Historical divergence and gene flow: Coalescent analyses of mitochondrial, autosomal and sex-linked loci in passerina buntings

Evolution

Volumn 64, Issue 6, 2010, Pages 1762-1772

  Carling, Matthew D ^a,b,c   Lovette, Irby J ^b,c   Brumfield, Robb T ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

^b Fuller Evolutionary Biology Program   (United States)

^c Cornell University ^*  (United States)

Author keywords

Divergence population genetics; Indigo bunting; Isolation with migration; Lazuli Bunting

Indexed keywords

ALLOPATRY; DIVERGENCE; FITNESS; GENE FLOW; GENETIC ANALYSIS; GENETIC MARKER; HYBRID; MITOCHONDRIAL DNA; PARAMETERIZATION; PASSERINE; REPRODUCTIVE ISOLATION;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; GENE FLOW; GENE LOCUS; GENETICS; MITOCHONDRIAL GENE; SONGBIRD; SPECIES DIFFERENTIATION;

ANIMALS; GENE FLOW; GENES, MITOCHONDRIAL; GENETIC LOCI; GENETIC SPECIATION; MODELS, GENETIC; SONGBIRDS;

AVES; CARDINALIDAE; EMBERIZA; PASSERINA AMOENA; PASSERINA CYANEA;

EID: 77953908260     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2010.00954.x     Document Type: Article

References (55)

1. Abrams M. Fire and the development of oak forests. Bioscience 1992, 42:346-353.
2. Avise J C, Walker D, Johns G C. Speciation durations and Pleistocene effects on vertebrate phylogeography. Proc. R. Soc. Lond. B 1998, 265:1707-1712.
3. Axelsson E, Smith N G C, Sundstrom H, Berlin S, Ellegren H. Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and turkey. Mol. Biol. Evol. 2004, 21:1538-1547.
4. Baker M C, Boylan J T. Singing behavior, mating associations and reproductive success in a population of hybridizing Lazuli and Indigo buntings. Condor 1999, 101:493-504.
5. Becquet C, Przeworski M. Learning about modes of speciation by computation approaches. Evolution 2009, 63:2547-2562.
6. Borge T, Webster M T, Andersson G, Saetre G P. Contrasting patterns of polymorphism and divergence on the Z chromosome and autosomes in two Ficedula flycatchers. Genetics 2005, 171:1861-1873.
7. Brumfield R T, Liu L, Lum D E, Edwards S V. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data. Syst. Biol. 2008, 57:719. 731
8. Carling M D, Brumfield R T. Haldane's rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal and sex-linked loci across the Passerina bunting hybrid zone. Evolution 2008a, 62:2600-2615.
9. Carling M D, Brumfield R T. Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings. Genetics 2008b, 178:363-377.
10. Carling M D, Brumfield R T. Speciation in Passerina buntings: introgression patterns of sex-linked loci identify a candidate gene region for reproductive isolation. Mol. Ecol. 2009, 18:834-847.
11. Charlesworth B, Coyne J A, Barton N. The relative rates of evolution of sex chromosomes and autosomes. Am. Nat. 1987, 130:113-146.
12. Coyne J A, Orr H A. Two rules of speciation. Speciation and its consequences 1989, 180-207. Otte D, Endler J A. Pp., , eds., Sinauer Associates, Inc., Sunderland, MA
13. Coyne J A, Orr H A. Speciation 2004, Sinauer Associates, Inc., Sunderland, MA
14. Edwards S V, Beerli P. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 2000, 54:1839-1854.
15. Ellegren H. Molecular evolutionary genomics of birds. Cytogenet. Genome Res. 2007, 117:120-130.
16. Emlen S T, Rising J D, Thompson W L. Behavioral and morphological study of sympatry in Indigo and Lazuli buntings of the Great Plains. Wilson Bull. 1975, 87:145-179.
17. Excoffier L, Laval G, Schneider S. Arlequin ver 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online 2005, 1:47-50.
18. Geraldes A, Basset P, Gibson B, Smith K L, Harr B, Yu H T, Bulatova N, Ziv Y, Nachman M W. Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Mol. Ecol. 2008, 17:5349-5363.
19. Graur D, Li W H. Fundamentals of molecular evolution 2000, Sinauer Associations, Inc., Sunderland, MA
20. Greene E, Muehter V R, Davison W. Lazuli Bunting. The Birds of North America Online. 1996, http://bna.bird.cornell.edu, (A. Poole, ed.) Ithaca: Cornell Lab of Ornithology; Retrieved from The Birds of North America Online database
21. Hagen R H, Scriber M. Sex-linked diapause, color, and allozyme loci in Papilo glaucus: linkage analysis and significance in a hybrid zone. J. Hered. 1989, 80:179-185.
22. Haldane J B S. Sex ratio and unisexual sterility in animal hybrids. J. Genet. 1922, 12:101-109.
23. Harrigan R J, Mazza M E, Sorenson M D. Computation vs. cloning: evaluation of two methods for haplotype determination. Mol. Ecol. Res. 2008, 8:1239-1248.
24. Hey J. Recent advances in assessing gene flow between diverging populations and species. Curr. Opin. Genet. Dev. 2006, 16:592-596.
25. Hey J, Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 2004, 167:747-760.
26. Hey J, Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 2007, 104:2785-2790.
27. Johnson N K, Cicero C. New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds. Evolution 2004, 58:1122-1130.
28. Kane N C, King M G, Barker M S, Raduski A, Karrenberg S, Yatabe Y, Knapp S J, Reiseberg L H. Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent Helianthus species. Evolution 2009, 63:2061-2075.
29. Klicka J, Zink R M. The importance of recent ice ages in speciation: a failed paradigm. Science 1997, 277:1666-1669.
30. Klicka J, Fry A J, Zink R M, Thompson C W. A cytochrome-b perspective on Passerina bunting relationships. Auk 2001, 118:611-623.
31. Kroodsma R L. Hybridization in buntings (Passerina) in North-Dakota and eastern Montana. Auk 1975, 92:66-80.
32. Lee J Y, Edwards S V. Divergence across Australia's Carpentarian barrier: statisitical phylogeography of the Red-Backed Fairy Wren (Malurus melanocephalus). Evolution 2008, 62:3117-3134.
33. Lovette I J. Glacial cycles and the tempo of avian speciation. Trends Ecol. Evol. 2005, 20:57-59.
34. Nadachowska K, Babik W. Divergence in the face of gene flow: the case of two newts (Amphibia: Salamandridae). Mol. Biol. Evol. 2009, 26:829-841.
35. NatureServe Explorer: an Online Encyclopedia of Life, Version 6.1. 2006, http://www.natureserve.org/explorer, NatureServe
36. Nei M. Molecular evolutionary genetics 1987, Columbia Univ. Press, New York City
37. Nei M, Li W H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 1979, 76:5269-5273.
38. Nielsen R, Wakeley J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 2001, 158:885-896.
39. Niemiller M L, Fitzpatrick B M, Miller B T. Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies. Mol. Ecol. 2008, 17:2258-2275.
40. Nosil P. Speciation with gene flow could be common. Mol. Ecol. 2008, 17:2103-2106.
41. Payne R B. Indigo Bunting. 2006, http://bna.birds.cornell.edu, (A. Poole, ed.) Ithaca: Cornell Lab of Ornithology; Retrieved from The Birds of North America Online database
42. Ridgely R S, Allnutt T F, Brooks T, McNicol D K, Mehlman D W, Young B E, Zook J R. Digital distribution maps of the birds of the Western hemisphere, version 1.0 2003, NatureServe, Arlington, VA
43. Ross-Ibarro J, Tenaillon M, Gaut B S. Historical divergence and gene flow in the genus Zea. Genetics 2009, 181:1399-1413.
44. Rozas J, Sanchez-DelBarrio J C, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497.
45. Saetre G P, Borge T, Lindroos K, Haavie J, Sheldon B C, Primmer C, Syvanen A C. Sex chromosome evolution and speciation in Ficedula flycatchers. Proc. R. Soc. Lond. B 2003, 270:53-59.
46. Sibley C G, Short L L J. Hybridization in the buntings (Passerina) of the Great Plains. Auk 1959, 76:443-463.
47. Stephens M, Donnelly P. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 2003, 73:1162-1169.
48. Stephens M, Smith N, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 2001, 68:978-989.
49. Strasburg J L, Rieseberg L H. Molecular demographic history of the annual sunflowers Helianthus annus and H. petiolarus-large effective population sizes and rates of long-term gene flow. Evolution 2008, 62:1936-1950.
50. Strasburg J L, Rieseberg L H. How robust are " Isolation with Migration" analyses to violations of the IM model? A simulation study. Mol. Biol. Evol. 2010, 27:297-310.
51. Tajima F. Evolutionary relationships of DNA sequences in finite populations. Genetics 1983, 105:437-460.
52. Tucker P K, Sage R D, Warner J, Wilson A C, Eicher E M. Abrupt cline for sex-chromosomes in a hybrid zone between two species of mice. Evolution 1992, 46:1146-1163.
53. Weir J T, Schluter D. Calibrating the avian molecular clock. Mol. Ecol. 2008, 17:2321-2328.
54. Won Y J, Hey J. Divergence population genetics of chimpanzees. Mol. Biol. Evol. 2005, 22:297-307.
55. Zink R M, Slowinski J B. Evidence from molecular systematics for decreased avian diversification in the Pleistocene Epoch. Proc. Natl. Acad. Sci. USA 1995, 92:5832-5835.