Testing founder effect speciation: Divergence population genetics of the Spoonbills Platalea regia and Pl. minor (Threskiornithidae, Aves)

Molecular Biology and Evolution

Volumn 28, Issue 1, 2011, Pages 473-482

  Yeung, Carol K L ^a   Tsai, Pi Wen ^a   Chesser, R Terry ^b   Lin, Rong Chien ^a   Yao, Cheng Te ^c   Tian, Xiu Hua ^d   Li, Shou Hsien ^a  

^a NATIONAL TAIWAN NORMAL UNIVERSITY   (Taiwan)

^b DEPARTMENT OF PALEOBIOLOGY   (United States)

^c ENDEMIC SPECIES RESEARCH INSTITUTE   (Taiwan)

^d NORTHEAST FORESTRY UNIVERSITY   (China)

Author keywords

approximate Bayesian computation; founder effect speciation; Platalea; postdivergence gene flow; spoonbills

Indexed keywords

ANIMAL TISSUE; ARTICLE; ASIA; AUSTRALIA AND NEW ZEALAND; BAYES THEOREM; BIRD; BOTTLENECK POPULATION; CONTROLLED STUDY; FOUNDER EFFECT; GENE FLOW; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; MALE; NONHUMAN; PLATALEA MINOR; PLATALEA REGIA; POPULATION SIZE; SIMULATION; SPECIES DIFFERENTIATION; VALIDITY;

ANIMALS; AUSTRALASIA; BIOLOGICAL EVOLUTION; BIRDS; FAR EAST; FOUNDER EFFECT; GENE FLOW; GENETIC SPECIATION; GENETICS, POPULATION; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC;

AVES; PLATALEA; PLATALEA MINOR; PLATALEA REGIA; THRESKIORNITHIDAE;

EID: 78650482579     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq210     Document Type: Article

References (77)

1. Backström N, Brandström M, Gustafsson L, Qvarnström A, Cheng H, Ellegren H. 2006. Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): conserved synteny but gene order rearrangements on the avian Z chromosome. Genetics 174:337-386.
2. Balakrishnan CN, Edwards SV. 2009. Nucleotide variation, linkage disequilibrium and founder-faciliated speciation in wild populations of the zebra finch (Taeniopygia guttata). Genetics 181:645-660.
3. Barraclough TG, Vogler AP. 2000. Detecting the geographical pattern of speciation from species-level phylogenies. Am Nat. 155:419-434.
4. Bearhop S, Fiedler W, Furness RW, Votier SC, Waldron S, Newton J, Gabriel JB, Berthold P, Farnsworth K. 2005. Assortative mating as a mechanism for rapid evolution of a migratory divide. Science 310:502-504.
5. Beaumont MA. 2008. Joint determination of topology, divergence time and immigration in population tree. In: Matsumura S, Forster P, editors. Simulation, genetics and human prehistory. Cambridge: University of Cambridge. p. 135-154.
6. Beaumont MA, Zhang W, Balding DJ. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
7. Becquet C, Przeworski M. 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17:1505-1519.
8. Bequet C, Przeworski M. 2009. Learning about modes of speciation by computational approaches. Evolution 63:2547-2562.
9. Benjamini Y, Yekutieli D. 2001. The control of the false discovery rate under dependency. Ann Stat. 29:1165-1188.
10. Boucher VL, Nash TH III. 1990. Growth patterns in Ramalina menziesii in California: coastal vs. inland populations. Bryologist 93:295-302.
11. Chesser RT, Yeung CKL, Yao CT, Tian XH, Li SH. 2010. Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA. Zootaxa 2603:53-60.
12. Chesser RT, Zink RM. 1994. Modes of speciation in birds: a test of Lynch's method. Evolution 48:490-497.
13. Clegg SM, Degnan SM, Kikkawa J, Moritz C, Estoup A, Owens IPF. 2002. Genetic consequences of sequential founder events by an island-colonizing bird. Proc Natl Acad Sci. 99:8127-8132.
14. Coyne JA, Orr HA. 2004. Speciation. Sunderland (MA): Sinauer Associates.
15. Figuerola J. 1999. Effects of salinity on rates of infestation of waterbirds by haematozoa. Ecography 22:681-685.
16. Friesen VL, Anderson DJ. 1997. Phylogeny and evolution of the Sulidae (Aves: pelecaniformes): a test of alternative modes of speciation. Mol Phylogenet Evol. 7:252-260.
17. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
18. Gavrilets S. 2004. Fitness landscapes and the origin of species. Princeton (NJ): Princeton University Press.
19. Gemmell NJ, Akiyama S. 1996. An efficient method for the extraction of DNA from vertebrate tissues. Trends Genet. 12:338-339.
20. Grant PR, Grant BR, Peetren K. 2001. A population founded by a single pair of individuals: establishment, expansion, and evolution. Genetica 112-113:359-382.
21. Hamilton G, Stoneking M, Excoffier L. 2005. Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations. Proc Natl Acad Sci. 102:7476-7480.
22. Hancock JA, Kushlan JA, Kahl MP. 1992. Storks, ibises and spoonbills of the world. London: Academic Press.
23. Hendry AP, Nosil P, Rieseberg LH. 2007. The speed of ecological speciation. Funct Ecol. 21:455-464.
24. Hey J. 2005. On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biol. 3:e193.
25. Hornfeldt B, Hipkiss T, Fridolfsson A-K, Eklund U, Ellegren H. 2000. Sex ratio and fledging success of supplementary-fed Tengmalm's owl broods. Mol Ecol. 9:187-192.
26. Hudson R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338.
27. Hudson RR, Kreitman M, Aguadé M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
28. Hudson RR, Slatkin M, Maddison WP. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583-589.
29. Jeffreys H. 1961. The theory of probability, 3rd ed. Oxford: Oxford University Press.
30. Knowles LL, Futuyma DJ, Eanes WF, Rannala B. 1999. Insight into speciation from historical demography in the phytophagous beetle genus Orphraella. Evolution 53:1846-1856.
31. Kondo B, Peters JL, Rosensteel BB, Omland KE. 2008. Coalescent analyses of multiple loci support a new route to speciation in birds. Evolution 62:1182-1191.
32. Li JW, Yeung CKL, Tsai PW, et al. (11 co-authors). 2010. Rejecting strictly allopatric speciation on a continental island: prolonged post-divergence gene flow between Taiwan (Leucodioptron taewanus, Passeriformes Timaliidae) and Chinese (L. canorum canorum) hwameis. Mol Ecol. 19:494-507.
33. Losos JB, Glor RE. 2003. Phylogenetic comparative methods and the geography of speciation. Trends Ecol Evol. 18:220-227.
34. Lowry DB, Rockwood RC, Willis JH. 2008. Ecological reproductive isolation of coast and inland races of Mimulus guttatus. Evolution 62:2196-2214.
35. Machado CA, Kliman RM, Markert JA, Hey J. 2002. Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Mol Biol Evol. 19:472-488.
36. Maddison DR, Maddison PW. 2000. MacClade 4: analysis of phylogeny and character evolution. Sunderland (MA): Sinauer Associates.
37. ST comparisons. J Evol Biol. 20:1705-1719.
38. Mattern MY, McLennan DA. 2000. Phylogeny and speciation of felids. Cladistics 16:232-253.
39. Mayr E. 1942. Systematics and the origin of species. New York: Columbia University Press.
40. Mayr E. 1954 Changes in genetic environment and evolution. In: Evolution as a process. Huxley JS, Hardy AC, Ford EB, editors. London: Allen & Unwin. p. 156-180.
41. Mayr E. 1963. Animal species and evolution. Cambridge (MA): Harvard University Press.
42. Mayr E. 1970. Populations, species and evolution. Cambridge (MA): Harvard University Press.
43. Mayr E. 1976. Evolution and the diversity of life: selected essays. Cambridge (MA): Harvard University Press.
44. Mayr E. 1982. Speciation and macroevolution. Evolution 36:1119-1132.
45. McVean G, Awadalla P, Fearnhead P. 2002. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160:1231-1241.
46. Moya A, Galiana A, Ayala FJ. 1995. Founder-effect speciation theory: failure of experimental corroboration. Proc Natl Acad Sci. 92:3983-3986.
47. Nielsen R, Wakeley J. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885-896.
48. Niemiller ML, Fitzpatrick BM, Miller BT. 2008. Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: gyrinophilus) inferred from gene genealogies. Mol Ecol. 17:2258-2275.
49. Osada N, Wu C-I. 2005. Inferring the mode of speciation from genomic data. Genetics 169:259-264.
50. Paulay G. 2002. Diversification in the tropical Pacific: comparisons between marine and terrestrial systems and the importance of founder speciation. Integr Comp Biol. 42:922-934.
51. Pulido F. 2007. The genetics and evolution of avian migration. Bioscience 57:165-174.
52. Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW. 1999. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol Biol Evol. 16:1791-1798.
53. Provine W. 1989. Founder effects and genetic revolutions in microevolution and speciation. A historical perspective. In: Gidding LV, Kaneshiro KY, Anderson WW, editors. Genetics, speciation and the founder principle. New York: Oxford University Press. p. 43-76.
54. ST in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient. Mol Ecol. 16:891-905.
55. Raymond M, Rousset F. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered. 86:248-249.
56. Ross-Ibarra J, Wright S, Foxe J, Kawabe A, DeRose-Wilson L. 2008. Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS ONE. 3:e2411.
57. Rozas J, Sánchez-DelBarrio JC, Messegyer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
58. Rundle HD, Nosil P. 2005. Ecological speciation. Ecol Lett. 8:336-352.
59. Simmons MP, Ochoterena H. 2000. Gaps as characters in sequence-based phylogenetic analysis. Syst Biol. 49:369-381.
60. Stadler T, Arunyawat U, Stephan W. 2008. Population genetics of speciation in two closely related wild tomatoes. (Solanum Section Lycopersicon). Genetics 178:339-350.
61. Stephens M, Scheet P. 2005. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet. 76:449-462.
62. Stephens M, Smith N, Donnelly P. 2001. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 68:978-989.
63. Strasburg JL, Rieseberg LH. 2010. How robust are "Isolation with Migration" analyses to violation of the IM model? A simulation study. Mol. Biol. Evol. 27:297-310.
64. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
65. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics analysis (MEGA) software. version 430. Mol. Biol. Evol. 24:1596-1599.
66. Tavare S, Balding DJ, Griffiths RC, Donnelly P. 1997. Inferring coalescence times from DNA sequence data. Genetics 145:505-518.
67. Thornton K, Andolfatto P. 2006. Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172:1607-1619.
68. Turner TL, Hahn MW, Nuzhdin SV. 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biol. 3:e285.
69. Vincek V, O'Huigin C, Satta Y, Takahata N, Boag PT, Grant PR, Grant BR, Klein J. 1997. How large was the founding population of Darwin's finches? Proc R Soc B Biol Sci. 264:111-118.
70. Wakeley J, Hey J. 1997. Estimating ancestral population parameters. Genetics 145:847-855.
71. Walsh HE, Jones IL, Friesen VL. 2005. A test of founder effect speciation using multiple loci in the auklets (Aethia spp.). Genetics 171:1885-1894.
72. Weir JW, Schluter D. 2008. Calibrating the avian molecular clock. Mol Ecol. 17:2321-2328.
73. Welker JM. 2000. Isotopic (d18O) characteristics of weekly precipitation collected across the USA: an initial analysis with application to water source studies. Hydrol Process. 14:1449-1464.
74. Won Y-J, Hey J. 2005. Divergence population genetics of chimpanzees. Mol Biol Evol. 22:297-307.
75. Wright S. 1931. Evolution in Mendelian populations. Genetics 16:97-159.
76. Wu C-I. 2001. The genic view of the process of speciation. J Evol Biol. 14:851-865.
77. Yeung CK-L, Yao C-T, Hsu Y-C, Wang J-P, Li S- H. 2006. Assessment of the historical population size of an endangered bird, the black-faced spoonbill (Platalea minor) by analysis of mitochon-drial DNA diversity. Anim Conserv. 9:1-10.