Introduction to Conservation Genetics Richard Frankham, Jonathan D

Cambridge University Press 0521630142 - Introduction to Conservation Genetics Richard Frankham, Jonathan D. Ballou and David A. Briscoe Index More information

Index

Acionyx lubatus see cheetah Alouatta seniculus see red howler autopolyploidy 373–4, 533 acorn woodpecker 331, 516 monkeys autotetraploid 88 Acrocephalis (Bebornis) sechellensis see Alpine ibex Capra ibex 464 autozygosity 257, 533 Seychelles warbler Amazon basin, extinction rates, birds average heterozygosity 48, 533 adder Vipera berus 36, 286, 300, 306, 5 401 Amazona vittata see Puerto Rican parrot B allele, blood groups 167–8 additive genetic variance 109, 110–11, American bison see bison backcross 273, 533 533 Ammodramus maritimus nigrescens see Baiji dolphin 345 additivity 533 dusky seaside sparrow Baird’s beaked whale Berardius bairdii Aepyceros melampus see impala amphibians 472–3 African wild dog Lycaon pictus 65 allozyme diversity 62 Balaenoptera endeni see Bryde’s whale Agrostis tenuis see bent grass genetic distances, means/ranges Balaenoptera musculus see blue whale Ailuropoda melanoleuca see giant panda 69 Balaenoptera physalus see fin whale Aix sponsa see wood duck percentage endangered 3 balancing selection 199, 204, 534 Aleutian goose Branta canadensis amphidiploid 533 bald eagle Haliaeatus leucocephalus 352, leucopareia 464 amplified fragment length 464 Algonquin wolf 369 polymorphism (AFLP) 55–6, Bali starling Leucopsar rothschildi 345, allele frequency 48, 73–4, 139–41 64–6 496 computer simulation 193–4, Amur leopard Panthera pardus orientalis bandicoot, Eastern barred Perameles 195–6 425 gunnii 61 divergence over time, population Anas laysanensis see Laysan duck (teal) Banksia brownii see Brown’s banksia fragmentation 319–20 angiosperms, polyploidy 29 Banksia cuneata see matchstick banksia equilibrium 171–2 Anser caerulescens see snow goose barnacle goose Branta leucopsis 117 favourable allele 142 Anser fabalis see bean goose barred owl Strix varia 15 genetic drift 179–87 Anthoxanthum odoratum see bunch bat, ghost Macroderma gigas 487 inbreeding 260 grass bay checkerspot butterfly Euphydryas and migration 169–73 Aotus trivirgatus see owl monkey editha bayensis 30, 130, 506, and mutation 158–60 Apalachicola rosemary Conradina 509 recessive allele 62 glabra 345 bean goose Anser fabalis 464 alleles Arabian oryx Oryx leucoryx 67, 184, 354, Bebornis (Acrocephalis) sechellensis see deleterious 60–1 385, 425, 431, 464 Seychelles warbler directional selection 215 case study 466 bee-eater 117 effective number 201 Arabidopsis thaliana see thale cress bent grass Agrostis tenuis, tolerance to effectively neutral 214–16, 327 Argyroxiphium sandwicense var. heavy metals 129, 148, 170–1, lethal 261–2, 275–6, 293–4 sandwicense see Mauna Kea 212 mismatch analysis 481 silversword Berardius bairdii see Baird’s beaked allelic diversity (A) 48, 62, 80–3, 533 artificial insemination 442 whale Allen’s rule, clines 170 Aruba Island rattlesnake Crotalus Bergmann’s rule, clines 170 alligator, American Alligator unicolor 345 Bidens, Hawaiian 345, 494 mississippiensis 65 asexual species 414–16 bighorn sheep Ovis canadensis 332, allopatric speciation 372, 533 associative overdominance 219–20, 513 allopolyploidy 237–9, 373–4, 533 533 small vs. large populations 33 allotetraploid 89 assortative mating 85, 533 binomial distribution 534 allozygous 257, 533 Astragalus see sentry milk-vetch binomial sampling 180 allozymes 61–2, 533 Astrocaryum mexicanum 513, 514 biodiversity diversity 219 Attwater’s prairie chicken conservation 2–3 electrophoresis 49–50, 52 Tympanuchus cupido attwateri defined 2 heterozygosity 246 345, 352 bioresources 2 indicators of hybridization 411 Australian bush rat Rattus fuscipes 217 biparental inbreeding 494–6, 534

© Cambridge University Press www.cambridge.org Cambridge University Press 0521630142 - Introduction to Conservation Genetics Richard Frankham, Jonathan D. Ballou and David A. Briscoe Index More information

608 INDEX

birds Brown’s banksia Banksia brownii 272, preservation following extinction allozyme diversity 62 415 in wild 420 avian malaria 498 brush-tailed bettong Bettongia reintroductions 448–70 extinction rates 4 penicillata 354 shortage of space 337 Amazon basin 5 Bryde’s whale Balaenoptera endeni stages 422–3 genetic distances, means/ranges 69 472–3 zoos 421–2 heritabilities of fitness, body size, buffalo, African Syncerus caffer 65, 127, Caretta caretta see loggerhead turtle bill size 117 486 Caribbean flamingo 354 inbreeding depression 282 bullfrog (American) Rana catesbeiana carrier frequency 83–4 percentage endangered 3 354 Castanea dentata see chestnut, sex determination 497 bumble bee Bombus terrestris 39 American birthweight, humans, stabilizing bunch grass Anthoxanthum odoratum Catalina mahogany Cercocarpus selection 149–50 465 traskiae 345, 411–12 bison tolerance to heavy metals 129, 148, catastrophes 504, 515, 534 American Bison bison 176 170–1, 212 Cerastium fischerianum var. molle 66 European Bos bonasus 176, 184, 425 butterflies, Finland, extinctions 31, Cercocarpus traskiae see Catalina Biston betularia see peppered moth 313 mahogany black lion tamarin Leontopithecus Cercocebus atys see sooty mangabey chrysopygus 430 California condor Gymnogyps chafer beetles Prodontia modesta and P. black sea bass 490 californianus 61, 83, 134–6, 143, bicolorata 367 black stilt Himantopus novaezelandiae 184, 260–1, 352, 431, 444–5, 496 Chamaecrista fasciculata 387 345 case study 467 Chatham Island black robin Petroica black-footed ferret Mustela nigripes 99, chondrodystrophy 83, 134–6, 260–1, traversi 184, 302, 400 184, 352, 425, 431, 463 444–5 cheetah Acionyx lubatus 61, 159, 300, case study 466–7, 517 genetic disease, management 444–5 431, 485, 517 black-footed rock wallaby Petrogale California spotted owl Strix occidentalis chestnut, American Castanea dentata lateralis 13, 34–6, 285, 315, 316, occidentalis 14–15 38, 148, 402 401–3, 408 Canada goose Branta canadensis 117 chi-square test 77–8 island and mainland populations canine distemper virus (Morbillivirus) chimpanzee Pan troglodytes 64, 80 34, 408 499, 515, 517 eastern Pan t. schweinfurthii 472 loss of genetic diversity 285, 315, Canis lupus see gray wolf chloroplast DNA (cpDNA) 237, 534 316 Canis rufus see red wolf Choeropsis see pygmy hippopotamus reintroductions 13, 401–3 Canis simiensis see Ethiopian wolf chondrodystrophy, condors 83, 134–6, blackcap Sylvia atricapilla 129 Capra ibex see ibex 260–1, 444–5 blood groups, B allele 167–8 capricorn silvereye Zosterops lateralis chromosomal diversity 59–60 blue whale Balaenoptera musculus chlorocephala 509 Cichlidae 372, 375 472–3 captive population breeding cinereous vulture 431 Bombus terrestris see bumble bee programmes 419–47 CITES (Convention on International Bos bonasus see bison extent 420–1 Trade in Endangered Species) Bos gaurus see gaur founding 423–4 503 bottlenecks 19, 183–7, 304, 482–5, genetic adaptation in captivity clade 534 533 452–9 Clarkia pulchella see evening primrose Branta leucopsis see barnacle goose genetic changes in captivity 452 Clethrionomys glareolus see bank vole Branta canadensis leucopareia see genetic deterioration 455 clines 167, 169–73 Aleutian goose genetic goals 352–7 cloning 442–3 Branta canadensis see Canada goose genetic management 427–39 clover Branta sandvicensis see nene (Hawaiian growth 426–7 rose Trifolium hirtum 460 goose) inbreeding depression 108, 428 white Trifolium repens 129 Brassica sp. 62 avoiding 431–5 co-dominance, defined 48, 534 Brazil, Atlantic forest fragmentation management of groups 439–41 coalescence 475–80, 534

309 maximizing Ne/N 430–1 effective population size 485 bridled nailtail wallaby Onychogalea maximum avoidance of inbreeding coalescence times 478 fraenata 65 (MAI) 431–41 coancestry 433, 534 brown bear Ursus arctos 332 minimizing kinship 433–9 see also kinship Pyrenean race 480, 498 plant propagation 420–1 cobra, blacknecked 354

INDEX 609

collared flycatcher 117 crow see Mariana crow; raven dog, hybridization see Ethiopian wolf collared lizard Crotaphytus collaris 381, Cryan’s buckmoth 391 (simian jackal) 462 cryopreservation 442 dog see African wild dog; colonial pocket gopher Geomys colonus Cuvier’s gazelle Gazella cuvieri 287 dominance, degrees of 140–1 12, 217–18, 378 Cynomys spp. see prairie dogs dominance variance 109, 111, 122, 535 Columba mayeri see Mauritius pink Dorcas gazelle Gazella dorcas 270–1, pigeon Daphnia see water flea 301 computer simulation 28–30, 193–4, Darwin’s cactus finch Geospiza Drosophila melanogaster see fruit fly 195–6, 253, 507–9 scandens 117, 243, 244, 484 Dusicyon fulvipes see Darwin’s fox allele frequency 193–4, 195–6, 253 Darwin’s fox Dusicyon fulvipes 345 dusky seaside sparrow Ammodramus PVAs 507–9 Darwin’s medium ground finch maritimus nigrescens 367, 490, condor see Californian condor Geospiza fortis 115, 117, 129, 244 504 Connochaetes see wildebeest DDT control 400 Conolphus subcristatus see Galapagos deer mouse Peromyscus maniculatus 39, Eastern barred bandicoot Perameles iguana 288, 289 gunnii 61, 244, 345 Conradina glabra see Apalachicola deleterious alleles 60–1 ecological exchangeability 389–91 rosemary deleterious mutation 162, 198 ecosystem services 535 conservation biology 9 demographic history, and population value 1–2 Conservation Breeding Specialist size 480–5 ecotypes 129, 535

Group (CBSG), IUCN 534 demographic stochasticity 28, 504, effective number of alleles (ne ) 201, conservation genetics 513, 535 535

definition/scope xiii, 1, 9–10 Dendrocopus medius see middle spotted effective population size (Ne ) 189–90, management of endangered species woodpecker 228, 239–51, 535 16–18 desert topminnow Poeciliopsis monacha estimating 250 structure and content 10 25, 284–5, 401 fluctuating populations 247–8 Convention on International Trade in deterministic factors, endangered inbreeding 250 Endangered Species (CITES) 503 species 503 unequal sex ratio 241–3 convergent evolution 535 Diceros bicornis see rhinoceros, black variance 250 Cook’s kok’io Kokia cookei 176, 420 die-back fungus Phytophthora variation in family sizes 243–6 copepod, Tigriopus californicus 387 cinnamomi 97–8 effectively neutral alleles 214–16, 535 Copsychus sechellarum see Seychelles dik-dik Madoqua sp. 367, 386 eider duck Somateria mollissima 73 magpie robin directional selection 114, 145, 146–8, Elaphurus davidianus see Père David’s cord grass see Spartina 191, 215, 535 deer correlation, defined 102 disease Eld’s deer 513 corridors 404 inherited diseases 443–4 electrophoresis 51–3 Corrigan grevillea Grevillea scapigera species boundaries 127 elephant 345 disease resistance 129–30 African Loxodonta africana 391 Corvus corax see raven and genetic diversity 39 Asian Elephas maximus 30, 243, Corvus kubaryi see Mariana crow and MHC 209 413–14 cotton (cultivated) Gossypium dispersal emperor goose 499 barbadense and G. hirsutum 411 evolutionary changes 129–30 endangered species 2–8 cotton-top tamarin Saguinus oedipus and gene flow 330 defined 6–7, 8, 535 112, 119 dispersal distances 331 deterministic factors 503 Coturnix coturnix japonica see Japanese disruptive selection 145–6 extent of endangerment 3–4 quail DNA genetic diversity 65–6, 158–9 coyote 65 non-intrusive sampling for genetic IUCN categories 7 crane analysis 12, 475–6 microsatellite genetic diversity hooded 431 sequence variation 62–4 65–6 red-crowned 244, 431 sequencing 57–9 regeneration of genetic diversity whooping 67, 184, 345 phylogenetic trees 382–4 158–9 cricket Gryllus firmus 425 see also microsatellites; stochastic factors 504 critically endangered species 535 mitochondrial DNA Endangered Species Acts, legal crossing over 93 DNA fingerprints (minisatellites) protection 7, 371, 421, 526 Crotalus see rattlesnake 54–6, 64–5, 535, 540 endemic species 34, 536 Crotaphytus collaris see collared lizard dodo Raphus cucullatus 23 Enhydris lutra see sea otter

610 INDEX

environmental stochasticity 504, 536 island/mainland/ocean (1660 to fox environmental variation 99 present) 4 Darwin’s Dusicyon fulvipes 345 partitioning 105–6 population viability analysis 506–28 San Joaquin kit Vulpes macrotis epistasis 536 recorded (1660 to present) 4 mutica 481 epistatic variance 536 sixth extinction 2 silver Vulpes vulpes 147–8 Equus, horse, evolution 148 stochastic factors 504 Frankel, Sir Otto 9 Equus grevyii see Grevy’s zebra Franklin tree Franklinia alatamahu 176, Equus przewalskii see Przewalski’s horse F, Wright’s inbreeding coefﬁcient 536 420 ethics, justiﬁcation for preservation of F statistics frequency-dependent selection 199,

genetic diversity 1–2 FIS 324–7, 537 207–11, 537

Ethiopian wolf (simian jackal) Canis FIT 324–7, 537 fruit ﬂy Drosophila melanogaster 63, 67

simiensis 12, 65, 81, 169, 345, 411 FST 324–7, 537 bottlenecks 185, 304 eucalypts, glaucousness 212–13 Falco araea see Seychelles kestrel Buri’s increase in variance in allele Eucalyptus coccifera see Tasmanian snow Falco peregrinus see peregrine falcon frequencies over time 321 gum Falco punctatus see Mauritius kestrel clines 170 Eucalyptus gigantea see gigantic false poison sumach Rhus michauxii directional selection 191 eucalypt 414 family size 246 Eucalyptus gunnii see gunni eucalypt family sizes 243–7 genetic drift 324 Eucalyptus marginata see jarrah tree impact on effective population size heritabilities, mean 118 Eucalyptus urnigera see urn gum 243–6 inversion polymorphism 211–12 Euperipatoides leuckartii see velvet worm Felis concolor coryi see Florida panther mutational accumulation 350 Euphydryas editha bayensis see bay Festuca ovina, tolerance to heavy speed 148 checkerspot butterfly metals 129, 148, 170–1, 212 full-sib mating 261, 537 euro Macropus robustus erubescens 34, fin whale Balaenoptera physalus 472–3 Furbish’s lousewort Pedicularis 285 Finland, Glanville fritillary butterfly furbishiae 61, 519 evening primrose Clarkia pulchella 31 31, 313 evolution fishes G6PD (glucose-6-phosphate adaptive 128 allozyme diversity 62 dehydrogenase), deficiency 197, convergent 129 genetic distances, means/ranges 69 207 large populations 126–53, 154–74 inbreeding depression 282 Galapagos, see also Darwin’s finches small populations 175–96 parasite load 38 Galapagos iguana Conolphus evolutionarily effective population percentage endangered 3 subcristatus 464 size 485 fitness see reproductive fitness Galapagos Island cotton Gossypium evolutionarily significant units (ESU) fixation 142, 217 darwinii 411 388–9, 536 selective sweeps 479 Galapagos tortoise Geochelone

evolutionary potential 341–3, 536 fixation index FST 331, 536 elaphantopus 464 and heritability 111–18 Florida panther Felis concolor coryi 11, Gambusia holbrooki see mosquito-fish impact of population size 347–8 345, 367–8, 397–9, 460 gaur Bos gaurus 443 ex situ conservation 441, 536 case study 518 Gazella cuvieri see Cuvier’s gazelle exons 62, 536 flour beetle Tribolium castaneum, Gazella dorcas see Dorcas gazelle

expected heterozygosity (He ) 78, 201, T. confusum 32, 303, 179 Gazella spekei see Speke’s gazelle 536 extinction due to inbreeding 32, gene diversity, expected

extinction rates 303 heterozygosity (He ) 78, 201, 536 plants 5 genetic drift 179 gene dropping 537 projections 5–6 fluctuating asymmetry 300 gene flow 329–31 extinction vortex 32, 505, 536 flycatchers 117 population structure 485–91 extinctions 23–44 forensic biology 13, 470–501, 536 gene trees, and coalescence 475–80, causes founder effect 537 537 circumstantial evidence 32 founder relationships 496–7 genetic characterization methods 476 human-associated factors 7–8 founders 183 genetic distance 48, 379–81, 537 inbreeding depression 28, 32–3 captive populations 423–4 genetic diversity 45–71 loss of genetic diversity 36–9 small numbers 424–6 changes over time 228 stochastic factors 8 founding events 192 characterization, quantitative deterministic factors 503 effect on genetic diversity 423–6 variation 96–125

INDEX 611

conservation 198 Glanville fritillary butterfly, Finland Halichoerus grypus see grey seal defined 47–50, 537 31, 313 Halocharpus bidwilli 236 and disease resistance 39 glaucous gull Larus hypoboreus 499 Haloragodendron lucasii 414, 493 endangered species 65–6, 158–9 global warming 127 haplo-diploids 415–16 extent 60–7 Globicephalis melas see long-finned pilot haploid loci 142 justification for preservation whale haplotype networks 486, 538 1–2 Gloger’s rule, clines 170 haplotypes 91, 537 in large populations 199–200 Glossary 533–45 Hardy—Weinberg equilibrium 75–89, loss 225–6 glucose-6-phosphate dehydrogenase 538 maintenance 197–224 deficiency 197, 207 and carriers 83–4 measurement 50–60 golden hamster Mesocricetus auratus deviations 84–6, 493 origin and regeneration 155–6 356 extensions 86–8 partitioning 105–6 golden lion tamarin Leontopithecus and inbreeding 84 reproductive fitness 220–1 rosalia 30, 163, 178, 244, recessive allele frequency 62, 82–3 single locus 348–9 249–50, 283, 345, 351, 354 sex-linked loci 88–90 time for regeneration 158–9 captive breeding 423–5, 450–2, 461 harmonic mean 538 variation in space/time 67–71 computer simulation, PVA 508 Harris’s hawk Parabuteo unicinctus 464 genetic drift 178–87, 218, 324 genetic management 450–2 harvesting, impacts 412–14 defined 537 reintroductions 463 Hawaiian Bidens 345, 494 and selection 114, 145, 146–8 inbreeding depression 454 Hawaiian crow 302 genetic issues in reserve design minimum habitat area 525–6 Hawaiian duck 411 410–11 gopher see pocket gopher Hawaiian goose see nene genetic load 155, 162–7, 537 gorilla Gorilla gorilla 427 Hawaiian monk seal 511 genetic management 419–47 Gossypium barbadense and G. hirsutum heath hen Tympanuchus cupido cupido endangered species 16–18 see cotton (cultivated) 33 reintroductions 448–70 Gossypium darwinii see Galapagos heavy metals, tolerance to 129, 148, genetic markers 375–9 Island cotton 170–1, 212 reproductive systems 492 grasses see species names Helianthus see sunflower genetic problems, diagnosis 401 grassland daisy Rutidosis heliconius butterfly Heliconius erato 87 genetic stochasticity 505 leptorrhynchoides 88, 229–30, hemizygosity 538 genetics 373 heritability and minimization of extinctions gray wolf Canis lupus 65, 163, 332, 369 defined 102, 112, 118, 538 11–15 great tit Parus major 117 estimating 118–20 and population viability analysis greater prairie chicken 25, 36, 231–2, and evolutionary potential 111–18 (PVA) 511–12 285, 300, 306, 401, 482, 505–6, magnitudes 116–18 genome 48 516 precision 120 genome resource banks 441–3, 537 Grevillea scapigera see Corrigan realized 542 genome uniqueness 438, 537 grevillea hermaphrodite 75, 538 genotype frequency 76–8, 259–61 Grevy’s zebra 244, 431 Heterocephalus glaber see mole-rat genotype ϫ environment interaction grey seal Halichoerus grypus 65 heterosis 300, 305 106, 537 Grus americana see whooping crane heterozygosity (H) 48 genotypes 48 Gryllus firmus see cricket allozyme 246 Gentiana pneumonanthe 30 Guadalupe Island lupine Lupinus average 48 Geochelone elaphantopus see Galapagos guadalupensis 465 bottlenecks 185–7 tortoise Guam rail Rallus owstoni 176, 184, 468 equilibrium 202 Geomys colonus see pocket gopher gunni eucalypt Eucalyptus gunnii 213 expected 78, 201 Geomys pinetus see pocket gopher Gymnogyps californianus see California rates of loss 237–9 ghost bat Macroderma gigas 487 condor loss of 186, 232–5, 321–4 giant panda Ailuropoda melanoleuca gymnosperms, polyploidy 29 observed 74, 234 345, 404 and population size 202 gigantic eucalypt Eucalyptus gigantea habitat area, minimum 525 heterozygote advantage 204–7, 538, 213 habitat fragmentation 310 541 giraffe Giraffa camelopardis, inbreeding haemophilia 166 Himantopus novaezelandiae see black depression 25–7 Haliaeatus leucocephalus see bald eagle stilt

612 INDEX

hitchhiking 538 in species that regularly inbreed Kirtland’s warbler 345 HIV-1 and HIV-2 499 290, 431–41 koala Phascolarctos cinereus 65, 408–10, homozygosity 48, 538 susceptibility 120–1 482–3, 491 honeycreeper, Hawaiian Vestiaria 45, variability 288–90 Kokia cookei see Cook’s kok’io 130, 375 indigo bunting 117 komodo dragon Varanus komodoensis honeysuckle, roundleaf Lambertia industrial melanism 37, 126, 129, 65, 345 orbifolia 493–4 137–9, 144–5, 171 Hong Kong lady’s tresses orchid inherited diseases 443–4 lakeside daisy Hymenoxys acaulis var. Spiranthes hongkongensis 373–4 insecticide resistance 130 glabra 38, 352, 407 horse, evolution 148 interaction variance 109, 111, 538 Lambertia orbifolia see honeysuckle, horseshoe crab 381 International Species Information round-leaf housefly Musca domestica, inbreeding System (ISIS) 422 Lanius lucovicianus mearnsi see San depression 285 introgression 16, 168, 411, 538 Clemente Island loggerhead Howellia aquatilis 61 introns 62, 539 shrike human population inversion polymorphism 211–12, Larus hypoboreus see glaucous gull growth 8 539 Laysan duck (teal) Anas laysanensis total 8 Ipomopsis aggregata see scarlet gilia 491 humpback whale Megaptera island extinctions, recorded (1660 to Laysan finch Telespiza cantans 65, 74, novaeangliae 345, 472–3 present) 4 79, 86 hybridization, detecting 12, 168, 369, island populations 19, 33–6, 313–17 Leontopithecus chrysopygus see black lion 411, 476 bottleneck to genetic diversity 19 tamarin Hymenoxys acaulis var. glabra see extinction proneness 33–6 Leontopithecus rosalia see golden lion lakeside daisy Isle Royale gray wolf Canis lupus 183, tamarin 267–8, 347–8, 509 Lepidochelys kempii see Kemp’s ridley sea ibex Capra ibex 385–6 isolating factors, origin of species turtle idealized population 188, 538 372–3 Lepus americanus see snowshoe hare identity by descent 257, 538 isozymes 539 lesser snow goose see snow goose illegal hunting/collecting 472–5 IUCN (World Conservation Union) lethal alleles 261–2, 275–6 impala Aepyceros melampus 486 aims 2, 420 inbreeding depression 293–4 in situ conservation 538 CAMPs 422 lethal equivalents (B) 301–4, 539 inbreeding 254–79, 538 captive breeding policy 422 lethal mutations 158, 162, 192 and extinction 286 CBSG 534 Leucopsar rothschildi see Bali starling genetic consequences 258–62 classification of endangerment 7 light-footed clapper rail Rallus and migration 328–31 PVAs 508 longirostris levipes 66 parentage 494–6 Species Survival Commission 422 Limonium duforii 414 and selection 297 lineage sorting 383, 539 small populations 263–8 Japanese quail Coturnix coturnix linkage (dis)equilibrium 90–3, 219 see also self-fertilization japonica, inbreeding depression coefficient of 534, 539 inbreeding coefficient F 25, 256–8, 538 27–8, 288 lion average F 26 jarrah tree Eucalyptus marginata 97–8, African Panthera leo 49, 499 indirect estimation 267–8 103 Asiatic Panthera leo persica 50, 244–5, inbreeding depression 24–7, 187, 226, disease resistance 97–8 345 248–9, 280–308 lizards see collared lizard; sleepy captive populations 108 kangaroo see euro; red kangaroo lizard characteristics 287–95 Kemp’s ridley sea turtle Lepidochelys loci 48, 539 computer projections 29–30 kempii 366 mutations 157 defined 538 kestrels 65, 177 loggerhead shrike Lanius lucovicianus detection and measurement king penguin 117, 431, 431 65 299–302 King’s lomatia Lomatia tasmanica 61, see also San Clemente Island examples 282 414 loggerhead shrike

minimization of extinction risk 11 kinship (kij ) loggerhead turtle Caretta caretta 13, purging 295–9 captive populations 433–9 470, 488–9, 495, 517 rate, and extinction risk 28 defined 539 Lomatia tasmanica see King’s lomatia recovering 305–6 mean 435 long-finned pilot whale Globicephalis and reproductive fitness 18 minimizing 457 melas 488

INDEX 613

long-footed potoroo Potorous longipes Mauna Kea silversword Argyroxiphium Mongolian wild horse see Przewalski’s 65, 375–6 sandwicense var. sandwicense 176, horse Lord Howe Island woodhen 345, 407 monomorphic 48, 540 Tricholimnas (Gallirallus) sylvestris case study 469 monophyletic classifications 371, 540 176, 345, 352, 400, 425 Mauritius kestrel Falco punctatus 65, Monte Carlo simulations 193–4 case study 468–9, 518–19 67, 79, 176–7, 184, 302 Morbillivirus see canine distemper Loxodonta africana see elephant Mauritius pink pigeon Columba virus Lupinus guadalupensis see Guadalupe (Nesoenas) mayeri 184, 244, 302, mosquito-fish Gambusia holbrooki, Island lupine 345, 425 extinction due to inbreeding Lycaon pictus see African wild dog maximum avoidance of inbreeding 32, 303 lynx Lynx canadensis 247, 504 (MAI) 431–41 muntjac deer Muntiacus spp. 59, 370, Lysimachia minorcicensis 66, 460 mean, defined 101 376 mean kinship (mk) 435, 539 Musca domestica see housefly Macroderma gigas see ghost bat Megaptera novaeangliae see humpback Mustela nigripes see black-footed ferret Macropus robustus erubescens see euro whale mutation 156–67 Madoqua sp. see dik-dik melanism, industrial pollution 37, balancing selection 199 mahogany see Catalina mahogany; 126, 129, 137–9, 144–5, 171 beneficial 199 royal mahogany Meleagris gallopavo see turkey deleterious 198 maize Zea mays merino sheep Ovis aries 112 human 162 inbreeding depression 282, 295 Mesocricetus auratus see golden hamster lethal 158, 162, 192 quantitative trait loci (QTL) 100, meta-analysis 539 neutral 156, 199, 200–3 123 mammals, example 18 reverse 160 two-way selection 149 metapopulations 313, 332–3, 539 small populations 191–2 major histocompatibility complex Mexican wolf Canis lupus mexicanus 65, mutation load 162–7, 540 (MHC) 38, 90, 92, 207–10, 539 108, 289, 367, 497 defined 155 drift 218 microsatellites 53–7, 63–6, 539 mutation rate selection coefficient s 145 genetic characterization methods examples 157 Malacothamnus fasciculatus var. 476 from mutation–selection balance nesioticus see Santa Cruz Island paternity determination 494–6 165–6 bush mallow middle spotted woodpecker and stable equilibrium 160 malaria 196, 204–7 Dendrocopus medius 33 mutation–selection balance 162–7, avian 498 migration 167–73 275–7, 540 malheur wirelettuce Stephanomeria detecting immigrants 488–9 and fitness 166 malheurensis 176, 415 and inbreeding 328–31 polyploids 164–5 mallee 414 migration corridors 404 mutational meltdown 349, 540 Malurus splendens see splendid fairy migration–selection equilibrium myxoma virus, rabbit 129–30 wren frequency 171–2 mammals minimum viable population size Nasella pulchra 460 allozyme diversity 62 (MVP) 337–9, 506–7, 524–6, natural selection 540 extinction rates 4 539 see also selection genetic distances, means/ranges 69 minisatellite (VNTR) 54–6, 64–5, 535, Nei’s genetic distance 379–81, 540 inbreeding depression 282 540 Nei’s genetic similarity 540 percentage endangered 3 Mirounga angustrostris see northern nene (Hawaiian goose) Branta management of captive populations elephant seal sandvicensis 67, 184, 400, 482, 439–41 Mirounga leonina see southern elephant 484 management units, defining 12, seal neutral mutation 156, 199, 200–3, 388–92 mitochondrial DNA (mtDNA) 540 540 management of wild populations analysis 59–60, 378–9, 476 Nicotiana see tobacco 394–418 scats 13, 480–1 Ninox novaeseelandiae undulata see Mariana crow Corvus kubaryi 65 evolutionarily significant units Norfolk Island boobook owl mass extinctions 504 (ESU) 388–9 non-synonymous substitution 540 sixth extinction 2 mole-rat, naked Heterocephalus glaber, Norfolk Island boobook owl Ninox matchstick banksia Banksia cuneata inbreeding depression 272–3 novaeseelandiae undulata 273–4, 509, 519–20 molecular genetics, forensic biology 367, 382–3, 490, 498 mathematical models, role 132–3 13, 470–501, 536 normal distribution 96, 100, 540

614 INDEX

northern elephant seal Mirounga penguin 117 Poisson distribution 189, 243, 541 angustrostris 61, 176, 183–4, peppered moth Biston betularia, polar bear Thalarctos 65 241–2, 248, 339, 484–5 industrial melanism 37, 126, polyandry 541 inbreeding 266–7 129, 137–9, 144–5, 171 polygamy 541 northern right whale Eubalaena Perameles gunnii see Eastern barred polygyny 541 gracialis 345 bandicoot polymerase chain reaction (PCR) 58–9, northern spotted owl see spotted owl percentage of loci polymorphic (P) 541 541–2 nucleotide substitutions 201 Père David’s deer Elaphurus davidianus polymorphism nyala Tragelaphus angasi 354 184, 420 allozyme electrophoresis 49–50 peregrine falcon Falco peregrinus 65, defined 542 observed heterozygosity 74, 540 352, 464 inversion 211–12 Ochotona princeps see pika Peripatus see velvet worm loci 48 okapi Okapia johnstoni 302–3, 431 peripheral characters 108, 541 transient 199 old-field mouse Peromyscus polionotus Peromyscus leucops see white-footed polyphyletic classifications 371, 542 288, 289 mouse polyploidy 60, 88–90, 373–4 Onychogalea fraenata see bridled nailtail Peromyscus maniculatus see deer mouse genetic management 416 wallaby Peromyscus polionotes see old-field and inbreeding depression 29, orangutan Pongo pygmaeus 367, 371, mouse 276–7, 294–5 377–8 pesticide resistance 130 mutation–selection balance 164–5 Oryctolagus cuniculus see rabbit Petrogale see wallaby rates of loss of heterozygosity 237–9 Oryx dammah see scimitar-horned oryx Petroica traversi see Chatham Island Pongo pygmaeus see orangutan Oryx leucoryx see Arabian oryx black robin population fragmentation 85–6, 226, outbreeding depression 10, 385–8, 541 Phascolarctos cinereus see koala 309–335, 404–10 overdominance 199, 204–7, 296, 541 phenotypic intermediates 149–50 degree 318–19 associative 219–20 phenotypic variance 105 distribution of alleles 317–18 Ovis aries see merino sheep Photinia 499 divergence in allele frequencies Ovis canadensis see bighorn sheep phylogenetic trees 382–4 over time 319–20

owl monkey Aotus trivirgatus 367, 386 phylogeography 541 FST 324–7, 537 owl see barred owl; spotted owl Phytophthora cinnamomi see die-back genetic adaptation in captivity fungus 457–9 Pacific ridley turtle Lepidochelys olivacea Picoides borealis see red-cockaded genetic management 404–10 366 woodpecker population size 176–96 Pacific yew Taxus brevifolia 249, 326, pied flycatcher Ficedula hypoleuca 117 bottlenecks 183–7, 304, 482–5 494 pika Ochotona princeps 488 census (N) 240 Palo Verdes blue butterfly 345 pink pigeon Columba (Nesoenas) mayeri demographic history 480–5

Pan troglodytes see chimpanzee 184, 244 effective (Ne ) 189–90, 228, 239–51, panda see giant panda; red panda Pinus torreyana see Torrey pine 535 panmictic 541 plagues 127 estimating 250–1, 339–41 Panthera leo persica see lion, Asiatic plant collections 421 fate <500 344–8 Panthera leo see lion, African ex situ conservation 441 evolutionarily effective 485 Panthera pardus orientalis see Amur plant propagation, breeding genetic viability 336–59 leopard programmes 420–1 see also population viability Panthera tigris see tiger plants, allozyme diversity 62 analysis (PVA) Parabuteo unicinctus see Harris’s hawk Platanus platanoides see sycamore harmonic mean 247 parasite load, ﬁshes 38 pleiotropy 541 idealized 188 parentage, paternity determination poaching 413–14 increasing in wild populations 494–6 pocket gopher 399–401 partial dominance 541 colonial Geomys colonus 12, 217–18, large, and evolution 126–53, Partula taeniata and P. tenuis101, 103, 378 154–74 113, 354, 420 southeastern Geomys pinetus 12, loss of genetic diversity 227–53

heritabilities 119 217–18, 378 maximizing Ne/N 430–1 Parus, titmice 117 Poeciliops occidentalis see topminnow measuring 187–90 Pedicularis furbishiae see Furbish’s ﬁsh reduction effects 225–6 lousewort Poeciliopsis monacha see desert single large or several small (SLOSS) pedigrees 269–71, 541 topminnow 311, 314, 410

INDEX 615

small, and evolution 175–96 Prodontia modesta and P. bicolorata see realized heritability 542 threatened populations 343–4 chafer beetles recessive allele frequency, population structure, gene flow proteins Hardy–Weinberg equilibrium 485–91 neutral mutation rate 202 62, 82–3 population viability analysis (PVA) 18, variation 61–2 recessive lethal selection 134–6 502–28 see also allozymes recombination 93 defined 542 Przewalski’s horse Equus przewalskii 61, red grouse Lagopus lagopus 117 exercises 527–8 163, 183, 244, 425, 496 red kangaroo Macropus rufus 504 extinctions 506–28 case study 467 red panda Ailurus fulgens 431 and genetics 511–12 inbreeding 255–6 Red Queen hypothesis 127 limitations 523–4 pseudogene 542 red wolf Canis rufus 289, 369 minimum viable population size Pseudoryx nghetinhensi see saola (Vu red-cockaded woodpecker Picoides (MVP) 337–9, 506–7, 524–6 Quang bovid) borealis 311–12, 345, 352, 379, predictions 520–3 Puerto Rican parrot Amazona vittata 395, 509 Potentilla glandulosa see sticky 30, 184, 345, 425, 515–16 red-crowned crane 244, 431 cinquefoil Puerto Rican plain pigeon 66 red-ruffed lemur 61, 163, 184, 425 potoroo Potorous tridactylus 375–6 puma see Florida panther red-tailed hawk 302, 356 Potorous longipes see long-footed purging 275, 295–9, 542 regression, defined 102 potoroo puritan tiger beetle 392 reintroductions 13, 543 prairie chicken see Attwater’s; greater pygmy hippopotamus Choeropsis 256 genetic management 448–70 prairie dogs Cynomys spp. 517 Pyrenean brown bear Ursus arctos 480, individuals, choice 460–3 primer, defined 542 498 sites probe 542 choice 459–60 Problems quail Coturnix coturnix japonica, identification by DNA 12–13 allele frequency 94, 153 inbreeding depression 27–8, success 463–5 bottlenecks 500 288 reproductive fitness 97, 213, 536, 543 cloning 447 quantitative genetic variation 96–125, heritabilities 116–18 dominance 153 542 and inbreeding depression 18, 281 endangered species 527 correlation with molecular relation to genetic diversity 220–1 evolutionary potential 358 variation 121–2 retention 339–41 genetic adaptation 470 detecting 103–5 reproductive isolation, genetic genetic diversity 70–1, 222 organization 122 distance 379–81 genetic management 417 partitioning 105–6, 108–11 reproductive systems, genetic markers Hardy–Weinberg equilibrium 94 vs. qualitative genetic variation 99 492 heritability 124 quantitative trait locus (QTL) 100, 123, reproductive technology 441–3 heterozygosity (H) 124, 252 542 reptiles heterozygote advantage 222 range of dominance 123 allozyme diversity 62 inbreeding 279, 308, 417 genetic distances, means/ranges 69 IUCN catgeories 21–2 rabbit Oryctolagus cuniculus 129–30, percentage endangered 3 kinship 446 463 reserves, design 410–11 lethal equivalents 308 Rallus longirostris levipes see light-footed resistance, evolution of 130 linkage (dis)equilibrium 95 clapper rail restriction enzyme 543 Mendelian inheritance 21 Rallus owstoni see Guam rail restriction fragment length mutation 173–4 Rana catesbeiana see bullfrog polymorphism (RFLP) 56, 485, population fragmentation 334 (American) 543 population size 252 random genetic drift 542 Rhagoletis pomonella see hawthorn fly probability and statistics 21, 124, random mating, defined 542 rhinoceros 195 randomly amplified polymorphic black Diceros bicornis 65, 391, 405, reintroductions 470 DNA (RAPD) 55, 64–5, 542 512 revision 531–2 RAPD 469 Javan Rhinoceros sondaicus 6, 345, 352 selection 151–3 Raphus cucullatus see dodo one-horned (Indian) Rhinoceros selection differential 125 rattlesnake Crotalus viridis 100 unicornis 184, 186, 327, 336, self-incompatibility 223 Aruba Island Crotalus unicolor 345 337–8, 400, 425 taxonomy 393 Rattus fuscipes see Australian bush rat Rhus michauxii see false poison sumach Solutions 546–66 raven Corvus corax 65 Rodriguez fruit bat 431

616 INDEX

rose pink Sabatia angularis 288 self-fertilization 84–5, 248–9, 281, 415, sparrow see dusky seaside sparrow; royal mahogany 65 543 song sparrow Rutidosis leptorrhynchoides see grassland self-incompatibility 543 Spartina, polyploidy 89 daisy alleles 37–8, 210–11, 217, 229–30 speciation 544 sensitivity analysis 516–17, 543 allopatric 372 Sabatia angularis see rose pink sentry milk-vetch Astragalus 67 instantaneous 373–4 Saguinus oedipus see cotton-top tamarin sex determination 497 sympatric 372 salmon sex ratio 241–3 species Atlantic 65 sex-linked loci 543 defined 370–1, 544 chinook 240, 373, 519 Hardy–Weinberg equation 88–90 delineating using genetic markers coho 12 sexing, molecular 497–8 375–9 sockeye 373 Seychelles kestrel Falco araea 65, 177 lifespan 5 San Clemente Island loggerhead Seychelles magpie robin Copsychus management units, defining 12 shrike Lanius lucovicianus sechellarum 302, 345 origin mearnsi 65 Seychelles warbler Acrocephalis allopatric/sympatric 372 San Joaquin kit fox Vulpes macrotis sechellensis 99, 283, 345, 400 instant speciation 373–4 mutica 481 sheep isolating factors 372–3 Santa Cruz Island bush mallow bighorn 33, 332, 513 slow speciation 374–5 Malacothamnus fasciculatus var. merino 112 sibling 381 nesioticus 414–15, 493 Soay 38, 288, 521–3 species survival plans (SSPs) 421 saola (Vu Quang bovid) Pseudoryx sibling species 381, 543 spectacled eider duck Sommateria nghetinhensi 377 sickle cell anaemia 204–7 fischeri 499 scarlet gilia Ipomopsis aggregata 288, silent substitution 62, 156, 543 Speke’s gazelle Gazella spekei 425 401 silver fox Vulpes vulpes 147–8 Sphenodon guntheri, S. punctatus see scats, mtDNA analysis 13, 480–1 simian jackal see Ethiopian wolf tuatara Schiedea haleakalensis 345 single large or several small (SLOSS) Spiranthes hongkongensis 373–4 scimitar-horned oryx Oryx dammah 310, 311, 314, 410, 544 Spiranthes sinensis 373–4 176, 244, 431 single locus genetic diversity 348–9 Spiranthes spiralis 373–4 sea otter Enhydris lutra, target single nucleotide polymorphism (SNP) spix macaw 431 population size 352 56, 544 splendid fairy wren Malurus splendens selection 133–50 single strand conformational 283, 496 adaptation 136–9 polymorphism (SSCP) 56 spotted owl Strix occidentalis long-term 148 sixth extinction 2 Californian Strix o. occidentalis balancing 199, 204 sleepy lizard Tiliqua rugosa 65 14–15 directional selection 114, 145, small scabious Scabiosa columbaria northern Strix o. caurina 14–15, 61, 146–8 405 509 disruptive selection 145–6 snow goose, lesser Anser caerulescens SSCP see single strand conformational frequency-dependent 207–11 117, 119, 120, 489–90, 495 polymorphism natural selection 128 snow leopard Panthera pardus orientalis SSPs see species survival plans 421 on mutations 160–7 425 stabilizing selection 145, 149–50, quantitative characters 145–6 snowshoe hare Lepus americanus 247 544 recessive lethal 134–6 Soay sheep 38, 288, 521–3 stable equilibrium 160, 544 small populations 190–1 Socorro dove Zenaida graysonii 176 standard deviation, defined 102 stabilizing selection 145–6, Socorro Island red-tailed hawk 302, starling 149–50 356 Bali Leucopsar rothschildi 345, 496 selection coefficient (s) 137, 139, Somateria mollissima see eider duck European Sturnus vulgaris 100, 117 143–5, 543 song sparrow 117 Stephanomeria malheurensis see malheur major histocompatibility complex sooty mangabey Cercocebus atys 499 wirelettuce (MHC) 145 Soulé, Michael 9 stickleback, three-spined 373 selection differential (S) 114, 543 source–sink 333, 544 sticky cinquefoil Potentilla glandulosa selection response, prediction southeastern pocket gopher Geomys 107 115–16 pinetus 12, 217–18, 378 stochastic evolution 177 selective sweep 543 Southern blot 544 stochastic factors selectively neutral alleles 214–16, 327, southern elephant seal Mirounga endangered species 504 543 leonina 241–2 interactions 505–6

INDEX 617

stochasticity Tigriopus californicus 387 Wahlund effect 322, 545 defined 544 Tiliqua rugosa see sleepy lizard wallaby demographic 28, 504, 513 titmice Parus 117 allied 65 Strix occidentalis see spotted owl tobacco Nicotiana 103, 104–5 Petrogale brachyotis 365, 375 Strix varia see barred owl topminnow fish Poeciliops occidentalis Petrogale godmani 365 Sturnus vulgaris see starling 300 Petrogale lateralis see black-footed Styrax texana see Texas snowbell Torrey pine Pinus torreyana 61 rock wallaby subspecies, defined 371 toxoplasmosis Toxoplasma gondii 127 warbler see Kirtland’s; Seychelles sunflower trans-species polymorphism 545 warbler Californian Helianthus exilis 366 transient polymorphisms 199, 544 water flea Daphnia 129–30 Texan Helianthus paradoxus 367 translocations 404–7, 545 whale meat, forensic biology 472–4 supportive breeding 465–6, 544 transposons 156, 545 white-footed mouse Peromyscus leucopes sycamore Platanus platanoides 374 tree swallow 117 354 Sylvia atricapilla see blackcap Tribolium see flour beetle white-naped crane Grus vipio 354 sympatric species 372, 544 Tricholimnas sylvestris see Lord Howe white-winged wood duck Aix sponsa Syncerus caffer see buffalo Island woodhen 431, 464 synonymous substitution 544 Trifolium see clover whooping crane Grus americana 67, tuatara Sphenodon punctatus and S. 184, 345 Taita thrush Turdus helleri 498 guntheri 367 wild populations, management Take-home messages 529–30 Turdus helleri see Taita thrush 394–418 tandem repeats 54–6, 64–5, 535, turkey, wild Meleagris gallopavo 288 wildebeest Connochaetes 127 544 Tympanuchus see Attwater’s prairie wolf see Algonquin wolf; Ethiopian Tasmanian snow gum Eucalyptus chicken; heath hen wolf; gray wolf; Isle Royale coccifera 213 wolf; red wolf taxon 544 urn gum Eucalyptus urnigera 213 Wollemi pine Wollemia nobilis 1, 11, 66, taxonomic status 365–94 Ursus arctos see brown bear 102, 346, 403 flowchart of questions 17 wombat management units 399 Varanus komodoensis see komodo northern hairy-nosed Lasiorhinus and minimization of extinction risk dragon krefftii 65, 176, 227, 236, 237, 11–12 variable number tandem repeats 250–1, 345, 400, 475 susceptibility to inbreeding (VNTR, minisatellite) 54–6, reintroduction sites 12–13 depression 29 64–5, 535, 540 southern hairy-nosed Lasiorhinus Taxus brevifolia see Pacific yew variance latifrons 65, 227 Telespiza cantans see Laysan finch defined 101, 545 wood duck Aix sponsa 431, 464 Texan sunflower Helianthus paradoxus dominance variance 109, 111, 122 woodpecker 367 effective sizes 250 acorn 331, 516 Texas snowbell Styrax texana 346 partitioning 109–11 middle spotted 33 Thalarctos see polar bear velvet worm red-cockaded 311–12, 345, 352, 379, thalassaemia 197, 207 Euperipatoides leuckartii 72, 86 395, 509 thale cress Arabidopsis thaliana 100 Peripatus 72, 86, 366, 385 World Conservation Union see IUCN Thomomys see pocket gophers Vestiaria see honeycreeper, Hawaiian threatened populations vicariance 545 Y-specific probes 488 defined 544 vinegar fly see fruit fly Drosophila yellow-bellied marmot 271 recovering 516–17 melanogaster size 343–4 Vipera berus see adder Zea mays see maize threatened species, defined 6, 544 Vu Quang bovid (saola) Pseudoryx zebra, Grevy’s Equus grevyi 244, 431 tiger beetle 392, 490 nghetinhensi 377 Zenaida graysonii see Socorro dove tiger Panthera tigris vulnerable, defined 545 Zieria prostrata 491 Bengal 386 Vulpes macrotis mutica see fox, San zoos 421–2 Siberian 184, 354, 386, 425 Joaquin kit Zosterops lateralis chlorocephala see Sumatran 244 vulture, cinereous 431 Capricorn silvereye