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Population Management 2000 User`s Manual - Training

1. vULE 2f3 2 083 190 0 26 SDF i 3 073 1303 YUL A O M TNI ORLAR IIR Oo i o Aa TUA BY KELIR Afye 0 11 Curarty sonec oy AK Curarty sores w AK Individuals 1 w vin rad inths tak 3 shown akavatovs besar usec 1e 30st one isir y Wate Ther Alternatives 1 lype ing pairing of your choice W Inclide nffspring in aga strin 2 Import pairs froma pairing fila w Apply pairs and culls to Mat Select one animal trom each ot the above tables Males and Females Information about the offspring WHAT TO DO and changes tu the populaliun slalisues us uresull uf lhe pulenta miulding we displayed iri He bugul ahaye right Click Mata Tham tn sonfinn the mating and praducea an offspring MK 0071 Figure 13 Pairing screen To sort the list of animals click on the appropriate column heading Click on it again if you want to sort in the reverse order You can then test the effects on the genetic status of the population of producing offspring from any pair of animals Click on the male and the female that you may want to pair to see how Gene Diversity Gene Value and Founder Genome Equivalents would change if that pair produced offspring Once you decide to use a pairing hit the Accept button Instead of choosing Pairs from the lists you can also Type in a Pairing of your Choice by clicking on that label This option allows you to type in pairs that might be hard to find in a very long list of animals You may also test pairings of dead anim
2. 123 but an unknown sire the sire P123 would be created and given parents UNK An exception to this occurs if the dam is herself wild caught In that case it is assumed that the dam was pregnant wen captured and the sire P123 is given parents WILD 15 Individual Statistics The screen at this next tab lists all the living animals in the selected population along with some basic information parentage age etc and various measures of current genetic value to the breeding program You can get more information about the various genetic measures reported by PM2000 by reading the Population Management Manual If any values in the table are 1 000 this means that the number could not be calculated or was not applicable For example founders do not get a value for the GU Desc the Genome Uniqueness among descendants not counting the founders Crarmetis Aanlyn for OKAPLA ICHNS TON sucoocew vex se Dar As csesor wo verso i w Oy aa l berere rt ee 315 F IILI WD r Sue 0 3 130 03 0 C30C 3 0139 Cy 44 o c3sC 1 0070 Em X la DG LEG O C 130 3 OCOC 1 027 CW OCHE 1 0020 Par ve iy ki 144 H YRR N Wit Tutt Wt Wil Ika I thks I IHF II Ibh T3 263 k 21 249 23 SALLeE O63 130 03 OCOC 3 0753 C37 OCA 0 030 aa 229 K 213 E7 22 IINA 0 0 130 03 0 0300 3 0057 Cnel 0 CIEL 0 C3 0 2 2025 aa F td ek 14 WILA izi LELLE I N Weds l be at Wt A a Wee 317 F 2 7 c 19 SALLa 0 23 130 03 0 C30C 1
3. Current Potential Founders 2b OQ additional living Nesrendants 74 00 Gene Diversity 0 r267 02a Cene Value IZo Fnunder Ganame Cquivalants GAR 10 53 Fuunder Genomes Suviviny 10 44 10 53 Mean Inbreeding tH U71 m Currant N 76 Known 100 00 GD 0 8 G7 MK 0 07R GY 0 9767 fga 6 83 Pairs 01 Figure 10 Population Statistics screen At the bottom of the screen you will notice that there are listed a few of the more useful measures of the genetic status of the population This footnote will be displayed on each of the Genetics screens and the values may change as you make recommendations for breedings and or cullings 14 Founder Statistics This screen shows a list of all founders and some statistics about their genetic contributions to the living captive born population On this screen as in most tables in PM2000 you can sort the list on any of the listed measures by clicking on that column heading If you click on a column heading for a second time the list will be sorted in descending order Sort the founder list by the Living Dead column in order to see if there are any living founders If there are you might take note of them now Living founders should probably be given preference in breeding over non founders that have similar or larger mean kinships Genin Anlyxen far OKAPIA IOHNS TON Fogasa or static o E emesa steticr s Ir orsec ve cirship te strx sir ves cuties Lttectre gt Forse
4. copy puts the animal into the new population but still leaves it also as a member of the old population To move or copy an animal highlight its current source population on the left hand list then right click on the animal on the right Then drag the animal to the recipient population You will be prompted to specify whether you wish to Copy or Move the animal or to Test one of these actions If you test the action PM2000 will first tell you what new gene diversity would result and then it will ask if you wish to proceed with the Move or Copy 25 Metapopulation comparisons Clicking on the comparisons icon will open a screen for making population comparisons On this screen you highlight the populations you want included in the comparisons and the program will display a table of all pairwise between population comparisons Below the diagonal on this table is the genetic divergence between each pair of populations as measured by an Fst value Fst is a measure of what proportion of the total gene diversity of the two populations is present as between population divergence rather than within population diversity Above the diagonal are the between population differences as measured by the mean of all kinships between animals in the two different populations On the diagonal are the gene diversities within each population Below the table are given the total gene diversity of the metapopulation GDt the mean within population gene di
5. Definitions PM2000 provides a dictionary of terms used in genetic and demographic analyses You can access this dictionary by clicking on Definitions within the Help menu To look up a word scroll through the list of defined terms and highlight the term to be defined If any terms within a displayed definition are not clear to you you may highlight the term in the definition box and then click on Define term from above definition lesen JETT eT i gt wec emnes ue Io clanenms oh Tac ww Sights sere ho repree uct ys cape icar Ve ths valas Meech of le i e een w yum a Alih kanl awah sabe pijpnrhnjpnad h iherioncs loss 3 gere diar t soyadi he ite fe ice eukse yar yenergcn slenmss a 3 alr u irla iiri lin Ah ranh crbyn lel san aida avers Dr Farar sere 2 offsa ngepecee tr scyenic anime s cite ese salir Su itui ve F TF rower Tories Jete carn iro nys daii Sec iwoughike lis terms otles ordy seika de ritica ci igat Clickwwe Je e corn Serr rar 220ve cStir 7 2r autor 73 38 the i Saniry ofe arntour dirn catir gt ar 304 sa Figure 24 Definition look up window EXITING PM2000 To exit your PM2000 session either click on the x icon in the upper right corner of the PM2000 window or select Quit from the File Menu PM2000 automatically asks whether you want to save the changes to your Project 30 References on management of pedigreed populations Ballou J 1983 Calculating inbreeding co
6. 12 13 0 66 45 41 36 34 34 ER 51 45 40 36 34 34 33 29 29 27 22 0 0 OO w O G G 000 000 000 000 000 000 No O OvOr S OO OC COO Or7Os OC G ODOOAANDFAIO OO COMO OW OOO BR DAO OO COO OO OD 5 5 4 4 3 3 2 2 1 a 0 0 0 Filter conditions in effect Locations N AMERICA Dates During 01 01 1960 lt date lt 23 05 2000 Figure 25 Sample prn file with demographic data 34 Genetic data Genetic data are provided to PM2000 via a database dbf file created by dBase FoxPro or a similar database program The necessary fields for the dbf file containing pedigree data are Info 6 character name or ID label 6 character name for the sire 6 character name for the dam 0O female 1 mal T F indicating whether the animal should be included in the analysis T F indicating if the animal is dead T dead Birth date or date of entry into the population Death date iogical iogical Date Date HDAT EOUT LOCATION Date C Date of exit from the po usually the same as dea pulation thdate Location of the animal or any other pertinent info that you want attac hed as a label he following fields must exist but can be blank 2000 will place data from each living animal into these fields 3 0 an integer code for age 8 Inbreeding coefficient F 8 Propo
7. Animals with sex m or f rather than M or F are contracepted males and females respectively You may then want to sort on location and then scan down the list to see if it includes animals at any institutions that are not participating in the management plan Click on animals from either list to move them over to the other side Check the box Use Selection for Age Structure and Demographic Projections if you want any changes you make in the selected animals to be carried over to the age pyramid and population projections screens under Demography Click on Accept when you have the lists as you want them to be You can edit the sex age or location of animals at this screen but be aware that these changes only affect pm2000 s genetic calculations and tables they do not change the data back in your studbook You can also add new animals to the pedigree at this screen To do this click on Create New and then fill in the basic information for each new animal If you leave any fields except ID blank PM2000 will fill them in with default values when it creates the animal For example unspecified parents are assumed to be UNK for unknown an unspecified location is UNKNOWN and an unspecified birth year is 2000 Animal scicction CGurreot Panulatian Size 76 Unselieeted Individuals 64 Sie dbe ob ax age Lacstion mule 20047 sex ga pts he 2 7 k 2 Hy BROH tre F ELLI Z 20 v a DAL_A3 37H H CALL v
8. COC O 090 3 009 55 0S4 COC CITER FFT F 34 Mo aE RE EM MA rath Sh EM Ti KAN EGEZ 7 BEAT Aung mace rans yuan ony AR J p to this point Import culls trom a culling tile SC AF Pr ADHS SAh JELCZ AGU 90 0005 CLA IOMA AEA SE war AGN 0 0006 SAR AICGCZ GD 0 9311 BY 0 9315 Slo eels a 7 26 oe W Apply cullings to sge structure deta hy bd Salant an individual or qraup of individuals from tha Current Panulation tahle at left and clink the Cull WHAT TO D Button to cull them trom the population You can cull multiple animals at once even though the provaewe ul lhe changes Ww the populalion slats will nul reflec this LETCE TLE gt O amp Knuwn 10000 GD MK Cua GY Figure 14 Culling screen In addition you may use this screen to identify additional animals that should be removed from the population in order to further the genetic management If there is limited space available to maintain animals you may want to remove genetically redundant animals sometimes called surplus to make room for production of new and more valuable animals Sometimes you need to identify some animals that can be 18 safely removed from your population for use in release programs or for export At this screen you can sort the list of animals by any one of several measures of genetic importance MK mean kinship KV kinship value GU genome uniqueness P lost probability of allele loss FOKE first order kin e
9. Use of animals with unknown ancestries in scientifically managed breeding programs Zoo Biology 12 161 172 Willis K 2001 Unpedigreed populations and worst case scenarios Zoo Biology 20 305 314 32 Appendix A Using PM2000 on databases created without SPARKS When you create a PM2000 Project the program obtains demographic data the life table from text files with the extension prn and obtains pedigree information and data on the living managed population from a database dbf file The easiest way to create these files for PM2000 is to use the SPARKS studbook program developed by ISIS International Species Information System http www isis org to manage the pedigree data and then to export the demographic and genetic data via the Reports gt Analysis gt Export Data menus However the files with demographic and pedigree data can be created outside of SPARKS using text editors database programs or other applications if care is taken to create files of the precise format In addition it is possible to enter demographic and pedigree data directly into PM2000 Entering demographic and pedigree data directly into PM2000 When you create a PM2000 Project you have the option of specifying that no demographic data will be imported and or that no genetic data will be imported If you specify that no demographic data will be imported then PM2000 starts with a simple life table of survival and fecundity rates and creates file
10. When you created your Project PM2000 read in demographic data from prn files and performed a number of analyses You click on the Demography heading to begin your demographic analyses The following sections describe each tabbed page available within Demography Male and Female Life Tables The life tables for males and females are created from the data exported from SPARKS The Life Table screens show the average survival and reproductive rates for males over the time period you selected when exporting the data from SPARKS PM2000 also calculates the population growth rate lambda and r for a stable population under these conditions as well as generation length T current number of males N and projected number of males twenty years from now N20 Note that unknown sex animals are counted as 50 male 50 female so you may have fractional males Also shown are the sample sizes animals at risk used to calculate the Mx and Px values life expectancy Ex and reproductive value Vx On the left side of the Life Table screen is the ACTUAL life table These are the data exported from SPARKS On the right is the MODEL life table The Mx fecundity and Px Survival rates on the screen are initially the same as the ACTUAL screen However the you can use the MODEL screen to smooth the to data by clicking the text below the table You can also change the Px and Mx values in the MODEL life table but not in the ACTUAL table Desrangnphin Annlyrie
11. cations w aey M yb dicke yrophtor me ocveicec plicis Figure 22 Sample Graph with Graph Control toolbox 27 When you create a graph PM2000 first shows you a small version of the graph lets you set details of the lay out and lets you define axis labels and titles The click Plot to see the final graph You can send this graph to the Clipboard return to reset the titles click on Options or go to advanced Graph Control options by right clicking on the graph to set chart type data used for plotting and many other options DEMOGRAPHY GRAPHS The pre set demography graphs help evaluate and visually compare the Actual and Model life tables As mentioned above small population sizes and small sample sizes often results to unrealistic life tables The purpose of smoothing is to try to make more realistic these types of problematic life tables Graphs allow you to compare the MODEL vs ACTUAL values of Mx Px and Lx separately for males and females Use these to help you modify Mx or Px values in the MODEL life tables and evaluate the effect of the smoothing Also available in the Demography Graphs is a plot of Male vs Female Reproductive values Vx used to calculate the Kinship Values used elsewhere in the program and projections of males females and total population size over time The projection graphs are also available on the Projections tab in the Demography section GENETICS GRAPHS There are a number of pre set genetics
12. graphs in PM2000 accessible through the Graphs gt Genetics menu and you can create your own custom graphs of genetic and or demographic data via the Graphs gt Custom menu Within Graphs gt Genetics there are 3 categories of graphs Population Data Founder Data and Individual Data Population Data Graphs A WARNING It is very important to note that the population data have been calculated from only the animals that were in the selected set imported into PM2000 Therefore if you selected only living animals for your genetic analyses a common and quite reasonable thing to do the genetic data plotted in these graphs will show how genetic variation has changed among those animals that are still alive today Animals that were in the population but are now dead will not be included in the tallies of past genetic variation because you excluded them from your PM2000 analyses This will typically result in meaningless and perhaps highly misleading graphs of historic trends In order to obtain useful graphs of historic trends in measures of genetic variability you need to include in your selected set of animals all those animals that were alive in your population at any time in the date window for which you care to plot the trends During an export of genetic data from SPARKS this can be accomplished by specifying a Geographic view if desired specifying only Living animals and specifying a time window that includes the period of interest Anim
13. of captive breeding This estimate will represent an average N over those generations The second estimate of N is based simply on the number of living males and living females that have produced offspring This estimate will reflect the current Ne but often it will overestimate Ne because some of the animals that have bred may no longer be breeders or may breed only poorly Click on the Send to Clipboard icon to record these estimates in your report Census If you ran a Census Report within Sparks then PM2000 will fetch those data and display them in a table and in a graph on the Census screen Genetic Anulyses tur OKAPIA JOHNSTONI Fug ile ou ale x hi mh Sheds ae ale m hin su Su hapi be ah an n Caullu Files des sip tle n Pill rili iteases 301 Syaz Mese Penoles 2 bar 14 t 3 Bee 14 3 3 3 1 T 7 a Blk iii Skid 14 1 F T 635 23 12 E 20 56 E 0 7 Wes ba 14 1 T ae c38 E 1 E 39 1 1 5 ey zal y u ee ee A J F nals ETa 17 1 3 AEDEP D D ererrrerrerece TA E z y hea 14 1 d j ear Figure 15 Census screen 19 GENETICS OPTIONS In the Settings gt Genetics gt General Options menu you can change some of the assumptions made by PM2000 for genetic analyses Unless you are have special analysis needs and you are very familiar with how the genetic analyses are calculated you should probably not change any of these settings other than perhap
14. subpopulation from your list With the list of populations on the left are given the number of animals in each population and the gene diversity present within that population Papulations as x nkapi emo W933 AC 0 6267 Sex Z LF CICIR AT N 30 7675 aE r O C 16S 0 i 1F LILES NAV GEE ir F Wit it t A Me as el SD 3 9225 a M 0 0352 0 1 A Fenoles N C SD 1 0096 202 H OOK iat Ay BRIM Mek sh TET ryt H IEZ E oa ie ef 3D 8E39 Tt F 0 0792 0 paps SD wal 4 13 G OS 7 r IFAN 0 WL Pe e NH aD Lee i H WL elle Ta UBL SEU TES Pale a det 3D 7299 336 M Ocre 0 Seb DECC iF CALI SPRE z E l aF BRJKELI 1 30 25 WE r 0 C361 ia I nhF HaT COL Ske JS Nee ii DATS ihl F ile asl He U ie a PHILS DELP 4 3D 3 0 y H 0 33 0 CILI ay DERSE NAV ul 1h ivr t MEERI Ti URL APUG a OMAHA dee SDI 7622 382 F 0 C726 xe MENE 47 DISK EY 24 N 2 SD 2 6075 30 cr 0 03 E SALIGE Mesa iri ink H Wie 11 O ad 39C F 0 0442 03 LLIE 391 H 0 C207 0 WLC iH M Wah om BUCH 1 396 F 0 0793 ILAE 397 r 0 0367 0 CILHILS iMr H TERRI i sie a Current Population Intormation N 6 GU 0 926 tge 5 83 Figure 19 Metapopulations screen Moving or copying individuals between populations You can use the Metapopulation screen to test what would happen if you were to copy or move an animal from one population to another A move puts the animal in the new population and removes it from the old A
15. t in which case it will show you how much you can hope to retain If you can t meet this goal then you need to change some values to see how large a population you will need Start by increasing the Maximum Allowed Population Size to a larger but reasonable number If this doesn t work you can experiment with increasing generation length population growth rate and or effective population size Play around with changing values but keeping them within reason until you have a sense for how large a population you will need or how many new founders are needed It may be that you still can t meet the goals even with reasonable changes For example if your gene diversity is already below the goal no amount of changes will help In this case it is worth considering adding new founders Find the line labeled New Founders and change the value to 1 This will activate the lines below Set the Maximum Allowed Population size and a reasonable number and select New Founders from the Solve For list The program will automatically calculate the number of founders you need to add within the next year to meet your goals You can also change the number of times or years you 22 hope to add new founders as well as the frequency Again play around with these options until you have an understanding of how adding new founders will help you achieve your genetic goals If you still find that adding founders is impossible or an unreasonab
16. those lines is not important to PM2000 The lines of data must follow the format shown in the text box above with each line giving for an age sex class n the number of animals alive note PM2000 does not use this number for anything as it calculates the number of animals of each age from the pedigree data file described below the annual mortality rate the annual fecundity equal to the number of same sex offspring produced by a female of that age the age class the sample size number of animals that had been at risk for mortality the sample size for fecundity a5 gt DD For reasons that have to do with the way in which SPARKS presents demographic rates the fecundities given to PM2000 must be the expected number of same sex progeny produced by an animal that reaches the midpoint not the beginning of the age class A blank line then separates the above data from a trailer that defines the subset of the database that was used for the demographic calculations Studbook Data for TEST DATA SPECIES female Data exported on 24 May 2000 Data compiled by John Doe Data current thru 7 Jan 2000 Scope of data World captive population Number Alive Qx Mx Age Class Sample Size Qx Sample Size Mx 000 000 000 000 000 000 0 000 0 0 0 0 0 1 000 0 1 0 0 0 0 0 0 000 000 500 500 500 500 500 29 500 30 500 27 000 10 11 233 000 11 12 0 000
17. 0733 C 3653 0 C39C 0 C320 2 2026 3 r 2l4 E39 10 Oh ICA Ta 1390 03 0 0300 3 0730 C363 OC BE O CIES 220 J ara ly vr tech Th SANDI SPI 1 Wii HIE TK 1 HI Ht wil Wt ul wil lt 2 z ras ce 15 23a O65 6130 03 0 00 MES Casts EE ocro cea JXl r 2l4 33 l4 JILCC 0 02 130 03 0 0300 3 0717 C jel 0 036 O CIES 2 2020 aka be vri mle TY Wan eh Tit I the H44 A a Wt i Wt Wil Ws 377 k E e33 12 Er eaa 5 35 130 0 0 C30C 3 0530 C3922 o crc o cyo a0 J r J lt 42 2 Qe Of 190 0 0 C90C GI Coco OCOC 0 0300 Ea E iri F 471 rvi Wo WRB hs LELLE 1 ut I H ls HL Ak HW eh wy 363 rae ce T EeNDIECSZ 2 190 0 C20C 2 0619 C39C3 DCE 0 0300 a 33 y JI c72 1 LCC TE 130 03 0 0300 1 0270 C3313 0 035 OCES 220 5 wl re 1h L eet Wl als Tit Wi wil Wk 44 1 ied Wt i HL as 11 limn yurin ony Hn we Currant N 76 Sm Known 100 00 GD 0 8 6 hale OMIKI GY 0 S963 i Pairs Figure 12 Individual Statistics screen Inbreeding The Inbreeding tab displays a list of the inbreeding coefficients symbolized by F of the analyzed population You can use this list to assess whether more inbred animals have shorter life spans if you Selected Living and Dead animals when you exported the genetic data from SPARKS or you can ignore this screen and go on to more interesting parts of the genetic analysis Brackets around an ID indicates that the animal is dead the age given for a dead animal is the age at which it died Kinship Mat
18. On the Pairings screen all males and females in your population are listed in tables You can sort either list by any one of several measures of genetic importance MK mean kinship KV kinship value GU genome uniqueness P lost probability of allele loss FOKE first order kin equivalents or Rel MK the relative mean kinship You change the measure of genetic importance shown on the table by going to Settings gt Genetics gt Weigh Pairings By and checking the desired measure Although only one measure will be displayed on the list of animals for possible pairing you can see all of the genetic information about any animal by double clicking on that animal on the list Crarmtis Anly for OKAPLA JOHNSTONI gt pulane i Ste shes ourse Stanctics individual stas sies aiz esdima vor osmasi Fa ings Jus ye zerve gt pulane i tize iter Iris menzu a Males Fermales a MAE SE w wialuiri a AE ese mialuiri 3 7 3 EAEE ESEN AEIR NST tesulting Ottspring Generated Uttspring hid WT THT DFR 4 Hki UE Shan F 0 00000 339 amp 215 0070 4 amp 3 3031 190 09 DALAS 362 2027 1300 1 ALEE ETE jana 4 2 2 001 190 03 C YUL 42 JOTI IJO C AHCIR YAT Slulislius I er TT A Aee ei TE E SEEEN 511 3 023 130 03 Fh BRIE 422 2053S 1206 4 TUL 5I 3 0e7 190 03 YULI 4 3 JOCI 130 03 I CIR YT art ME TWEE 4 CAMERA awl HET TMNT RRES i 423 2 054 190 0 7 STLCIIS 487 3061 130 02
19. Population Management 2000 a User s Manual PM2000 version 1 163 14 July 2002 Robert C Lacy Chicago Zoological Society Jonathan D Ballou National Zoological Park Smithsonian Institution Software developed by Jonathan D Ballou Robert C Lacy and JP Pollak Cornell University Support provided by American Zoo and Aquarium Association The Walt Disney Company Foundation Chicago Zoological Society National Zoological Park Cornell University Lincoln Park Zoo Manual citation Lacy R C and J D Ballou 2002 Population Management 2000 User s Manual Chicago Zoological Society Brookfield IL Software citation Pollak J P R C Lacy and J D Ballou 2002 Population Management 2000 version 1 163 Chicago Zoological Society Brookfield IL 2000 2002 Chicago Zoological Society INTRODUCTION TO PM2000 The Population Management 2000 PM2000 software package provides a suite of tools for genetic and demographic analysis and management of pedigreed animal populations a studbook PM2000 combines the capability of the MS DOS programs GENES written by Robert Lacy Chicago Zoological Society DEMOG written by Laurie Bingaman Lackey and Jon Ballou National Zoological Park and CAPACITY written by Jon Ballou as well as adding some new features PM2000 was developed by JP Pollak Cornell University Bob Lacy and Jon Ballou Support for the development of PM2000 was provided by the American Zoo and Aquariu
20. airing non selected animals the genetic calculations will be slower but you will be able to use non selected animals in pairs Do not update genetic measures as pairs are created Normally PM2000 adds hypothetical offspring to the population as you create pairings and updates the measures of genetic value e g Mean Kinship Kinship Value to reflect the contribution of these new animals This will cause the paired animals and their relatives to decline in genetic value However if pairs to be tested have only a low probability of successfully breeding it may be more realistic not to assume that they will add offspring to the population In 20 this case they and their relatives would not drop in value Checking this option will cause PM2000 to not create hypothetical offspring of chosen pairs and not update genetic measures Count unknowns as wilds Normally pm2000 excludes unknown animals from genetic analyses and considers only the known portion of pedigrees of partly known animals This option specifies that animals with unknown parents should be treated as wild caught founders Allow pairing dead animals If you wish to test the effects of producing offspring from dead animals perhaps from cryopreserved gametes or embryos you need to check this option before selecting the pairs Use input matrix of coefficients of relatedness or kinship among founders These options allow you to specify that founders are not unrelated as is usu
21. ally assumed but instead have a specified matrix of relatedness or kinship Founder kinships could arise because of known familial relationships e g a litter of siblings or because molecular genetic evidence indicates close kinship among some founders If this option is chosen there must be in the project folder a file called related txt or kinships txt as appropriate for the option selected The file must be an ASCII DOS text file with the following format First line is a number stating how many founders are in the relationship or kinship matrix Any founders not in the matrix will be assumed to be unrelated to all other founders Subsequent lines give one per line the studbook numbers for each founder in the relationship or kinship matrix Following the list of founders the matrix is specified Each line lists the relationship or kinship coefficients to each founder with a space separating each value The full symmetrical matrix must be given For example the following kinship file information would indicate that founders 23 35 67 and 101 are full siblings kinships of 0 25 but are not themselves inbred kinships to self 0 5 101 0 50 0 25 0 25 0 25 0 25 0 50 0 25 0 25 0 25 0 25 0 50 0 25 0 25 0 25 0 25 0 50 Create output file for use with MateRx This option specifies that PM2000 should after completing genetic analyses create a file of genetic data for later use in the program MateRx see below Run Gene Drop simu
22. als or of animals not in your selected population if you previously chose those options under Genetics Settings see below After each pair is selected the measures of genetic value of the remaining animals will be updated l e the new parents and any of their kin will become less valuable than they had been before the pairing This updating is not done if the Genetics Option see below is set to specify that genetic measures should not change as pairs are created 17 Any animals used in pairings will be highlighted in red If you change your mind after you Accept a pair you can un pair it by highlighting it on the list of pairs and then hitting the Remove button If you want to start over with selecting pairs hit the Reset button As you pair animals you will see that the summary statistics of the population will be updated at the bottom of the screen When you are done selecting pairs you should send your list of pairs to your PM Clipboard Also send to the Clipboard the new Population Statistics at the bottom of the screen You can specify that the hypothetical offspring produced by your pairs should be included in the Age Structure and Population Projection screens by checking the indicated box You can also specify that these new offspring are to be included in any data file produced for MateRx see below When you exit PM2000 your selected Pairs will be printed to a file called project prs You can later ask PM2000 to add th
23. als that are now dead will be used for historic analyses but will not affect genetic measures on the current population Note however that this view will include within the current living population all animals that were ever in the selected geographic region and who are still alive This may include some animals that have been exported from the region There is one way to trick SPARKS and PM2000 into giving correct historic and current genetic analyses Kill any animals that leave the selected geographic region on the date that they depart Once you are sure that you have selected the historic population of interest you can plot graphs showing Genetic Diversity vs Time Founders vs Time Founder Genome Equivalents vs Time or Mean Inbreeding vs Time 28 Founder Data Graphs From this menu you can select histogram plots showing any of the following statistics for each founder Representation the number of copies of each founder s genes present in the living descendant population Descendants the number of living descendants Contribution the proportion of the genes in the living descendant population that are derived from each founder Retention the probability that each founder s alleles are still present in at least one living descendant and Potential Retention the probability that each founder s alleles are present in the descendants or in the founder itself if it is still alive Individual Data Graphs From this m
24. ed ly ve SIAE rancve seh H l iaf 315 21 MICK MAT 23 hd zi Hef k ui z DALAS EE 52 i f7 U ae ae DAL AN fan H ld Ft z5 k cE AELAF Shes 214 td 13 BLIZE w c poe Create ve a r 1 CAL Hd t H KANI HOZ a H 14 FAILI 2 os SD WAP 226 hd 17 CEILGE EH a1 a t TUL E r 17 WSIL iki We oe Vl AS m Fie F l kE 377 k o CALI SPRE 743 bd 13 KEBE Hant J a E OKLA ava fg IH H l4 FOTCA2AH IF Ursc ted 2 L isortec ma F Use Salentinn for Age Structure and Demographic Projections h de dak dee aayain answa ti lanabe alsde Select an animal or animals trom the Current l opulation table at lett and click Iemove to exclude WHAT TO DO lhem fun unakhyses Tu udd unimas buek intu the vunent population selegl Weir Groce tHe buble al right and nalink Add Click Anneapt when finished tn ennfirm the selactians Figure 9 Animal Selection screen If you made any changes to the selected animals this is a good time to go back to the Clipboard and write down what changes you made in the selected animals If you don t write it down now you can be sure that you won t remember later why you included some animals and excluded others 13 Population Statistics After you accept your Animal Selection PM2000 proceeds with the genetic analyses When it is done it takes you to the Population Statistics screen This screen displays the basic summary statistics describing the genetic health of your population Take time to look at how many founder
25. ed to get to your desired or target population size In the upper left corner of this screen you specify the target size and the desired rate or amount of time to reach that target If you need to increase population size PM2000 will use the population growth rate from the demographic analyses to determine how fast you can grow the population and thus how long it will take you to get to your target size The numbers in the table at the upper right show you how many births you need this year next year the year after etc to get to and maintain the population at the target size The Model life tables you set up earlier are used to make these calculations These calculations take into consideration the neonatal mortality rates so the table really does show the number of births needed as opposed to the number of surviving births You can change any of the values to explore various options If you need to decrease the population size the table may show negative numbers These are the number of animals you must remove from the population to cause the population to decline to the target size Mrara mpral Araibewin far OKAPIA JOHNS TOMI Masb s lars tenale ate sble nce Luctzahe 1 trate Moieste 12 e male sers Ies eroiections 2raduerve sr ung rer me 99 Reproductive Planning How many births are required lo reach a desired population size Births naadad ta ineraase the panulation from a cunmant siza nf eh th a new s
26. efficients from pedigrees Pages 509 520 in C M Schonewald Cox S M Chambers B MacBryde and W L Thomas eds Genetics and Conservation A Reference for Managing Wild Animal and Plant Populations Benjamin Cummings Menlo Park California Ballou J D 1987 Small populations genetic diversity and captive carrying capacities Proceedings 1987 AAZPA Annual Conference 1987 33 47 Ballou J D amp T J Foose 1996 Demographic and genetic management of captive populations Pages 263 283 in D G Kleiman M E Allen K V Thompson amp S Lumpkin eds Wild Mammals in Captivity University of Chicago Press Chicago Ballou J D and R C Lacy 1995 Identifying genetically important individuals for management of genetic diversity in pedigreed populations Pages 76 111 in J D Ballou M Gilpin and T J Foose eds Population Management for Survival amp Recovery Analytical Methods and Strategies in Small Population Conservation Columbia University Press New York Caughley G 1977 Analysis of Vertebrate Populations John Wiley amp Sons New York Darwin C 1868 The variation of animals and plants under domestication John Murray London Ebert T A 1999 Plant and Animal Populations Methods in Demography Academic London Foose T J and J D Ballou 1988 Population management theory and practice Inter Zoo Yearbook 27 26 41 Foose T J R Lande N R Flesness G Rabb amp B Read 1986 Propagation plans Zoo B
27. enu you can plot a frequency histogram of the distribution of mean kinships in the population This will allow you to quickly see where the extreme values of mean kinship lie whether there are gaps in the distribution and how many animals fall at each level of mean kinship CUSTOM GRAPHS The Custom Graphs under the Graphs menu gives you the capability to plot almost any data from your PM2000 Project analyses On the left side of the Custom Graphs window is a list of the variables that can be graphed Each variable is associated with either Years e g Population Projections and Gene Diversity Age classes e g Mx Px and Vx or Individual IDs e g Inbreeding and Mean Kinship The default graphs will plot any selected variable against the appropriate one of Years Age classes or Individual IDs You also have the option of selecting a Frequency Histogram or a Cumulative Frequency Plot or plotting a variable against any other variable that is associated with the same type of data Years Age classes or Individuals While the Custom Graphs allows you to make any of a very large number of graphs be aware that many graphs you might choose would be largely meaningless or very had to interpret Even for meaningful graphs you will often need to open up the Graph Control Toolbox by right clicking on the initial graph and change graph settings in order to create a useful graph For example a graph of Mean Kinships vs Genome Uniqueness would
28. eral Projects from alternative sets of demographic and genetic information from a given studbook All the information associated with a Project will be stored in files in a project folder or directory _ Population Management 2000 iof x File Help Population Mat nd agement ot Come Unie n Robert C Lacy of the Brookfiel cal Park ger prey An bay gt Move the mouse around and help or instructions will appear here Figure 1 Opening screen of PM2000 PM2000 Wizard Mode PM2000 can be run in either a Wizard mode or Standard mode To create a Project in Wizard mode select Let the Wizard Help Me from the opening screen In Wizard mode PM2000 will guide you through a logical sequence for completing analyses and making decisions about managing your population At each screen the Wizard will provide a message box with instructions about what to do at that step The message screen shows only about 5 lines of text but it can be scrolled to show the rest of each message At the bottom of each message provided by the PM2000 Wizard you must either hit Next to proceed with your guided analysis hit Back to return to the previous Wizard page hit Exit Wizard to end the Wizard and use PM2000 in its Standard mode At any screen within Wizard mode you can jump back to earlier screens by clicking on the page number of the desired screen The label of each screen will appear as your cursor moves over its number When y
29. ese pairs or any pairs that have been listed in a prs file to any Project by choosing to Import Pairs from a File on the screen The pairs you have chosen will automatically be reloaded with your Project when you later Open the Project Culling The Culling screen allows you to identify which animals should be removed from the managed population and to test what effect those cullings will have on the genetic status of your population Any animals that were already known to be outside of the managed population or are incapable of breeding should probably have been removed already back at the Animal Selection screen before you began Genetic analyses However at this point you can remove more such animals by culling them here Craretis Anly for OKAPLA ICHN SS TON gt pulahe i Ste shes oure saisies Individual Stes shes als coding hash o Matic Be ings Lt oe anrerve gt pulane i tize iter Iris enza tk ol Mold nainn Praview af Population Culler Individuals Sex AE oy AL Plasi C lt E Pelik sKaca eye Location Statistics Atter EEEE 302 CIM OCIO 3 03 FF CIO C3 0C Mi Mi POM M MA vake Sa N 5C3 3 069 C39C 0 090 9 0C 3 6 0 32 CI 0C JOSI CIM OCIO JOCI 377 Of 36 COC Uei LMM NNI vi e NPR LN 3089 CIs OCP JOCI 234E 0 675 COC Loca CI0C OCIS e Esee OE CI 0C iee Mi dae MM MA valie tA 7EAN He OSPR lye a 3 083 C387 0 095 9 0C 25 37 0 635 CI 0C CENVER Aye 0 05 E 4 amp 5 zoc
30. from the SPARKS studbook software SPARKS automatically names this file exchange dbf Alternatively you may have created your own dbf file containing a pedigree for analysis with PM2000 see Appendix A After the first time that you use exchange dbf or another dbf file for sending genetic information to PM2000 PM2000 will create a text file called project ped with project replaced by the name of your project that contains the pedigree information from the dbf file The advantage of this file is that it is saved with a name that associates it with your project and it can be used again in the future if you need again to read the genetic information into your PM2000 project Therefore if you subsequently export more genetic information from SPARKS SPARKS will over write your exchange dbf file but you will still have a saved copy under the name of project ped of the pedigree information that was used in your PM2000 project If you ever need to restore the pedigree information in your PM2000 project back to the pedigree that was first read in you can do so by going to Data gt Genetics gt Reset on the menu If you wish to replace your pedigree information with data from a different pedigree information file you can do so by going to Data gt Genetics gt NewData on the menu Before beginning your genetic analyses you might note that the Clipboard automatically contains a line that specifies what file was used for genetic informat
31. gram that uses a new rating system being developed by SPMAG to calculate an index which indicates how good or bad any pair in a population is relative to several measures of genetic importance The MateRx software is designed and developed to be a genetic tool that will guide population management decisions For every male female pair in the population MateRx calculates a single numeric index indicating the relative genetic benefit or detriment to the population of breeding that particular pair This index the mate suitability index or MSI is calculated from considering the pairs mean kinship values the difference in the male and females mean kinship the inbreeding coefficient of the offspring produced and the amount of unknown ancestry in the pair MateRx is designed to simplify the decisions about which pairs should be bred by condensing all that we know about the genetics of a pair into a single number The program can be used to produce a table showing the MSI values for all male female pairings which then can be accessed through word processing software and printed and distributed or can be used interactively to search for specific mates as needed MSI values are labeled as beneficial scores 1 2 or 3 or detrimental scores 4 5 or 6 to the population Beneficial MSIs denote no detrimental effects relative to the genetic values of that pair and MSI values of 4 5 or 6 indicate at least one detrimental effect MSI Score Defini
32. h basic text editing tools for cutting and pasting or adding and deleting text To edit you can use standard Windows short cut keys or select actions from the Report Menu On the Clipboard you will accumulate text tables and graphs that document your analyses and management decisions It is a good idea to send information liberally to the Clipboard as you work in PM2000 and then later to go back to edit and delete unnecessary information On each screen in PM2000 and for some subsections of screens there is a Send to Report icon Clicking on that icon will send the associated text tables and or graphs to your Clipboard Often times formatting of tables and text is modified when they are sent to the Clipboard You can later edit the report either in the PM2000 Clipboard or in other programs to obtain formatting you like It is also useful to copy to the clipboard data that you may wish to analyze graph or use in spread sheet programs Excel PowerPoint First Send to report the data you wish to use then select the data from the Clipboard and copy it directly into the spread sheet program The Clipboard report can be printed or saved as an rtf file via the File Menu You can also retrieve previously saved reports into your Clipboard Because the Clipboard is saved as an rtf file in pm2000 projects project project rtf it can be opened in WORD WORDPERFECT or other word processing programs for further editing Ho
33. h should be evaluated carefully You can reset the values to original values imported from SPARKS by selecting the Data gt Demography gt Reset option on the menu bar Once you are happy with the life table or can explain away all its peculiarities copy it to the Clipboard You may want to cut and paste the life table from the Clipboard to a spreadsheet program to enhance graphics Age Distribution The Age Distribution screen shows the number males left and females right in different age classes Each bar is a one year age class Under the age distribution is the total number of male female and unknown aged animals currently in the population The table shows the actual numbers and the numbers expected for a stable age distribution A stable age distribution is the number of animals in each age class that we would expect if the life table rates had been constant over time You can change the numbers of animals in different age classes Unknown sex animals are assigned to be 0 5 male and 0 5 female Demographic Analyses for OKAPIA JOHNSTONI Male Life Table Female Life Table Male Projections Female Projections Total Projections Reproductive Planning Other Info Graphs Females Age Class WB actual stable Number of individuals FS Total Males 38 0 Unknown Age Males 0 0 ames os ResetAge Distributions to the imported values Total Females 38 0 Unknown Age Females 0 0 2 Figure 5 Age Dis
34. hie OKAPIA IOHNST ONI Lite lable Amix Fx vix a 130 3 0C C3 C 3 0C ta li 1 4 Vl c C72 alig t 0 C 2 Jr Wea Ie 1H Eslinrules C39 pi 7 oO C59 1 27 airiai t U1 1 44 Ive A 1045 E 0 04 C39 1 3 os ec 2 T 10 44 11 uL 1 All 1 N 38 00 12 Fatal C35 J2 D oO C35 22 Macas 19258 14 Wei ah sk 15 C3 C50 3 3 15 0 03 C50 J2 1 re 1 44 Ver 13 0 64 C38 7 13 3 C2 3 0 vl TTI i E LAI hese data have haen smanthed Ox me aas j a aoe ef x Smooth tha data none mnre Figure 4 Life Table screen At this screen you should first check that the smoothing of the Mx and PX is reasonable The object is to derive a Mx and Px curve and hence Lx curve that reflects the characteristics of the population to the best of your knowledge Poor data quality and quantity are a problem in many studbooks Smoothing the data can help to provide more reasonable estimates of life table rates However smoothing can sometimes lead to unreasonable values You need to check the life table for any smoothing problems and modify the smoothed Px or Mx values if this is the case So check the following Is there reproduction in pre or post reproductive ages If so zero these out Check the graphs of Actual vs Model Mx and Actual vs MODEL Px Use knowledge of the species biology husbandry and management to modify the Mx values as needed Modifications that significantly change lambda or generation lengt
35. ile Parents must come before their offspring in the file but otherwise the file need not be chronologically or otherwise ordered 35 Providing a census data file PM2000 obtains historic census data used only in the Census table and graph within the Genetics section but not in other calculations from a text file called exchcens txt This file is created by SPARKS whenever a Census report is produced but it can also be generated manually with any text editor If the file is created outside of SPARKS PM2000 will look for it in the same folder that contains the genetic and demographic data files The format of the exchcens txt file is given below Following the year the numbers provide the total population size the number of males the number of females and the number of animals of unknown sex Caution the format if this file is undergoing revision so the format specified here may no longer be correct by the time that you read this LOT TaD 1978 1 1979 1 1980 1 1981 1 1982 1 1983 1 1984 1 1985 21 12 1986 21 10 11 198721 40 11 1988 24 10 14 1989 30 12 18 1990 34 13 21 1991 39 18 21 1992 39 18 21 1993 42 18 24 0 1994 47 21 26 0 19957 535 26727 0 1996 56 26 30 0 1997 60 28 32 0 1998 64 29 35 0 Figure 27 Format of the exchcens txt file with historic census data 36
36. iology 5 139 146 Frankham R amp D A Loebel 1992 Modeling problems in conservation genetics using captive Drosophila populations Rapid genetic adaptation to captivity Zoo Biology 11 333 342 Keyfitz N 1968 Introduction to the Mathematics of Populations Addison Wesley Reading Mass Lacy R C 1987 Loss of genetic diversity from managed populations Interacting effects of drift mutation immigration selection and population subdivision Conservation Biology 1 143 158 Lacy R C 1993 Impacts of inbreeding in natural and captive populations of vertebrates Implications for conservation Perspectives in Biology and Medicine 36 480 496 Lacy R C A M Petric amp M Warneke 1993 Inbreeding and outbreeding depression in captive populations of wild species Pages 352 374 in N W Thornhill ed The natural history of inbreeding and outbreeding Univ of Chicago Press Chicago Lacy R C 1994 Managing genetic diversity in captive populations of animals Pages 63 89 in M L Bowles and C J Whelan eds Restoration and Recovery of Endangered Plants and Animals Cambridge University Press Cambridge Lacy R C 1995 Clarification of genetic terms and their use in the management of captive populations Zoo Biology 14 565 577 Lacy R C 1997 Importance of genetic variation to the viability of mammalian populations Journal of Mammalogy 78 320 335 31 Lacy R C 2000 Should we select genetic alleles in our conservat
37. ion and Additional genetic information specifies what View criteria were used when the genetic data were exported from SPARKS You might add any further notes to the growing report on your Clipboard as necessary or useful to document the genetic analyses that you are conducting A warning It is extremely hard to remember when you look back at a project months after it was first created why certain animals were included or not in your analysis and why you made other particular decisions about the population analysis and management USE YOUR CLIPBOARD to document your analyses You click on the Genetics heading to begin your genetic analyses The following sections describe each tabbed screen available within Genetics 12 Animal Selection Although you specified in SPARKS what animals should be included in the genetic analysis you did this when you set the View Criteria for the Export you now have a chance to touch up this selection The left hand list shows the animals in the population to be analyzed In the right hand list are those animals not in the selected set The lists can be sorted on any of the columns by clicking on the column heading Click again to sort in the reverse order To find out if any sterile animals are in the selected set click twice on the Sex column heading and check for animals that are listed as being sex s You probably want to remove these animals from the set selected for genetic management
38. ion breeding programs Zoo Biology 19 279 282 Lacy R C J D Ballou F Princ e A Starfield and E Thompson 1995 Pedigree analysis Pages 57 75 in J D Ballou M Gilpin and T J Foose eds Population Management for Survival amp Recovery Analytical Methods and Strategies in Small Population Conservation Columbia University Press New York Lande R and G F Barrowclough 1987 Effective population size genetic variation and their use in population management Pages 87 123 in M E Soul ed Viable Populations for Conservation Cambridge University Press Cambridge Miller P S amp P W Hedrick 1993 Inbreeding and fitness in captive populations Lessons from Drosophila Zoo Biology 12 333 351 Odum R A and B R Smith 2001 The effects of prorating risk in the development of life tables Zoo Biology 20 279 291 Ralls K amp J Ballou 1983 Extinction lessons from zoos Pages 164 184 in C M Schonewald Cox S M Chambers B MacBryde amp W L Thomas eds Genetics and conservation A reference for managing wild animal and plant populations Benjamin Cummings Menlo Park California Ralls K J D Ballou amp A Templeton 1988 Estimates of lethal equivalents and the cost of inbreeding in mammals Conservation Biology 2 185 93 Soul M Gilpin M Conway W and T Foose 1986 The Millennium Ark how long a voyage how many staterooms how many passengers Zoo Biology 5 101 113 Willis K 1993
39. iza nf gt with a grwth rate nf 1 Mid onver the next 1 yaars r Assumed sex ratin at hirth F tl Mala 1 Pamala omer gasart of err sls 3 ull Birt Needed 135 Litter Clutch Size I Prob Pair breeds C30 Size Puis Needed 12 6 Fopulation k Appl these reproductie plans to the projections pears Figure 7 Reproductive Planning screen To simply maintain population size a zero population growth management plan all you will need to do is produce enough births to balance the death rate Set the target size at the current size and lambda will change to 1 0 The number of births needed to replace expected deaths will be shown in the table Once you have the number of births needed you need to determine how many breeding pairs or groups you need to set up to produce these numbers of births Use your experience and knowledge of the biology husbandry and behavior as well as your knowledge of the individuals in the population to specify in the lower left part of the screen the expected mean litter or clutch size and the probability that a pair will breed PM2000 will apply these numbers to its calculation of the number of births needed in order to determine for you how many pairs you should put together for breeding 10 At the lower right of the Reproductive Planning screen is a graph that shows the projected growth and then stability of your population assuming that all goes according to the plans you ha
40. l currently disabled is the goal to retain at least X of the gene diversity throughout a period of Y Years The program will start by determining what population size you need to meet this goal Notice that the program has retrieved data from other parts of the program to use in these calculations Prrpealitiar Olga diwas for OKAMA JOHNSTONI How can you meet your genetic goals aiae fc ms oe Population Variables Management Goals Generation Length Mudrniuin Pulenuial Pupulutiuon Growl Rule z i Ariaast dil Gana Niversiy DURING f 111 Years Current Panulatinn Size Current Ettective Size Ruliu uf Nu De Current Gane Diversity Maximum Allowable Population Size iy 3 3 ak 4 New Paundars per Addition vent Year to Start Adding Founders Youu Ww Stup Adding Founders Yaars Gatwrean Addition Pvants c l I I ont C75 0 1 20 23 20 SC 30 7C 20 9C 130 ear FGE tecruited per New Founder Pupulauun Sier Needed lu Merl Guals Nuvded 282 cu alnere Sia Pha du iHi dts rals E GD ut vrnd uf 100 yeurs 90 Figure 17 Goals screen At the start the Maximum Allowed Population Size is set at the current size At the bottom of the screen next to the Solve for you can see if maintaining the population at the current size under the existing conditions Ne and generation length can maintain your desired goal The answer will either be that you can with this number or even fewer animals or that you can
41. lation for nnn iterations PM2000 normally uses 1 000 iterations of the gene drop simulation to estimate the genetic diversity remaining in a population and the genome uniqueness values for each animal This is enough to provide reasonable precision usually to better than 1 accuracy without requiring an unreasonable amount of computer time for most studbooks Analyses will be faster if a smaller number of iterations is chosen Analyses will be more accurate if a larger number is chosen Number of offspring produced per pair When you select pairs for breeding the effect of those breedings on the genetic status of the population depends on the number of offspring produced by each pair Before starting to select pairs for breeding you may need to specify how many offspring are produced per pair Here you should specify how many offspring are produced in each litter clutch or brood for your species After you change any of the General Options under the Genetics Settings and then click on OK PM2000 will redo the genetic calculations using the settings you have selected 21 GOALS This part of PM2000 allows you to explore various options for meeting a specific genetic goal First specify in the upper right hand corner a genetic goal in terms of the amount of genetic diversity you wish to retain over a given time period A typical goal is to maintain 90 of the wild gene diversity for 100 years This is the default in PM2000 An alternative goa
42. le number are needed then consider changing your goal For very small populations with no hope of adding new founders it may only be possible to maintain 87 of gene diversity for 100 years The goal can be changed by decreasing the amount of gene diversity to retain shortening the time period or both For some populations it might even be reasonable to set the genetic goals higher than the 90 for 100 years A large well managed population with long generation length and with the option of periodically adding new founders may be able to retain 95 gene diversity for 200 years Don t forget to send to the Clipboard various scenarios you want to present in your final report Finally set the screen to the scenario you accept as the most reasonable way to meet your goal number of new founders if appropriate desired population size any changes in lambda or N or T required The target population size for the last scenario tested will carry over to other parts of the program e g Clipboard s Analyses Completed Reproductive Planning as your goal for population size Multiple comparisons Sometimes it is useful to explore how a range of values in a parameter or pair of parameters affects the goal The Multiple Comparisons option available through clicking on the Multiple Comparison text allows you to simultaneously select a range of values for two parameters and create a table of results So for example if you were interested i
43. ly property set After upgrading to a new version of pm2000 create new projects rather than trying to load any existing projects see below PM2000 may not display well with some Settings of computer screens If labels of PM2000 run off the edge of the screen or the screens otherwise are problematic you should try alternative Display Settings These Settings can be accessed via the Control Panel gt Display gt Settings Usually PM2000 displays well with a Screen Display Area of 1024x768 A Screen Area of less than 800x600 will often cause problems Font size accessed through the Advanced button of the Display Settings in Win98 seems to work well when it is set at Large fonts For some monitors however settings other than those described above may be better The MS Office menu bar may cover part of the PM2000 display If that happens set the Office bar to AutoHide Support Help in using PM2000 can be obtained from the Population Management Manual Wiese and Willis in prep and from Help messages screen prompts and Wizards built into the program Members of the AZA Small Population Management Advisory Group will often be able to provide assistance to users of PM2000 The staff of the AZA Population Management Center in Chicago can also field questions regarding use of PM2000 The Population Management Center can be reached at pmc brookfieldzoo org Any reports of apparent bugs in the software should be sent to pm2000 ix netcom com but the
44. m Association The Walt Disney Company Foundation the Chicago Zoological Society the National Zoological Park Cornell University and the Lincoln Park Zoo PM2000 is copyrighted but it is distributed as freeware for use by anyone who has a need for it It is illegal for anyone to sell in whole or in part PM2000 without prior permission from the Chicago Zoological Society PM2000 is a Windows program and it can run on Pentium class computers running Win95 Win98 Win2000 or WinNT It requires about 2 MB of disk space for the program files and up to about 7 MB of space for system files that it may need to load onto the computer It may not run on computers with 32 MB RAM and it will run best if there is at least 64MB of RAM More memory is needed to analyze very large studbooks more than about 4000 animals Installation PM2000 is normally distributed on a CD To install PM2000 run the SETUP program on the CD The installation is available for downloading at hitp www2 netcom com pm2000 pm2000 html Updates of the program will be posted on this site as well During installation it is recommended that newer system files already on the computer should not be over written If Access Violation errors occur during installation they can usually be safely Ignored and the installation will still proceed successfully Prior to installing a new version make sure that no files in the existing pm2000 folder or the Sparks studbook folder have the read on
45. mography analyses you can then modify these defaults to test the effects of other demographic rates A genetic information file is specified next PM2000 will first look for a file named sparks projecfiproject ped or sparks projeciexchange dbf If these are not found or you wish to use a different file you would specify that file The project ped file is a file created by PM2000 when you first create a Project It is a text file version of the information in the exchange dbf file By saving the pedigree information in the ped file PM2000 allows you to later retrieve the pedigree data on which a Project was originally based perhaps for creating a new Project from the same genetic data even if you have overwritten the exchange dbf file created by SPARKS You can specify that no genetic information will be imported into your Project In that case when you begin genetic analyses you will need to type in the animals and their parentage for your population It should be noted that the genetic information file will be used for more than just obtaining the parentage data for genetic analyses This file also provides data as to which animals are in the selected subset of the population that will be the focus of management Thus not only genetic analyses but also age structure and the starting population for population projections will be based on this managed subset of the population The prn files with demographic information will be used only t
46. n determining how changes in Generation Length and changes in lambda might affect the target population size select Generation Length on the top of the table to set the columns to different values and select Max Potential Lambda to set the rows at different lambda values Usually PM2000 will set the middle value as the currently defined value for a parameter however these values can be changed by clicking on the cell The table will fill with the target sizes needed for every combination of T and lambda These results can also be sent to the clipboard Pipin letini Ckajwiclivwe foe OKAPIA IOHNST ONE How can you meet your genetic goals rale te yeenzen gt GeneroiciLengh Binlagical Variahlas eie or 21071 Maxin an thelial Py in amir tae Bal i Zarar opulotic i Size fea Fotenie mbes g Sarar 3c ve 23 se Py Tamar Gere Diver y Aaviir sir A mwak 3 Fogle or 23 qual asi i ah dhe ad Gur i Sulve Fur Pupulutiun Size Needed lu Meel Guuls Mew Four dere ser Ade or Ivet A50 410 Gararstion Lar yr sol 3m Fa O AA l 105 107 Ae a A Program Ohjentivas Papulalion Size Needed to Meel Goals ie 3 Gene Drvarsity atthe CHE 31 IOC Yeas e ses JO 5s Tene Divers DL UNC 10C Years Figure 18 Multiple Comparisons screen 23 MateRx PM2000 is designed to export data to an independent DOS based program called MateRx Ballou Earnhardt and Thompson 2000 MateRx is a pro
47. ned you can click on the MateRx tab to create or re create a dataset to run the MateRx program This dataset will incorporate any removals new pairings or culls that you have imposed on the population MateRx will run in a DOS window at the same time as PM2000 and thus can serve as an additional tool for use in developing a population management plan See the MateRx documentation for details on running MateRx 24 METAPOPULATIONS The last component of PM2000 is a section on Metapopulation analyses In this section you can partition your population into subsets including nested or overlapping subsets if you wish and look at the gene diversity within and between these subpopulations Creating subpopulations For the population highlighted on the left side of the screen initially this will be the total project population as that is the only one available the animals in that population will be listed on the right This list can be sorted by clicking on a column heading To create a subpopulation use your mouse to select the animals you wish to include and then click on the subset icon to create your new subpopulation The program will prompt you to name the subpopulation You can very quickly create a subpopulation for each Location by clicking on the map icon The information icon gives you a snapshot of information about any animal you highlight while the delete icon removes an animal from a population or removes a
48. o provide the mortality and fecundity rates for demographic analysis Therefore in creating the genetic information file from SPARKS or otherwise it is very important to pay close attention to which animals are selected for analysis After specifying the files with input data you can add any notes to a Comments section of the Create New Project screen These comments will be automatically transferred to your Clipboard report It would be useful to use these notes as an opportunity to document any assumptions you made or other special considerations about the data that you imported into your Project When working on a PM2000 Project you can move among six sections of the program the PM2000 Clipboard Demography Genetics Goals MateRx and Metapopulations PM2000 can also create a set of pre formatted reports for the breeding and transfer recommendations of population management it provides a variety of graphs and it contains Help and a dictionary with Definitions of genetic and demographic terms YOUR PM2000 CLIPBOARD After you have entered all the information needed to create your Project you click on the Create button and PM2000 takes you to the Clipboard a report editor Automatically transferred to the Clipboard will be documentation of the Project name and date the files used for demographic and genetic information and any text describing the data view used when the data were exported from SPARKS The Clipboard provides you wit
49. or 22 1 me riof enu suczec m vex aye vom ator Rep csciteror Allele ser aema ket Lacccxcor ie P I Ile ell vb u tat TAL Ill ait 10 E c 3 0230 BRAK C1845 1 645 35 0 Il H E 3 0230 I C 17e5 J 745 36 0 Tie F I Hk h Kral 1 Ala rth all 38 hd 5 3 0625 G ed4c C7305 3 7225 37 0 39 J C 3 0230 2 13931 C220 1 2230 36 0 th H i Hl all babi tft baie ah ihl l 54 3 0115 0 52C C3925 2 0635 35 0 32 H Cc 3 0129 JE C3963 J J 40 03 a H I Vile a mel 1 14F 1 I gt ell ihl l 257 bd Ec 3 0152 125C c 252 3 2520 9 0 JE F 2 3 0230 anoc C3 1 0030 6 0 all F I He 14 baal tea 1 17 th Vill 152 Id 1 0236 3 275C C 48 1 4640 43 0 IS r C 3 0052 6 275 C 49 5 J435 32 0 The E I Wey HTAA Ia 1271h wi 38 bd C 3 07 3138C 256 3 2530 32 0 asc H C 1 0271 2 030C C5003 2 5030 0 0 z Uicronlby ah dlre Sh dlu ik Current 75 Koow 10000 GD 0M2 0 0 GI 1 928 fye iPas 0 Figure 11 Founder Statistics screen If you specify that UNKnown animals are to be treated as WILD see Genetic Options below then the founders that have UNK parents will be indicated with a U after the studbook You may see some founders with studbook numbers of Pxxx in which xxx is another animal s studbook number These are pseudo animals that had to be created by PM2000 to complete the pedigree These animals are the UNKnown parents of animals whose other parent is the xxx animal Thus if an animal has dam
50. ou close and save a Project that is in Wizard mode PM2000 will remember where you were in the Project If you later Open the Project it will open in Wizard mode and will resume at the screen where you last left it Help A Help utility can be opened from the PM2000 menu bar This allows you to search the text of a Help manual essentially the text of this PM2000 manual and the text shown in Wizard mode You can also scroll through the documentation to find needed information Creating a Project When you start PM2000 and select Create a New Project from the opening menu PM2000 first asks for a Project name The name may be the same as your studbook or you may use variants on the studbook name to identify Projects that contain different versions of the analysis After you specify the Project name you need to specify the folder that will store the Project By default PM2000 sets the folder to one with the same name as the Project as a subfolder of the PM2000 Projects folder You may change the Project folder to something else if you wish by typing in a different name or browsing to a different existing folder On the Create New Project screen you also have the option of specifying a Date for Calculations This date will be used to determine the ages of animals The default date is the date that the project is created You may wish to complete demographic and genetic analyses for ages calculated relative to some other date Project Name oka
51. pi Date for Calculations 8 5 97 Project Folder D PM2000 Projects okapi Ehaesar The following file will be used for gathering demographic information on females D sparks okapi fokapi pm Browse Species OKAPIA JOHNSTONI Filter conditions The following file will be used for gathering demographic information on males D sparks okapi mokapi pm Browse Species OKAPIA JOHNSTONI Filter conditions I Check this box if no demographic data will be imported for this project The following file will be used for gathering genetic information D SPARKS OKAPI Exchange dbt TORM I Check this box if no genetic data will be imported for this project Comments j notes about the project would go here a Create Cancel Figure 2 Create New Project window Next you must specify the names and locations of the files with demographic information on females and males By default PM2000 will look for files named the sparks project fproject prn and sparks projecimproject prn with projec replaced by the name of your project If the files do not exist with these names or if you wish to use other demographic data files you specify those files by typing in the filenames or browsing to find the files If you have not previously prepared prn files with demographic information you can specify that no demographic data will be imported into your Project PM2000 will then use default demographic data Within De
52. program is provided without any guarantee that bugs will be fixed Further development and support of PM2000 will depend on resources being provided for that purpose Starting PM2000 Before running PM2000 files with data on the demographic rates and with data on the pedigree must be created The easiest way to create these is to use the SPARKS program developed by ISIS International Species Information System http www isis org to manage the studbook data From the Reports gt Analysis gt Export menu of SPARKS you can export the needed files for demographic and genetic analysis Sample files fdefault prn mdefault prn and default dbf are provided in the PM2000 installation Care should be taken in determining exactly which data to export from SPARKS PM2000 will use the animals defined in the SPARKS View for the Genetic Export as the managed population although animals can be removed and added from that View before genetic analyses are run To use PM2000 with a dataset that was created outside of SPARKS see Appendix A ape To start PM2000 double click on the pm2000 exe program file or short cut x Initially you must create a new PM2000 Project Your Project will be a set of analyses and reports associated with a data set You may create several Projects from a data set perhaps using different options for the analyses or making management recommendations based on different assumptions or goals and you may create sev
53. quivalents or Rel MK the relative mean kinship To sort the list of animals click on the appropriate column heading Click on it again if you want to sort in the reverse order You can then test the effects on the genetic status of the population of removing any animal Click on an animal that you may want to remove to see how Gene Diversity Gene Value and Founder Genome Equivalents would change if that animal were culled Once you decide to cull an animal hit the Accept button After each animal is removed the measures of genetic value of the remaining animals will be updated l e kin of the culled animal will become more valuable than they had been before the culling If you want to un cull all the animals you had selected hit the Reset button You can specify that the animals to be culled should be removed from the Age Structure and Population Projection screens by checking the indicated box As you cull animals you will see that the summary statistics of the population will be updated at the bottom of the screen When you are done with culling you should Send to the Clipboard your list of culled animals and the new Population Statistics at the bottom of the screen Effective Population Size The effective population size Ne is based on the past history of the population but its primary use is in predicting future genetic changes The first estimate of Ne is based on the amount of gene diversity lost through the generations
54. rix The kinship coefficients between every pair of animals in the population are displayed in a table accessed by the Kinship Matrix tab Most of the numbers shown in the genetic analyses can be calculated from the table of kinships For very large studbooks the kinship table is not shown as it is too large to be easily viewed However it will always be stored as a file named project kin in your Project folder so you can view it later if you wish If you want to find the kinship between any two animals click on the option below the table The kinship between two animals is also the inbreeding coefficient of any offspring produced by mating the two animals Thus this option allows you to examine whether a potential mating would produce inbred progeny 16 Pairings This screen allows you to select the optimal pairs of animals to breed and to test what effect those breedings will have on the genetic status of your population When you select pairs for breeding the effect of those breedings on the genetic status of the population depends on the number of offspring produced by each pair Before starting to select pairs for breeding you may need to specify how many offspring are produced per pair You can specify how many offspring are produced in each litter clutch or brood for your species in the Settings gt Genetics gt General Options menu If you change this number you must then click on the message to reset genetics options and data
55. rtion of the genome traceable to wild caught as opposed to Unknown founders Inbreeding coefficient omitting unknown genes ean Kinship K omitting unknown genes Kinship value KV omitting unknown genes Reproductive value Proportional of genome unique among living animals Proportion of genome unique among living descendants non founders Probability that an allele in that individual will be lost from the next generation Any miscellaneous notes about a record PM2000 will use the information in this field as additional identifiers for an animal Figure 26 Fields for a pedigree data file The ID must be a 1 to 6 character field and the dam and sire names are the 6 character ID numbers of the parents These IDs can be any combination of numerals letters and printable symbols e g punctuation If the name is less than 6 characters long the rest of the field can be padded with blanks If an animal is a founder parents are off the top of the pedigree and unknown the dam and sire names should be given as WILD Note that the WILD label must be right justified If one or both parents of an animal are unknown but thought to be within the pedigree population rather than being ancestors preceding the pedigree the unknown parent s should be given names UNK or any name of 1 to 6 characters that does not match any other animal in the data f
56. s have contributed to your captive born population how much gene diversity there is in the captive population relative to the wild population from which the founders came the number of founder genome equivalents how many wild caught animals would have the same gene diversity as the captive born population and the mean inbreeding level of the population Take time also to look at what these values could become the Potential if you could perfectly control all breeding production of offspring and which genes are transmitted to offspring Unless you bring in new founders you can never reach this theoretical potential rather it is an upper limit that gives you an indication of how much scope there might be for improvement The number of Living Descendants may be less than you expected and may even be a fractional number This is because PM2000 normally excludes all animals with unknown parents from genetic analyses and includes only those parts of animals which can be traced back to known founders For example an animal with a known dam but an unknown sire will be tallied as half an animal in genetic analyses As will be explained later you can change the way that PM2000 handles unknown parentage by going to the Settings gt Genetics gt General Options menu Gimni Anly for OAC JOHNS TON zj ourcler tanstics Individual ste shes as c gt ding Rira mMe Fae naz un e a 2erve gt pulane i Sire n gt roj sanau
57. s names fdefault prn and mdefault prn to hold these values The default demographic data are such that the population will have virtually zero population growth Within the Demography section on Model Data of the Male Life Table and Female Life Table tabs you can then change the default survival and fecundity rates to model populations with other demographic characteristics If you specify that no genetic data will be imported into your PM2000 Project then the program will ask you to create individuals and identify their identifier or name sire dam sex alive dead status birth year death year and location Only the first five of these data types are essential for the analyses as PM2000 can treat the others as missing data 33 Creating input data files outside of SPARKS For any but the smallest datasets it is not recommended that you create the input data within PM2000 Instead you should provide to PM2000 prn files with demographic data and a dbf file with pedigree data The formats of the data for these files are illustrated below Demographic data The format of the prn files is a ASCII text file with lines of data shown in the Figure 25 These data are the default demographic rates in file fdefault prn Of the first 8 lines of header information only the third line the sex to which these data apply is important The other lines are just there to better describe the data set you are using and the formats and content of
58. s the number of offspring to be produced per pair i Genetics Options x Settings for Genetic Calculations F Include founders in all genetic measures F Allow pairing non selected animals r Do not update genetic measures as pairs are created F Count Unknowns as Wilds F Allow pairing of dead animals I Use input matrix of coefficients of relationship among founders F Use input matrix of coefficients of kinship among founders F Create output file for use with MateRx l Run gene drop simulation for iterations gt For pairings use a litter size of 1 OK Figure 16 Genetics General Options window The available settings are Include founders in all genetic analyses Normally the wild caught or imported founders are not included in tallies of the genetic status GD GV and FGE of your population Instead the measures show the genetic status of the descendant animals produced within your captive population If you wish to include the founders themselves in the tallies of genetic status check this option Allow pairing non selected animals Non selected animals are not included in measures of genetic status that is why they were not selected but you may test them in Pairings if you check this box so that PM2000 will keep information about them in its database For example you might wish to test the effect of importing an animal not presently in your population to use in future pairings If you check the option to allow p
59. tions 1 very beneficial pair 2 moderately beneficial pair 3 slightly beneficial pair 4 slightly detrimental pair 5 detrimental pair should only be used if demographically necessary 6 very detrimental pair should only be used if demographic considerations override preservation of genetic diversity per se so detrimental the pair should never be made Because the MateRx process is automated the software is limited in several ways MateRx does not address demographics behavior or logistics of a pairing MateRx is not intended for use with all captive managed species Many species have unusual population histories and structures that require the expertise and attention of a trained population biologist These populations may have characteristics such as few founders many captive generations extremely small numbers or many unknown origins or parentage data that prohibit generic management see MateRx documentation for more details MateRx is time sensitive the MSI rankings are only valid as long as there are no substantial changes in the population This report should be considered invalid after one year following its date of creation The MateRx program file MATERX EXE needs to be loaded into your Project folder The program is currently set up to assume that your projects are each in a separate folder within the Projects folder While running PM2000 at any time after the initial Genetics tab is ope
60. tribution screen Take a look at the age distribution Are there any impossibly old animals if so check your SPARKS data Does the age structure show a baby boom or is it top or bottom heavy Are there enough animals in breeding age classes to provide the desired amount of reproduction How does the actual age distribution compare to the stable age distribution If they are quite different then population growth may behave unpredictably in the future Male and Female Projections The Projections screens show the expected number of males or females in the future given the model life table and the actual age distribution The projected numbers if the age structure was stable are also shown The difference between the actual and stable projections shows the impact of the age distribution For example a population with fewer breeders than expected if the population were stable might actually decrease in size in the near future as a result even though the life table predicts a positive growth rate lambda gt 1 0 Total Projections On the Total Projections screen the projections for males and females are combined Pix rerirygriapebian Amalyxix fnr OKAMA JOHNSTONI Size Cc 2 _ w a A O Q a tt tt tt tt ttt VTLS edger VUVTh Ve RERAD Years actual stable Figure 6 Projections screen Reproductive Planning Use the Reproductive Planning screen to determine how many births or culls you ne
61. usually be changed from the default line plot to a scatter plot S Cacate Cuctom Graph Data tn pint Plot Ayeiast Yeor iuli mE o l beni Irdi deslezAye Cless err sle h des diak eye Cie ini hir Siak sll al Irate d aisee ye Cicsstor Stok 2C st Ace Me s uri xih rah bdc Hel Ly Molel Medel La err sle Mi dlie hdc del Fe nole Medel Cx He 3 Hi del x Fi rah 1 Arse vty Polel Ace th ier ole bar dish ee She ales kic del hex Fame Gara C ve sity War ne Roniwerolb ncm nagiisa e lin FAE Seer Timel Hesr ive Tinei h wh Bipa aae n Sow nterna a ii dale iph tleo tenvel Figure 23 Custom Graphs selection window Freyueruy Hislugrarn wilh EJ ines vials Cumulative Frequency lot with 20 EOE 29 FILE MENU The File Menu provides a few ways to save projects or reports If you select New Report PM2000 will ask if you want to first save the old report and then will clear the Clipboard to let you start a fresh report Open Report allow you to retrieve a previously saved report for further work Save All saves the project and the report under the current names Save Project As allows you to save your project under a new name Save Report As will save the report under a new name Print Report will print your report HELP MENU The Help feature provides quick access to text that describes each component of PM2000 The Help text is a searchable on line version of this manual
62. ve specified If you check the box at the bottom left PM2000 will then transfer this projection to the Population Projection screens Standard Demography Graphs The last tabbed screen available in the Demography section provides a set of four standard graphs The graphs provided are age specific rates of fecundity Mx reproductive value Vx mortality Qx and survivorship Lx The data for these graphs are taken from the Model Data in the Life Table screens Unless you smoothed the data in your life tables the lines on the graphs may be rather jagged and hard to interpret You can use the smoothness of these graphs as an indication of whether it may be useful to smooth your demography data further MasLb gt lars lenale ate sbie ane Luctizabey teste Foiezhe 1s e male me ser ors lest Hrojections lt e sraduerc Asana sho rio Ureghz Model Mx oss aR 2 insler Forces A emeles FatTraM HAAN HHA AM DS TL 3 a Sa EGALITE EIEE m i 2 SM 62 TARE PP Pane ea e Age Class x Age Class x x lt g ch p o er 1 appels 4 eriles Laaya Cincom 4 SERS P95 Food CIS IaslsIET Age Class x Age Class x Figure 8 Demography Graphs screen 11 GENETIC ANALYSES Getting Started with genetics When you created your PM2000 project you specified a file to be used for gathering genetic information This file was either a dbf file or a ped file Most users will export a file for genetic analysis
63. versity GDw the overall Fst the mean between population kinship MKb and the mean within population kinship MKw Metapopulation Comparisons 0 0552 0 0734 i 0 0314 0 0332 0 0332 0 8918 0 0512 j 0 0342 0 0272 0 0272 0 0586 0 0528 0 0684 0 0628 0 0849 0 0849 0 8353 0 1323 0 1227 0 1109 0 1109 0 7209 0 189 0 5 Choose subpopulations from the list at left and comparison information will be displayed at right Close Figure 20 Metapopulation Comparisons screen The metapopulation comparisons can be used to determine which subpopulations are genetically least similar and therefore may be considered for exchanges that would benefit both Or by subsetting each population into its males and females you could determine which populations have animals that could be safely shifted into a new population without any risk of inbreeding with a related animal in the recipient population GRAPHS PM2000 provides the capability to plot a large number of different types of graphs that summarize trends and relationships in your data In the Graph Menu there are a set of default Demography graphs a set of default Genetics graphs and the option of creating Custom graphs of almost any two variables Mx Actual vs Model Males cl r 420 8 Xx Lee C2 7 Figure 21 Options Settings for a Graph r le Pom ZAR F Voge Age Liss tl s Ms MP SSI GM aman te e eree Age Class x Clic the ction ot Tar 13 rai mto the
64. wever after editing a PM2000 rtf file in another program you should either save it under another name or save it as an rtf file so that PM2000 can read the original or edited file if the Project is re opened At the right side of the Clipboard is a list of Analyses Completed This list will accumulate key descriptors of your managed population as you work through your analyses In addition clicking on any variable in the list will take you directly to the screen where that variable can be found or calculated Fopulsaton Management ZULU okapi le Kopet Usa cest Gens Iip Cw lu PM2000 Clipboard Demogauphy Genetics Guals MateRx Metapopeletions PM7010 Clapetar eared Population Management 2000 Analyses Completed Cuslomized report Project okapi Report compiled under Populwion Managerment 2000 version 1 13 9 55 59 AM 1114 01 C OLUICILS Date to be used tor calculations 3 7 01 Demographic data from ssparks okapiimokapi pm and D sparkstokapi tokapi pro Cienetic data fram ssparks okaptakapi ped Addition demographic information Data exported on 19 Jml 20411 Data compiled by Charles Darvin Dulu current Uru 7 Mer 2001 Scope of data World captive populatian Click on any descriptor to determine values or make changes 72 This is Une repurl for Uw current projec Yuu vuan send dula lu lhis seport by sight clicking un u yruplity table ele Figure 3 The PM2000 Clipboard DEMOGRAPHIC ANALYSES

Population Management 2000 User`s Manual - Training

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