Conservation genomics of threatened animal species

Annual Review of Animal Biosciences

Volumn 1, Issue , 2013, Pages 261-281

  Steiner, Cynthia C ^a   Putnam, Andrea S ^a   Hoeck, Paquita E A ^a   Ryder, Oliver A ^a  

^a INSTITUTE FOR CONSERVATION RESEARCH   (United States)

Author keywords

adaptive variation; disease susceptibility; hybridization; inbreeding depression; population demography

Indexed keywords

ANIMAL; ANIMAL DISPERSAL; ENDANGERED SPECIES; ENVIRONMENTAL PROTECTION; GENOMICS; POPULATION DYNAMICS;

ANIMAL DISTRIBUTION; ANIMALS; CONSERVATION OF NATURAL RESOURCES; ENDANGERED SPECIES; GENOMICS; POPULATION DYNAMICS;

EID: 84893741469     PISSN: 21658102     EISSN: 21658110     Source Type: Journal    
DOI: 10.1146/annurev-animal-031412-103636     Document Type: Review

References (154)

1. Ekblom R, Galindo J. 2011. Applications of next generation sequencing in molecular ecology of nonmodel organisms. Heredity 107:1-15
2. Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nat. Rev. Genet. 11:697-709
3. Avise J. 2010. Perspective: conservation genetics enters the genomics era. Conserv. Genet. 11:665-69
4. Frankham R. 2010. Challenges and opportunities of genetic approaches to biological conservation. Biol. Conserv. 143:1919-27
5. Frankham R. 2010. Where are we in conservation genetics and where do we need to go? Conserv. Genet. 11:661-63
6. Hudson ME. 2008. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol. Ecol. Resour. 8:3-17
7. Kohn MH,Murphy WJ, Ostrander EA, Wayne RK. 2006. Genomics and conservation genetics. Trends Ecol. Evol. 21:629-37
8. Ouborg NJ, Angeloni F, Vergeer P. 2009. An essay on the necessity and feasibility of conservation genomics. Conserv. Genet. 11:643-53
9. Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma R, Hedrick PW. 2010. Conservation genetics in transition to conservation genomics. Trends Genet. 26:177-87
10. Primmer CR. 2009. From conservation genetics to conservation genomics. Ann. N. Y. Acad. Sci. 1162:357-68
11. Schwartz MK, Luikart G, Waples RS. 2007. Genetic monitoring as a promising tool for conservation and management. Trends Ecol. Evol. 22:25-33
12. Shokralla S, Spall JL, Gibson JF, Hajibabaei M. 2012. Next-generation sequencing technologies for environmental DNA research. Mol. Ecol. 21:1794-805
13. Stapley J, Reger J, Feulner PGD, Smadja C, Galindo J, et al. 2010. Adaptation genomics: the next generation. Trends Ecol. Evol. 25:705-12
14. Windig J, Engelsma K. 2010. Perspectives of genomics for genetic conservation of livestock. Conserv. Genet. 11:635-41
15. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, et al. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469:529-33
16. Excoffier L, Hofer T, Foll M. 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103:285-98
17. Jensen P. 2005. Genomics: the chicken genome sequence. Heredity 94:567-68
18. Nei M, Suzuki Y, Nozawa M. 2010. The neutral theory of molecular evolution in the genomic era. Annu. Rev. Genomics Hum. Genet. 11:265-89
19. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-95
20. Lohmueller KE, Bustamante CD, Clark AG. 2011. Detecting directional selection in the presence of recent admixture in African-Americans. Genetics 187:823-35
21. Verdu P, Rosenberg NA. 2011. A general mechanistic model for admixture histories of hybrid populations. Genetics 189:1413-26
22. Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andres AM, et al. 2009. Darwinian and demographic forces affecting human protein coding genes. Genome Res. 19:838-49
23. Thornton KR, Jensen JD. 2007. Controlling the false-positive rate in multilocus genome scans for selection. Genetics 175:737-50
24. Li J, Li H, Jakobsson M, Li S, Sjödin P, Lascoux M. 2012. Joint analysis of demography and selection in population genetics: Where do we stand and where could we go? Mol. Ecol. 21:28-44
25. Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, et al. 2007. Recent human effective population size estimated from linkage disequilibrium. Genome Res. 17:520-26
26. Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, et al. 2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528-32
27. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, et al. 2008. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet. 4:e1000083
28. Gutenkunst RN, HernandezRD, Williamson SH, Bustamante CD. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5:e1000695
29. Gray MM, Granka JM, Bustamante CD, Sutter NB, Boyko AR, et al. 2009. Linkage disequilibrium and demographic history of wild and domestic canids. Genetics 181:1493-505
30. Engelhardt BE, Stephens M. 2010. Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet. 6:e1001117
31. Kirk H, Freeland JR. 2011. Applications and implications of neutral versus non-neutral markers in molecular ecology. Int. J. Mol. Sci. 12:3966-88
32. Pool JE, Hellmann I, Jensen JD, Nielsen R. 2010. Population genetic inference from genomic sequence variation. Genome Res. 20:291-300
33. Frankham R. 2005. Genetics and extinction. Biol. Conserv. 126:131-40
34. Reed DH, Frankham R. 2003. Correlation between fitness and genetic diversity. Conserv. Biol. 17:230-37
35. Vila C, Sundqvist AK, Flagstad O, Seddon J, Bjornerfeldt S, et al. 2003. Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc. Biol. Sci. 270:91-97
36. Gompert Z, Forister ML, Fordyce JA, Nice CC, Williamson RJ, Buerkle CA. 2010. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Mol. Ecol. 19:2455-73
37. vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR, et al. 2011. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res. 21:1294-305
38. Rohland N, Reich D, Mallick S, Meyer M, Green RE, et al. 2010. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biol. 8:e1000564
39. Bowden R, MacFie TS, Myers S, Hellenthal G, Nerrienet E, et al. 2012. Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population. PLoS Genet. 8:e1002504
40. Becquet C, Patterson N, Stone AC, Przeworski M, Reich D. 2007. Genetic structure of chimpanzee populations. PLoS Genet. 3:e66
41. Gonder MK, Locatelli S, Ghobrial L, Mitchell MW, Kujawski JT, et al. 2011. Evidence from Cameroon reveals differences in the genetic structure and histories of chimpanzee populations. Proc. Natl. Acad. Sci. USA 108:4766-71
42. Nielsen R, Paul JS, Albrechtsen A, Song YS. 2011. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12:443-51
43. Lawson DJ, Hellenthal G, Myers S, Falush D. 2012. Inference of population structure using dense haplotype data. PLoS Genet. 8:e1002453
44. Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, et al. 2011. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics 12:231
45. Pritchard JK. 2011. Whole-genome sequencing data offer insights into human demography. Nat. Genet. 43:923-25
46. Manel S, Joost S, Epperson BK, Holderegger R, Storfer A, et al. 2010. Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Mol. Ecol. 19:3760-72
47. Vandersteen TymchukW,O'Reilly P, Bittman J, MacDonald D, Schulte P. 2010. Conservation genomics of Atlantic salmon: variation in gene expression between and within regions of the Bay of Fundy. Mol. Ecol. 19:1842-59
48. Hoffmann AA, Sgró CM. 2011. Climate change and evolutionary adaptation. Nature 470:479-85
49. Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK. 2000. Considering evolutionary processes in conservation biology. Trends Ecol. Evol. 15:290-95
50. Parchman T, Geist K, Grahnen J, Benkman C, Buerkle CA. 2010. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180
51. Elmer KR, Kusche H, Lehtonen TK, Meyer A. 2010. Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes. Philos. Trans. R. Soc. B Biol. Sci. 365:1763-82
52. Ekblom R, Balakrishnan CN, Burke T, Slate J. 2010. Digital gene expression analysis of the zebra finch genome. BMC Genomics 11:219
53. Kunstner A, Wolf JBW, Backstrom N, Whitney O, Balakrishnan CN, et al. 2010. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol. Ecol. 19:266-76
54. Tarazona S, Garcia-Alcade F, Dopazo J, Ferrer A, Conesa A. 2011. Differential expression in RNA-seq: a matter of depth. Genome Res. 21:2213-23
55. Tzika AC, Helaers R, Schramm G, Milinkovitch MC. 2011. Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles. EvoDevo 2:19
56. Milano I, Babbucci M, Panitz F, Ogden R, Nielsen RO, et al. 2011. Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake. PLoS ONE 6:e28008
57. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57-63
58. Gilad Y, Pritchard JK, Thornton K. 2009. Characterizing natural variation using next-generation sequencing technologies. Trends Genet. 25:463-71
59. Salem M, Vallejo RL, Leeds TD, Palti Y, Liu S, et al. 2012. RNA-seq identifies SNP markers for growth traits in rainbow trout. PLoS ONE 7:e36264
60. Ballou JD, Lacy RC. 1995. Identifying genetically important individuals for management of genetic diversity in pedigreed populations. In Population Management for Survival and Recovery, ed. JD Ballou, M Gilpin, TJ Foose, pp. 76-111. New York: Columbia Univ. Press
61. Stinchcombe JR, Hoekstra HE. 2008. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100:158-70
62. Schielzeth H, Forstmeier W, Kempenaers B, Ellegren H. 2012. QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers. Mol. Ecol. 21:329-39
63. Steiner CC, Weber JN, Hoekstra HE. 2007. Adaptive variation in beach mice produced by two interacting pigmentation genes. PLoS Biol. 5:1880-89
64. Protas M, Tabansky I, Conrad M, Gross JB, Vidal O, et al. 2008. Multi-trait evolution in a cave fish, Astyanax mexicanus. Evol. Dev. 10:196-209
65. Garvin MR, Saitoh K, Gharrett AJ. 2010. Application of single nucleotide polymorphisms to non-model species: a technical review. Mol. Ecol. Resour. 10:915-34
66. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, et al. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376
67. Peterson BK,Weber JN, Kay EH, Fisher HS, Hoekstra HE. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping inmodel and non-model species. PLoSONE 7:e37135
68. Miller M, Brunelli J,Wheeler P, Liu S, Rexroad CE, et al. 2012. A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Mol. Ecol. 21:237-49
69. Anderson TM, vonHoldt BM, Candille SI, Musiani M, Greco C, et al. 2009. Molecular and evolutionary history of melanism in North American gray wolves. Science 323:1339-43
70. Johnson HE, Mills LS, Wehausen JD, Stephenson TR, Luikart G. 2011. Translating effects of inbreeding depression on component vital rates to overall population growth in endangered bighorn sheep. Conserv. Biol. 25:1240-49
71. Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton J. 2009. Gene mapping in the wild with SNPs: guidelines and future directions. Genetica 136:97-107
72. Barrett RDH,Hoekstra HE. 2011. Molecular spandrels: tests of adaptation at the genetic level. Nat. Rev. Genet. 12:767-80
73. Oleksyk TK, Smith MW, O'Brien SJ. 2010. Genome-wide scans for footprints of natural selection. Philos. Trans. R. Soc. B Biol. Sci. 365:185-205
74. Renaut S, Bernatchez L. 2011. Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. Salmonidae). Heredity 106:1003-11
75. Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 6:e1000862
76. Linnen CR, Kingsley EP, Jensen JD, Hoekstra HE. 2009. Onthe origin and spread of an adaptive allele in deer mice. Science 325:1095-98
77. Nielsen R. 2005. Molecular signatures of natural selection. Annu. Rev. Genet. 39:197-218
78. Ujvari B, Belov K. 2011. Major Histocompatibility Complex (MHC) markers in conservation biology. Int. J. Mol. Sci. 12:5168-86
79. Siddle HV, Deakin JE, Coggill P, Whilming LG, Harrow J, et al. 2011. The tammar wallaby major histocompatibility complex shows evidence of past genomic instability. BMC Genomics 12:421
80. Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrom M, et al. 2011. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477:207-10
81. Aguilar A, Roemer G, Debenham S, Binns M, Garcelon D, Wayne RK. 2004. High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proc. Natl. Acad. Sci. USA 101:3490-94
82. Xu T-J, Sun Y-N, Chen S-L. 2010. Allelic variation, balancing selection and positive selected sites detected from MHC class I alpha gene of olive flounder. Genetica 138:1251-59
83. Burri R, Salamin N, Studer RA, Roulin A, Fumagalli L. 2010. Adaptive divergence of ancient gene duplicates in the avian MHC class II b. Mol. Biol. Evol. 27:2360-74
84. Hedrick PW, Parker KM, Gutiérrez-Espeleta GA, Rattink A, Lievers K. 2000. Major histocompatibility complex variation in the Arabian oryx. Evolution 54:2145-51
85. Kelley J, Walter L, Trowsdale J. 2005. Comparative genomics of major histocompatibility complexes. Immunogenetics 56:683-95
86. Keller LF, Waller DM. 2002. Inbreeding effects in wild populations. Trends Ecol. Evol. 17:230-41
87. Charlesworth D, Willis JH. 2009. The genetics of inbreeding depression. Nat. Rev. Genet. 10:783-96
88. Paige KN. 2010. The functional genomics of inbreeding depression: a new approach to an old problem. Bioscience 60:267-77
89. Charlier C, Coppieters W, Rollin F, Desmecht D, Agerholm JS, et al. 2008. Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat. Genet. 40:449-54
90. Karlsson EK, Baranowska I,Wade CM, Salmon Hillbertz NH, Zody MC, et al. 2007. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat. Genet. 39:1321-28
91. Hagenblad J, Olsson M, Parker HG, Ostrander EA, Ellegren H. 2009. Population genomics of the inbred Scandinavian wolf. Mol. Ecol. 18:1341-51
92. Glaubitz JC, Rhodes OE, Dewoody JA. 2003. Prospects for inferring pairwise relationships with single nucleotide polymorphisms. Mol. Ecol. 12:1039-47
93. Lynch M, Ritland K. 1999. Estimation of pairwise relatedness with molecular markers. Genetics 152: 1753-66
94. Gasbarra D, Pirinen M, Sillanpaa MJ, Arjas E. 2007. Estimating genealogies from linked marker data: a Bayesian approach. BMC Bioinformatics 8:411
95. Li M-H, Stranden I, Tiirikka T, Sevon-Aimonen M-L, Kantanen J. 2011. A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population. PLoS ONE 6:e26256
96. Roca AL, Georgiadis N,O'Brien SJ. 2005. Cytonuclear genomic dissociation in African elephant species. Nat. Genet. 37:96-100
97. Halbert ND, Derr JN. 2007. A comprehensive evaluation of cattle introgression into US federal bison herds. J. Hered. 98:1-12
98. Grant BR, Grant PR. 2010. Conspecific versus heterospecific gene exchange between populations of Darwin's finches. Philos. Trans. R. Soc. B Biol. Sci. 365:1065-76
99. Fitzpatrick BM, Johnson JR, Kump DK, Shaffer HB, Smith JJ, Voss SR. 2009. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders. BMC Evol. Biol. 9:176
100. Abi-Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, et al. 2011. The shaping of modern human immune systems by multiregional admixture with archaic humans. Science 333:89-94
101. Twyford AD, Ennos RA. 2012. Next-generation hybridization and introgression. Heredity 108:179-89
102. Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, et al. 2012. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl. Acad. Sci. USA 109:14295-96
103. Collins FS. 1999. Shattuck lecture: medical and societal consequences of the Human Genome Project. N. Engl. J. Med. 341:28-37
104. Savage AE, Zamudio KR. 2011.MHCgenotypes associate with resistance to a frog-killing fungus. Proc. Natl. Acad. Sci. USA 108:16705-10
105. Li J, Boroevich KA, Koop BF, Davidson WS. 2011. Comparative genomics identifies candidate genes for Infectious Salmon Anemia (ISA) resistance in Atlantic salmon (Salmo salar). Mar. Biotechnol.13:232-41
106. Ralls K, Ballou JD, Rideout BA, Frankham R. 2000. Genetic management of chondrodystrophy in California condors. Anim. Conserv. 3:145-53
107. Romanov MN, Tuttle EM, Houck ML, Modi WS, Chemnick LG, et al. 2009. The value of avian genomics to the conservation of wildlife. BMC Genomics 10(Suppl. 2):S10
108. Romanov MN, Koriabine M, Nefedov M, de Jong PJ, Ryder OA. 2006. Construction of a California condor BAC library and first-generation chicken-condor comparative physical map as an endangered species conservation genomics resource. Genomics 88:711-18
109. Wong PBY, Wiley EO, Johnson WE, Ryder OA, O'Brien SJ, et al. 2012. Tissue sampling and standards for vertebrate genomics. GigaScience 1:8
110. Ryder OA, Benirschke K. 1984. Value of frozen tissue collections for zoological parks. In Collections of Viable Tissues: Value, Management, and Future, ed. HC Dessauer, MS Hafner, pp. 6-9. Lawrence, KS: Am. Assoc. Syst. Collect.
111. Ryder OA, McLaren A, Brenner S, Zhang Y-P, Benirschke K. 2000. DNA banks for endangered species. Science 288:275-77
112. Wildt DE, Rall WF, Critser JK, Monfort SL, Seal US. 1997. Genome resource banks. Bioscience 47: 689-98
113. Tovar H, Navarrete F, Rodríguez L, Skewes O, Castro FO. 2008. Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell. Dev. Biol. Anim. 44:309-20
114. KaramanM, HouckM, Chemnick L, Nagpal S, Chawannakul D, et al. 2003. Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts. Genome Res. 13:1619-30
115. Frankham R, Ballou JD, Dudash MR, Eldridge MDB, Fenster CB, et al. 2012. Implications of different species concepts for conserving biodiversity. Biol. Conserv. 153:25-31
116. Kristensen TN, Pedersen KS, Vermeulen CJ, Loeschcke V. 2010. Research on inbreeding in the 'omic' era. Trends Ecol. Evol. 25:44-52
117. Davey J, Hohenlohe P, Etter P, Boone J, Catchen J, Blaxter M. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12:499-510
118. Myllykangas S, Natsoulis G, Bell JM, Ji HP. 2011. Targeted sequencing library preparation by genomic DNA circularization. BMC Biotechnol. 11:122
119. Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G, Dickson M, et al. 2005. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307:1928-33
120. Mackay TFC, Stone EA, Ayroles JF. 2009. The genetics of quantitative traits: challenges and prospects. Nat. Rev. Genet. 10:565-77
121. Weetman D, Wilding CS, Steen K, Morgan JC, Simard F, Donnelly MJ. 2010. Association mapping of insecticide resistance in wild Anopheles gambiae populations: major variants identified in a low-linkage disequilibrium genome. PLoS ONE 5:e13140
122. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, et al. 2008. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 9:356-69
123. Seddon N, Amos W, Adcock G, Johnson P, Kraaijeveld K, et al. 2005. Mating system, philopatry and patterns of kinship in the cooperatively breeding subdesert mesite Monias benschi. Mol. Ecol. 14:3573-83
124. Saillant E, Patton JC, Gold JR. 2005. Genetic variation, kinship, and effective population size in a captive population of the endangered Cape Fear shiner, Notropis mekistocholas. Copeia 2005:20-28
125. Blouin MS. 2003. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends Ecol. Evol. 18:503-11
126. Ivy JA, Lacy RC. 2012. A comparison of strategies for selecting breeding pairs to maximize genetic diversity retention in managed populations. J. Hered. 103:186-96
127. Araki H, Cooper B, Blouin MS. 2007. Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild. Science 318:100-3
128. Pemberton JM. 2008. Wild pedigrees: the way forward. Proc. R. Soc. B Biol. Sci. 275:613-21
129. Kirkpatrick B, Li SC, Karp RM, Halperin E. 2011. Pedigree reconstruction using identity by descent. J. Comput. Biol. 18:1481-93
130. Nunes VL, Beaumont MA, Butlin RK, Paulo OS. 2011. Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient. Mol. Ecol. 20:193-205
131. Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, et al. 2012. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 22:602-10
132. Ellegren H, Sheldon BC. 2008. Genetic basis of fitness differences in natural populations. Nature 452:169-75
133. Pertoldi C, Wojcik JM, Tokarska M, Kawalko A, Kristensen TN, et al. 2010. Genome variability in European and American bison detected using the BovineSNP50 BeadChip. Conserv. Genet. 11:627-34
134. Wetzel DP, Stewart IRK, Westneat DF. 2012. Heterozygosity predicts clutch and egg size but not plasticity in a house sparrow population with no evidence of inbreeding. Mol. Ecol. 21:406-20
135. David P. 1998. Heterozygosity-fitness correlations: new perspectives on old problems. Heredity 80:531-37
136. Slate J, Pemberton JM. 2002. Comparing molecular measures for detecting inbreeding depression. J. Evol. Biol. 15:20-31
137. Miller JM, Poissant J, Hogg JT, Coltman DW. 2012. Genomic consequences of genetic rescue in an insular population of bighorn sheep (Ovis canadensis). Mol. Ecol. 21:1583-96
138. Johnson WE, Onorato DP, Roelke ME, Land ED, Cunningham M, et al. 2010. Genetic restoration of the Florida panther. Science 329:1641-45
139. Halbert ND, Ward TJ, Schnabel RD, Taylor JF, Derr JN. 2005. Conservation genomics: disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations. Mol. Ecol. 14:2343-62
140. Wolf JBW, Bayer T, Haubold B, Schilhabel M, Rosenstiel P, Tautz D. 2010. Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Mol. Ecol. 19:162-75
141. Roca AL, Schook LB. 2011. Genomics: captive breeding and wildlife conservation. In Encyclopedia of Biotechnology in Agriculture and Food, ed. DR Heldman, DG Hoover, MB Wheeler, pp. 320-25. New York: Taylor & Francis
142. Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, et al. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc. Natl. Acad. Sci. USA 106:18644-49
143. Perelman P, Johnson WE, Roos C, Seuanez HN, Horvath JE, et al. 2011. A molecular phylogeny of living primates. PLoS Genet. 7:e1001342
144. Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361-75
145. Steele PR, Pires JC. 2011. Biodiversity assessment: state-of-the-art techniques in phylogenomics and species identification. Am. J. Bot. 98:415-25
146. Brinkmann H, Philippe H. 2008. Animal phylogeny and large-scale sequencing: progress and pitfalls. J. Syst. Evol. 46:274-86
147. Singh ND, Larracuente AM, Sackton TB, Clark AG. 2009. Comparative genomics on the Drosophila phylogenetic tree. Annu. Rev. Ecol. Evol. Syst. 40:459-80
148. Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, et al. 2010. Resolving postglacial phylogeography using high-throughput sequencing. Proc. Natl. Acad. Sci. USA 107:16196-200
149. McCormack JE, Maley JM, Hird SM, Derryberry EP, Graves GR, Brumfield RT. 2012. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Mol. Phylogenet. Evol. 62:397-406
150. Knowles LL. 2009. Statistical phylogeography. Annu. Rev. Ecol. Evol. Syst. 40:593-612
151. Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, et al. 2011. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res. 21:1640-49
152. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-75
153. Ureta-Vidal A, Ettwiller L, Birney E. 2003. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4:251-62
154. Miller W, Makova KD, Nekrutenko A, Hardison RC. 2004. Comparative genomics. Annu. Rev. Genomics Hum. Genet. 5:15-56