DNA-based approaches for evaluating historical demography in terrestrial vertebrates

Biological Journal of the Linnean Society

Volumn 112, Issue 3, 2014, Pages 367-386

  Fahey, Anna L ^a   Ricklefs, Robert E ^b   Dewoody, J Andrew ^a  

^a PURDUE UNIVERSITY   (United States)

^b UNIVERSITY OF MISSOURI ST LOUIS   (United States)

Author keywords

Amphibians; Birds; Coalescence; Mammals; Mitochondrial genes; Neutrality test statistics; Nuclear genes; Reptiles; Sex biased dispersal; Substitution rates

Indexed keywords

COALESCENCE; DEMOGRAPHIC HISTORY; DISPERSAL; EFFECTIVE POPULATION SIZE; GENETIC DIFFERENTIATION; MITOCHONDRIAL DNA; TERRESTRIAL ENVIRONMENT; VERTEBRATE;

AMPHIBIA; AVES; MAMMALIA; REPTILIA; VERTEBRATA;

EID: 84902536539     PISSN: 00244066     EISSN: 10958312     Source Type: Journal    
DOI: 10.1111/bij.12259     Document Type: Article

References (124)

1. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecology and Systematics 33: 707-740.
2. Avise JC, Walker D. 1998. Pleistocene phylogeographic effects on avian populations and the speciation process. Proceedings of the Royal Society of London Series B, Biological Sciences 265: 457-463.
3. Axelsson E, Webster MT, Smith NGC, Burt DW, Ellegren H. 2005. Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Research 15: 120-125.
4. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376.
5. Ballard JWO, Whitlock MC. 2004. The incomplete natural history of mitochondria. Molecular Ecology 13: 729-744.
6. Barker BS, Waide RB, Cook JA. 2011. Deep intra-island divergence of a montane forest endemic: phylogeography of the Puerto Rican frog Eleutherodactylus portoricensis (Anura: Eleutherodactylidae). Journal of Biogeography 38: 2311-2325.
7. Bazin E, Glemin S, Galtier N. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science 31: 570-571.
8. Bellemain E, Bermingham E, Ricklefs RE. 2008. The dynamic evolutionary history of the bananaquit (Coereba flaveola) in the Caribbean revealed by a multigene analysis. BMC Evolutionary Biology 8: 240.
9. Bensch S, Irwin DE, Irwin JH, Kvist L, Åkesson S. 2006. Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers. Molecular Ecology 15: 161-171.
10. Bos DH, Gopurenko D, Williams RN, DeWoody JA. 2008. Inferring population history and demography using microsatellites, mitochondrial DNA, and major histocompatibility complex (MHC) genes. Evolution 62: 1458-1468.
11. Brace S, Barnes I, Powell A, Pearson R, Woolaver LG, Thomas MG, Turvey ST. 2012. Population history of the Hispaniolan hutia Plagiodontia aedium (Rodentia: Capromyidae): testing the model of ancient differentiation on a geographically complex Caribbean island. Molecular Ecology 21: 2239-2253.
12. Bromham L, Penny D. 2003. The modern molecular clock. Nature Reviews Genetics 4: 216-224.
13. Brown WM, George M, Wilson A. 1979. Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America 72: 1967-1971.
14. Cheviron ZA, Hackett SJ, Capparella AP. 2005. Complex evolutionary of a Neotropical lowland forest bird (Lepidothrix coronata) and its implications for historical hypotheses of the origin of Neotropical avian diversity. Molecular Phylogenetics and Evolution 36: 338-357.
15. Clark AG. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Molecular Biology and Evolution 7: 111-122.
16. Congdon BC, Piatt JF, Martin K, Friesen VL. 2000. Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes. Evolution 54: 974-986.
17. Crawford AJ. 2003. Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Molecular Ecology 12: 2525-2540.
18. CSAC. 2005. Chimpanzee sequencing and analysis consortium initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
19. D'Horta FM, Cabanne GS, Meyer D, Miyaki CY. 2011. The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine. Molecular Ecology 20: 1923-1935.
20. Dickerson BR, Ream RR, Vignieri SN, Bentzen P. 2010. Population structure as revealed by mtDNA and microsatellites in northern fur seals, Callorhinus ursinus, throughout their range. PLOS ONE 5: e10671.
21. Drovetski SV, Zink RM, Ericson PGP, Fadeev IV. 2010. A multilocus study of pine grosbeak phylogeography supports the pattern of greater intercontinental divergence in Holarctic boreal forest birds than in birds inhabiting other high-latitude habitats. Journal of Biogeography 37: 696-706.
22. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution 22: 1185-1192.
23. Dupuis JR, Roe AD, Sperling FAH. 2012. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Molecular Ecology 21: 4422-4436.
24. Edwards SV, Kingan SB, Calkins JD, Balakrishnan CN, Jennings WB, Swanson WJ, Sorenson MD. 2005. Speciation in birds: genes, geography, and sexual selection. Proceedings of the National Academy of Sciences of the United States of America 102: 6550-6557.
25. Ellegren H. 2007. Molecular evolutionary genomics of birds. Cytogenetic and Genome Research 117: 120-130.
26. Eo SH, DeWoody JA. 2010. Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles. Proceedings of the Royal Society B 277: 3587-3592.
27. Fahey AL, Latta SC, Ricklefs R, DeWoody JA. 2012. Comparative historical demography of migratory and nonmigratory birds from the Caribbean island of Hispaniola. Evolutionary Biology 39: 400-414.
28. Felsenstein J. 1992. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genetical Research 59: 139-147.
29. Ferrero ME, Blanco-Aguiar JA, Lougheed SC, Sánchez-Barbudo I, de Nova PJG, Villafuerte R, Dávila JA. 2011. Phylogeography and genetic structure of the red-legged partridge (Alectoris rufa): more evidence for refugia within the Iberian glacial refugium. Molecular Ecology 20: 2628-2642.
30. Firestone KB, Elphinstone MS, Sherwin WB, Houlden BA. 1999. Phylogeographical population structure of the tiger quolls Dasyurus maculatus (Dasyuridae: Marsupialia), an endangered carnivorous marsupial. Molecular Ecology 8: 1613-1625.
31. Förster DW, Gündüz İ, Nunes AC, Gabriel S, Ramalhinho MG, Mathias ML, Britton-Davidian J, Searle JB. 2009. Molecular insights into the colonization and chromosomal diversification of Madeiran house mice. Molecular Ecology 18: 4477-4494.
32. Fu Y. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
33. Fu Y, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693-709.
34. Galbreath KE, Cook JA, Eddingsaas AA, DeChaine EG. 2011. Diversity and demography in Beringia: multilocus tests of paleodistribution models reveal the complex history of arctic ground squirrels. Evolution 65: 1879-1896.
35. Galtier N, Nabholz B, Glémin S, Hurst GDD. 2009. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18: 4541-4550.
36. Gehring PS, Pabijan M, Randrianirina JE, Glaw F, Vences M. 2012. The influence of riverine barriers on phylogeographic patterns of Malagasy reed frogs (Heterixalus). Molecular Phylogenetics and Evolution 64: 618-632.
37. Girman DJ, Vilá C, Geffen E, Creel S, Mills MGL, McNutt JW, Ginsberg J, Kat PW, Mamiya KH, Wayne RK. 2001. Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus). Molecular Ecology 10: 1703-1723.
38. Greenwood PJ. 1980. Mating systems, philopatry and dispersal in birds and mammals. Animal Behaviour 28: 1140-1162.
39. Gvoždík V, Moravec J, Klütsch C, Kotlík P. 2010. Phylogeography of the Middle Eastern tree frogs (Hyla, Hylidae, Amphibia) as inferred from nuclear and mitochondrial DNA variation, with a description of a new species. Molecular Phylogenetics and Evolution 55: 1146-1166.
40. Hare MP, Cipriano F, Palumbi SR. 2002. Genetic evidence on the demographic of speciation in allopatric dolphin species. Evolution 56: 804-816.
41. Harpending HC, Sherry AR, Rogers AR, Stoneking M. 1993. Genetic structure of ancient human populations. Current Anthropology 34: 483-496.
42. Ho SYW. 2007. Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology 38: 409-414.
43. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. 2011. Time-dependent rates of molecular evolution. Molecular Ecology 20: 3087-3101.
44. Ho SYW, Shapiro B. 2011. Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources 11: 423-434.
45. Hoelzer GA. 1997. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees revisited. Evolution 51: 622-626.
46. Hofmann S, Fritzsche P, Solhøy T, Dorge T, Miehe G. 2012. Evidence of sex-biased dispersal in Thermophis baileyi inferred from microsatellite markers. Herpetologia 68: 514-522.
47. 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 Genetics 6: e1000862.
48. Hope AG, Speer KA, Demboski JR, Talbot SL, Cook JA. 2012. A climate for speciation: rapid spatial diversification within the Sorex cinereus complex of shrews. Molecular Phylogenetics and Evolution 64: 671-684.
49. Hope AG, Waltari E, Fedorov VB, Goropashnaya AV, Talbot SL, Cook JA. 2011. Persistence and diversification of the Holarctic shrew, Sorex tundrensis (Family Soricidae), in response to climate change. Molecular Ecology 20: 4346-4370.
50. Hulva P, Fornůsková A, Chudárková A, Evin A, Allegrini B, Benda P, Bryja J. 2010. Mechanisms of radiation in a bat group from the genus Pipistrellus inferred by phylogeography, demography and population genetics. Molecular Ecology 19: 5417-5431.
51. Jackson ND, Austin CC. 2009. The combined effects of rivers and refugia generate extreme cryptic fragmentation within the common ground skink (Scincella lateralis). Evolution 64: 409-428.
52. Johansson H, Surget-Groba Y, Thorpe RS. 2008. Microsatellite data show evidence for male-biased dispersal in the Caribbean lizard Anolis roquet. Molecular Ecology 17: 4425-4432.
53. Johns GC, Avise JC. 1998. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution 15: 1481-1490.
54. Ju J, Yang M, Xu S, Zhou K, Yang G. 2012. High level population differentiation of finless porpoises (Neophocaena phocaenoides) in Chinese waters revealed by sequence variability of four nuclear introns. Molecular Biology Reports 39: 7755-7762.
55. Karl SA, Toonen RJ, Grant WS, Bowen BW. 2012. Common misconceptions in molecular ecology: echoes of the modern synthesis. Molecular Ecology 21: 4171-4189.
56. Lane A, Shine R. 2011. Intraspecific variation in the direction and degree of sex-biased dispersal among sea-snake populations. Molecular Ecology 20: 1870-1876.
57. Lee JY, Edwards SV. 2008. Divergence across Australia's Carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus). Evolution 62: 3117-3134.
58. Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
59. Liberg O, von Schantz T. 1985. Sex-biased philopatry and dispersal in birds and mammals: the Oedipus hypothesis. American Naturalist 126: 129-135.
60. Lim HC, Sheldon FH. 2011. Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia. Molecular Ecology 20: 3414-3438.
61. Lloyd BD. 2003. The demographic history of the New Zealand short-tailed bat Mystacina tuberculata inferred from modified control region sequences. Molecular Ecology 12: 1895-1911.
62. Lopes IF, Miño CI, Del Lama SN. 2007. Genetic diversity and evidence of recent demographic expansion in waterbird populations from the Brazilian Pantanal. Brazialian Journal of Biology 67: 849-857.
63. Lovette IJ. 2004. Mitochondrial dating and the mixed support for the '2% rule' in birds. The Auk 121: 1-6.
64. Mao X, He G, Hua P, Jones G, Zhang S, Rossiter SJ. 2012. Historical introgression and the persistence of ghost alleles in the intermediate horseshoe bat (Rhinolophus affinis). Molecular Ecology 22: 1035-1050.
65. Marin JC, González BA, Poulin E, Casey CS, Johnson WE. 2012. The influence of the arid Andean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) in South America. Molecular Ecology 22: 463-482.
66. Martínez-Solano Í, Peralta-García A, Jockusch EL, Wake DB, Vázquez-Domínguez E, Parra-Olea G. 2012. Molecular systematic of Batrachoseps (Caudata, Plethodontidae) in southern California and Baja California: mitochondrial-nuclear DNA discordance and the evolutionary history of B. major. Molecular Phylogenetics and Evolution 63: 131-149.
67. Merilä J, Björklund M, Baker AJ. 1997. Historical demography and present day population structure of the greenfinch, Carduelis chloris-an analysis of mtDNA control-region sequences. Evolution 51: 946-956.
68. Meyer M, Stenzel U, Hofreiter M. 2008. Parallel tagged sequencing on the 454 platform. Nature Protocols 3: 267-278.
69. MGSC. 2002. Mouse genome sequencing consortium: initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
70. Moore JA, Miller HC, Daugherty CH, Nelson NJ. 2008. Fine-scale genetic structure of a long-lived reptile reflects recent habitat modification. Molecular Ecology 17: 4630-4641.
71. Moore WS. 1995. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49: 718-726.
72. Moritz C, Dowlin TE, Brown WM. 1987. Evolution of animal mitochondrial DNA: relevance for population biology and systematic. Annual Review of Ecology and Systematics 18: 269-292.
73. Nabholz B, Glémin S, Galtier N. 2008. Strong variation of mitochondrial mutation rate across mammals-the longevity hypothesis. Molecular Biology and Evolution 25: 120-130.
74. Nadachowska K, Babik W. 2009. Divergence in the face of gene flow: the case of two newts (Amphibia: Salamandridae). Molecular Biology and Evolution 26: 829-841.
75. Nei M. 1987. Molecular evolutionary genetics. New York, NY: Columbia University Press.
76. Neumann K, Michaux JR, Maak S, Jansman HAH, Kayser A, Mundt G, Gattermann R. 2005. Genetic spatial structure of European common hamsters (Cricetus cricetus)-a result of repeated range expansion and demographic bottlenecks. Molecular Ecology 14: 1473-1483.
77. Norgate M, Chamings J, Pavlova A, Bull JK, Murray ND, Sunnucks P. 2009. Mitochondrial DNA indicates late Pleistocene divergence of populations of Heteronympha merope, an emerging model in environmental change biology. PLoS ONE 4: e7950.
78. O'Neill EM, Schwartz R, Bullock CT, Williams JS, Shaffer HB, Aguilar-Miguel X, Parra-Olea G, Weisrock DW. 2012. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Molecular Ecology 22: 111-129.
79. Palumbi SR, Baker CS. 1994. Contrasting population structure from the nuclear intron sequences and mtDNA of humpback whales. Molecular Biology and Evolution 11: 426-435.
80. Palumbi SR, Cipriano F, Hare MP. 2001. Predicting nuclear gene coalescence from mitochondrial data: the three-times rule. Evolution 55: 859-868.
81. Paupério J, Herman JS, Melo-Ferreira J, Jaarola M, Alves PC, Searle JB. 2012. Cryptic speciation in the field vole: a multilocus approach confirms three highly divergent lineages in Eurasia. Molecular Ecology 21: 6015-6032.
82. Peters JL, Gretes W, Omland KE. 2005. Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method. Molecular Ecology 14: 3407-3418.
83. Portik DM, Bauer AM, Jackman TR. 2011. Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa. Molecular Ecology 20: 1744-1758.
84. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C. 2013. Great ape genetic diversity and population history. Nature 499: 471-475.
85. Prugnolle F, de Meeus T. 2002. Inferring sex-biased dispersal from population genetic tools: a review. Heredity 88: 161-165.
86. Ptak SE, Przeworski M. 2002. Evidence for population growth in humans is confounded by fine-scale population structure. Trends in Genetics 18: 559-563.
87. Puritz JB, Addison JA, Toonen RJ. 2012. Next-generation phylogeography: a targeted approach for multilocus sequencing of non-model organisms. PLoS ONE 7: e34241.
88. Pybus OG, Rambaut A, Harvey PH. 2000. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155: 1429-1437.
89. Qu Y, Lei F, Zhang R, Lu X. 2010. Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau. Molecular Ecology 19: 338-351.
90. Qu Y, Zhang R, Quan Q, Song G, Li SH, Lei F. 2012. Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the vinous-throated parrotbill (Paradoxornis webbianus). Molecular Ecology 21: 6117-6133.
91. Ramírez-Soriano A, Ramos-Onsins SE, Rozas J, Calafell F, Navarro A. 2008. Statistical analysis of neutrality tests under demographic expansions, contractions, and bottlenecks with recombination. Genetics 179: 555-567.
92. Ramos-Onsins SE, Rozas J. 2002. Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution 19: 2092-2100.
93. Rato C, Carranza S, Harris DJ. 2011. When selection deceives phylogeographic interpretation: the case of the Mediterranean house gecko, Hemidactylus turcicus (Linnaeus, 1758). Molecular Phylogenetics and Evolution 58: 365-373.
94. Reding DM, Freed LA, Cann RL, Fleischer RC. 2010. Spatial and temporal patterns of genetic diversity in an endangered Hawaiian honeycreeper, the Hawaii Akepa (Loxops coccineus coccineus). Conservation Genetics 11: 225-240.
95. Rogers AR. 1995. Genetic evidence for a Pleistocene population explosion. Evolution 49: 608-615.
96. Rogers AR, Harpending HC. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552-569.
97. Rout PK, Thangraji K, Mandal A, Roy R. 2012. Genetic variation and population structure in jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes. Scientific World Journal 2012: 2012-618909.
98. Ruokonen M, Aarvak T, Chesser RK, Lundqvists AC, Merilä J. 2010. Temporal increase in mtDNA diversity in a declining population. Molecular Ecology 19: 2408-2417.
99. Schneider S, Excoffier L. 1999. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152: 1079-1089.
100. Sequeira F, Sodré D, Ferrand N, Bernardi JAR, Sampaio I, Schneider H, Vallinoto M. 2011. Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from the mtDNA and nuclear markers. BMC Evolutionary Biology 11: 264-278.
101. Slatkin M, Hudson RR. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
102. Sly ND, Townsend AK, Rimmer CC, Townsend JM, Latta S, Lovette IJ. 2010. Phylogeography and conservation genetics of the Hispaniolan endemic Palm-Tanagers (Aves: Phaenicophilus). Conservation Genetics 11: 2121-2129.
103. Smith MA, Green DM. 2006. Sex, isolation and fidelity: unbiased long-distance dispersal in a terrestrial amphibian. Ecography 29: 649-658.
104. Smith SA, Donoghue MJ. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86-89.
105. Stephens M, Smith NJ, Donnelly P. 2001. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 68: 978-989.
106. Stone AC, Battistuzzi FU, Kubatko LS, Perry Jr GH, Trudeau E, Lin H, Kumar S. 2010. More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 365: 3277-3288.
107. Strimmer K, Pybus OG. 2001. Exploring the demographic history of DNA sequences using the generalized skyline plot. Molecular Biology and Evolution 18: 2298-2305.
108. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
109. Tchaicka L, Eizirik E, de Oliveira TG, Cândido JF Jr, Freitas TRO. 2007. Phylogeography and population history of the crab-eating fox (Cerdocyon thous). Molecular Ecology 16: 819-838.
110. Tollis M, Ausubel G, Ghimire D, Boissinot S. 2012. Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis historical demography of a genomic model species. PLoS ONE 7: e38474.
111. Townsend AK, Rimmer CC, Latta SC, Lovette IJ. 2007. Ancient differentiation in the single-island avian radiation of endemic Hispaniolan Chat-Tanagers (Aves: Calyptophilus). Molecular Ecology 16: 3634-3642.
112. Tucker AD, McCallum HI, Limpus CJ, McDonald KR. 1998. Sex-biased dispersal in a long lived polygynous reptile (Crocodylus johnstoni). Behavior Ecology and Sociobiology 44: 85-90.
113. van Tuinen M, Hedges SB. 2001. Calibration of avian molecular clocks. Molecular Biology and Evolution 18: 206-213.
114. Turchetto-Zolet AC, Pinheiro F, Salgueiro F, Palma-Silva C. 2012. Phylogeographical patterns shed light on the evolutionary process in South America. Molecular Ecology 22: 1193-1213.
115. Wang Y, Lane A, Ding P. 2012. Sex-biased dispersal of a frog (Odorrana schmackeri) is affected by patch isolation and resource limitation in a fragmented landscape. PLoS ONE 7: e47683.
116. Wares JP. 2009. Natural distributions of mitochondrial sequence diversity support new null hypotheses. Evolution 64: 1136-1142.
117. Weir JT, Schluter D. 2008. Calibrating the avian molecular clock. Molecular Ecology 17: 2321-2328.
118. Wilson RE, Peters JL, McCracken KG. 2012. Genetic and phenotypic divergence between low- and high-altitude populations of two recently diverged cinnamon teal subspecies. Evolution 67: 170-184.
119. Wu Y, Wang Y, Jiang K, Hanken J. 2013. Significance of pre-Quaternary climate change for montane species diversity: insights from Asian salamanders (Salamandridae: Pachytriton). Molecular Phylogenetics and Evolution 66: 380-390.
120. Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution 46: 409-418.
121. You Y, Sun K, Xu L, Wang L, Jiang T, Liu S, Lu G, Berquist SW, Feng J. 2010. Pleistocene glacial cycle effects on the phylogeography of the Chinese endemic bat species, Myotis davidii. BMC Evolutionary Biology 10: 208.
122. Zhan XJ, Pan SK, Wang JY, Dixon A, He J, Muller MG, Ni PX, Hu L, Liu Y, Hou HL, Chen YP, Xia JQ, Luo Q, Xu PW, Chen Y, Liao SG, Cao CC, Gao SK, Wang ZB, Yue Z, Li GQ, Yin Y, Fox NC, Wang J, Bruford MW. 2013. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nature Genetics 45: 563-566.
123. Zhou WW, Wen Y, Fu J, Xu YB, Jin JQ, Ding L, Min MS, Che J, Zhang YP. 2012. Speciation in the Rana chensinensis species complex and its relationship to the uplift of the Qinghai-Tibetan Plateau. Molecular Ecology 21: 960-973.
124. Zink RM, Barrowclough GF. 2008. Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology 17: 2107-2121.