Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.


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Literature Cited

  1. Int. Union Conserv. Nat. Nat. Resour 2014. The IUCN Red List of Threatened Species, Version 2014.2. Cambridge, UK: Int. Union Conserv. Nat. Nat. Resour. http://www.iucnredlist.org
  2. Duellman WE, Trueb L. 1994. Biology of Amphibians Baltimore, MD: Johns Hopkins Univ. Press [Google Scholar]
  3. Wells KD. 2010. The Ecology and Behavior of Amphibians Chicago: Univ. Chicago Press [Google Scholar]
  4. Vitt LJ, Caldwell JP. 2013. Herpetology: An Introductory Biology of Amphibians and Reptiles San Diego, CA: Acad. Press [Google Scholar]
  5. Nunney L, Elam DR. 1994. Estimating the effective population size of conserved populations. Conserv. Biol. 8:1175–84 [Google Scholar]
  6. Schwartz MK, Tallmon DA, Luikart G. 1998. Review of DNA-based census and effective population size estimators. Anim. Conserv. 1:4293–99 [Google Scholar]
  7. Palstra FP, Ruzzante DE. 2008. Genetic estimates of contemporary effective population size: What can they tell us about the importance of genetic stochasticity for wild population persistence?. Mol. Ecol. 17:153428–47 [Google Scholar]
  8. Wang IJ, Savage WK, Shaffer HB. 2009. Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense). Mol. Ecol. 18:71365–74 [Google Scholar]
  9. Funk WC, Blouin MS, Corn PS, Maxell BA, Pilliod DS et al. 2005. Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape. Mol. Ecol. 14:2483–96 [Google Scholar]
  10. Storfer A, Murphy MA, Evans JS, Goldberg CS, Robinson S et al. 2006. Putting the “landscape” in landscape genetics. Heredity 98:3128–42 [Google Scholar]
  11. Mockford SW, Herman TB, Snyder M, Wright JM. 2007. Conservation genetics of Blanding’s turtle and its application in the identification of evolutionarily significant units. Conserv. Genet. 8:1209–19 [Google Scholar]
  12. Holyoake A, Waldman B, Gemmell NJ. 2001. Determining the species status of one of the world’s rarest frogs: a conservation dilemma. Anim. Conserv. 4:129–35 [Google Scholar]
  13. Shaffer HB, Fellers GM, Magee A, Voss SR. 2000. The genetics of amphibian declines: population substructure and molecular differentiation in the Yosemite toad, Bufo canorus (Anura, Bufonidae) based on single-strand conformation polymorphism analysis (SSCP) and mitochondrial DNA sequence data. Mol. Ecol. 9:3245–57 [Google Scholar]
  14. Lande R, Barrowclough GF. 1987. Effective population size, genetic variation, and their use in population management. Viable Populations for Conservation Soulé ME. 87–124 Cambridge, UK: Cambridge Univ. Press [Google Scholar]
  15. Frankham R. 2007. Effective population size/adult population size ratios in wildlife: a review. Genet. Res 89:Spec. Issue 5–6491–503 [Google Scholar]
  16. Griffiths RC, Tavare S. 1994. Sampling theory for neutral alleles in a varying environment. Philos. Trans. R. Soc. B Biol. Sci. 344:1310403–10 [Google Scholar]
  17. Minin VN, Bloomquist EW, Suchard MA. 2008. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 25:71459–71 [Google Scholar]
  18. Funk WC, Tallmon DA, Allendorf FW. 1999. Small effective population size in the long-toed salamander. Mol. Ecol. 8:101633–40 [Google Scholar]
  19. Phillipsen IC, Funk WC, Hoffman EA, Monsen KJ, Blouin MS. 2011. Comparative analyses of effective population size within and among species: ranid frogs as a case study. Evolution 65:102927–45 [Google Scholar]
  20. Myers EA, Weaver RE, Alamillo H. 2013. Population stability of the northern desert nightsnake (Hypsiglena chlorophaea deserticola) during the Pleistocene. J. Herpetol. 47:3432–39 [Google Scholar]
  21. Guiher TJ, Burbrink FT. 2008. Demographic and phylogeographic histories of two venomous North American snakes of the genus Agkistrodon. Mol. Phylogenet. Evol. 48:2543–53 [Google Scholar]
  22. Mönkkönen M, Reunanen P. 1999. On critical thresholds in landscape connectivity: a management perspective. Oikos 84:2302–5 [Google Scholar]
  23. Manel S, Schwartz MK, Luikart G, Taberlet P. 2003. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol. Evol. 18:4189–97 [Google Scholar]
  24. Clark RW, Brown WS, Stechert R, Zamudio KR. 2008. Integrating individual behaviour and landscape genetics: the population structure of timber rattlesnake hibernacula. Mol. Ecol. 17:3719–30 [Google Scholar]
  25. Spear SF, Peterson CR, Matocq MD, Storfer A. 2005. Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum). Mol. Ecol. 14:82553–64 [Google Scholar]
  26. Howes BJ, Brown JW, Gibbs HL, Herman TB, Mockford SW et al. 2009. Directional gene flow patterns in disjunct populations of the black ratsnake (Pantheropis obsoletus) and the Blanding’s turtle (Emydoidea blandingii). Conserv. Genet. 10:2407–17 [Google Scholar]
  27. Manier MK, Arnold SJ. 2005. Population genetic analysis identifies source–sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis). Mol. Ecol. 14:133965–76 [Google Scholar]
  28. McCartney-Melstad E, Waller T, Micucci PA, Barros M, Draque J et al. 2012. Population structure and gene flow of the yellow anaconda (Eunectes notaeus) in northern Argentina. PLOS ONE 7:5e37473 [Google Scholar]
  29. Savage WK, Fremier AK, Shaffer HB. 2010. Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time. Mol. Ecol. 19:163301–14 [Google Scholar]
  30. Tolley KA, Makokha JS, Houniet DT, Swart BL, Matthee CA. 2009. The potential for predicted climate shifts to impact genetic landscapes of lizards in the South African Cape Floristic Region. Mol. Phylogenet. Evol. 51:1120–30 [Google Scholar]
  31. Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nat. Rev. Genet 11:697–709 [Google Scholar]
  32. Fraser DJ, Bernatchez L. 2001. Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Mol. Ecol. 10:122741–52 [Google Scholar]
  33. De Guia APO, Saitoh T. 2007. The gap between the concept and definitions in the evolutionarily significant unit: the need to integrate neutral genetic variation and adaptive variation. Ecol. Res. 22:4604–12 [Google Scholar]
  34. Moritz C. 1994. Defining “evolutionarily significant units” for conservation. Trends Ecol. Evol. 9:10373–75 [Google Scholar]
  35. Driscoll DA, Hardy CM. 2005. Dispersal and phylogeography of the agamid lizard Amphibolurus nobbi in fragmented and continuous habitat. Mol. Ecol. 14:61613–29 [Google Scholar]
  36. Palsbøll PJ, Bérubé M, Allendorf FW. 2007. Identification of management units using population genetic data. Trends Ecol. Evol. 22:111–16 [Google Scholar]
  37. Richards CL, Knowles LL. 2007. Tests of phenotypic and genetic concordance and their application to the conservation of Panamanian golden frogs (Anura, Bufonidae). Mol. Ecol. 16:153119–33 [Google Scholar]
  38. Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK. 2000. Considering evolutionary processes in conservation biology. Trends Ecol. Evol. 15:7290–95 [Google Scholar]
  39. Emel SL, Bonett RM. 2011. Considering alternative life history modes and genetic divergence in conservation: a case study of the Oklahoma salamander. Conserv. Genet. 12:51243–59 [Google Scholar]
  40. US Dep. Int., US Dep. Commer 1996. Policy regarding the recognition of distinct vertebrate population segments under the Endangered Species Act. Fed. Regist. 61:4722–25 [Google Scholar]
  41. Monsen KJ, Blouin MS. 2003. Genetic structure in a montane ranid frog: restricted gene flow and nuclear–mitochondrial discordance. Mol. Ecol. 12:123275–86 [Google Scholar]
  42. Shaffer HB, Pauly GB, Oliver JC, Trenham PC. 2004. The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense. Mol. Ecol. 13:103033–49 [Google Scholar]
  43. Funk WC, McKay JK, Hohenlohe PA, Allendorf FW. 2012. Harnessing genomics for delineating conservation units. Trends Ecol. Evol 27:489–96 [Google Scholar]
  44. Fitzpatrick BM, Placyk J, John S, Niemiller ML, Casper GS, Burghardt GM. 2008. Distinctiveness in the face of gene flow: hybridization between specialist and generalist gartersnakes. Mol. Ecol. 17:184107–17 [Google Scholar]
  45. Storfer A, Mech SG, Reudink MW, Ziemba RE, Warren J et al. 2004. Evidence for introgression in the endangered Sonora tiger salamander, Ambystoma tigrinum stebbinsi (Lowe). Copeia4783–96 [Google Scholar]
  46. Riley SPD, Shaffer HB, Voss SR, Fitzpatrick BM. 2003. Hybridization between a rare native tiger salamander (Ambystoma californiense) and its introduced congener. Ecol. Appl. 13:51263–75 [Google Scholar]
  47. Luquet E, Garner T, Léna J, Bruel C, Joly P et al. 2011. Genetic erosion in wild populations makes resistance to a pathogen more costly. Evolution 66:1942–52 [Google Scholar]
  48. Rosenblum EB, Poorten TJ, Settles M, Murdoch GK. 2012. Only skin deep: shared genetic response to the deadly chytrid fungus in susceptible frog species. Mol. Ecol. 21:133110–20 [Google Scholar]
  49. Thorpe RS, Reardon JT, Malhotra A. 2005. Common garden and natural selection experiments support ecotypic differentiation in the Dominican anole (Anolis oculatus). Am. Nat. 165:4495–504 [Google Scholar]
  50. Schneider CJ, Smith TB, Larison B, Moritz C. 1999. A test of alternative models of diversification in tropical rainforests: ecological gradients vs. rainforest refugia. PNAS 96:2412869–73 [Google Scholar]
  51. Freedman AH, Thomassen HA, Buermann W, Smith TB. 2010. Genomic signals of diversification along ecological gradients in a tropical lizard. Mol. Ecol. 19:173773–88 [Google Scholar]
  52. Rosenblum EB, Römpler H, Schöneberg T, Hoekstra HE. 2010. Molecular and functional basis of phenotypic convergence in white lizards at White Sands. PNAS 107:52113–17 [Google Scholar]
  53. Babik W, Pabijan M, Arntzen JW, Cogalniceanu D, Durka W, Radwan J. 2009. Long-term survival of a urodele amphibian despite depleted major histocompatibility complex variation. Mol. Ecol. 18:5769–81 [Google Scholar]
  54. Ogden R, Thorpe RS. 2002. Molecular evidence for ecological speciation in tropical habitats. PNAS 99:2113612–15 [Google Scholar]
  55. Bonin A, Taberlet P, Miaud C, Pompanon F. 2006. Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Mol. Biol. Evol. 23:4773–83 [Google Scholar]
  56. Fritz SA, Rahbek C. 2012. Global patterns of amphibian phylogenetic diversity. J. Biogeogr. 39:81373–82 [Google Scholar]
  57. Isaac NJB, Redding DW, Meredith HM, Safi K. 2012. Phylogenetically-informed priorities for amphibian conservation. PLOS ONE 7:8e43912 [Google Scholar]
  58. Austin JD, Gorman TA, Bishop D, Moler P. 2011. Genetic evidence of contemporary hybridization in one of North America’s rarest anurans, the Florida bog frog. Anim. Conserv. 14:5553–61 [Google Scholar]
  59. 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. 9:1176 [Google Scholar]
  60. Fitzpatrick BM, Johnson JR, Kump DK, Smith JJ, Voss SR, Shaffer HB. 2010. Rapid spread of invasive genes into a threatened native species. PNAS 107:83606–10 [Google Scholar]
  61. Fitzpatrick BM, Shaffer HB. 2007. Introduction history and habitat variation explain the landscape genetics of hybrid tiger salamanders. Ecol. Appl. 17:2598–608 [Google Scholar]
  62. Fitzpatrick BM, Shaffer HB. 2007. Hybrid vigor between native and introduced salamanders raises new challenges for conservation. PNAS 104:4015793–98 [Google Scholar]
  63. Ryan ME, Johnson JR, Fitzpatrick BM, Lowenstine LJ, Picco AM, Shaffer HB. 2013. Lethal effects of water quality on threatened California salamanders but not on co-occurring hybrid salamanders. Conserv. Biol. 27:195–102 [Google Scholar]
  64. Johnson JR, Fitzpatrick BM, Shaffer HB. 2010. Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders. BMC Evol. Biol. 10:1147 [Google Scholar]
  65. Rodriguez D, Cedeño-Vázquez JR, Forstner MRJ, Densmore LD. 2008. Hybridization between Crocodylus acutus and Crocodylus moreletii in the Yucatan Peninsula: II. Evidence from microsatellites. J. Exp. Zool. A Ecol. Genet. Physiol. 309A:10674–86 [Google Scholar]
  66. Sanders KL, Rasmussen AR, Guinea ML. 2014. High rates of hybridisation reveal fragile reproductive barriers between endangered Australian sea snakes. Biol. Conserv. 171:200–8 [Google Scholar]
  67. Pasachnik SA, Fitzpatrick BM, Near TJ, Echternacht AC. 2009. Gene flow between an endangered endemic iguana, and its wide spread relative, on the island of Utila, Honduras: When is hybridization a threat?. Conserv. Genet. 10:51247–54 [Google Scholar]
  68. Parham JF, Papenfuss TJ, van Dijk PP, Wilson BS, Marte C et al. 2013. Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers. Mol. Phylogenet. Evol. 67:1176–87 [Google Scholar]
  69. Spinks PQ, Shaffer HB. 2007. Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci. Conserv. Genet. 8:3641–57 [Google Scholar]
  70. Nosil P. 2012. Ecological Speciation New York: Oxford Univ. Press [Google Scholar]
  71. Rice WR, Hostert EE. 1993. Laboratory experiments on speciation: What have we learned in 40 years?. Evolution 47:61637–53 [Google Scholar]
  72. Losos J, Warhelt KI, Schoener TW. 1997. Adaptive differentiation following experimental island colonization in Anolis lizards. Nature 387:70–73 [Google Scholar]
  73. Graham CH, Ron SR, Santos JC, Schneider CJ, Moritz C. 2004. Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs. Evolution 58:81781–93 [Google Scholar]
  74. Smith TB, Grether GF. 2008. The importance of conserving evolutionary processes. Conservation Biology: Evolution in Action Carroll SP, Fox CW. 85–98 Oxford: Oxford Univ. Press [Google Scholar]
  75. Wiens JJ, Graham CH. 2005. Niche conservatism: integrating evolution, ecology, and conservation biology. Annu. Rev. Ecol. Evol. Syst. 36:1519–39 [Google Scholar]
  76. Kozak KH, Wiens JJ. 2006. Does niche conservatism promote speciation? A case study in North American salamanders. Evolution 60:122604–21 [Google Scholar]
  77. Wang IJ, Summers K. 2010. Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog. Mol. Ecol. 19:3447–58 [Google Scholar]
  78. Wake DB. 2009. What salamanders have taught us about evolution. Annu. Rev. Ecol. Evol. Syst. 40:1333–52 [Google Scholar]
  79. Freedman AH, Buermann W, Mitchard ETA, DeFries RS, Smith TB. 2010. Human impacts flatten rainforest-savanna gradient and reduce adaptive diversity in a rainforest bird. PLOS ONE 5:91–9 [Google Scholar]
  80. Muñoz MM, Crawford NG, McGreevy TJ, Messana NJ, Tarvin RD et al. 2013. Divergence in coloration and ecological speciation in the Anolis marmoratus species complex. Mol. Ecol. 22:102668–82 [Google Scholar]
  81. Rosenblum EB, Harmon LJ. 2011. “Same same but different”: replicated ecological speciation at White Sands. Evolution 65:4946–60 [Google Scholar]
  82. Rissler LJ, Apodaca JJ. 2007. Adding more ecology into species delimitation: Ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Syst. Biol. 56:6924–42 [Google Scholar]
  83. Smith TB, Kark S, Schneider CJ, Wayne RK, Moritz C. 2001. Biodiversity hotspots and beyond: the need for preserving environmental transitions. Trends Ecol. Evol. 16:8431 [Google Scholar]
  84. Kawecki TJ, Ebert D. 2004. Conceptual issues in local adaptation. Ecol. Lett. 7:121225–41 [Google Scholar]
  85. Helmuth B, Kingsolver JG, Carrington E. 2005. Biophysics, physiological ecology, and climate change: Does mechanism matter?. Annu. Rev. Physiol. 67:1177–201 [Google Scholar]
  86. Rosenblum EB, Hoekstra HE, Nachman MW. 2004. Adaptive reptile color variation and the evolution of the MC1R gene. Evolution 58:81794–808 [Google Scholar]
  87. Johnson JR, Johnson BB, Shaffer HB. 2010. Genotype and temperature affect locomotor performance in a tiger salamander hybrid swarm. Funct. Ecol. 24:51073–80 [Google Scholar]
  88. Voss SR, Prudic KL, Oliver JC, Shaffer HB. 2003. Candidate gene analysis of metamorphic timing in ambystomatid salamanders. Mol. Ecol. 12:51217–23 [Google Scholar]
  89. Voss SR, Smith JJ. 2005. Evolution of salamander life cycles: A major effect QTL contributes to both continuous and discrete variation for metamorphic timing. Genetics 170:275–81 [Google Scholar]
  90. Voss SR, Kump KD, Walker JA, Shaffer HB, Voss GJ. 2012. Thyroid hormone responsive QTL and evolution of paedomorphic salamanders. Heredity 109:293–98 [Google Scholar]
  91. Richter-Boix A, Quintela M, Kierczak M, Franch M, Laurila A. 2013. Fine-grained adaptive divergence in an amphibian: genetic basis of phenotypic divergence and the role of nonrandom gene flow in restricting effective migration among wetlands. Mol. Ecol. 22:51322–40 [Google Scholar]
  92. Bi K, Vanderpool D, Singhal S, Linderoth T, Moritz C, Good JM. 2012. Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics 13:1403 [Google Scholar]
  93. Miller HC, Biggs PJ, Voelckel C, Nelson NJ. 2012. De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus). BMC Genomics 13:1439 [Google Scholar]
  94. Bar-Yaacov D, Bouskila A, Mishmar D. 2013. The first chameleon transcriptome: comparative genomic analysis of the OXPHOS system reveals loss of COX8 in iguanian lizards. Genome Biol. Evol. 5:101792–99 [Google Scholar]
  95. Wall CE, Cozza S, Riquelme CA, McCombie WR, Heimiller JK et al. 2011. Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation. Physiol. Genomics 43:269–76 [Google Scholar]
  96. Yang W, Qi Y, Bi K, Fu J. 2012. Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: a comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris. BMC Genomics 13:588 doi:10.1186/1471-2164-13-588 [Google Scholar]
  97. Daugherty CH, Cree A, Hay JM, Thompson MB. 1990. Negected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature 347:6289177–79 [Google Scholar]
  98. Engstrom TN, Shaffer HB, McCord WP. 2002. Phylogenetic diversity of endangered and critically endangered southeast Asian softshell turtles (Trionychidae: Chitra). Biol. Conserv. 104:2173–79 [Google Scholar]
  99. Hay JM, Sarre SD, Lambert DM, Allendorf FW, Daugherty CH. 2010. Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia). Conserv. Genet. 11:31063–81 [Google Scholar]
  100. Spinks PQ, Thomson RC, Hughes B, Moxley B, Brown R et al. 2012. Cryptic variation and the tragedy of unrecognized taxa: the case of international trade in the spiny turtle Heosemys spinosa (Testudines: Geoemydidae). Zool. J. Linn. Soc. 164:4811–24 [Google Scholar]
  101. Winter M, Devictor V, Schweiger O. 2013. Phylogenetic diversity and nature conservation: Where are we?. Trends Ecol. Evol. 28:4199–204 [Google Scholar]
  102. Cadotte MW, Davies TJ. 2010. Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Divers. Distrib. 16:3376–85 [Google Scholar]
  103. Vane-Wright RI, Humphries CJ, Williams PH. 1991. What to protect?—systematics and the agony of choice. Biol. Conserv. 55:3235–54 [Google Scholar]
  104. Crawford AJ, Lips KR, Bermingham E. 2010. Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of Central Panama. PNAS 107:13777–82 [Google Scholar]
  105. Smith KG, Lips KR, Chase JM. 2009. Selecting for extinction: nonrandom disease-associated extinction homogenizes amphibian biotas. Ecol. Lett. 12:101069–78 [Google Scholar]
  106. Corey SJ, Waite TA. 2008. Phylogenetic autocorrelation of extinction threat in globally imperilled amphibians. Divers. Distrib. 14:4614–29 [Google Scholar]
  107. Böhm M, Collen B, Baillie JEM, Bowles P, Chanson J et al. 2013. The conservation status of the world’s reptiles. Biol. Conserv. 157:372–85 [Google Scholar]
  108. Hidasi-Neto J, Loyola RD, Cianciaruso MV. 2013. Conservation actions based on Red Lists do not capture the functional and phylogenetic diversity of birds in Brazil. PLOS ONE 8:9e73431 [Google Scholar]
  109. Ernst R, Linsenmair KE, Rödel M-O. 2006. Diversity erosion beyond the species level: dramatic loss of functional diversity after selective logging in two tropical amphibian communities. Biol. Conserv. 133:2143–55 [Google Scholar]
  110. Velo-Antón G, Wink M, Schneeweiß N, Fritz U. 2011. Native or not? Tracing the origin of wild-caught and captive freshwater turtles in a threatened and widely distributed species (Emys orbicularis). Conserv. Genet. 12:2583–88 [Google Scholar]
  111. Fritz U, Gong S, Auer M, Kuchling G, Schneeweiß N, Hundsdörfer AK. 2010. The world’s economically most important chelonians represent a diverse species complex (Testudines: Trionychidae: Pelodiscus). Org. Divers. Evol. 10:3227–42 [Google Scholar]
  112. Welton LJ, Siler CD, Linkem CW, Diesmos AC, Diesmos ML et al. 2013. Dragons in our midst: phyloforensics of illegally traded southeast Asian monitor lizards. Biol. Conserv. 159:7–15 [Google Scholar]
  113. Austin C, Spataro M, Peterson S, Jordan J, McVay D. 2010. Conservation genetics of Beolen’s python (Morelia boeleni) from New Guinea: reduced genetic diversity and divergence of captive and wild animals. Conserv. Genet. 11:889–96 [Google Scholar]
  114. Ballou JD. 1993. Assessing the risks of infectious diseases in captive breeding and reintroduction programs. J. Zoo Wildl. Med. 24:3327–35 [Google Scholar]
  115. Bloxam QMC, Tonge SJ. 1995. Amphibians: suitable candidates for breeding-release programmes. Biodivers. Conserv. 4:6636–44 [Google Scholar]
  116. Kraaijeveld-Smit FJL, Griffiths RA, Moore RD, Beebee TJC. 2006. Captive breeding and the fitness of reintroduced species: a test of the responses to predators in a threatened amphibian. J. Appl. Ecol. 43:2360–65 [Google Scholar]
  117. Ralls K, Ballou J. 1986. Captive breeding programs for populations with a small number of founders. Trends Ecol. Evol. 1:19–22 [Google Scholar]
  118. Miller HC, Miller KA, Daugherty CH. 2008. Reduced MHC variation in a threatened tuatara species. Anim. Conserv. 11:3206–14 [Google Scholar]
  119. Kriger K, Hero J-M. 2006. Survivorship in wild frogs infected with chytridiomycosis. EcoHealth 3:171–77 [Google Scholar]
  120. Burlibaşa L, Gavrilă L. 2011. Amphibians as model organisms for study environmental genotoxicity. Appl. Ecol. Environ. Res. 9:11–15 [Google Scholar]
  121. Poletta GL, Larriera A, Kleinsorge E, Mudry MD. 2009. Genotoxicity of the herbicide formulation Roundup® (glyphosate) in broad-snouted caiman (Caiman latirostris) evidenced by the comet assay and the micronucleus test. Mutat. Res. Toxicol. Environ. Mutagen. 672:295–102 [Google Scholar]
  122. Relyea RA. 2009. A cocktail of contaminants: how mixtures of pesticides at low concentrations affect aquatic communities. Oecologia 159:2363–76 [Google Scholar]
  123. Shinn C, Marco A, Serrano L. 2008. Inter- and intra-specific variation on sensitivity of larval amphibians to nitrite. Chemosphere 71:3507–14 [Google Scholar]
  124. Schlaepfer MA, Hoover C, Dodd CK. 2005. Challenges in evaluating the impact of the trade in amphibians and reptiles on wild populations. Bioscience 55:3256–64 [Google Scholar]
  125. Ogden R, Dawnay N, McEwing R. 2009. Wildlife DNA forensics—bridging the gap between conservation genetics and law enforcement. Endanger. Species Res. 9:179–95 [Google Scholar]
  126. Waples RS. 2002. Definition and estimation of effective population size in the conservation of endangered species. Population Viability Analysis Beissinger SR, McCullough DR. 147–68 Chicago: Univ. Chicago Press [Google Scholar]
  127. Nei M, Maruyama T, Chakraborty R. 1975. The bottleneck effect and genetic variability in populations. Evolution 29:11–10 [Google Scholar]
  128. Peery MZ, Kirby R, Reid BN, Stoelting R, Doucet-Bëer E et al. 2012. Reliability of genetic bottleneck tests for detecting recent population declines. Mol. Ecol. 21:143403–18 [Google Scholar]
  129. Rodríguez-Zárate CJ, Rocha-Olivares A, Beheregaray LB. 2013. Genetic signature of a recent metapopulation bottleneck in the olive ridley turtle (Lepidochelys olivacea) after intensive commercial exploitation in Mexico. Biol. Conserv. 168:10–18 [Google Scholar]
  130. Johnson JR, Thomson RC, Micheletti SJ, Shaffer HB. 2010. The origin of tiger salamander (Ambystoma tigrinum) populations in California, Oregon, and Nevada: Introductions or relicts?. Conserv. Genet. 12:2355–70 [Google Scholar]
  131. Ryan ME, Johnson JR, Fitzpatrick BM. 2009. Invasive hybrid tiger salamander genotypes impact native amphibians. PNAS 106:2711166–71 [Google Scholar]
  132. Kolbe JJ, Lavin BR, Burke RL, Rugiero L, Capula M, Luiselli L. 2013. The desire for variety: Italian wall lizard (Podarcis siculus) populations introduced to the United States via the pet trade are derived from multiple native-range sources. Biol. Invasions 15:4775–83 [Google Scholar]
  133. Kolbe JJ, Glor RE, Rodríguez Schettino L, Lara AC, Larson A, Losos JB. 2004. Genetic variation increases during biological invasion by a Cuban lizard. Nature 431:7005177–81 [Google Scholar]
  134. Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:7357493–96 doi:10.1038/nature10231 [Google Scholar]
  135. Frankam R. 2008. Stress and adaptation in conservation genetics. J. Evol. Biol. 18:750–55 [Google Scholar]
  136. Moore J, Nelson N, Keall S, Daugherty C. 2008. Implications of social dominance and multiple paternity for the genetic diversity of a captive-bred reptile population (tuatara). Conserv. Genet. 9:1243–51 [Google Scholar]
  137. Milinkovitch M, Monteyne D, Gibbs J, Fritts T, Tapia W et al. 2004. Genetic analysis of a successful repatriation programme: giant Galapagos tortoises. Proc. R. Soc. B Biol. Sci 271:341–45 [Google Scholar]
  138. Longcore L, Pessier A, Nichols D. 1999. Batrachochytrium dendrobatidis gen. et sp. nov., a chytrid pathogenic to amphibians. Mycologia 91:219–27 [Google Scholar]
  139. Vancraeynest D, Pasmans F, Martel A, Chiers K, Meulemans G et al. 2006. Inclusion body disease in snakes: a review and description of three cases in boa constrictors in Belgium. Vet. Rec. 158:757–60 [Google Scholar]
  140. Lips K, Diffendorfer J, Mendelson J III, Sears M. 2008. Riding the wave: reconciling the roles of disease and climate change in amphibian declines. PLOS Biol 6:3e72 [Google Scholar]
  141. McCoy ED, Mushinsky HR, Lindzey J. 2007. Conservation strategies and emergent diseases: the case of upper respiratory tract disease in the gopher tortoise. Chelonian Conserv. Biol. 6:2170–76 [Google Scholar]
  142. Odum R, Goode M. 1994. The species survival plan for Crotalus durissus unicolor: a multifaceted approach to conservation of an insular rattlesnake. Captive Management and Conservation of Amphibians and Reptiles Murphy JB, Adler K, Collins JT. 363–68 Ithaca, NY: Soc. Study Amphib. Reptil [Google Scholar]
  143. Savage AE, Kiemnec-Tyburczy KM, Ellison AR, Fleischer RC, Zamudio KR. 2014. Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes. Gene 542:98–108 [Google Scholar]
  144. Ellison AR, Savage AE, DiRenzo GV, Langhammer P, Lips KR, Zamudio KR. 2014. Fighting a losing battle: vigorous immune response countered by pathogen suppression of host defenses in a chytridiomycosis-susceptible frog. Genes Genomes Genet 19:1275–89 [Google Scholar]
  145. Van Straalen NM, Timmermans MJTN. 2002. Genetic variation in toxicant-stressed populations: an evaluation of the “genetic erosion” hypothesis. Hum. Ecol. Risk Assess. Int. J. 8:5983–1002 [Google Scholar]
  146. Maes GE, Raeymaekers JAM, Pampoulie C, Seynaeve A, Goemans G et al. 2005. The catadromous European eel Anguilla anguilla (L.) as a model for freshwater evolutionary ecotoxicology: relationship between heavy metal bioaccumulation, condition and genetic variability. Aquat. Toxicol. 73:199–114 [Google Scholar]
  147. Sparling DW, Gorsuch JW. 2010. Ecotoxicology of Amphibians and Reptiles Boca Raton, FL: CRC Press/Taylor & Francis [Google Scholar]
  148. Burlibaşa L, Zarnescu O. 2013. In vivo effects of Trichostatin A—a histone deacetylase inhibitor—on chromatin remodeling during Triturus cristatus spermatogenesis. Anim. Reprod. Sci. 142:1–289–99 [Google Scholar]
  149. Yin XH, Li SN, Zhang L, Zhu GN, Zhuang HS. 2008. Evaluation of DNA damage in Chinese toad (Bufo bufo gargarizans) after in vivo exposure to sublethal concentrations of four herbicides using the comet assay. Ecotoxicology 17:4280–86 [Google Scholar]
  150. Schaumburg LG, Poletta GL, Siroski PA, Mudry MD. 2012. Baseline values of micronuclei and comet assay in the lizard Tupinambis merianae (Teiidae, Squamata). Ecotoxicol. Environ. Saf. 84:99–103 [Google Scholar]
  151. Caliani I, Campani T, Giannetti M, Marsili L, Casini S, Fossi MC. 2014. First application of comet assay in blood cells of Mediterranean loggerhead sea turtle (Caretta caretta). Mar. Environ. Res. 96:68–72 [Google Scholar]
  152. Nikoloff N, Natale GS, Marino D, Soloneski S, Larramendy ML. 2014. Flurochloridone-based herbicides induced genotoxicity effects on Rhinella arenarum tadpoles (Anura: Bufonidae). Ecotoxicol. Environ. Saf. 100:275–81 [Google Scholar]
  153. Pérez-Iglesias JM, Ruiz de Arcaute C, Nikoloff N, Dury L, Soloneski S et al. 2014. The genotoxic effects of the imidacloprid-based insecticide formulation Glacoxan Imida on Montevideo tree frog Hypsiboas pulchellus tadpoles (Anura, Hylidae). Ecotoxicol. Environ. Saf. 104:120–26 [Google Scholar]
  154. Thomassen HA, Fuller T, Buermann W, Mila B, Kieswetter CM et al. 2011. Mapping evolutionary process: a multi-taxa approach to conservation prioritization. Evol. Appl. 4:397–413 [Google Scholar]
  155. Moritz C. 2002. Strategies to protect biological diversity and the evolutionary processes that sustain it. Syst. Biol. 51:2238–54 [Google Scholar]
  156. Branch LC, Clark A, Moler PE, Bowen BW. 2003. Fragmented landscapes, habitat specificity, and conservation genetics of three lizards in Florida scrub. Conserv. Genet. 4:199–212 [Google Scholar]
  157. Vasconcelos R, Brito JC, Carvalho SB, Carranza S, Harris DJ. 2012. Identifying priority areas for island endemics using genetic versus specific diversity—the case of terrestrial reptiles of the Cape Verde Islands. Biol. Conserv. 153:276–86 [Google Scholar]
  158. Genome 10K Community Sci 2009. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J. Hered 100:6659–74 [Google Scholar]
  159. Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y et al. 2013. The draft genomes of the soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat. Genet 45:6701–6 [Google Scholar]
  160. Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC et al. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 14:3R28 [Google Scholar]
  161. St. John JA, Braun EL, Isberg SR, Miles LG, Chong AY et al. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 13:1415 [Google Scholar]
  162. Wan QH, Pan SK, Hu L, Zhu Y, Xu PW et al. 2013. Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator. Cell Res 23:91091–105 [Google Scholar]
  163. Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L et al. 2011. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477:7366587–91 [Google Scholar]
  164. Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR et al. 2013. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. PNAS 110:5120645–50 [Google Scholar]
  165. Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ et al. 2013. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. PNAS 110:5120651–56 [Google Scholar]
  166. Gilbert C, Meik JM, Dashevsky D, Card DC, Castoe TA, Schaack S. 2014. Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes. Proc. Biol. Sci 281:179120141122 [Google Scholar]
  167. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J et al. 2010. The genome of the Western clawed frog Xenopus tropicalis. Science 328:5978633–36 [Google Scholar]
  168. Kim S, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T et al. 2011. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinform. 12:1231 [Google Scholar]
  169. Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J. 2012. SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLOS ONE 7:7e37558 [Google Scholar]

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