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BIRDD - BioQUEST Curriculum Consortium

1. Cerro Media Luna Bellavista farm Lava tube MER E Charles Darwin Research Station Bah a Tortuga Grassy Drier fern grass sedge summit grassland lt 1 m high Puerto Ayora gt Miconia Mossy evergreen scrub dominated by Miconia only on St Cruz St Crist bal Moist Most or influenced by Scalesia Closed canopy evergreen forest dominated by A cl aar a Humid 9 Scalesia 12 20 m clouds amp Transition Open canopy semi deciduous woodland xerophytic misty rain trees growing higher than cacti 7 9 m Arid Coastal dry tree like cactus forest 4 m high amp scrub Coastal Zone salt tolerant shrubs saltbush mangroves in low sheltered bays Map Source modified from Healy 1996 FileName ISLANDS BRD page 1 Galapagos Archipelago Summary of Island Names Isl ID Common English Official Other Names Alb Albany Balt_SS Baltra S Seymour Baltra Seymour Sur Brto_Brth Bartolom Bartholomew Bartolom Bele Beagle Beagle Cldw Caldwell Cmp Campe n Champion Camp on Cocos Cocos Cocos Cwly Cowley Cowley DMaj Daphne Major Daphne Major DMin Daphne Minor Drwn Clp Darwin Culpepper Darwin Guerra Edn Ed n Ed n Endrb Enderby Enderby Esp Hd Espafiola Hood Espa ola Frn_Nrb Fernandina Narborough Fenandina Plata Flor_Chrl Floreana Charles Santa Mar a Grd_EsHd Gardner Esp Hood Grd_FICh Gardner Flor Charles Gnov_Twr Genovesa Tower Genovesa Ew
2. EGANISM Mitochondrion Cactospisa pallida 385 bp gion partial sequence Eukaryota Metazoa Chordata Craniata Wertebrata Archosauria nes Heognathae Passeriformes Fringillidae Emberizinae Cactospiza REFERENCE l bases l to 385 AUTHORS Fr land J K and BEoag P T TITLE Phylogenetics of Darwin s finches Paraphyly in the tree finches and two divergent lineages in the Warbler Finch JOURNAL Suk 19939 In press REFERENCE Z bases l to 255 AUTHORS Freeland J K and Boag P T TITLE JOURNAL Submitted 02 SEP 12933 SMS University of Reading Whiteknights Reading Berks Rei 64 UK FEATURES Location Qualifiers Direct Submission Source 1 385 forganism Cactospisa pallida No mitochondrion fdb xref taxon 48878 Scroll Bar fnote Erom Santa Crus Island Galapagos misc feature x1 2385 LEO SAN ooh fei Preview Preview page 5 T int all H Ti the Print All s How To Pages button on the Table o Navigating Around BIRDD Pines Preview Mode Preview mode is appropriate for viewing data summary lists amp statistics In Browse mode these displays look blank The pictures below show a summary list in both modes Browse mode incorrect Note that no data are visible and red instructions show in header Preview mode correct LU UU sii DEMORPHBRD REELRSEESPSSSESSSSUDSUSSSUDNUS P Click to List of
3. Tarsus Length Length of leg Actually the majority of a bird s leg is a single bone the tibiotarsus that extends from the ankle joint to the toes or phalanges printer 10 10 2000 page 3 Notes on Darwin s Finch Morphology Data Sources used a variety of English island names we display island names in our Common English format All measurements are in millimeters There are a number of duplicate museum catalog numbers within the Snodgrass amp Heller data and between the S amp H Sulloway and Swarth data The measurements of these birds typically differ because of inherent variability in the way measurements are are made e g how much pressure is applied to a wing as well as to differences in definitions of measurement e g whether culmen is defined as from tip to feathers or from tip to skull We have tried to note duplicates in the Notes field for each bird but left the data as in the original tables Museum Abbreviations Museum abbreviations mostly used by sources BM NH British Museum Natural History Brit Mus British Museum UMZC University Museum of Zoology Cambridge LRNH Leiden Rijksmuseum van Natuurlijke Historie Stanf Univ Mus Stanford University Museum Calif Acad Sci California Academy of Sciences U S Nat Mus United States National Museum W Johnson private collection of Captain W Johnson of San Francisco Snodgrass amp Heller 549 specimens Snodgrass am
4. added Dataset Choice buttons on table of contents to allow views of subsets of data added diagrams of measurements added new lists of original and modern taxa names FileName DFMAIN BRD page 22 Notes on BIRDD Molecular Sequence Database added over 150 new records from GenBank with sequences of six new molecules added data from two potential sister taxa added Dataset Choice buttons on table of contents to allow views of subsets of data added added summary display of list of molecules amp numbers of sequences from each species modified display of GenBank records to accommodate longer sequences added compact synopsis display of each sequence in browse mode for buttons to allow copying of clean sequences switching to display of full GenBank record etc added summary listing of primary references with sequences studied removed aligned and consensus sequences removed export of consensus and clean sequences modified export of GenBank records to allow export of subsets Species Database added images of skulls and muscles to species descriptions added summary views of just skull amp muscle images added notes on skull images with muscles labeled modified table of islands occupied by each species added button to allow display of the Islands database s table of species on each island from within the species database Vocalization Database modified How To pages add
5. 1961 Morphological differentiation and adaptation in the Gal pagos finches University of California Publications in Zoology 58 1 302 Bowman R I 1963 Evolutionary patterns in Darwin s finches Occas Papers California Acad Sci 44 107 140 Castor I C and A Phillips 1996 A guide to the Birds of the Gal pagos Islands Princeton NJ Princeton University Press Curio E and P Kramer 1964 Vom Mangrovefinken Cactospiza heliobates Snodgrass und Heller Zeits Tierpsychol 21 223 234 Gould J 1837 Description of new species of finches collected by Darwin in the Galapagos Proc Zool Soc Lond 5 4 7 Grant P R 1986 Ecology and Evolution of Darwin s Finches Princeton NJ Princeton University Press Harris M P 1973 The Gal pagos avifauna The Condor 75 265 278 Harris M P 1982 A Field Guide to Birds of Gal pagos London Collins Lack D 1945 The Gal pagos finches Geospizinae a study in variation Occasional Papers of the California Academy of Sciences 21 1 159 Lack D 1969 Subspecies and sympatry in Darwin s Finches Evolution 23 252 263 Rothschild W Hartert E 1899 A review of the ornithology of the Galapagos Islands With notes on the Webster Harris expedition Novit Zool Lond 6 85 205 Salvin O 1876 On the avifauna of the Gal pagos archipelago Trans Zool Soc Lond 9 447 510 Snodgrass R E 1902 The relation of the food to the size and shape
6. In addition to the camera tripod and computer we needed for our work we were travelling with a group of students and professors heading to Genovesa Island to do their own geologic research Professor Karen Harpp and student Dan Korich of Colgate Professor Carl Wirth and student Bryan Kennedy and student Daniel Andrade of Escuela Politecnica Nacional of Ecuador were planning to spend ten days on the small island mapping and collecting rock samples as part of a separate project on the origins of the Galapagos Islands As a result we were also carrying a number of bags containing sampling equipment mapping tools and all the gear that would be needed to spend a week and a half on an uninhabited island So all the equipment as well as two members of our group were loaded onto the back of the pick up and we set off for the Darwin Station After about fifty minutes of travel across paved and gravel roads we found ourselves in Puerto Ayora the main town both on the island of Santa Cruz and the Galapagos Islands as a whole Because of a large number of visiting scientists the dormitories that the Station has to rent were full As a result we ended up in the Castro Hotel as small family run establishment about a mile from the Darwin Station Janna and I settled into our room that we would call home for the next week while the other members of the group prepared to leave for Genovesa sometime within the next three days Our first goal upon arriv
7. NSF Division of Undergraduate Education Grant DUE 9950740 an Instructional Technology Grant from the Division of Instruction Technology at the University of Wisconsin Madison Educational Research and Development Centers Program PR Award Number R305A60007 administered by the Office of Educational Research and Improvement U S Department of Education and by the Wisconsin Center for Education Research School of Education University of Wisconsin Madison Beloit College Beloit WI Hamilton College Clinton NY Special thanks for services above and beyond go to the staffs of the interlibrary Loan and Reference Departments of Hamilton College s Burke Library The opinions findings and conclusions do not necessarily reflect the views of the supporting agencies FileName DFMAIN BRD page 6 Notes on BIRDD Bibliography Benson D A M S Boguski D J Lipman J Ostell B F F Ouellette B A Rapp and D L Wheeler 1999 GenBank Nucl Acids Res 27 1 12 17 Freeman S and J Herron 1998 Evolutionary Analysis Upper Saddle River NJ Prentice Hall Harvey P and M Pagel 1991 The Comparative Method in Evolutionary Biology Oxford Oxford University Press Lack D L 1945 The Gal pagos finches Geospizinae a study in variation Occasional Papers of the California Academy of Sciences 21 1 159 Lack D L 1947 Darwin s Finches Cambridge England Cambridge University Press Spro
8. This takes you to a display in Browse mode where you can inspect individual sequences Scroll to a specimen you are interested in and click in the Copy This Sequence button Switch to DNA Electrophoresis or other program and select Paste from the Edit menu or press Command V Sequences from multiple finches can be pasted into the Scrap Book Stickies or other handy storage location To export GenBank records Select a dataset in the Dataset Choice box on the Table of Contents Click the View Full GenBank Records button to verify your choice Return to the Table of Contents and click the Export GenBank Records button Type a name for the file to receive the exported records All of the selected records will be exported to a text file that may be opened with a text editor or most sequence analysis programs 4 GR 4 File Name DFDNA BRD p 2 Notes On The Molecular Sequence Database Version History Version 2 Many new sequences of a variety of molecules added Aligned and consensus sequences could not be done on the new data so these fields have been removed and left as an exercise for the student Viewing and printing of GenBank data were moved to different layouts because many new records were so long they have to be printed at small font sizes These sizes could not be viewed clearly on many computer screens Viewing of individual records is now done on a screen sized layout in Browse mode and a button ha
9. 032303 gagca acorbcaacgig diaatageacocag aoccaatataadigadeaiggaccaagdaccoera pp pata pcp caadebeceorpgaga g ccgibxttgacgg To fix this problem switch from Preview to Browse Hace gUE goce spera i AAA 1 select Browse or 2 press or 3 select from the Mode FB Mac Browse from the Mode menu pop up Alt B Win d Browse Browse Layout Preview Layout MIA ECT Preview Revert Record FileName DFMAIN BRD page 7 Wee ew en Navigating Around BIRDD dials Canceling Lengthy Operations Some operations in BIRDD may take a long time Where possible BIRDD will warn you and allow you to cancel the operation It may take a minute or two to setup all the pages for this dataset Shall I continue If you do continue lengthy operations are indicated by a cursor Mac or a flashing esc Win To cancel such an operation press the 3 amp keys Mac or the Esc key Win When you cancel an operation there are a number of possible results 1 Everything may look fine but the number of pages will be replaced by a question mark You can go ahead and page through the data but be careful about printing some datasets print thousands of pages To see how many pages will print drag the bookmark to the bottom of the book control see page 2 If you don t wish to print an entire dataset enter numbers into the Print pages from to boxes of the Print dialog Pag
10. All Data Sources view cata Data Source Number Data Source Mumber 2 Lack CAS onodgrass amp Heller 1904 oullovay 1982 swarth 1931 DFMORPH BRD Filename imlo ph brd page E E SS EEE A ea To fix this problem switch from Browse to Preview You may 1 Click on the instructions in the upper left hand corner or 2 select Preview from the Mode pop up or 3 press or 4 select Preview from the CMEZZXES N 100 laa E Browse ag U Mac Mode menu Apud m Alt U Win peeteat S Sort ET Replace a Relookup Revert Record FileName DFMAIN BRD page 6 Navigating Around BIRDD Browse Mode Browse mode is appropriate when you need to select items or when buttons are needed Examples include these Help pages all of the Table of Contents displays GenBank displays shown on page 4 where a Print button is needed and the example below where buttons allow you to copy the sequence and switch between the synopsis and the full GenBank record Browse mode correct Preview mode incorrect Note lack of Buttons DO gt prFDNA BRD 5 Sm r Table of GenBank Synopsis of Each Sequence ET Brent All gd This eem 165 Rihosomal RNA zene partial Taxor Camarhynchus pallida gd eM BLAEN APERE EIR EAEE N E PAPEI EA AFA FEA PEFFE EEEN E PEERAA AEE TEREA EFFE FEAE AENEAN EEA EAA j Locus Mame Seg Size Date EnterediMaodified Accession Version E Synopsis of Each Sequence j
11. B B B m 4 Isa Alb B B B B B B B BB BIB u Plazas a B B BI 3 LHrm Crsm o i Mrch Bndl B B 8 BB BIB 7 Pnt_Abng B B B B B B B BIB 9 Pnz Dnc B x B B BB B p 6 Rab Jrv B B B BBB BIB s Bainb ooo B 1 SCris Chat B Bix BB BJ B e SCru Inde B B B B x B BB BIB 9 SFe_Bmgt B B B 8B BB B 7 Snti_Jams B B B B B B B B Bj B 10 Seym NS BB 2 Trtu Brat op B8B 1 WIf Wnm B B B s s B a4 FileName Islands B breeding p possibly breeding o breeds occasionally page 1 s straggler x bred in past now extinct Beagle Investigations Return Darwinian Data The Darwin s Finch Data Resource DFDR Weather Table of Contents wersion 2 0 8IRDD v2 To return to this location Select Go to Weather Table of Contents under the Script menu View All Weather Data View Rainfall Data Graph 1950 1989 1950 1989 Monthly Rainfall View Avg Rainfall Export 1950 1989 1950 1989 Monthly RainFall View Monthly Export Monthly Stats by Location Statistics Return to Main Table of Contents Notes on Weather Data About the Database This database contains a variety of weather data The major data include 40 Years 1950 89 Data on Rainfall on San Cristobal These data may be viewed as raw data or more usefully exported for summarizing and analysis in other programs These data are also summarized by month The average rainfall 1s reported in both the Rainfall field for consistency with oth
12. Book Jaurnal Article Map Ref Type Thesis been entered click the Perform Find button Most of the fields are just text boxes that you can type in The Reference Type field however provides a list for you to select from Find criteria can be complex but many finds are simple Any single value entered into a field will retrieve references with that value Examples Year Title Ref Type Retrieves all web sites in the database Author Title Ref Type Retrieves works published in 1990 A number of special symbols can make criteria more flexible Lessthan gt Greater than lt Less than or equal gt Greater than or equal Exact match Entire field 1 character 1 or more characters Range text Exact text Examples Year lt 1900 Year gt 1900 Published before 1900 Published during or after 1900 ven 1889 e 7900 ven Ts NM Published beliesn 1850 and Published in 1890 1990 1900 inclusive wi oe Smith Smithson Smithers Smith but not Smithson or Smithers Lessthan lt Less than or equal Exact match 1 character Range More Examples gt Greater than gt Greater than or equal Entire field 1 or more characters text Exact text Grant and initials R and P anywhere among authors 96 in this database Grant P R and any other authors 48 in this database effectively P R Grant as first author Grant P R as
13. Contents that will display and print a summary of the IDs taxonomic names synonyms and common names In data sets e g DFMorph derived from published sources we have included taxon names used by original authors as well as our standardized names FileName DFMAIN BRD page 9 Notes on BIRDD USING BIRDD Much of the following can be found in the help information provided by the How To buttons in the various databases You should examine those displays whenever you first open a database and when you are uncertain about how to proceed Navigating the Databases Click the Notes on the How To Navigate Around BIRDD button on the Main table of contents for annotated images of BIRDD s tables of contents data windows and controls etc Tables of Contents Opening the BIRDD application icon brings up the Main Table of Contents for all of the files It contains a number of buttons which display background information or take you to relevant data files and displays Click once on a button and the appropriate information or database will appear The main table of contents mirrors the organization of most of the other databases Notes Button In the upper left is a wide button that takes you to background text describing the data e g these Notes on BIRDD How To Button In the upper right there is a square How To button that displays information on how to use the database and how to interpret the data Display Buttons In
14. a broad frequency range a Softest chip shown by the short spike on the waveform trace and faint sonogram trace b Loudest chip shown by the taller spike and darker sonogram File Name DFVOCAL BR p 3 Beagle Investigation Return Darwinian Data The Darwin s Finch Data Resource DFDR Island Table of Contents version 2 0 BIRDD v2 To return to this location Select Go to Islands Table of Contents under the Script menu View Archipelago View All Data on Finches Inhabiting Islands Inhabited Maps Each Island Each Island By Each Species View Map of View Vegetation Zones Island Summaries View All Island Names View Islands Vegetation Zones Return to Export Island Main Table of Contents Data Notes on Island Database About the Database This data file contains information about individual islands Data on area species of plants etc can help provide ideas for students study of the finch distributions Maps can be printed for reference and the blank map can be copied and used to draw species distribution etc Map images can be pasted into programs like NIH Image available on the BioQUEST Library CD ROM for additional manipulation to measure topographic diversity for example Bibliography Maps amp Geographic Data Cox A 1983 Ages of the Galapagos Island Patterns of Evolution in Galapagos Organisms R I Bowman M Berson and A E Leviton San Francisco CA Pacific Division AAAS
15. but could not understand any English and had difficulty deciphering our broken Spanish Luckily Tuan an American Peace Corps volunteer accompanied us serving as our translator and guide Tuan was definitely up for a chuck full day of panoramas and exploration Our driver on the other hand did not seem to welcome the prospect of a siesta less day without a warm lunch until we bought him some chocolate bars at the Puerto Ayora grocery store Since he napped in the truck at each site we didn t worry too much about him being sleep deprived Following our food stop we went to the lava tunnel to retake the panorama that was lost when the computer crashed We crept back into the tunnel and spun the camera one more time Once finished we jumped back into the red pick up to visit some farms that Tuan had worked on for a sustainable agriculture Peace Corps project The farms were incredible It seemed like every imaginable fruit and vegetable was growing on each plot of land goyaba trees were dispersed between orange trees and pineapples grew across from the coffee Guava pera peppers tomatoes beans papaya and mango were everywhere The daughter of the man who owned the farm was giving us a taste of every fruit imaginable We twisted open the long brown goyaba bean and ate out the white fruit from around the seed The red pera was like a cross between an apple and a pear All of it was delicious We sampled everything that we could plunge our teeth
16. buttons to go to information or data sets boldface buttons are functional To return to this location from anywhere in BIRDD Click a Return to Main Table of Contents button or Select Go to Main Table of Contents under the Script menu Print All How To Pages Skeletal Data EE E Pictures amp Panoramas Island Data For technical support comments and suggestions contact Frank Price by phone 315 853 5233 or by e mail fprice hamilton edu B mee Return with Danvinian Dara The Darwin s Finch Data Resource version 2 0 October 2000 A BioQUEST Library Collection First Review Module Copyright Frank Price Hamilton College amp Beloit College Samuel Donovan U Wisc Madison James Stewart U Wisc Madison John Jungck Beloit College BioQUEST Curriculum Consortium Beloit College Ph 608 363 2743 700 College Street E mail bioquest beloit edu Beloit WI 53511 Web http www beloit ed bquest Published by Academic Press For technical support contact Frank Price the Developer ph 315 853 5233 e mail fprice hamilton edu Warning This solution contains password s which may only be provided by the Developer identified above Acknowledgements Funding Version 2 0 NSF Grant DUE 9950740 Version 1 0 the Division of Instruction Technology at the University of Wisconsin Madison in the form of an Instructional Technology Grant Additional support was provided by the Educa
17. hgx CourierNew sit hqx If the above URL doesn t work go to the Microsoft homepage http www microsoft com Find the search page and enter the string Arial sit hgx TimesNew sit hgx CourierNew sit hqx then click on A words to find the files Your browser should decompress the fonts and you can drag them onto your System Folder icon FileName DFMAIN BRD page 15 Notes on BIRDD Screen Resolution and Color Depth The tables of contents screens are configured for viewing at 800 x 600 or better resolution Data displays typically show pages as they would be printed and are best viewed at higher resolution 1152 x 870 allows viewing of entire pages without using the Zoom out control On many computers there is a trade off between higher screen resolution and smaller number of visible colors You should choose the highest resolution that provides more than 256 colors While 256 colors are acceptible for most of BIRDD s screens color images are better if you can display 16 bit color or better thousands or millions of colors Printing Printing from PCs has been tested with only HP amp Apple PostScript laser printers The most common problem involves displays such as tables of contents that are intended to print in wide landscape orientation will print in tall portrait orientation Similarly tall displays such as notes on databases may appear as wide See the Troubleshooting note in BIRDD s button Introduction
18. into before looking at the green houses It was interesting to see the plastic covered sheds of vegetables In addition it was strange to see COWS goats dogs and chickens roaming around There were so many introduced species of flora and fauna It raised many conservation issues in our minds Visiting the farms on Santa Cruz allowed us to see the grave affects of human impact on the Galapagos Islands Next we set off for the lower transition zone Driving along the road it was very difficult to differentiate the zones of vegetation In addition to the prescence of introduced species the limitations of our equipment made it difficult to find an appropriate site After numerous here s and I don t know s we settled on a spot a few meters away from the main road The dense low lying brush made it difficult to set up the equipment So we jumped around and stomped on the surrounding vegetation After guiltfully clearing an ample circumference for ourselves we took the shots File Name GALPICS BRD p 7 Notes On The Image Database Then we journey to the other side of the island As we drove over the peak of the volcano the dense gar a faded into blue skies and sunshine The leeward side was absolutely beautiful The Scalescia trees were larger and the shrubbery was lower Therefore it was easy to pick a spot right off the road to jump out and take the pictures In order to get a panorama minus the big red pick up truck the driver z
19. island per month from 1979 into 1997 Island Names amp Abbreviations The islands of the Gal pagos archipelago are referred to by a bewildering variety of names that derive from sources that range from pirates to W W II military personnel Much of the older literature refers to English names while more recent literature tends to employ common names used by the local inhabitants Many writers use a mixture Because of this confusion we have decided to use as Island name a combination of the common name and the English name used in the classic literature However students should be aware that some confusion is inevitable For example Seymour may refer to North Seymour this appears to be the modern usage or to Baltra also known as South Seymour and Seymour Sur Wherever possible island names are displayed as Common Name English Name to help you learn both When space is at a premium we use a shorter Island ID that contains shortened forms of both Thus Baltra 1s displayed as Baltra South Seymour when there is space and Balt SS when necessary Finch Names amp Abbreviations Similarly names of finches are spelled out fully where possible Where space is limited we use an abbreviated ID that 1s the first three characters of the genus specific name and subspecies name if appropriate For example the Large tree finch is designated by Camarhynchus psittacula or by Cam psi There 1s a button in the DFTaxa Table of
20. lateral and ventral skulls w muscles and beak cross sections Added counts of number of islands where breeding where uncertain and where extinct Revised Status on Island display added number of islands counts Version 1 1 Font and layout changes as covered in notes to Main file All images converted and reimported to work on Windows computers See notes in Main file _ M Geospiza magnirostris y M add ext sup M pter d lat 4 M add ext prof mandibular T X S A2 rhamphotheca GUI N Lig jugomand ext eer M add post Nu ind i pter v lat yo M add ext med M add ext sup M depr mand Lig jugomand art Superficial jaw muscles Geospiza fortis Proc palato max Left Side deep jaw muscles Right side superficial jaw muscles mandibular Proc t l PR Y roc transpa M pseudotemp prof M pter v lat M add ext med M pter v med M pter d lat ESTE sd V Dterygoid J i p lt ll E PEN NA P M d d er y M pter d med acu Lig jugomand art M pter v lat M depr mand M retr pal Certhidea olivacea M pseudotemp prof M pter v med M pter d lat e A a TA 1 M pter d med Abbreviation Lig jugomand art Lig jugomand ext M M M M M M M M M M M Mandibular Rhamphotheca add ext med add ext prof add ext sup add post depr man
21. only author 17 in this database i e entire field contains only Grant P R Shortcut You can also enter symbols and get a reminder of their functions by using the Symbols pulldown menu and selecting the desired symbol less than less than or equal greater than greater than or equal exact match Fange duplicates today s date invalid date or time nne character zero nr more characters m oH Do not use these controls liter al text field content match AND searches When you need to find references which each have more than one criterion put those criteria in a single request Examples T rM KC UT ON LL Der T Grant P R AND B R Grant in author vear 1980 1990 field 20 In this database i e field z contains both Grant P R as well as B Grant P R as first author AND published R Grant between 1980 and 1990 21 in this database Same between 1980 and 1990 AND a complete book i e not a chapter in an edited book 1 in this database Ie How to Find References Multiple Criteria OR Searches OR searches When you need to find references which have alternative criteria put the criteria in multiple requests by clicking on the Add OR button under Criteria Example a search for all references with BOTH B R Grant AND P R Grant as authors would look like this BIBLIO BRD Makes previous Find Enter Criter
22. raw sequences can be cut and pasted into other programs e g the DNA Electrophoresis program on the BioQUEST Library CD GenBank records can also be exported and read by other DNA analysis programs The data were downloaded from the GenBank Web site Benson D A et al 1999 http www ncb1 nlm nih gov These data were deposited by individual research groups working on a variety of projects see Bibliography The layout of the Table of Contents display like that of the Morphology database differs from most others in that there is a Dataset Choice box that allows you to determine which subset of data you wish to view The View Table of Sequences amp Data button allows you to see a listing of all of the molecules and species in the database and how many specimens of each are available The View Full GenBank Records button displays each complete record Many of these records are long enough that they won t fit on a screen or even a printed page A scroll bar allows you to view a complete record Note that you should not use the regular File gt Print command to print GenBank records but rather the Print button in the header The View Synopsis of Each Sequence button allows you to inspect a summary of information from each GenBank record This display is easier to read although less complete than the original GenBank records Included in this display is the molecular sequence with spaces and numbers removed A button will copy th
23. similar strategy select the printer use the Properties to select a generic LaserWiriter driver Solution If the name of your laser printer does not include the word or string laser then rename it to something that includes the string without quotes Solution If all of the above fail you can still do a manual Page Printer Setup before each print Note that if you must do this How to pages must be printed one at a time from each page not by using the Print All button on the table of contents Solution Contact Frank Price phone 315 853 5233 e mail fprice hamilton edu for help FileName DFMAIN BRD page 20 Notes on BIRDD Panoramas don t work Probable Cause These will not work within BIRDD itself and we hope to post updates on the BIRDD website soon Solution Panoramas and sounds can be played from within QuickTime and some other softwere see Panoramas and Sounds topic in the Main database Sounds Do not work on Windows PCs Solution 1 If you have FileMaker version 4 for Mac or 5 for Windows open BIRDD from within the FileMaker application 1 Open your FileMaker application 2 Select Open Existing File or if FileMake is already running select the Open command from the File menu 3 Navigate or browse to the folder containing BIRDD 4 Type DFMAIN BRD into the file name box and click the Open button 5 At the Main menu click on the Vocalizations button and play the sounds 6 If you see a message l
24. students cannot analyze them further raw data are hard to find Even if raw data are available in printed form students or instructors must first enter and proofread them a daunting task for even a moderately large data set The DFDR lowers the threshold for using raw data by collecting them and providing them in electronic form for review and export of other software The databases provide A body of background information e g island names taxonomic names maps A large volume of diverse data e g beak dimensions molecular sequences Simple statistics and information displays help students understand the data Sources of data for other software allow use of data in other programs An easy consistent user interface facilitates moving around viewing and printing data and background information FileName DFMAIN BRD page 2 Notes on BIRDD The Instructional Resources While data resources are obviously an important part of helping students experience problem solving in evolutionary biology data alone do not constitute a rich educational experience Because BIRDD is designed to support the broadest possible range of uses new users both students and teachers may not know how to get started To help orient new users we have begun to collect examples of some of the different ways BIRDD has been used in a variety of institutions and courses Clearly understanding evolutionary theory 1s an essential compon
25. the display then return Zoom Box File Edit Mode Select Format Script Window DFInun Layout pop up menu Camarhynchus heliobates Appearanc Mode pop up menu Status Area control Hamis 1942 Flare 5 5 p 118 Resize Box had Preview E Es Zoom out control In some situations you may wish to use the Zoom in control the Mode pop up menu or the Zoom controls See the Next page for more FileName DFMAIN BRD page 4 To print all How To pages use the Print All Navigating Around BIRDD How To Pages button on the Table of Contents Browse vs Preview Modes Most BIRDD displays are in Preview mode a few are in Browse mode Usually BIRDD sets up displays correctly but errors may sometimes lead to the wrong mode The left hand image shows a GenBank display in Browse mode the right hand image shows the same display in Preview mode The latter is not appropriate for printing this type of record must be done using the Browse mode button Watch for cues shown in red Browse Mode Display Buttons Margins not visible Instructions visible FOE BAD Don t print from the File menu A Aj j Ben pant PEMAN Mitoch Control Region short button on the right If the button is nat visible select Browse mode from the Mode menu DNA 285 bp 2ros3730 DEFINIT ICRA piza pallida mitochond region partial sequence ACCESO I N AF049790 1 NID 74191252 VE
26. was soaked So the three of us began to climb up to the highest point At one branching of the trail Sarah pointed out the trail to Media Luna and Cerro Crocker then headed off to her area of introduced grasses We asked if we should use our Global Positioning System but she assured us that there was no way we could get off the trail or get lost She would meet us in eight hours in the spot where we were standing So we were on our own We continued to climb and the gar a began to pick up again along with driving winds We continued to climb upward until finally we reached the highest point We were soaked The rain was a fine mist being blown forcefully at us from every direction The mist was so fine that it quickly blew through our jeans and rain jackets When we had asked sarah about what to wear she had forgot to mention the true amount of rain we would face So there we were at the top of the mountain soaked and in the middle of a rain storm We couldn t take out the digital camera in that much rain so we decided to head back down the volcano and hope that eventually the rain would stop After slipping down the incredible muddy trails that slid beneath our feet we reached a point that would make a great panorama Having prepared so thoroughly for the rain we got out the umbrella We quickly realized that it seemed as though the rain was coming up the slope So eventually we tried to guard the camera from the rain as best we could duri
27. 10 Galapagos Locations Data are from Hoffmann J A J 1975 Atlas climatico de America del Sur mapas de temperaturas y precipitaciones medias Climatic atlas of South America maps of mean temperature and precipitation World Meteorological Organization UNESCO Cartographia Unfortunately the time frame of the data used to generate the monthly averages were not reported so the Years were coded as Unk FileName WEATHER BR page 1 Notes on Weather Data Exported Monthly Rainfall data Exporting the 1950 1989 rainfall data produces a tab delimited text file with the following data Field Column Heading Comment Island ID The short name of the island Location The name of the weather station location Year The 4 digit year Month The 1 or 2 digit month Year Month The decimal equivalent of the middle of the month 1 e month 12 0 5 This facilitates graphing the date Rain mm The total rainfall that month in mm Exported Monthly Average data Exporting the average stats data produces a tab delimited text file with the following data Field Column Heading Comment Data Source Name of source of data Island ID Short name of Island Location Name of location of weather station Year 4 digit year or year range if known Month 1 or 2 digit month Elev Elevation of weather station 1n meters AvgMaxTemp AvgMinTemp AvgTemp appropriate statistic temperatures in C SeaTemp HrsSun Rain mm Procedu
28. 4g Foraging Habitat Foraging Location plants ground ticks on tortoises iguanas all zones common in humid on central isls arid on N 1sls Length 16 5cm Wt 35g Foraging Habitat Foraging Location arid zone more in trees shrubs less on ground Length 14 0cm Wt 21 Foraging Habitat Foraging Location arid zone usu 1n cactus No Islands Breed Uncertain Extinct 16 l 0 Breeding Habitat lowlands not highlands No Islands Breed Uncertain Extinct 27 2 0 Breeding Habitat No Islands Breed Uncertain Extinct 11 2 l Breeding Habitat No Islands Breed Uncertain Extinct 14 0 0 Breeding Habitat Opuntia Prickly Pear Cactus FileName DFTAXA BRD p 3 Pinaroloxias inornata little known probably insects nectar fruit Platyspiza crassirostris fleshy fruits soft medium hard seeds leaves flowers Cocos F Foraging Method little known probably pecking Vegetarian F Foraging Method peck from plant Length Wt Foraging Habitat Foraging Location tropical rainforests among leaves on ground Length 16 5cm Wt 34g Foraging Habitat Foraging Location transition zone occ arid coastal amp Scalesia trees bushes occasionally ground No Islands Breed Uncertain Extinct 1 0 0 Breeding Habitat No Islands Breed Uncertain Extinct 9 1 0 Breeding Habitat Beagle Investigations Return Darwinian Data The Darwin s Finch Data Resourc
29. AF089782 ATF hp 28 JAIN 1999 AFUS9 702 AFUS9782 1 GI 419 1375 JE sequence cannot be selected amp copied with the mouse E 165 Ribosomal RNA gene partial Taxon Camarhynchus pallida Definition Cactospiza pallida 165 ribosomal RNA gene mitochondrial gene for l Nu mitochondrial RNA partial sequence Locus Mame Seq Size Date Entered Modified ACCeSsion Version AF089782 4Te hp 26 JAN 1999 AF039782 A4F089782 1 Keywords GI 4191375 Reference 1 Freeland J R and Boag P T Phylogenetics of Darwin s finches Paraphyly Definition Cactospiza pallida 165 ribosomal RNA gene mitochondrial gene for in the tree finches and two divergent lineages in the Warbler Finch Auk mitochondrial RNA partial sequence 1999 In press j Keywords 2 Reference 1 Freeland J R and Boag P T Phylogenetics of Darwin s finches Paraphyly Reference 2 Freeland J E and Boag P T Direct Submission in the tree finches and two divergent lineages in the Warbler Finch Auk E 1999 In press Reference 2 Freeland J R and Boag P T Direct Submission Sequence A A Jhodha paar Pate 2000 29021235924 Ob 230 00 crac bc cra 0 0 ol M E Sequence M ae Y o lr 2 urgoggiatodigaccgigeaaaggtagegcabeaatigicocataaategagadagiatgaatggaaaacgaggidiaadgbieiatacaggeaateggt gaaxtigatetordigtacaaaagregggatgagoocataagargagaag accdgiggaadicaaaaccag cg accacgttaaadeacatacica ecco ggglicadgacacrtaagocadiggiocgegititicggitg ggpcgacctiggagca2230122300607233331 3g 300 so0
30. BIRDD Beagle Investigations Return with Darwinian Data Version 2 0 RioQUEST 4 SN et o Ee ae ch iy ie Librarv VH User Notes Frank Price Samuel Donovan Hamilton College University of Wisconsin Madison A BioQUEST Library VII Online module published by the BIOQUEST Curriculum Consortium The BioQUEST Curriculum Consortium 1986 actively supports educators interested in the reform of undergraduate biology and engages in the collaborative development of curricula We encourage the use of simulations databases and tools to construct learning environments where students are able to engage in activities like those of practicing scientists Email bioguest beloit edu Website http bioquest org Editorial Staff Editor Managing Editor Associate Editors John R Jungck Ethel D Stanley Sam Donovan Stephen Everse Marion Fass Margaret Waterman Ethel D Stanley Amanda Everse Sue Risseeuw Online Editor Editorial Assistant Beloit College Beloit College BIoQUEST Curriculum Consortium University of Pittsburgh University of Vermont Beloit College Southeast Missouri State University Beloit College BIoQUEST Curriculum Consortium Beloit College BIoQUEST Curriculum Consortium Beloit College BIoQUEST Curriculum Consortium Editorial Board Ken Brown University of Technology Sydney AU Joyce Cadwallader St Mary of the Woods College Eloise Carter Oxford College Angelo Collins Knowles Science Teaching
31. Defense Mapping Agency 1993 Pacific Ocean Ecuador Archipelago de Colon Galapagos Islands Hydrographic Topographic Center Bethesda MD map 22000 Names used on the maps are the official names Healey K H Bradt et al 1996 Kevin Healey s Travel Map of Galapagos Islands Vancouver B C Canada ITMB Publishing Biological Data Bowman R I 1961 Morphological differentiation and adaptation in the Galapagos finches University of California Publications in Zoology 58 1 302 Grant P R 1986 Ecology and Evolution of Darwin s Finches Princeton NJ Princeton University Press Harris M P 1973 The Galapagos avifauna The Condor 75 265 278 Harris M P 1982 A Field Guide to Birds of Galapagos London Collins citing Wiggins amp Porter 1971 for plants Harris M P 1982 A Field Guide to Birds of Galapagos London Collins Lack D L 1947 Darwin s Finches an essay on the general biological theory of evolution Cambridge England Cambridge University Press Lack D 1969 Subspecies and sympatry in Darwin s Finches Evolution 23 252 263 file Islands page 1 Notes on Island Database Notes About the Data Elevation Data There are considerable differences in published measurements up to more than 100 m in some cases Most elevations in m were read from the DMA map For a few low islands with no elevation indicated on the DMA map elevations from Healy ar
32. Foundation Terry L Derting Murray State University Roscoe Giles Boston University Louis Gross University of Tennessee Knoxville Yaffa Grossman Beloit College Raquel Holmes Boston University otacey Kiser Lane Community College Peter Lockhart Massey University NZ Ed Louis The University of Nottingham UK Claudia Neuhauser University of Minnesota Patti Soderberg Conserve School Daniel Udovic University of Oregon Rama Viswanathan Beloit College Linda Weinland Edison College Anton Weisstein Truman University Richard Wilson Emeritus Rockhurst College William Wimsatt University of Chicago Copyright 1993 2006 by Frank Price and Samuel Donovan All rights reserved Copyright Trademark and License Acknowledgments Portions of the BIoQUEST Library are copyrighted by Annenberg CPB Apple Computer Inc Beloit College Claris Corporation Microsoft Corporation and the authors of individually titled modules All rights reserved System 6 System 7 System 8 Mac OS 8 Finder and SimpleText are trademarks of Apple Computer Incorporated HyperCard and HyperTalk MultiFinder QuickTime Apple Mac Macintosh Power Macintosh LaserWriter ImageWriter and the Apple logo are registered trademarks of Apple Computer Incorporated Claris and HyperCard Player 2 1 are registered trademarks of Claris Corporation Extend is a trademark of Imagine That Incorporated Adobe Acrobat and PageMaker are trademarks of Adobe Systems Incorporated Mi
33. Page and Previous Page script commands For consistency we provide most data displays in Preview mode since that is required for statistical summaries Preview mode does not provide access to buttons or to individual records so the Table of Contents pages and How To pages are presented in Browse mode This should not be a major limitation as most of the user interface elements are standard and are covered in pages accessible from the How To Navigate around BIRDD button on the Main Table of Contents FileName DFMAIN BRD page 19 Notes on BIRDD Printing Problems Text or images are cut off Pages are too short wide or too narrow tall in screen displays or printouts Probable Cause BIRDD cannot yet work with printer selected in Chooser Mac or the default printer Windows BIRDD will work with the following printers Apple and Hewlett Packard HP postscript laser printers many Apple StyleWriters many HP DeskJet printers and many Epson Stylus 740 printers Solution Many postcript laser printers will work with the generic Apple Laserwriter print drivers Mac users should open their Chooser and select an appropriate printer icon e g LaserWriter or LaserWriter 8 select the appropriate printer name and click the Setup button Click the choice for manually choosing a PPD file and select Generic from the list This will often work even if the printer you ve selected is an HP or other postscript device Windows user can use a
34. RL Key Comments Go to lt this dbase s gt Table of Contents 1 go to current database s contents Go to Main Table of Contents 2 go to main table of contents View lt this dbase s gt Database Notes 3 view notes on current database First Page 4 jump to the top of a list Previous Page 5 move up in a long list Next Page 6 move down in a long list Last Page 7 move to the bottom of a long list 8 additional scripts appropriate to 9 the current database 0 Only the first ten scripts have keyboard equivalents Printing Typically printing is done by selecting Print from the File menu This will bring up the standard dialog box and you can select number of copies page ranges etc A few screens notably the How To pages must be printed from buttons just look for a Print button or notice Be aware that different printers have differing print areas and options Depending on your printer and default settings there may be differences between what you see on the screen and what is printed Printing from PCs has been tested with only HP amp Apple PostScript laser printers See Troubleshooting below if you are having printing problems FileName DFMAIN BRD page 11 Notes on BIRDD Selecting Subsets of Data BIRDD was designed to be a data repository that would allow students or faculty to get a general idea of the data available so that they could export those data to other software tools For this reason we have not provid
35. RS ION AAF09790 1 GI 4191382 y l KEYWORDS SOURCE woodpecker finch ORGEaH ISM Mitochondrion Cactospiza pallida Records Eukaryota Metazoa Chordata Craniata Vertebrata Archosauria nes Heognathae Passeriformes Fringillidae Emberiszinas Cactospiga REFERENCE l bases l to 255 AUTHORS Freland J k and BEoag F T TITLE Phylogenetics of Darwin s finches Paraphyly in the tree finches and two divergent lineages in the Warbler Finch JOURHAL Suk 1993 In press REFERENCE Z bases l to 255 BUTHORS Freeland J K and BEoag F T TITLE Direct Submission JOUBRHAL Submitted 02 SEP 1993 SHS University of Reading Whitehknights Reading Berks KCE BAJ UK FEATURES Location Qualifiers Source L 385 forganism Cactospisa pallida i mitochondrion D db xrief taxon 45575 Scroll Bar inote from Santa Crus Island Galapagos su misc feature lt 1 gt 255 e DFDMA BRD p 7 a es a o0 adl Browse UU AE Browse FileName DFMAIN BRD Preview Mode Display Margins visible A Fn 8 SS buttons Instructions s not visible GenBank Records Don t print from the Fil AAI i Sud M e menu Mitoch Control Region short button on the right If tha button is nat visible select Browse mode from the Made menu p 4 IMA 5 IAH 15933 AF089790 actospiza pallida mitochondrial co ACCESSION AF089770 MID 4131252 VERSION AF S3730 1 G1 4191352 KEYWORDS SOURCE woodpecker finch
36. Time for Macs or for Windows or an equivalent program 1 Note the location and name of the sound and its name in the File Location field on the displays 2 Switch to your QuickTime Movie Player program or an equivalent 3 Use the File Open command to open the sound file These are located in the BIRDD gt DFFiles gt Sounds gt E Sounds directory QuickTime Movie Player controls work as advertised in the next screens File Name DFVOCAL BR p 1 Controlling Sound Playback When you click on a picture of a sound a standard QuickTime playback control bar will appear nearby as shown below Click anywhere in this sound picture ih k LEN to activate its QuickTime control NN Slider LA N Pay top eunten Forward amp Reverse Speaker volume Control Frame advance Buttons don t work with sounds To start or stop the recording click the Play Stop button or press the space bar The slider will move along the picture as the sound plays Although not perfectly synchronized the slider s position along the picture will roughly correspond to the sound To adjust the sound level click on the Speaker Volume control You may also need to adjust your computer s Sound Control Panel consult the user s manual for your computer or contact your user support organization Tip To move the slider to a particular part of the recording click on that spot During playback clicking on a spot will return the playba
37. Time movie mov files These files are available in the original sounds O Sounds folder in the Raw Data folder Files were opened with Canary edited to remove verbal introductions long stretches of silence and some noise then saved in the edited sounds E Sounds folder as aiff files These are the sounds used to generate waveform and sonogram images and are played from within the database Edited sounds are saved in aiff format files in the Edited Sounds E Sounds folder inside the Raw Data folder Note these aiff files and their enclosing folders must remain within the DFDR Raw Data E Sounds series of folders or the sounds cannot be played Problems Hearing Sounds Sounds are not currently playable from within BIRDD itself although one image 1s visible We hope to provide an update soon check the BioQUEST website http www bioquest org for current information There are several ways to play these sounds click the nformation button 1n the Main Table of Contents and scroll down to the section on Panoramas and Sounds On some Windows machines and some Macs you may have to use a separate sound application e g QuickTime to play the sound files outside of BIRDD If you still have problems hearing sounds Make sure the Sound or Monitors and Sound control panel is configured properly and especially that the the volume control is turned up File Name DFVOCAL BRD p 4 Problems With Sounds This databa
38. a in the two requests Deleting the 2 request would find 42 articles by including those written by a Grant Beagle Investigations Return Darwinian Data The Darwin s Finch Data Resource DFDR Galapagos Tourists version 1 0 BIRDD v2 To return to this location Select Go to Tourists Table of Contents under the Script menu View All Data View Summary by Year View Summary by Month Return to Main Table of Contents Export Data Notes on Tourist Data About the Database This database contains data on the number of tourists visiting the Gal pagos islands in each month from January 1979 through May 1997 Data were downloaded from Tourists Visiting Gal pagos web page http www polaris net jpinson tourist tbl 1 html That page cites the Gal pagos National Park as the source of their data Notes About the Data Exported Monthly Data Exporting the data produces a tab delimited text file with the following data Field Column Heading Comment Year 4 digit year Month 3 character month name n Month l or 2 digit month Year Month decimal equivalent of year and middle of month 1 e n Month 12 0 5 this facilitates graphing the data by time N Tourists number of tourists visiting in that month FileName GalTrsts BRD page 1
39. across the lava tubes We ventured inside and despite some slick rocks were able to take a wonderful panorama showing the characteristic levels marks skylights and collapses of the lava tubes which form as the lava on the outside of a flow hardens while the lava inside continues to flow through until finally the molten rock runs out leaving the tube to drain From there we biked up hill some more until we finally reached the small town of Bellavista home of some of the largest accessible lava tubes on Santa Cruz Bellavista 1s a small town located about ten kilometers from Puerto Ayora We finally got to the 7 5km long tunnel with the help of some friendly town residents A kindly older man who spoke very rapid Spanish ran the tunnel entrance We were finally able to communicate that we wanted to go through it to take pictures at which point he showed us the large hand painted diagram of the tunnel and the collapse through which we were to emerge about 2 5km into the tube We were a bit skeptical and we had no idea where on the surface of the island we would emerge but the man handed us an extra flashlight in case ours died and we were on our way We entered the tunnel and quickly realized why he had given us the extra flashlight Once we had gotten a few hundred meters from the large entrance there was no light other than our rather weak flashlight It was the darkest dark imaginable and the silence was amazing We were the only people in
40. age 1 Notes on BIRDD The Data Resources Unlike most BIo0oQUEST modules BIRDD is neither a simulation nor a text module There are no predetermined experiments to run Instead there are rich data that can be used to develop investigations that explore evolutionary phenomena in a realistic manner These permit observational hypothesis testing in contrast to the experimental hypothesis testing that most people understand to be the scientific method Too often doing science is exclusively associated with collecting data while the analysis and interpretation of those data are underemphasized Evolutionary biology and ecology have always involved the integration of diverse data to identify new patterns and to build models to explain those patterns The Darwin s Finch Data Resource DFDR is the first BIRDD module and contains a collection of scientific data related to Darwin s Finches Our primary goal has been to compile as many raw data as possible and to organize them so they are easily accessible The aim 1s to put students in the position of John Gould who first named and described the finches and other scientists in England who received the specimens Darwin brought back from his voyage on HMS Beagle Of course the range of data and their presentation reflect 150 years of progress in science and technology Data printed in books and journals are difficult to use because they are typically processed statistics and tabulations and
41. and the locations of most of the images marked PANORAMAS Panoramas were created using QuickTime VR software These are not currently viewable from within BIRDD itself although one frame of each panorama is visible We hope to provide an update soon check the BioQUEST website http www bioquest org for current information There are several ways to play these images click the How To Use Panoramas button on the Table of Contents for this database You may also click on the nformation button in the Main Table of Contents and scroll down to the section on Panoramas and Sounds EXPORTING IMAGES Images cannot be exported as files but you may copy and paste images through your computer s clipboard Select the appropriate image and use the Copy command on the Edit menu Field Notes Most of these images were taken by Alicia Newton amp Janna Pistiner students from Colgate University in Hamilton NY Their field notes are attached to these database notes and provide modern students s reactions to some of the realities of field research in the Gal pagos File Name GALPICS BRD p 1 Notes On The Image Database Notes About the Data Field Notes by Alicia Newton amp Janna Pistiner Colgate University Hamilton NY Over this summer August 1999 we Alicia Newton and Janna Pistiner undergraduate students at Colgate University were given the opportunity to go to the Galapagos Islands and visually document the different ve
42. ared to be a branch in the path We weren t sure exactly which path to take but using our somewhat basic compass skills decided that we knew which path headed in the right direction and decided to take it We walked for almost twenty minutes without recognizing anything and without not recognizing anything Finally we began to head up again and we came to a pipeline that we knew we hadn t passed We decided it would be best to turn around Twenty minutes later we came to the same branch and took the other path At this point we weren t really sure we recognized anything So we kept walking hoping that the fact we were walking with the water current that was streaming down the path under our feet meant that 1f nothing else we were heading down in elevation Finally we came to a rise Fearing that this meant we were again heading up the volcano we stopped We were hungry and cold still soaked from the early morning rain We had the pineapple and the pocket knife So with few other options we half cut and half ripped the pineapple open chewing violently though the juicy fruit Pineapple strands stuck in out teeth and our cheeks stung from the acidic juice but we didn t care So after our meal we headed up the rise to find ourselves looking at the road we came in on as well as Bellavista We gratefully slid down the muddy path careful only not to hit the barbed wire fences of the farms that lined the road On our way into Bellavista
43. ble word processor standard BioQUEST form for providing feedback on BQ modules standard BioQUEST form for providing bug reports on BQ modules holds examples of how BIRDD has been used in a variety of courses tutorial to help faculty and students get started using BIRDD brief discussion of issues related to teaching evolution User Notes pdf file Adobe Acrobat file containing all of BIRDD s tables of contents information notes and How To screens an off line manual Install Info folder Mac holds record of installer setup actions Win also uninstall data ReadMe BIRDD pdf file Information on BIRDD installation and late breaking information FMTOOLS DLL CLPROOF DLL The following files are only needed on Windows computers and are not accessed by users CLLNGENU DLL FMENGINE DLL FMOLE DLL FM BRD DLL FileName DFMAIN BRD page 18 Notes on BIRDD Trouble shooting FileMaker Modes We created BIRDD with FileMaker Pro version 4 0 published by the FileMaker company We used the FileMaker Solutions Distribution Kit version 3 to bind the databases to the BIRDD stand alone application You need not own the FileMaker Pro application FileMaker has a number of features that novices find awkward Explaining these differences well enough for users to take advantage of them would we expect take time away from the biology that is our goal Our intent is to shield FileMaker novices from needing to learn much about FileMaker itse
44. cales that make it difficult for instructors to develop labs comparable to those in biochemistry physiology or behavior Yet we need only look to examples of evolution research to see how these obstacles have been overcome Evolution research involves the synthesis of many types of data and often does not directly test hypotheses with experimental protocols A great deal can be learned using comparative methods Making comparisons between species and looking for associations between traits and ecological conditions allows evolutionary biologists to test hypotheses about adaptations Harvey and Pagel 1991 Freeman and Herron 1998 We must not allow a narrow view of the nature of science to limit the opportunities that students have to learn about evolutionary phenomena through their own scientific inquiries BIRDD aims to lower the threshold for getting students actively involved with evolutionary problem solving by providing 1 raw data students may work with and 2 pedagogical ideas to help instructors structure appropriate experiences for their students One of the most difficult aspects of teaching biology 1s how to help students understand what it means to engage in evolutionary reasoning There are very few activities available that allow students to pursue investigations homologous to those of evolutionary biologists This project grew out of a belief in the value of these types of investigations for students FileName DFMAIN BRD p
45. ch as habitats food and foraging habits and illustrations of skull and jaw musculature At present most of the data are on the 13 species living on the Galapagos archipelago itself Additional data on genera subspecies and the Cocos Island Finch Pinaroloxias inornatus may be added later The notes on this file contain information about the bewildering variety of names that have been applied to Darwin s finches and explains names and abbreviations we use throughout the DFDR DFVocal vocalizations Songs and other vocalizations along with sonograms and waveform diagrams Islands information on islands Contains data about 39 of the islands in the Galapagos Archipelago Data include finches that live on the island vegetation zones physical dimensions and age There are also maps of the archipelago and of each island Weather mostly rainfall and temperature Contains about 40 years of monthly rainfall data at one location and monthly averages of temperature rainfall and other parameters at several locations and elevations FileName DFMAIN BRD page 8 Notes on BIRDD GalPics images Contains a number of habitat panoramas and pictures of habitats and organisms as well as notes by students who took many of the images Biblio Literature Contains a bibliography of over 300 entries on Darwin s finches and on the Gal pagos in general GalTrsts tourist visits Contains data on the number of tourists visiting the
46. check the volume control and click to another sound then back again You will only have to do this for the first sound in each session FileName DFMAIN BRD page 21 Notes on BIRDD VERSION NOTES 2 0 Modifications To Run On Windows Computers All images have been reprocessed to display properly on Windows computers Fonts changed from Helvetica and Times to Ariel and Times New Roman respectively This will require that computers have those fonts installed See nstallation Notes Size of most text was made smaller to fit space available on Windows Most text objects have vertical alignment set to Center Layouts have fixed 0 5 margins to permit printing on printers with wider non printable areas Other Changes Numerous changes to make BIRDD more user friendly additional error messages instructional notes on displays printed in red text additional How To pages Because BIRDD can export such a large number of different data sets and because it is so easy to export data we have removed the folder of exported data Exp Data Added BIRDD In The Classroom a separate text module to help users think about teaching with BIRDD Changes To Individual Data Sets In addition to minor changes in documentation internal bibliographies and various displays the following more substantive changes have been made Morphology Database added approx 6 700 new records from David Lack s studies of Darwin s finches
47. ck to that point and repeat from there File Name DFVOCAL BR p 1 Pictorial Displays Sonogram Display Graphs sound frequency or pitch on the vertical axis and time on the horizontal axis Pitch frequency is measured in kHz kilohertz thousands of cycles per second ak ihe WEE 3 Waveform Display Graphs sound pressure roughly loudness on the vertical axis and time on the horizontal axis Sound pressure is measured in Pa micropascals For both displays time is measured in seconds s or milliseconds ms click to play the recording File Name DFVOCAL BR p 2 1 4 Interpreting Pictorial Displays Annotated Sonogram amp Waveform Displays 1 4 5 24 5 6 6a 2 4 5 6b 3a42 123 4 5 424 5 6 6a2 4 5 6b 3a 4 2 Notes See notes with corresponding numbers below Three notes of the basic song 2 3 Silence a splice where recording was shortened Whistles start as a faint high mark on sonogram that rapidly descends in frequency and becomes stronger a The louder call indicated by the taller trace on the waveform and the darker sonogram trace White noise or static from wind other background noises and the recording apparatus The louder this background noise the broader the fuzzy band on the waveform and the darker the gray background in the sonogram The basic song a series of three quick low pitched chur or tur sounds followed by a fourth Chip a very brief sound with
48. co tourists So there we sat and sat It was hopeless After about two hours we settled for a half of a panorama and some cute tortoise action shots File Name GALPICS BRD p 6 Notes On The Image Database Following lunch at the station we went out to attempt to take our panorama of Tortuga Bay With our gear on backs and digital photos on our minds we set out for the bay again The narrow path ran up and down through the arid flora Although the sky started out as its hazey garua best it became increasingly cold and dark as we neared our coastal destination Turn around No way We had already done this once before to leave without a panorama again would be such a waste of our short time on the island Onward we walked When we could finally see ocean it began to drizzle So sit it out we decided There we sat and sat the unlucky theme of our day waiting for the sky to clear We wanted to get the incredibly gorgeous bay at its finest Unfortunately the sky became darker and darker We returned to the station that night panorama less hopeful that our excursions to come would be more successful Wednesday 8 11 99 Lava Tunnel Farms Lower Transition Upper Transition Birds Dock Los Gemalos After a quick station breakfast we set out for a cross island day trip Abandoning our bad gear induced bruised bum biking idea we arranged to have a driver take us to different locations on Santa Cruz The driver seemed really nice
49. crosoft Windows MS DOS and Windows NT are either registered trademarks or trademarks of Microsoft Corporation Helvetica Times and Palatino are registered trademarks of Linotype Hell The BIoQUEST Library and BIoQUEST Curriculum Consortium are trademarks of Beloit College Each BioQUEST module is a trademark of its respective institutions authors All other company and product names are trademarks or registered trademarks of their respective owners Portions of some modules software were created using Extender GrafPak by Invention Software Corporation Some modules software use the BIoQUEST Toolkit licensed from Project BIAoQUEST PREFACE This document contains all of the database notes and How To files from within BIRDD These can be printed to provide a manual for students to refer to Instructors can distribute copies of whichever pages are appropriate for the assignments they give their students These notes can also be viewed from within the BIRDD application by clicking on the How To button on the database Contents screens NOTE This document requires Version 4 0 or later of the Adobe Acrobat M Reader With earlier versions of the Reader some of the graphics will display poorly or not at all Version 4 0 of the Reader is available on the CD and can be installed from the Library Guide Beagle Investigations Return Darwinian Data The Darwin s Finch Data Resource DFDR Main Table of Contents version 2 0 Click
50. d pseudotemp prof pter d lat pter d med pter v lat pter v med etr pal Proc palato max Proc transpal Pterygoid Definition Jugomandibular Articular Ligament Jugomandibular Externus Ligament Adductor Mandibulae Externus Muscle Partes Medialis Adductor Mandibulae Externus Muscle Partes Profundus Adductor Mandibulae Externus Muscle Partes Superficialis Adductor Mandibulae Posterior Muscle Depressor Mandibulae Muscle Pseudotemporalis Superficialis Profundus Muscle Pterygoideus Dorsalis Muscle Partes Lateralis Pterygoideus Dorsalis Muscle Partes Medialis Pterygoideus Ventralis Muscle Partes Lateralis Pterygoideus Ventralis Muscle Partes Medialis Retractor Palatini horny keratinized covering of beak Palato Maxillary Process Transpalatus Process Pterygoid Bone Generalized Ventral View of Palate medial ridge lateral ridge intercalary lateral groove Cam hel Cam pal Cam par Cam pau Cam psi Cer oli Geo con Geo dif Geo for Geo ful Geo mag Geo sca Pin ino Pla cra Camarhynchus heliobates Mangrove F Camarhynchus pallidus Camarhynchus parvulus Camarhynchus pauper Camarhynchus psittacula Certhidea olivacea Geospiza conirostris Geospiza difficilis Geospiza fortis Geospiza fuliginosa Geospiza magnirostris Geospiza scandens Pinaroloxias inornata Platyspiza crassirostris Cactospiza heliobates Woo
51. dpecker F Cactospiza pallidus Cactornis pallidus pallidus Sclater amp Salvin striatipectus Swarth Small Tree F Geospiza parvula Gould salvini Ridgway Medium Tree F psittaculus Gould habeli Sclater amp Salvin affinis Ridgway Large Tree F Warbler F becki Rothschild mentalis Ridgway fusca Sclater amp Salvin olivacea Gould bifasciata Ridgway luteola Ridgway cinerascens Ridgway ridgwayi Rothschild amp hartert darwini Rothschild amp Hartert propinqua Ridgway conirostris Ridgway Large Cactus F Sharp beaked Ground nebulosa Gould F septentrionalis Rothschild amp Hartert difficilis Sharpe debilirostris Ridgway Medium Ground F Small Ground F Large Ground F strenua Gould Cactus Ground F Cactornis scandens Cocos F Vegetarian F Summary Table of Ecological Data Camarhynchus heliobates larg insects mangrove leaves Camarhynchus pallidus large insects often hidden some fruit Camarhynchus parvulus variety of ismall nsects fruits soft seeds Camarhynchus pauper little known between Cam psi amp Cam par FileName DFTAXA BRD Mangrove F Foraging Method pecking probing occ uses twig Woodpecker F Foraging Method pecking probing uses spines twigs Small Tree F Foraging Method shallow excavation hangs upside down Medium Tree F Foraging Method medium excavation Le
52. e DFDR Finch Vocalizations Table of Contents version 2 0 BIRDD v2 boldface buttons are functional To return to this location Select Go to DF Vocal Table of Contents under the Script menu Print All How To Pages Export data Notes On The Vocalization Database About the Database This database differs from others because of the nature of the data sounds require different controls Moreover there are pictures sonograms and waveform displays that can help you analyze sounds but which are probably unfamiliar Be sure to click on the How Play amp Interpret Sounds button on the Table of Contents and perhaps print the help pages In order to play sounds the program must be in Browse mode not Preview mode see Help screens in Main Table of Contents This means that this database performs somewhat differently from other DFDR databases In particular the Next and Previous Page commands as well as the Book pages move from one record 1 e vocalization to another In other databases these commands and controls move from one printed page to another File Name DFVOCAL BRD p 1 Notes On The Vocalization Database Background Vocalizations especially courtship territorial songs are common isolating mechanisms between species in organisms such as crickets frogs and birds This database contains a few examples of songs and calls of Darwin s finches The definitive work to date on vocal repertoires of Dar
53. e birds drinks blood Length 12 7cm Wt 18g Foraging Habitat Foraging Location moist zones rarely arid larger branches twigs Length 10 2cm Wt 8g Foraging Habitat Foraging Location all zones mostly trees bushes Scalesia Miconia zones Length 15 2cm Wt 28g Foraging Habitat Foraging Location arid zone G scandens digs gravel moves stones Length 12 7cm Wt 20g Foraging Habitat Foraging Location mostly on ground No Islands Breed Uncertain Extinct 9 1 1 Breeding Habitat No Islands Breed Uncertain Extinct 17 0 0 Breeding Habitat No Islands Breed Uncertain Extinct 5 0 0 Breeding Habitat No Islands Breed Uncertain Extinct f 0 3 Breeding Habitat Summary Table of Ecological Data Geospiza fortis various medium hard seeds few insects Geospiza fuliginosa various soft small seeds insects flowers fruit Geospiza magnirostris very hard seeds usu large few insects Geospiza scandens medium hard seeds fruit nectar pulp esp Opuntia cactus Medium Ground F Foraging Method scratch ground peck from plant Small Ground F Foraging Method scratch ground peck from plant Large Ground F Foraging Method scratch ground peck from plant Cactus Ground F Foraging Method scratch ground peck from plant Length 12 7cm Wt 20g Foraging Habitat Foraging Location all zones commonest mostly on ground in arid Length 11 4cm Wt 1
54. e or browse to the folder containing BIRDD 4 Type DFMAIN BRD into the file name box and click the Open button 5 At the Main menu click on the Pictures and Panoramas button and view the panoramas If you choose to listen with QuickTime for Macs or for Windows or an equivalent program 1 Note the location of the image and its name in the File Location field on the displays 2 Switch to your QuickTime Movie Player program or an equivalent 3 Use the File Open command to open the panorama file These are located in the B RDD DFFiles Gallmages Pans directory QuickTime Movie Player controls work as advertised in the next screen For more informaton click the nformation button in the Main Table of Contents and go to the section on Panoramas and Sounds File Name GALPICS BRD p 2 Controlling Panoramas When you click on a picture panorama image a standard QuickTime playback control bar will appear as shown below This image is inactive K Cylinder Rotates A Click anywhere in s this picture isible frame Hi of image to activate its QuickTime control gt HE NC N inactive Zoom Out button Zoom In Button inactive QuickTime panoramas are essentially windows looking out toward a cylindrical image The mouse cursor turns into a bull s eye if you hold the mouse button down on the image it becomes an arrow If you move the mouse while holding down the button the cylinder wil
55. e shown as highest contour line followed by a A few data were taken from M Jackson 1993 Island Areas Areas were measured using NIH Image to select islands on 300 dpi images scanned from the DMA map Extraneous symbols and numbers that touched island outlines were removed the default Threshold command was used then the wand tool was used to select the outside of the island outline The Measure command computed the area inside the outline as well as the outline The outline itself makes up a significant proportion of the area on small islands Assuming the middle of an outline is the actual border of the island our procedure overestimates island area However it 1s at least consistent We know of no other source of data for all of the islands and published sources vary significantly Ages of Islands Ages measured in millions of years were taken from the maximum values listed in Cox 1983 Finch Breeding Status Species were tabulated from Grant 1986 Harris 1973 1982 Lack 1947 1969 In general a species was recorded only if at least two different authors agreed on its status For some of the minor islands Grant 1986 was the only author to mention the island in these cases his data were used Vegetation Zones Data were compiled from Bowman 1961 and Harris 1982 Question marks indicate areas of disagreement Exported Data The export script and button produce a text file with the f
56. ed filename field to vocalization displays Islands Database added landmarks to Archipelago Landmarks map added locations where images and panoramas were taken to St Cruz vegetation zone map Weather Database no changes FileName DFMAIN BRD page 23 Notes on BIRDD Pictures Database New Provides 12 habitat panoramas and 17 still images of organisms habitats and landmarks Panoramic images can be rotated to see a 360 view of a scene Panoramas were created using QuickTime VR software and are not currently viewable from within BIRDD itself although one frame of each panorama is visible The notes in the database discusses several alternative ways to view these images Images may be viewed as small pictures with additional information about the image or as large images without the additional information Buttons allow switching between image SIZES A button on the table of contents displays a map of Santa Cruz island with the vegetation zones and the locations of most of the images marked Images cannot be exported as files but can be copied and pasted using the computer s clipboard or opened from the raw data file Bibliography Database New Contains over 300 references to books journal articles audiovisual materials and Web sites dealing with Darwin s finches amp or the Gal pagos islands References may be searched by author date title and type Citations can be copied individually or exp
57. ed sophisticated search or statistical functions and the various View buttons do not allow users to determine subsets of records or to select particular statistics Some databases do provide Dataset Choice buttons that let you focus displays at logical subsets of the data Faculty are familiar with the statistical and other tools of their trade and want their students to learn those tools We decided to make it easy for BIRDD users to export all records from as many data sets as possible Those data can then be imported into the appropriate programs for analysis of subsets FileName DFMAIN BRD page 12 Notes on BIRDD Exporting Data Many of BIRDD s data can be exported for use in other programs such as spreadsheets and statistics packages You can click on an export button and save data to a file with the name and location you specify In this version you have no choice of which data fields will be exported However all data analysis programs allow deletion of records and variables so you can delete those you do not wish to clutter your analyses Data are exported to tab delimited text files with each record e g a finch specimen or an island as a row and each field e g Sex BeakLength or island Area as a column These are plain text ASCII files whose data values are separated by tab characters and rows are ended by carriage returns This type of file can be read by most word processors databases spreadsheets and s
58. een s University Kingston Ontario Freeland J R and P T Y Boag 1999 The mitochondrial and nuclear genetic homogeneity of the phenotypically diverse Darwin s ground finches Evolution 53 5 1553 1563 GenBank Reference Petren K Microsatellite primers from Geospiza fortis and cross species amplification in Darwin s finches Mol Ecol 7 12 1782 1783 1998 Other Publications Petren K B R Grant et al 1999 A phylogeny of Darwin s finches based on microsatellite DNA length variation Proc R Soc Lond B 266 321 239 GenBank Reference Sato A C O hUigin et al 1999 Phylogeny of Darwin s finches as revealed by mitochondrial DNA sequences Proc Natl Acad Sci U S A 96 9 5101 5106 GenBank Reference unpublished Vincek V O Huigin C Satta Y Boag P T Grant P R Grant B R and Klein J How large was the founding population of Darwin s finches Unpublished Publication Vincek V C O Huigin et al 1997 How large was the founding population of Darwin s finches Proc Royal Soc London Series B Biol Sci 264 1378 111 118 File Name DFDNA BRD p 4 Notes On The Molecular Sequence Database Contacting GenBank GenBank National Center for Biotechnology Information Bldg 38A Rm 85 803 8600 Rockville Pike Bethesda MD 20894 U S A Tel 301 496 2475 Fax 301 480 9241 http www ncbi nlm nih gov NCBI Home Page File Name DFDNA BRD p 5 Beagle Inve
59. ent of learning biology Yet despite its central role teaching and learning evolution continues to be problematic Even without the confusion caused by the political and religious attacks on evolution education evolutionary concepts are both difficult to teach and difficult for students to understand We feel that 1s 1s important to allow students to move beyond textbook presentations of canonical evolution stories to experience for themselves how data are used to support scientific claims Without the opportunity to define and explore their own questions how can we expect students to understand scientific ways of knowing particularly the diverse and nuanced collection of approaches we call evolutionary biology The data available within BIRDD can be used to support realistic scientific inquiry into evolutionary phenomena Briefly some of the roles BIRDD might play in teaching and learning include Reference library a source of ideas and background information and summaries that can help students ask questions about evolutionary phenomena Data library a source of data to help answer questions asked by students Curricular resource a source teachers can use to develop custom exercises Source of presentation materials for maps images and data for lectures and reports The Documentation folder contains a Teaching Resources folder with additional resources to help users think about teaching and learning with BIRDD TeachingEvolut
60. er sources and in the AvgRain field unique to the NOAA BQ data Monthly averages from a variety of sources These data are taken from sources that are not consistent but do reflect the difficulty of comparisons Notes About the Data Monthly precipitation on San Crist bal from 1950 1989 NOAA 1997 United States National Oceanic and Atmospheric Administration National Climatic Data Center Global Historical Climatology Network Precipitation Data V1 URL http www ncdc noaa gov ghen ghcnV 1 CLIMVIS html visited 4 Dec 1997 Note This dataset 1s not for commercial distribution Those countries data summaries and products which are available at this site are intended for free and unrestricted use in research education and other noncommercial activities However for non U S locations data the data or any derived product shall not be provided to other users or be used for the re export of commercial services Forty year Average Monthly Precipitation on San Crist bal 1950 1989 Data are from the above source NOAA 1997 but have been summarized as part of this project and the source listed as NOAA BQ Run the View 1950 89 Rainfall Monthly statistics script to see this summary Six year Averages 1965 70 of Meteorological Readings by Charles Darwin Research Station Data are from Harris M P 1982 A Field Guide to Birds of Gal pagos London Collins Average Monthly Precipitation and Temperature at
61. ers that took us to Mark led us to the water tower located a five minute hike from the Botany building So in our slightly improving Spanish we talked with the volunteers learning more about the island and the places we would want to visit and photograph Because the center of the water tower had a large pole in the center we weren t able to set up the tripod to get a picture that didn t include the pole Our only option appeared to be setting up the tripod head on top of the already existing pole with the help of some string and a lot of duct tape But after this improvisation we had our first true panorama which we dutifully stitched on our computer and saved on a few Zip disks We showed off our panorama to the rest of our group then waved good bye as they left for Genovesa leaving us on our own for the next ten days File Name GALPICS BRD p 3 Notes On The Image Database Saturday 8 7 99 In addition to the vegetation zones we were told to take panoramas of anything interesting anything related to geology or even life in the town that would visually represent what the island was like We decided that lava tubes would be an interesting subject to photograph So after reading an article in the library we rented mountain bikes and headed in the general direction the article gave us After an extremely difficult fifteen minute ride up the side of the mountain in the mist called gar agar a with all our camera equipment we came
62. es All i From To s The display may be blank To get back to work either select Go To Table of Contents from the Script menu or press 1 Mac or CTRL 1 Win If you are still confused the ultimate fix is to return to the Main Table of Contents Select Go to Main Table of Contents from the Script menu FileName DFMAIN BRD page 8 Beagle Investigations Return Darwinian Data The Darwin s Finch Data Resource DFDR Finch Morphology Table of Contents version 2 0 8IRDD v2 To return to this location Select Go to DFMorph Table of Contents How To Onrintl Interpret under the Script menu Measurement Diagrams List All View Samples Statistics by Statistics by Data Sets From Each Island Species Subspecies wr View All Data on Statistics by Statistics by SE onoma Taxa Each Specimen Island Species Island Subspecies List Modern View Table of Statistics by Statistics by Species Morphology Data Species Island Subspecies Island List Modern Subspecies Ed x Eu WT Dataset Choice Export Selected Dataset This button lists all of the datasets Other buttons display only data from the subset selected in the Dataset Choice box See database Notes gt Notes on Darwin s Finch Morphology Data About the Database The DFMorph Darwin s Finch Morphology database contains data mostly morphological e g beak dimensions on individual Darwin s finches The data are from a number of publis
63. fferent zones and made the best of what summer weather on the Galapagos could give us Thursday 8 12 99 This was it We had every vegetation zone except for the coastal zone despite our two previous trips So we decided to grab our gear and head to Tortuga Bay The sun was shining and there didn t seem to be a cloud in the sky but we knew how quickly that could change We walked as fast as we could especially considering the amount of equipment we were carrying When we arrived at the beach it had gotten slightly overcast but no rain in sight We quickly hurried to the spot we had decided to take our panorama at the first time we visited Once there we learned it was a popular spot A group of eighth graders on a class trip from Quito were playing and a family had decided to picnic on the beach Considering the rather nice weather we decided to wait After about thirty minutes the school group had moved on after leaving some designs in the sand and the only people in our way were the family We finally asked them if they wouldn t mind moving for a few moments We then ended up explaining our project and showed them everything about the digital camera They were happy to help us out and even amused when we realized that a picture of one of their towels was in a mangrove picture We were done It as a relief to realize we had accomplished everything we had hoped to We decided to celebrate by going to the restaurant at the Hotel Sol y Ma
64. g consists of a drawn out raspy bizzzzzz that Bowman characterizes as a high pitched growl Abbreviate basic song is a shortened form of the basic song in which the extended middle buzz 1s shortened as in ree search ree search Derived song has two variants a polysyllabic form e g tee you tee you or chee tee chee tee a monosyllabic form e g churr churr churr chur Variations occurred within and between populations of one species and between different species Some populations borrowed calls from other species Harris 1982 noted that the range of variation within any one population is greater than the differences between species Also there are considerable inter island differences in song Clearly identifying species by songs alone is only for the very experienced File Name DFVOCAL BRD p 2 Notes On The Vocalization Database Bibliography Bowman R I 1983 The evolution of song in Darwin s finches Patterns of evolution in Gal pagos organisms R I Bowman Berson M amp Leviton A E San Francisco Pacific Division AAAS 237 537 Castro I C and A Phillips 1996 4 Guide to the Birds of the Gal pagos Islands Princeton NJ Princeton University Press Charif R A S Mitchell et al 1995 Canary 1 2 User s Manual Ithaca NY Cornell Laboratory of Ornithology Curio E and P Kramer 1964 Vom Mangrovefinken Cactospiza he
65. getation zones found on the islands The Galapagos and especially Santa Cruz Island presented an interesting location to do research Besides being incredibly remote Santa Cruz Island proved to have completely unpredictable weather unpredictable wildlife and plenty of completely unpredictable situations We began to prepare for our photography experience back at Colgate Over the course of three to four weeks we researched vegetation zones on the Galapagos Islands as well poring over countless maps and pictures trying to find the best places to get the pictures we were looking for We also had to find time to learn how to use our digital camera as well as the computer programs that would store the pictures we took and stitch them into digital panoramas computerized images that allow a viewer to see a full 360 view of an area After a few days of intensive camera and computer training we felt ready to handle at least the technical aspect of our job We were unsure on exactly where we should be taking pictures however While we were able to find many articles and web sites detailing the different zones as well as the different vegetation and wildlife we would find in them we were rarely able to locate anything that could tell us where we should be taking pictures We knew we were limited to Santa Cruz Island due to the difficulty of transportation between islands We also knew that the six zones that were represented on that island were all d
66. h L69 at the end of the field name In addition wherever possible we have also recorded the original author s name See references and notes in the Species database for more details Some of the taxonomic names are lengthy so we also have a more compact Species ID as well as a Subspecies ID where necessary The Species ID is made up of the first 3 letters of Lack s genus a period and the first 3 letters of Lack s species name For subspecies a period and the first 3 letters of Lack s subspecies name are added For example the specimens of sharp beaked ground finches on Darwin Culpepper have the following values Field Name Example Taxon Taxon Original Geospiza septentrionalis Taxon L69 Geospiza difficilis septentrionalis Genus L69 Geospiza Species L69 difficilis Subspecies L69 septentrionalis Species ID Geo dif Subspecies ID Geo dif sep Filename Dfmorph brd printer 10 10 2000 page 2 Filename Notes on Darwin s Finch Morphology Data Notes on Data Fields Attribute Age Plumage Wing Tail Culmen Gonys Basal Width of Bill Basal Depth of Bill Tarsus Dfmorph brd The terms beak and bill are used interchangeably Database Field and Notes Sex Here are notes on commonly used data and measurements Specific definitions and procedures for that source s data are described later Click on the Measurement Diagrams button on the Table of Contents to see pictures summarizing the vario
67. hed and unpublished sources Additional information includes the publication source of the specimen the original specific or subspecific name assigned by the author s museum location and catalog number and other information of historical importance In particular Sulloway s 1982 measurements of existing Beagle specimens have been included This version contains data from four sources The first three were in BIRDD version 1 the last is new with version 2 The largest published collection of measurements taken from Snodgrass amp Heller s important early work 1904 Sulloway s historically significant examination of the history of all surviving finch specimens collected by members of the Beagle expedition 1982 Measurements published in Swarth s 1931 monograph 2 Over 6 500 specimens that David Lack measured for his 1945 monograph and 1947 book Lack deposited copies of his measurements in the British Museum Natural History and the California Academy of Sciences CAS we optioned copies of the latter from the CAS Archives These more extensive data provide many opportunities for students to explore variation among individual finches and island populations and to try to understand how taxonomists separate specimens into species and subspecies There is considerable overlap among these subsets of data Some specimens such as those of the Beagle expedition may appear in all of them The Dataset Choice field on the Table of C
68. here are between species As Castor and Phillips 1996 note Clearly this fascinating group is in a state of almost visible evolutionary flux and much further study 1s needed Summary of Taxonomy Most modern authors stay close to Lack s scheme 1945 1947 1969 which was in turn based on Swarth s 1931 Lack recognized fourteen species with a total of about 30 distinct subspecies on the Gal pagos Since Swarth s and Lack s work there has been little disagreement about the delineation of the 14 species or about their general relationships There are some debate about a few names for example Sulloway 1982 argued for changing difficilis to nebulosa on historical grounds but difficilis 1s well ensconced in the literature and most modern authors stay with the traditional name The major point of discussion 1s about genera especially the genus for pallidus and heliobates Genera are rather arbitrary so this 1s a point on which reasonable people can disagree Lack 1969 followed by Harris 1973 1983 and others feel that 14 species should not be split into too many genera they lump pallidus and heliobates 1nto Camarhynchus Swarth 1931 Bowman 1961 1963 and Grant 1986 feel that pallidus and heliobates are distinctive enough e g 1n appearance ecology and song and deserve recognition as belonging to their own genus Cactospiza and pallidus becomes pallida for grammatical reasons At the other end of the lumper splitter spect
69. ia or next request Criteria active Click on the Add OR button to create the 2nd and 3rd requests Deletes the active request 1 Request P H first author AND B R elsewhere OR 2 Request B H first author AND P R elsewhere The heavy bar text cursor and field outlines mark this as the active request OR 3 Request P R AND B R as secondary authors The requests shown find 41 references with both authors as primary or secondary authors Deleting the 3 request finds 38 works with only those two authors and no other authors FileName BIBLIO BRD page 6 NOT searches when you need to find references which must NOT have some criteria put those criteria in multiple requests by clicking on the Add NOT button Example a search for all journal articles with the taxon names Geospiza Geospizidae and Geospizinae but which were NOT written by a Grant would look like this Find a Fefe Click on the Add NOT button to create the 2nd request Symbols 7 Scr ipt Cancel 1 Request geospiz finds geospiz in a title word followed by any number of characters a dae inae AND Journal Article NOT 2 Request Omit references with Grant in the author field X in the Omit box shows that this is a NOT request The heavy bar text cursor and field outlines mark this as the active request The requests shown find 21 references with all of the criteri
70. iddle rectrices to tip of the longest p 9 Culmen Upper Beak Length Measured in a straight line from a point where the feathers cease to hide the culmen to tip of maxilla the chord of the exposed culmen p 9 Depth of Bill at Base Beak Height measured from the base of culmen to angle formed by feathers at lower edge of ramus of mandible p 9 Width of Mandible Beak Width measured at base of lower mandible p 9 Tarsus Tarsus Length measured as a straight line from center of heel joint on posterior side to joint between metatarsus and middle toe on anterior side p 9 Middle toe with claw Middle Toe Length measured along upper side from joint between metatarsus and middle toe to tip of claw p 9 Swarth measured a small number of the type series of Geospiza magnirostris in the British Museum and these data are included There has been considerable confusion over the exact collection locality of Darwin s and other Beagle specimens Sulloway 1982 so those designations are enclosed in quotes and they should not be taken at face value See Sulloway s records for the best data on the Beagle collections Swarth provided a number of profiles of individual specimens mostly natural size These have been scanned and included in the dataon each finch Filename Dfmorph brd printer 10 10 2000 page 5 Notes on Darwin s Finch Morphology Data Sulloway 51 specimens Sulloway has s
71. ing that Wednesday was to try and find places to take pictures So we set off to find anyone in the station who could help us After asking for directions in the Station library we made our way to the Botany building located about fifty feet from the library We in our limited Spanish managed to ask if anyone knew someone who may be able to help us Two helpful station volunteers introduced us to Mark an Australian botanist who knew the island well He gave us a list of places that would offer the best representation of the vegetation zones Now we just needed to find out how to get there Thursday 8 5 99 On Thursday our search finally led us to Sarah a Canadian masters student whose specialty happened to be introduced grasses 1s the highlands or the uppermost area of the volcano After talking to her we learned that by venturing into the highlands we would be able to get excellent panoramas of both the Miconia Zone located at Media Luna a half crater on the side of the volcano and the Pampa Fern Sedge Zone located at Cerro Crocker the highest point of the volcano She was going up to the highlands the following Monday she said Would we like to come along Not knowing completely what we were getting into we agreed We would meet her outside our hotel Monday at 6 00 A M In the meantime we decided to search for the perfect panorama of the Arid Zone the zone in which the station and the town were located The same helpful volunte
72. ion pdf discusses some of the educational issues involved in teaching evolutionary biology ClassRmExamples pdf shows how BIRDD has been used in a variety of majors and non majors biology courses in large and small schools GettingStarted pdf contains tutorials illustrating how to use the BIRDD to 1 Navigate to find and print reference information data and summaries 2 Export numeric data and analyze them in other applications 3 Export non numeric data like images panoramas and sounds to other applicatons 4 Work through a question and analysis Our Web site http bioquest org birdd includes these and additional materials related to teaching and learning with BIRDD FileName DFMAIN BRD page 3 Notes on BIRDD Request for Feedback amp Suggestions This module is a work in progress As you will see we have collected and organized a variety of potentially useful data and materials but we plan to add more As the project evolves we hope BIRDD will support truly novel approaches to teaching evolution We are anxious for your feedback on the materials provided here your ideas for how these resources can be used in teaching biology and your suggestions for future directions of the project We are dependent on you to share your experiences and insight to make this module more useful While faculty and students using BIRDD cannot modify the contents of the data files we welcome suggestions for additional data We especia
73. is clean sequence to the computer s clipboard from which it can be copied to other programs File Name DFDNA BRD p 1 Notes On The Molecular Sequence Database About the Data There is considerable variation in how data were entered into GenBank records this is the inevitable consequence of the fact that different researchers are entering data on a variety of macromolecules In addition errors were made so that particular entries do not fit GenBank standards E g fields like DEFINITION and KEYWORDS should contain a period but some do not NCBI 1999 The raw GenBank records contain a number of inconsistencies e g scadens instead of scandens in the DEFINITION field These do not affect genus or species names in displays or printouts except in raw GenBank records Also the REFERENCE fields in GenBank records typically reflect publication status at the time records are entered into GenBank often unpublished or in press We made no attempt to update these fields but the Bibliography below groups the GenBank references with actual publications Exporting Sequence Data GenBank sequences displayed on screen and printed have nucleotide or amino acid numbers before each line and blanks inserted every 10 characters for readability To copy a single sequence without line numbers and blanks for use in programs such as the DNA Electrophoresis Bio QUEST module Select a dataset to view and click the View Sequence Summaries button
74. l Acrobat Reader version 4 0 or later Installers for the Acrobat Reader version 4 0 for both Macintosh and Windows are included on the Library CD FileName DFMAIN BRD page 14 Notes on BIRDD To use the Online Guide to install BIRDD 1 Insert the Library CD that is compatible with your computer system into your computer s CD drive If necessary locate the Acrobat Reader installer on the main level of the CD and install the Acrobat Reader Then locate and open the Online Guide document The Online Guide is located on the main level of The BioQUEST Library CD 2 To install BIRDD follow the Installing a Module instructions in either the Quick Start section on the Home page of the Guide or in the Using the Online Guide section Once BIRDD is installed on your hard drive 3 Check your fonts and monitor settings next topics 4 Double click on the BIRDD Mac or BIRDD EXE Win icon or shortcut to start BIRDD Fonts The fonts used in all layouts are Arial Courier New and Times New Roman If these fonts are not installed in your computer screens and printed pages will be poorly formatted and some information may be unreadable All Windows computers and Macintoshes with Microsoft software will have these fonts already installed If your computer does not have them you should download them from http www microsoft com typography fontpack default htm Scroll down the page and download Arial sit hqx TimesNew sit
75. l rotate to show more of the image in that direction The image will move left or right and up or down as you move the mouse The faster amp farther you move the mouse the faster the cylinder will rotate Click on the zoom buttons to bring the image closer or farther File Name GALPICS BRD p 1 Beagle Investigation Return Darwinian Data The Darwin s Finch Data Resource DFDR Bibliography Table of Contents version 1 BIRDD v2 To return to this location Select Go to Biblio Table of Contents under the Script menu Print All How To Pages Summary by Reference Type Summary by First Author List All Refs By Find By Author Date References Preview All Refs By Type Author Date po Ae Return to Main Table of Contents Notes on Bibliography Database About the Database INTRODUCTION This database contains over 300 references to literature and World Wide Web sites on the Gal pagos and on Darwin s finches This 1s a preliminary version of a more full fledged bibliography we hope to provide in a future edition of BIRDD Bibliographic databases are complex and while a number of them are available as stand alone programs e g EndNote and ProCite we hope however to provide significant functionality from within BIRDD so users do not need to buy additional software FINDING REFERENCES This database required somewhat more sophisticated search capabilities than other BIRDD databases so we have provided ex
76. lf New users should look at the How To Navigate Around BIRDD screens to learn what to look for If there is some confusion about where you are in BIRDD perssing Apple 1 Mac or CTRL 1 Win will take you back to the table of contents for the database you are using and clean up the screen display If you want more background understanding read the rest of this topic if not skip to the next one FileMaker has three operating modes one called Layout for changing the structure of the database and views of the data and Browse and Preview for viewing data Layout mode is used by programers and is protected by a password Students and instructors will use the other two and there are some inherent advantages and limitations in each that users should be aware of See the How To button on the Main Table of Contents for more details on how to use the modes In Browse mode you can see only individual records e g data on individual finches or islands The scroll bars and Status Area Book controls move through the entire database record by record Most importantly you cannot see summary information e g averages for a species The latter are visible only in Preview mode Preview mode allows you to see exactly what is going to print on a page but the horizontal and vertical scroll bars move only within that single printed page To see another page you must use the book icon in FileMaker s status area on the left of the screen or the Next
77. liobates Snodgrass und Heller Zeits Tierpsychol 21 223 234 Harris M P 1982 A Field Guide to Birds of Gal pagos London Collins Notes About the Data Data Sources The vocalizations in this database were provided by the Library of Natural Sounds at the Cornell Laboratory of Ornithology Waveform and sonogram images were produced using the Canary software program developed by the Bioacoustics Research Program also at the Lab of Ornithology Additional information on these fine organizations and their resources can be found at the following locations Library of Natural Sounds http www ornith cornell edu LNS LNS htm Bioacoustics Research Program BRP http www ornith cornell edu brp brp htm Cornell Laboratory of Ornithology http www ornith cornell edu 159 Sapsucker Woods Road 607 254 BIRD 607 254 2473 Ithaca NY 14850 1999 All sounds are copyrighted by the Cornell Laboratory of Ornithology Unless you obtain permission from the Laboratory you may not use or reproduce these sound except in the course of using this database for educational noncommercial purposes File Name DFVOCAL BRD p 3 Notes On The Vocalization Database Sound Files and Formats Raw sound files were provided by the Library of Natural Sounds on CD in audio CD format Each sound was converted to a Macintosh sound file 44 1 kHz sampling rate 16 bit amplitude resolution monaural using the SimpleSound application and saved as Quick
78. lity of his measurements see notes below for the Culmen Beak measurements were made with dial calipers to nearest 0 1 mm Culmen Upper Beak Length measured from the tip of the bill to the place where the culmen joins the skull This differed from Swarth s approach and with several species Lack was unable to estimate accurately the exact place where the culmen ended on the skull measurements of the same specimens taken a month or two later sometimes gave different results 1945 p 75 Unfortunately Lack appears to have decided to stop collecting or tabulating this measurement This reduces the comparability of his data with those of earlier workers Culmen From Nostril The distance from the anterior edge of the nostril to the tip of the upper beak This is the measurement that Lack and Sulloway decided to use in place of Swarth s exposed culmen In his published work Lack typically used culmen to refer to this measurement Bill Depth Bill Height measured at the base with the bill closed Some specimens had been stuffed with the bill slightly open and these were not measured Wing Length measured from the carpal joint to the end of the longest primary in the flattened wing measured with a millimeter rule to the nearest 1 mm Note that Lack and Sulloway flattened the wing while Swarth measured the wing in natural position Filename X Dfmorph brd printer 10 10 2000 page Notes on Darwin s Finch Morph
79. lly urge researchers with suitable raw data to contact us about adding more data Frank Price fprice Ohamilton edu gt Sam Donovan lt ssdonova students wisc edu FileName DFMAIN BRD page 4 Notes on BIRDD Historical Perspective on Darwin s Finches Early bird taxonomists did their work over the barrel of a gun and prepared stuffed study skins that form the core of most museum collections They usually based species descriptions on the morphology color etc of small numbers of specimens often only one Inherent in Darwin s theory of evolution was the idea that species were populations of individuals and that species descriptions should be based on statistically adequate samples Moreover there are many more important characteristics than the static morphology of a stuffed specimen e g soft tissue anatomy behavior life history biomolecular sequences etc From hindsight much of the early work was crude and of very limited scope nevertheless researchers such as John Gould Robert Ridgway and others paved the way toward our current conception of the evolution and taxonomy of Darwin s finches Collecting expeditions in the late 1800 s and especially the Hopkins Stanford Galapagos Expedition in 1905 6 provided most of the specimens of Darwin s finches available in museums With the development of new statistical techniques and the advent of population genetics in the 1930 s taxonomists began to examine larger number
80. n notes to Main file All images converted and reimported to work on Windows computers Filename Dfmorph brd printer 10 10 2000 page 8 Beak Height Beak Width Filename Measurements Used by Sources Upper Beak Length or Culmen Lower Beak Length Gonys Dfmorph brd Nostril Upper Beak Length Lack s method method of Snodgrass amp Heller Sulloway Swarth l Tarsus Length page 1 Beagle Investigations Return Darwinian Data The Darwin s Finch Data Resource DFDR Finch Molecular Sequence Table of Contents ion 2 0 iino v2 To return to this location Select Go to Sequence Table of Contents under the Script menu View Table of Sequences amp Taxa View List of Primary References View Synopsis of Each Sequence View Full GenBank Records Dataset Choice nm Export GenBank Records These buttons list all of the datasets Other buttons display only data from the subset selected in the Dataset Choice box See database Notes Notes On The Molecular Sequence Database Database Notes Introduction This database contains sequences of seven nucleic acids and proteins from 207 individual finches representing thirteen species and three or four genera It also includes sequences from 6 individuals of two suggested sister taxa of Darwin s finches Coerba flaveola and Tiaris olivacea Viewing the sequence data in this database is relatively uninteresting However
81. n to the station for the day to work on our other task of finding articles and pictures on and of the smaller more remote islands After completing some work in the library we returned to our hotel to try to stitch our lava tube pictures into a panorama File Name GALPICS BRD p 4 Notes On The Image Database It was then that we discovered our computer wouldn t turn on The garua and constant humidity had already proven to be too much for out little laptop to handle We spent the rest of the night talking to various people and trying to find out what options we had Almost all the pictures we had already taken were lost with the exception the water tower panorama We spent most of the night trying to figure out what we should do about saving pictures and having enough memory for all the pictures we planned to take At about 9 P M we realized that we were going to be going to the highlands for eleven hours the next day and we ought to bring something to eat with us Unfortunately it was 9 P M on a Sunday night We ended up with two oranges four pieces of bread and a small pineapple Monday 8 9 99 So Monday morning came and we got into the same pick up truck that brought us to the station and went off past Bellavista to the beginning of the trail to Media Luna and Cerro Crocker On the way to the trail we began to experience more and more gar a as we climbed in elevation When we got to the trail the mist had let up but the ground
82. nd paste methods to move images one at a time e g to NIH Image Note that images and sounds are copyrighted and may not be freely distributed Sound files are available 1n the Raw Data folder as either AIFF sound files or MOV QuickTime movie files FileName DFMAIN BRD page 13 Notes on BIRDD INSTALLATION amp TROUBLESHOOTING NOTES System Requirements Macintosh System 7 7 1 recommended 4MB available RAM QuickTime 3 to view panoramas Windows Windows 3 1 95 recommended 8 MB available RAM QuickTime 3 to view panoramas and play sound files Both 140 MB free hard disk space color monitor with 800 x 600 or better pixel resolution at 256 colors Installation Issues BIRDD will not run properly from the CD ROM it must be installed on each computer s hard disk The best way to install the BIRDD application is to use the BioQUEST Library Online Guide The Online Guide is an interactive Adobe Acrobat PDF document that provides access to the entire contents of The BioQUEST Library The Online Guide contains a short description of all of the software applications text modules datasets and tools in the Library with links to related documentation and to the module installers The Online Guide can be used on either a PC or a Macintosh computer In order to use the Online Guide you will need to have the Adobe Acrobat Reader installed on your computer For best results we suggest that you instal
83. nfall 1950 1989 on San Crist bal Total Monthly Rainfall Rainfall mm 400 300 200 no data no data 1980 1990 Summary by Month 625 500 extreme Y o outlier 3 5 O Rainfall o 6 mm O 250 O 8 125 X 9 O 0 LL 9 zum mmm D a a mm 1 2 3 4 5 6 7 8 9 10 11 12 Month FileName WEATHER BR page 1 Beagle Investigations Return Darwinian Data The Darwin s Finch Data Resource DFDR Galapagos Pictures Table of Contents wersion 1 0 pino v2 boldface buttons are functional To return to this location Select Go to Picture Table of Contents under the Script menu Print All How To Pages Map of Image View Habitat Locations Habitats Panoramas All Images small i S miman View Still Images All Images large vr si Contents Export data Notes On The Image Database About the Database INTRODUCTION This database contains a number of pictures of Gal pagos habitats organisms and data including panoramic images that allow you to rotate to see a 360 view of a scene Current keyword and search capabilities are crude but will be refined in future versions You may view images either as small pictures with additional information about the image or as large images without the additional information Buttons allow you to switch between image SIZES The Map of Image Locations Habitats button will show you a map of Santa Cruz island with the vegetation zones
84. ng a pause in the downpour After that adventure we decided to head to Media Luna We climbed up and down along the muddy paths falling a number of times all the while carrying our equipment Our brief respite from the garua was followed by a harder mist but with fewer winds Finally we came upon a casita or guard station that Sarah said marked the edge of the Miconia Zone We sat on the edge of the porch and ate the last of our bread It was 10 A M Hearing our voices one of the men inside of the casita came out Seeing the state we were in he invited us into the casita with him and his coworker to warm up and dry off In halting Spanish we explained our goal to the two men pest control agents working for the nation park service They took pity on us and gave us coffee offering to let us stay as long as we wanted We warmed up for about ten minutes then headed out to get our pictures It had stopped raining at that point allowing us to get a nice panorama of the Miconia Zone But even without the rain it seemed like there was constant condensation Thus the Wiper Method in which after every picture one of us would try to find a somewhat dry piece of clothing to wipe the water droplets of the camera lens We then decided to head back even though we had about five hours before we were to meet Sarah File Name GALPICS BRD p 5 Notes On The Image Database We followed the path past the guard house and continued down to what appe
85. ngth 140cm Wt 18g Foraging Habitat Foraging Location mangrove swamps tree trunks branches Length 15 2cm Wt 20g Foraging Habitat Foraging Location Miconia amp Scalesia transition arid coastal tree trunks large branches Length 11 4cm Wt 13g Foraging Habitat Foraging Location commonest in Scalesia transition some arid tips of small branches twigs more on ground than other Cam Length 12 7cm Wt 16g Foraging Habitat Foraging Location No Islands Breed Uncertain Extinct 2 0 0 Breeding Habitat Mangrove swamps No Islands Breed Uncertain Extinct 5 l 0 Breeding Habitat commonly in Miconia amp Scalesia zones less often 1n arid zone No Islands Breed Uncertain Extinct 9 0 0 Breeding Habitat No Islands Breed Uncertain Extinct 1 0 0 Breeding Habitat p 1 Camarhynchus psittacula variety of large insects Certhidea olivacea insects Geospiza conirostris more open ground than soft medium hard seeds large insects fruit nectar pulp Geospiza difficilis humid on central isls arid on N isls little known soft seeds insects flowers Large Tree F Foraging Method deep excavation twisting bill Warbler F Foraging Method pick from surface occ fly catch on wing Large Cactus F Foraging Method scratch ground peck from plant Sharp beaked Ground F Foraging Method scratch ground pick from plant pecks larg
86. of the Charles Darwin Research Station Farms folder images of farms Finches folder images of finches Sounds folder holds sound and other raw data files aiff files are audio files readable by many programs mov files are QuickTime files E_Sounds folder edited sound files used by the DF Vocal database O_Sounds folder original unedited sound files DFMAIN BRD file BIRDD s Main Table ofContents general introduction and notes DFMORPH BRD file finch morphology database DFTAXA BRD file species database skull and other species level images DFVOCAL BRD file vocalization database GALPICS BRD file images of habitats organisms amp locations GalTrsts BRD file tourist fisits database GBLines BRD file utility file of molecular sequence data used by DFDNA database to print amp export data not directly accesssed by users ISLANDS BRD file island database ISL_NAMS BRD file utility file of island names used by other files not directly accesssed by users MAPS BRD file utility file of map images used by other files not directly accesssed by users WEATHER BRD file weather database Documentation folder holds information about BIRDD and feedback forms Documents in MS Word folder Feedback Form pdf file Software Bug Report pdf file Teaching Resources folder ClassRmExamples pdf file GettingStarted pdf file TeachingEvolution pdf file holds editable copies of the following Adobe Acrobat pdf files requires MS Word or compati
87. of the bill in the Galapagos genus Geospiza Auk 19 367 381 Steadman D W 1982 The origin of Darwin s finches Fringillidae Passeriformes Transactions Of The San Diego Society Of Natural History 19 19 279 296 Sulloway F J 1982 The Beagle collections of Darwin s finches Geospizinae Bull Br Mus Nat Hist Zool 43 2 49 94 IM Notes About the Data Finch Status On Islands This table may be confusing as 1t attempts to present the data on which islands each species inhabits as compactly as possible Summary of numbers of islands are next to the species noame data for each species appear in two rows in the top row are the data for major islands and data for minor islands are in the second row Island names are shown in compact ID form The codes are as follows B known to breed regularly on the island well documented by several sources p possibly breeds on the island amp or sources disagree o known to occasionally breed on the island S believed to have been collected on island probably not a resident X known to breed in past but now extinct To summarize the distribution we have also totaled the number of islands for each species as breeding uncertain p o s and extinct Miscellaneous Notes Version History Version 2 0 List of species E subspecies revised slightly and expanded to subspecies AKA list expanded to include more synonyms but is still incomplete Added images of
88. ol your view of a single page page of data Click the top sheet The to page up Scroll Box Thumb Click on the bottom sheet and gray paga on Scroll Bar are visible only if part of the data window is not 1 current page number visible 26 total number of pages E Click in the gray part of the scroll Bookmark bar to move one windowful in Drag up or down to move more than one page at a time e g to top or bottom page i that direction Drag the scroll box to the top or bottom of the scroll bar to jump to the top or bottom of the window Gray Status Area A a C n Click the amp Book appear when PP Scroll arrows to move the there is more than one It the entire data window is windowipthatdirection page of data visible the scroll bar is empty Preview Browse Mode pop up menu like this horizontal bar use to switch between Preview amp Browse modes see pages 5 for more FileName DFMAIN BRD page 2 Navigating Around BIRDD Menus Three of the menus are of use within BIRDD If you select another menu command the data window may become confusing or empty If so select the Go to db Table of Contents Script menu command The File Menu allows you to Print many displays and to Quit from BIRDD y Mode Menu allows you to shift between browse and preview modes see pp 5 7 The Script Menu allows you to select various information displays Script menu y commands parallel the but
89. ollowing data fields Field Column Heading Is1 ID Island Name Area km Elev m Age No Ferns No FlPlants No LandBirds No Finches Zone Mangrove Zone Arid Zone Transition Zone Scalesia Zone Miconia Zone Grassy Comments Short Island ID code Long Common English name Area of island in square kilometers Maximum elevation of island in meters Maximum age of island in millions of years Number of species of ferns Number of species of flowering plants Number of species of land birds Number of species of Darwin s finches breeding ank gt zone not present on island X zone present on island 7 zone possibly present on island no zone data available for island j y bl j j j j file Islands page 2 Gal pagos Archipelago Islands Land Area Darwi O arwin Culpepper Cocos Isl oem UN Pinta Abingdon Length SUE Genovesa Tower 430 km 2 Roca Redonda Marchena Bindloe Length SW NE Bartolome Bartholomew 220 km Santiago o James ainbridge Rocks Daphne Major amp Minor Distance Seymour N Seymour to Mainland j A Baltra S Seymour 1000 km 14 c Guy e jon Fawkes Santa Cruz Fernandina Eden Indefatigable Narborough paS N Pinzon ieee Norte Plaza Sur Duncan Isabela Santa Fe Albemarle Barrington Sin Nombre Nameless ma Los Hermanos Crossman E Torttiga San Cristobal eran Camp on Champion Chatham Enderby 80 km n a Caldwell Es
90. ology Data Exported Data The export script and button produce a tab delimited text file with the following column headings Field Column Heading Comment Source Source of data IslandID Short name of island TaxonOrig Name of taxon assigned by author SpeciesID Short species name Gen spec SubspID Short subspecies name Gen spec subs Sex Sex of specimen Plumage Plumage state BodyL WingL TailL BeakW BeakH measurements described in Notes About the Data LBeakL UBeakL y N UBKL TarsusL MToeL Age is no longer exported see Notes on Data Fields above To avoid duplicate records in exported data the All dataset cannot be exported If the Export button is clicked when All is selected BIRDD provides an error message Miscellaneous Notes Version History Version 2 0 Lack s data stored at the California Academy of Sciences were added to the database Minor changes and corrections were to many layouts Added new statistical summaries Added buttons and scripts to list data sets and original taxa Changed most buttons and scripts to display the data from only one dataset Moved Sulloway Upper Beak data to the correct Nostril Culmen field instead of the incorrect Culmen field Modified list of exported data and rearranged columns removed Age modified to export data from only one dataset at a time Added diagram of measurements Version 1 1 Font and layout changes as covered i
91. ontents allows you to determine which set of data to examine and export Bibliography Lack D L 1945 The Gal pagos finches Geospizinae a study in variation Occasional Papers of the California Academy of Sciences 21 1 159 Lack D L 1947 Darwin s Finches an essay on the general biological theory of evolution Cambridge England Cambridge University Press Lack D L 1969 Subspecies and sympatry in Darwin s Finches Evolution 23 252 263 Snodgrass R E and E Heller 1904 Papers from the Hopkins Stanford Galapagos Expedition 1898 99 XVI Birds Proc Wash Acad Sci 5 231 372 Sulloway F J 1982 The Beagle collections of Darwin s Finches Geospizinae Bulletin of the British Museum Natural History Zoology series 43 49 94 Swarth H S 1931 The avifauna of the Galapagos Islands Occ Pap Calif Acad Sci 18 5 299 Filename Dfmorph brd printer 10 10 2000 page 1 Notes on Darwin s Finch Morphology Data Notes About the Data Taxon Names and IDs The initial confusion and debate over the classification of Darwin s finches settled down in 1931 with Swarth s monograph Lack made relatively minor changes 1945 1947 1969 and with some exceptions that is the system used by most modern workers We have elected to use Lack s 1969 classification as our standard Lack s names for genus and species names plus subspecies if appropriate are the modern taxa and are listed wit
92. oomed away for a while When we walked back to the truck Baltra was in clear view Near by Blue footed Boobies had a break from Frigate theft The Frigates were much too preoccupied A group of fishermen had just returned with their catch Frigates and cranes swarmed overhead in anticipation of some fresh seafood At the same time a new load of tourists came across from Baltra After watching the activity at the dock we decided to head back to get the final images for the day On the way back towards Puerto Ayora we stopped at Los Gemalos the twin pit craters Tourist buses came and went as we took pictures of the tremendous craters Tuan pointed out an avocado plant that sticks out of the very center of the pit This introduced tree seemed to peak out of nowhere Obscured by the thick mist the craters looked fantastically surreal Hesitant that the pictures would no do the striking scene justice we wanted to wait out what we thought was merely bad weather We thought that we could wait out the worst of the misty gar a surrounded us The driver told us otherwise In that case he told us we d be there the whole summer He advised us to just take the picture since the air didn t get much clearer through the dry season Taking his advice we took the pictures and then stood gasping at the impressive size of the craters for a while Then we were station bound after a successful day of tubes craters and vegetation panoramas We located the di
93. orted to text files There are extensive notes on how to use BIRDD s find capabilities Tourists Database New Contains the number of tourists visiting the islands per month from 1970 through the middle of 1997 Data may be viewed as a table or exported to a tab delimited text file for import into other software Version 1 0 This version of BIRDD 1s a first draft or prototype and we plan to make many changes as time and resources permit We encourage anyone using it to send feedback and suggestions to fprice hamilton edu Of course if you have questions or problems you should also write The user interface and controls are rather simplistic consisting of buttons and scripts with little that users can change The data are provided as is and users cannot change them or add to them If you know of other useful data sets please contact us This version has not been tested in multiuser mode Use in single user mode only Use it in multiuser mode at your own risk although we would appreciate feedback if you try it FileName DFMAIN BRD page 24 The Print command on File menu prints z only this one page To print all How To Navigating Arou nd BIRDD pages use the Print All How To Pages button on the Table of Contents Tables of Contents Hint All BIRDD databases have a Table of Contents similar to this one for information BIRDD Itself DFMAIN BRO Click for information about BIRDD Beagle Investigation
94. p Heller used the following approach to designating subspecies Trinomials are applied according to A O U canons of nomenclature i e when forms overlap in their variations regardless of the possibility or impossibility of their interbreeding they are called subspecies p 234 All measurements are in millimeters p 235 Measurements of length are in all cases of the specimen before being skinned p 235 These measurements must thus have been made in the field and recorded in catalogs or on specimen catalogs All other sources made measurements on dried specimens Filename Dfmorph brd printer 10 10 2000 page 4 Notes on Darwin s Finch Morphology Data Swarth 75 specimens Swarth made all measurements himself but did not repeat each measurement He noted that extremes were gone over several times Age Originally coded as black and streaked We originally followed Swarth usage and coded Adult for black and Juv for streaked We have left the data in the database but no longer export age data see Age in the table above Date We recoded collection date from Mon Day Year format to mm dd year Wing Length measured as the straight line from bend of closed wing to tip of longest primary with those feathers in their natural position not straightened p 9 This may differ from Sulloway s and Lack s flattened measurement Tail Length measured from point of insertion of m
95. pa ola gt all Hood 90 mi Floreana M Seas E Charles Santa Maria Gardner Watson Map Source Scanned from Harris M 1982 modifications amp changes from Grant P 1986 US Defense Mapping Agency 1985 Healey et al 1996 FileName ISLANDS BRD page 1 Gal pagos Archipelago Landmarks L and Area 8000 km Length NW SE 430 km Length SW NE Volcan 220 km Wolf Seymour Aeropuerto airport Volcan j Upper Distance Darwin crete to Mainland Lower transition site 1000 km i l Cerro Crocker Puerto Ayora amp Charles Darwin Research Station on Bah a Academy Elizabeth e Bellavista Lavatube Bahia site syn am Tortuga Puerto Baquer zo uerto Villami Moreno El Progreso 80 km La Playa is LLL REESE RS GRE ERE EE RE URN 90 mi La Paz a Map Source Scanned from Harris M 1982 and cleaned up modifications amp changes from Grant P 1936 US Defense Mapping i Agency 1985 Healey et al 1996 FileName ISLANDS BRD page 2 Gal pagos Archipelago Blank L and Area 8000 km Length NW SE 430 km Length SW NE 220 km Distance to Mainland Map_Source Scanned from Harris M 1982 modifications amp changes from Grant P 1986 US Defense Mapping Agency 1985 FileName ISLANDS BRD page 3 Map of Vegetation Zones on Santa Cruz Island e Ferry Landing Fact Upper Transition Lower Transition Pit Crater
96. r for tea The Sol y Mar also had a patio on the ocean home to a number of marine iguanas and crabs as well as blue footed boobies and pelicans We decided that it would be nice to have a visual documentation of a lot of the wildlife as well as the vegetation File Name GALPICS BRD p 8 Notes On The Image Database After our lunch we headed to the office of Howard and Heidi Snell the administrators of the Darwin Station who had agreed to help us with our computer troubles After a discussion we decided that the best approach would be to leave our picture cards with them so they could copy them onto zip disks Relieved we decided to head back to our room and organize all the data we had collected File Name GALPICS BRD If Panoramas Don t Work This database of pictures is something of a rough draft we expect future versions to be much improved In particular the panoramas are not currently viewable from within BIRDD itself although one frame of each panorama is visible We hope to provide an update soon check the BioQUEST website http www bioquest org for current information There are several alternative ways to play these images If you have FileMaker version 4 for Mac or version 5 for Windows you can open BIRDD from within the FileMaker application 1 Open your FileMaker application 2 Select Open Existing File or if FileMake is already running select the Open command from the File menu 3 Navigat
97. ractical experience The only way for students to learn how professionals pursue their craft 1s to work with the similar materials tools methods and questions For evolutionary biology this often requires access to data collected by someone else Traditionally publication of raw data has been too expensive and museum collections are inaccessible to most instructors and students Fortunately information technology has made it more practical to provide digital libraries of numeric data images sounds etc This was the original purpose behind the BIRDD project The recent emergence of vast quantities of publically available data such as molecular sequence data Benson et al 1999 and data from the LTER Long Term Ecological Research sites Sprott 1998 will continue to increase the need for students to understand how to mine data resources in meaningful ways Moreover access to archives of raw data can be important for professionals as well as for students Museum collections have always been important for evolutionary biologists but they are becoming even more important because original collecting has become very difficult for fiscal legal bureaucratic and ethical reasons Professionals will also benefit from having data available for reexamination BIRDD will make more canonical data sets like those of Swarth Lack and others more available Acknowledgments Funding and other support and for this project was provided in part by
98. re used to retrieve NOAA data Point Web browser to http www ncdc noaa gov ghen ghcnV 1 CLIMVIS html Select Graph Type Graph precipitation for the entire period of record Select Region click on South America Select a country or station group click on Ecuador in country list Click Okay button Select a station click 1950 to 1989 SAN CRISTOBAL GALA 0 908 89 6W Click Okay button Select metric units button click Graph Period of Record button Click View the Dataset button Use browser s File gt Save command to save data to disk file Comparable temperature data were not available FileName WEATHER BR page 2 Notes on Weather Data Bibliography NOAA 1997 United States National Oceanic and Atmospheric Administration National Climatic Data Center Global Historical Climatology Network Precipitation Data V1 URL http www ncdc noaa gov ghen ghenV I CLIMVIS html visited 4 Dec 1997 Note monthly summaries of these data were prepared by BioQUEST members These summary data are noted as NOAA BQ in the Source field Harris M P 1982 A Field Guide to Birds of Gal pagos London Collins Hoffmann J A J 1975 Atlas climatico de America del Sur mapas de temperaturas y precipitaciones medias Climatic atlas of South America maps of mean temperature and precipitation World Meteorological Organization UNESCO Cartographia FileName WEATHER BR page 3 Monthly Rai
99. res GFwak Guy Fawkes Isa_Alb Isabela Albemarle Isabella Santa Gertrudis Plazas Islas Plazas Plaza LHrm Crsm Los Hermanos Crossman Los Hermanos Mrch Bndl Marchena Bindloe Marchena Torres Pnt Abng Pinta Abingdon Pinta Geraldino Pnz Dnc Pinz n Duncan Pinz n Dean Pitt Pitt Rab Jrv R bida Jervis R bida RcaPat Roca Pateadora RcaRed Roca Redonda Bainb Rocas Bainbridge Bainbridge Rocks SCris Chat San Crist bal Chatham San Crist bal Dassigney Grande SCru Inde Santa Cruz Indefatigable Santa Cruz Bolivia Norfolk Porter Valdez Ch ves San Clemente SFe Brngt Santa F Barrington Santa F Snti Jams Santiago James San Salvador Olmedo Gil York Seym NS Seymour N Seymour Seymour Norte SNmb Nmls Sin Nombre Nameless Sin Nombre Trtu Brat Tortuga Brattle Tortuga Watson Watson WIf Wnm Wolf Wenman Wolf Nufiez Gasna Genovesa Ewres FileName ISLANDS BRD page 1 Finch Status on Islands No Cam Cam Cam Cam Cam Cer Geo Geo Geo Geo Geo Geo Plat Species Isl ID hel pal par pau psit oliv coni diff fort fuli mag scan cras Breeding Balt SS Bi q B Bp B 4 Brto Brth ooo o 1 Bele ooo B 1 Claw ee B 1 Cmp B B 2 Cocos PO IO RN ee Cwly ee B 1 DMaj o B oo B 2 DMin BB 2 Drwn Clp BiB B8 3 Edn ee B i Endrb o B 1 Esp Hd BiB x B 3 Fm Nb B B B B B BB B B B w Flor Chrl s B B B B x B Bx BIB s Grd EsHd Bao B 3 Grd_FICh ee B 1 Gnov Twr EN
100. rum Steadman 1982 would join all 13 Gal pagos species into the single genus Geospiza a practice common among earlier taxonomists Gould 1837 Salvin 1876 Rothschild and Hartert 1899 Snodgrass 1902 FileName DFTAXA BRD p 1 Here is a summary of the taxonomy used in DFDR 1 Geospiza Ground finches Uo 7 Platyspiza Vegetarian finch oo Camarhynchus Tree finches 9 10 subgenus Cactospiza 11 Camarhynchus 12 13 Certhidea Warbler finch 14 Pinaroloxias Species magnirostris fortis fuliginosa difficilis scandens conirostris crassirostris psittacula pauper parvulus pallidus heliobates olivacea inornata Subspecies magnirostris strenua nebulosa difficilis debilirostris septentrionalis scandens rothschildi abingdoni intermedia un named conirostris propinqua darwini psittacula affinis habeli parvulus salvini pallidus productus striatipectus olivacea bifasciata luteola ridgwayi fusca cinerascens becki mentalis extinct not used because no other living subspecies extinct Lack 1969 suggests one additional island population may be sub specifically distinct but hasn t been formally described Lack lumps pallidus amp heliobates in Camarhynchus but recognizes that they are less closely related to the Tree finches Some authors designate Cactospiza as a full genus Bibliography Bowman R I
101. s Printing Selecting Subsets of Data Exporting Data INSTALLATION amp TROUBLESHOOTING Installation Issues To use the Online Guide to install BIRDD Fonts Screen Resolution and Color Depth Printing Panoramas And Sounds File Organization Trouble shooting Printing Problems Text or images are cut off Panoramas don t work Sounds Do not work on Windows PCs Sounds Do not work on Macs VERSION NOTES 2 0 Modifications To Run On Windows Computers Other Changes Changes To Individual Data Sets Morphology Database Molecular Sequence Database Species Database Vocalization Database Islands Database Weather Database no changes Pictures Database New Bibliography Database New FileName DFMAIN BRD page 2 Notes on BIRDD Topics Tourists Database New Version 1 0 FileName DFMAIN BRD page 3 Notes on BIRDD INTRODUCTION The primary goal of the BIRDD Beagle Investigations Return with Darwinian Data project is to provide students and instructors with a variety of resources related to evolution research and to the teaching of evolution It is difficult for students to understand evolution unless they have an opportunity to study it as they study other areas of biology by doing what professionals in the discipline do in labs in museums or in the field Unfortunately labs have been rare in courses dealing with evolution and with some justification Evolutionary phenomena involve time and geographic s
102. s Return Darwinian Data including contact The Darwin s Finch Data Resource DFDR Information Main Table of Contents version lt lt gt_Version gt gt Click buttons to go to information or data sets boldface buttons are functional Red text provides To return to this location from anywhere in BIRDD hints about viewing Click a Return to Main Table of Contents button A click here and navigating El brought you to Select Go to Main Table of Contents maa Gale Gall these notes under the Script menu Click for documentation about the database Print All How To Pages Click to print all of these notes for reference Finch Morphology DNA Sequence SERA DES Data Data Data Island Weather Pictures amp Data Data Panoramas Data For technical support comments and suggestions a contact Frank Price by phone 315 853 5233 or by e mail fprice hamilton edu 100 fuaa Browse Click boldface buttons to go to named databases Plain buttons are not yet functional Click to leave BIRDD Contact information for support Buttons to move around among How to pages FileName DFMAIN BRD page 1 Navigating Around BIRDD Data Windows and Their Controls Data displayed by a Table of Contents button typically look like printed pages Here are the controls you use to manage them The Book controls which page is viewed It appears if there is more than one Scroll Bars contr
103. s been added to print records with a full page sized layout Because of the new sequences a Dataset Choice box has been added to the Table of Contents You may select any individual molecular sequence or all of them together The View Table of Sequences amp Taxa button always operates on the entire dataset of sequences All Other buttons including Export GenBank Records display print or export only the selected dataset Version 1 1 Font and layout changes as covered in notes to Main file File Name DFDNA BRD p 3 Notes On The Molecular Sequence Database Bibliography Information About GenBank Benson D A M S Boguski D J Lipman J Ostell B F F Ouellette B A Rapp and D L Wheeler 1999 GenBank Nucl Acids Res 27 1 12 17 NCBI National Center for Biotechnology Information 1999 NCBI GenBank Flat File Release 114 0 ftp ncb1 nlm nih gov genbank gbrel txt visited 12 21 1999 GenBank Reference in press Freeland J R and Boag P T Phylogenetics of Darwin s finches Paraphyly in the tree finches and two divergent lineages in the Warbler Finch Auk 1999 In press Publication Related Publications Freeland J R and P T Y Boag 1999 Phylogenetics of Darwin s finches Paraphyly in the tree finches and two divergent lineages in the warbler finch Auk 116 3 577 588 Freeland J R Y 1997 The genetic evolutionary history of the Darwin s finches Aves Geospizinae Ph D thesis Qu
104. s of specimens In the late 1920s Harry Swarth attempted to examine at least ten specimens of each species from each island and his 1931 monograph was a milestone that set the foundation of our taxonomy of the finches His work was an intermediate step in the late 1930 s David Lack measured every specimen he could get his calipers on He also made pioneering field observations and was the first to do major taxonomic work after having seen living finches in the wild He made relatively minor changes in Swarth s taxonomy on the basis of his larger samples more significantly he used the finches as a test case for a number of larger questions such as the roles of competition geographic isolation and environmental diversity in evolution His works Lack 1945 1947 are classics and a foundation for subsequent studies In the 1950 s and 60 s researchers followed up on issues raised by Lack Workers such as Robert Bowman and Peter and Rosemary Grant and their students began studies that continue to expand our understanding of evolution See Weiner 1994 for a very readable account of some of this work Diagrams from Lack and Grants work are canonical illustrations of evolution and adaptive radiation in many introductory textbooks FileName DFMAIN BRD page 5 Notes on BIRDD Data Archives and Digital Libraries While research such as that sketched above is important it does not by itself provide material that students can use to gain p
105. s table reports both the island on the specimen s label and his best determination from other sources e g field notes museum catalogues and specimen measurements We report his best guess in the Island field and his full report in the record s Note field Sulloway presented the label s locality first followed by a colon Where an island name alone follows the colon Sulloway determined locality on the basis of manuscript evidence Where the colon is followed by island form of subspecies the locality was estimated based on the specimen s measurements and plumage which coincide with only one possible island form given the various islands known to have been visited by the collector Filename X Dfmorph brd printer 10 10 2000 page 6 Notes on Darwin s Finch Morphology Data Lack 6 758 specimens David Lack s monograph 1945 and book 1947 have had an enormous impact on evolutionary research and his illustrations have become icons in textbooks The data in BIRDD are from a copy of his measurements deposited in the archives of the California Academy of Science Here are salient points on Lack s methodology 1945 Lack specifically tried to exclude specimens that had just left the nest although he notes that it was impossible to determine whether they were sexually mature Lack doesn t state whether he took multiple measurements and averaged them as Sulloway did It s clear however that he tried to assess the reliabi
106. say it can t find a particular file and ask you to locate it Take note of its File Location field and navigate to the appropriate location Panorama files are located in the following path Mac BIRDD or PC BIRD Folder DFFiles folder GalPics folder Pans folder mov files viewable with QuickTime software Sound files are located in the following path Mac BIRDD or PC BIRD Folder DFFiles folder sounds folder E Sounds folder mov files playable with QuickTime software aiff files playable with other software FileName DFMAIN BRD page 17 Notes on BIRDD File Organization The files and folders within the BIRDD folder must remain as shown below Most folders contain a ReadMe txt file containing late breaking news and descriptions of their contents Slashes separate files that have different names on Mac amp Windows computers Notes Folder File Type Mac BIRDD Win BIRD folder holds all of the following BIRDD alias shortcut file shortcut to the BIRDD application BIRDD Files folder holds the actual BIRDD databases sounds and images BIBLIO BRD file bibliography database BIRDD BIRDD EXE file application file opened when the alias shortcut is double clicked DFDNA BRD file DNA amp protein sequence database DFFiles folder holds image and sound files Gallmages folder holds image files Baltra folder images from Isla Baltra Pans folder panorama files StCruz folder images from Isla Santa Cruz CRDS folder images
107. se of sounds is something of a rough draft we expect future versions to be much improved In particular sounds are not playable on a Windows computer On Macs there is a bug that may cause you to see a message filename could not be found and is required when you first click on a sound 1 Note the name of the file e g Chel aiff and click on the OK button 2 You will see a message Please locate the file Navigate to the B RDD DFFiles Sounds E Sounds folder 3 Select the file with the name you noted above and click the Convert button 4 f you see a message This field is not modifiable click OK 5 If the sound won t play as described on the following screens check the volume control and click to another sound then back again You will only have to do this for the first sound in each session If you have FileMaker version 4 for Mac or version 5 for Windows you can open BIRDD from within the FileMaker application Here s how 1 Open your FileMaker application 2 Select Open Existing File or if FileMake is already running select the Open command from the File menu 3 Navigate or browse to the folder containing BIRDD 4 Type DFMAIN BRD into the file name box and click the Open button 5 At the Main menu click on the Vocalizations button and play the sounds 6 If you see a message filename could not be found and is required follow steps 1 5 above If you choose to listen with Quick
108. stigations Return Darwinian Data The Darwin s Finch Data Resource DFDR Species Table of Contents version 2 0 BIRDD v2 boldface buttons are functional To return to this location Select Go to Species Table of Contents under the Script menu Notes on Species Skull Images Print All DataBase Notes Skull Image Notes View List of View All Data on Species Names Each Species View Table of View Skulls Islands by Species amp Muscles Only View Ecological Data View Some Evolutionary Trees Export Species Data Go To Vocalization Database Notes on Finch Taxon Data File About the Database This database contains summary data on the taxa genera species amp subspecies of Darwin s finches Data include species recognition distribution on islands and general ecology We have relatively little on the Cocos Island Finch This prototype contains only data on species plus a few notes on genera data on subspecies may be added later The data in the Taxa database are not suitable for export so this function has not been implemented Note that the unit of observation in this database is a species data on individual finches 1s contained in other databases such as the morphology and sequences databases The taxonomy of Darwin s finches was in considerable flux for over 100 years so reading the old and some new literature can be quite confusing Some species can show greater variations between island populations than t
109. t can read text files Preview Pages Button Most of the listings of references are shown in Browse mode so you can use the various buttons If you want to see what the printed pages will look like and how many there will be click this button to go to Preview mode You may return to Browse mode and see the buttons by selecting Browse from the Mode menu or from the Mode pop up menu EXPORTING REFERENCES Exporting is done from the Export Found References in the Listing of References display Each citation is exported as a single line of text with hard returns between lines citations Additional formatting can be done with the word processor or other program that you use to manipulate the exported file Clicking the Find References button on the Table of Contents brings up The Find Screen Click to add delete and Click to find references Click to cancel and return move between criteria meeting the criteria to the Table of Contents Search Criteria are like data records You may type entries into one or more search requests The book icon SS SSS shows the number of requests eek 2 2 in this example and which request is active 2 Type criteria into fields OMIT NOT and Symbol Controls 2 request e D Capo i black bar on left amp visible a aD field outlines indicate this es ere feaiie sien a one Do not use these controls L BRek Edited
110. t filename gt could not be found and is required follow steps al a5 above Solution 2 If you have QuickTime for Macs or for Windows or an equivalent program 1 Note the location and name of the sound and its name in the File Location field on the displays 2 Switch to your QuickTime Movie Player program or an equivalent 3 Use the File gt Open command to open the sound file These are located in the BIRDD gt DFFiles gt Sounds gt E Sounds directory QuickTime Movie Player controls work as advertised in the vocaliztion database How To screens Sounds Do not work on Macs Probable Cause On Macs there is a bug that may cause you to see a message lt filename gt could not be found and is required when you first click on a sound Solution 1 1 Click on the OK button 2 You will see a message Please locate the file Click the Cancel button 4 Click Cancel in response to the continue script message 5 Click on another sound 1t should work then return to the sound that caused the problem Solution 2 1 Note the name of the file e g Chel aiff and click on the OK button 2 You will see a message Please locate the file Navigate to the BIRDD gt DFFiles gt Sounds gt E_Sounds folder 3 Select the file with the name you noted above and click the Convert button 4 If you see a message This field is not modifiable click OK 5 If the sound won t play as described on the following screens
111. tatistics programs The first row of an exported file contains the field column names many stat packages have a setting or option that will import the first row as the label variable name or column heading Missing data are blank and not coded because different programs a variety of ways of denoting missing data If your program requires something else you may open the file with a text editor and replace all combinations of lt tab gt lt tab gt with tab missing value code tab The export scripts allow you to specify a file name destination on the hard disk and preselects the Tab separated Text file type option Users can change any of these settings Select the disk folder and file name you would like to see Unless you know about specific alternative file types e g DIF you will probably find tab delimited to be the best file format As presently implemented the data that are to be exported are specified and cannot be changed Some of the databases contain a large number of fields used internally by scripts and special layouts that would be confusing for most users To avoid confusion we do not allow selection of subsets of fields or rows Most statistics and spreadsheet programs make it easy to delete columns and rows so we don t expect this to be a major problem BIRDD exports everything and you can just delete what you don t need At present you cannot export images or sound data If you need an image use standard cut a
112. tensive notes under the How To Find References button on the Table of Contents Be sure to read over those pages before trying to use the Find References button to do searches We would appreciate feedback from faculty and students on how we might improve this database and especially the search feature VIEWING BROWSING REFERENCES When you do a search or click on the View All References button you will see the Listing of References display in Browse mode Browse mode is appropriate for this display because it allows you to use the buttons described below Refer to the Navigating button on the Main Table of Contents for more on Preview and Browse modes Go To Table of Contents Button Returns to the Table of Contents Another Find Button Allows you do return to do another search of the database without going through the Table of Contents Copy One Selected Record Button If you have clicked to select a particular reference this will copy the text of the reference to your computer s clipboard and you can paste it into a word processor or other document You may then print your list of references as part of a report or to take to your library shelves FileName BIBLIO BRD page 1 Export Found Records Button Creates a text file with all of the references in it You can give the new file a name and determine where on your computer s hard drive the file 1s placed The file can be opened by a Word processor or any other file tha
113. the middle are buttons that take you to databases in individual database these buttons take you to different data displays Quit Back Button In the lower left is another wide button that quits from BIRDD in individual databases the lower left button returns to the main table of contents Each database has its own Table of Contents and appropriate buttons The first time you open BIRDD or any of its databases you should check out the Notes and How To buttons before using the display buttons Data Displays Most of BIRDD s data displays look like printed pages and window size and position are automatic Although BIRDD has the usual menus and window controls most of them need not be used Menus Only three of the menus are of significant use within BIRDD The File Menu allows you to Print the information you are viewing The Script Menu allows you to select various information displays and mostly parallel the buttons in the database s Table of Contents The Mode Menu allows you to move between Browse mode where you see raw data and buttons and Preview mode where you see printed pages and summary data FileName DFMAIN BRD page 10 Notes on BIRDD Standard Scripts on the Script Menu Each database also has a series of scripts visible on the Script menu The first seven scripts are the same in all databases and have the keyboard equivalents shown below Keyboard equivalent Mac Apple Key Script Menu Windows CT
114. the tube and soon decided that it might be best to turn around So we headed back out of the cave returned our flashlight and headed back to our hotel room We set up our computer to copy the pictures from the camera to the computer a rather long process on a laptop and went to dinner at the Station When we returned forty five minutes later we saved the files on the computer and cleared them from the camera in order to save space on the valuable picture cards We then went to sleep to prepare to take a panorama of the coastal zone the next day Sunday 8 8 99 When we woke up the sun was shining and we thought it would be a great time to head to Tortuga Bay the best place to photograph the mangrove trees that are so characteristic of the coastal zone By the time we had walked the 2 5 km to the beach from our hotel it had begun to get cloudy This was our first introduction to the power of the gar a the strange weather pattern that would dictate our lives for the next week Gar a is a driving mist common to the islands that have higher elevations during ironically the dry season As the moist air moves off the ocean and up into the higher elevations it cools resulting in an intense mist that results in constant clouds mist and humidity By the time we had set up our tripod it was hazy and beginning to mist We attempted to wait it out but after about an hour and a half decided it probably wouldn t clear up We decided to retur
115. tional Research and Development Centers Program PR Award Number R305A60007 as administered by the Office of Educational Research and Improvement U S Department of Education and by the Wisconsin Center for Education Research School of Education University of Wisconsin Madison Additional support provided by Beloit College and Hamilton College opecial thanks for services above and beyond go to the staffs of the Inter Library Loan and Reference Departments of Hamilton College s Burke Library The opinions findings and conclusions do not necessarily reflect the views of the supporting organizations Notes on BIRDD Topics INTRODUCTION The Data Resources The Instructional Resources Request for Feedback amp Suggestions Historical Perspective on Darwin s Finches Data Archives and Digital Libraries Acknowledgments Bibliography DATA Data Files DFMain a table of contents for all the project files DFMorph morphological measurements DFDNA DNA and protein sequences DFTaxa information about species DFVocal vocalizations Islands information on islands Weather mostly rainfall and temperature GalPics images Biblio Literature GalTrsts tourist visits Island Names amp Abbreviations Finch Names amp Abbreviations USING BIRDD Navigating the Databases Tables of Contents Data Displays Menus Standard Scripts on the Script Menu FileName DFMAIN BRD page 1 Notes on BIRDD Topic
116. to BIRDD General Notes FileName DFMAIN BRD page 16 Notes on BIRDD Panoramas And Sounds Panorama and sound files were created using QuickTime software Sounds are currently playable from within BIRDD on a Mac but not on Windows PCs Panoramas do not play on either platform although one frame of each panorama is visible We hope to provide an update soon check the BioQUEST website http www bioquest org birdd for current information There are several ways to play these images If you own the FileMaker Pro program Mac version 4 or Windows version 5 open the program and choose Open from the File menu navigate to the BIRDD folder and select DF Main BRD Windows users will have to view the contents of the BIRDD folder then type DFMAIN BRD into the filename box You can then use the main table of contents just as if you had double clicked on the BIRDD icon itself When you switch to the Vocalization or the Pictures databases the panoramas and sound should behave as documented in each of those files See the How To buttons in each database for details If you have QuickTime software installed on your computer open the folders shown below and double click on the appropriate mov file listed in the information for that image or sound If you have other software that plays mov or aiff files you may be able to use it as described for QuickTime The first time you try to view a panorama or listen to a sound BIRDD may
117. tons in the able of Contents amp File Edit M Select Format Script Window gt gt gt FTaHa Data on Each All databases have Tm _ standard script commands and keyboard equivalents m1 Mj iL A A A Keyboard equivalent commands Go to db Fable of Contents 31 bo to Main Table of Contents 362 Men gb Database Notes ae 3 the Table of Contents for the current database BIRDD s main Table of Contents buttons for different databases documentation specific to the current database First Page 36 4 first page of current data display equivalent to dragging bookmark to top Previous Page 5 previous page equivalent to clicking top page of Book Next Page 3665 next page equivalent to clicking on bottom page of Book Last Page 367 last page of current data display equivalent to dragging bookmark to bottom Below standard scripts each database has a number of did custom commands rna FileName DFMAIN BRD page 3 To print all How To pages use the Print All n How To Pages button on the Table of Navigating Around BIRDD Contents Other Controls Window size and position are automatic You should only use window controls amp menus described above If you click on another control esp the ones marked below in red gray in print the data window may become confusing or even empty If so select the Go to db Table of Contents Script menu command to clean up
118. tt Patricia 1998 U S Long Term Ecological Research Network U S Long Term Ecological Research Network Website http Iternet edu visited 2 22 2000 Swarth H S 1931 The avifauna of the Gal pagos Islands Occ Pap Calif Acad Sci 18 5 299 Weiner J 1994 The Beak of the Finch New York Knopf FileName DFMAIN BRD page 7 Notes on BIRDD DATA Data Files The data are organized in a number of separate database files and each database has a Notes display with additional information You needn t remember the names of files BIRDD handles file switching for you DFMain a table of contents for all the project files It displays a series of buttons that open other files or provide information about the entire system like these notes DFMorph morphological measurements Contains data from over 7 400 individual Darwin s finches The majority of the data are beak bill dimensions Included are measurements on 51 historically important specimens collected by Charles Darwin and others on HMS Beagle The file also contains buttons to display summary statistics of species and subspecies on different islands DFDNA DNA and protein sequences Data on seven molecules from over 200 individual finches and several possible sister species DFTaxa information about species The data include information on species recognition pictures descriptions islands inhabited ecological information su
119. tudied Darwin s Gal pagos collections and manuscripts and clarified many of the confusing points that confounded previous workers In particular Darwin neglected to record the localities where he collected his finches Sulloway tracked down and measured all of the existing Beagle specimens and his 1982 paper is the best source of data on the Beagle finch collections Sulloway tried as much as possible to use Lack s 1945 methodology in taking measurements Beak bill measurements were made with calipers accurate to better than 0 1 mm less than typical range of error in making repeated measurements Each beak measurement was taken six times on the specimen s right side the high and low were discarded and the remaining four were averaged Culmen Nostril Upper Beak Length measured from superficial anterior lip of nostril to tip of bill Depth of Bill measured from greatest height from base of bottom mandible to top of upper mandible before the curved culmen begins to descend i e not where mandible meets skull This may be different from those of other authors who were less specific about their procedures Wing Length measurements were taken from both wings when present using a millimeter rule the flattened wing was measured from carpal joint to tip of longest primary to the nearest 0 5 mm We report only the measurement of the right wing unless that wing was missing in which case we report the left wing Sulloway
120. ue to elevation But as to exact elevation or places that we could access at that elevation we were lost We along with our advisors Karen Harpp and Frank Price decided it would be best to get to Santa Cruz Island home of the Darwin Research Station and ask the scientists working there for advice Sunday 8 1 99 And so before we knew it August 1 1999 came around and we found ourselves on a plane actually many planes to Quito Ecuador The first obstacle came in getting to the island itself After a number of connecting flights and a few frantic runs through airports we found ourselves in Quito Ecuador in the middle of the night We managed to find taxis and after a few interesting wrong turns we arrived at the hostel that would be our home for the next few days while we worked out logistics with the Darwin Station Wednesday 8 4 99 Finally it was time to venture to the Galapagos From the Quito National Airport we flew onto Baltra Island a small island within sight of Santa Cruz From there we loaded our rather large amount of equipment onto a bus and headed for the Baltra dock From there we took a boat across the rather small channel to Santa Cruz Once on Santa Cruz a pick up truck from the Darwin Station picked us up and brought us to the other side of the 1sland File Name GALPICS BRD p 2 Notes On The Image Database One of the hardest aspects of travelling so much was the amount of equipment we had to bring
121. us measurements We coded as M F or U for unknown a few marked with in originals were coded as the indicated with the appropriate letter plus u for uncertain 1 e Mu and Fu Age Several authors coded Adult and Juvenile and we had previously accepted their designation However most of those assignments were based on plumage and the assumption that for Geospiza at least black males were adult and streaked or partially black males were juvenile This is now known to be incorrect so we no longer export age information Plumage Some authors designated Age as black or streaked we put these designations into Plumage Wing Length Tail Length Upper Beak Length Culmen is the technical term we use a more easily understood if longer term Note that Lack measured culmen from beak tip to where it joins the skull while Swarth measured exposed culmen beyond feathers Both of the above differ from Nostril to Maxilla Snodgrass amp Heller Culmen from Nostril Lack and Lip of nostril to tip of beak Sulloway To avoid confusion these latter are code in the Nostril Upper Beak Length field Lower Beak Length Again a technical term made more easily understood The lower beak typically is shaped like a Y the measurement is usually from the fork of the Y throat to the bottom tip of beak Beak Width Beak Height Depth may be interpreted as front to back length so we use height
122. we met up with the guards who we walked with into town When we got into town they signaled a pick up and we were given a ride back to Puerto Ayora and the Station We then walked back through town covered in the mud from Media Luna until we reached our rooms and collapsed Tuesday 8 10 99 Bright and early Tuesday morning we gathered up all of our gear and said farewell to the Castro Hotel After getting situated in our temporary Darwin Research Station abode we set out for the tortoise pens Our initial mission was to obtain a panorama of our large shelled friends So we positioned ourselves in the middle of the pen and set up our tripod Just as we finished leveling the camera a group of tourists flooded in and surrounded us We decided to wait it out and try to take the panorama right after they left As the group started wandering away all of the tortoises started charging our equipment Despite popular belief we discovered that tortoises can move those stumpy wrinkled legs of theirs pretty fast Mistaking our yellow camera bag for their usual banana treats the tortoises scurried towards us We would move and set up the equipment just in time for the tortoises to come towards us again When we finally figured out that the colorful bag was luring them in another tour group poured into the pen We covered everything yellow that we could find and decided not to give up With some patience we thought that we could out sit the influx of e
123. win s finches 1s a massive 300 page chapter by Bowman 1983 It contains a wealth of detail that we cannot hope to approach Bowman documented a variety of species specific vocalizations differing patterns within and between populations of one species on different islands as well as differences associated with differing motivational states social situation and habitat While this database contains only a one or two samples from a limited number of species it will let you examine the sounds visually and aurally We have also included Harris 1982 and Castro and Phillips 1996 descriptions of each species vocalizations to allow you to compare the limitations of textual descriptions to more informative images and sounds Bowman categorized three basic types of vocalizations each with a number of variations Whistle song a long continuous hissssssssss or seeeeeeeeee or a series of short notes see see see see that start at very high frequencies often inaudible to humans and descend gradually or rapidly to lower more audible frequencies This 1s produced during the breeding season and is structured to make it hard for predators like owls and hawks to locate Basic song has three variants 66 9 Basic song proper has syllables like chicago with a drown out buzzy a as in chic a a a a a a a go This 1s used in territorial defense and advertisement Special Basic son

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