Gene flow and species delimitation

Trends in Ecology and Evolution

Volumn 24, Issue 7, 2009, Pages 386-393

  Petit, Rémy J ^a,b   Excoffier, Laurent ^c  

^a UMR 1202 BIOGECO   (France)

^b UNIVERSITÉ DE BORDEAUX   (France)

^c UNIVERSITY OF BERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

GENE FLOW; GENOME; HYPOTHESIS TESTING; INTROGRESSION;

EID: 67649400420     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2009.02.011     Document Type: Article

References (91)

1. Sites J.W., and Marshall J.C. Delimiting species: a renaissance issue in systematic biology. Trends Ecol. Evol. 18 (2003) 462-470
2. de Queiroz K. Species concepts and species delimitation. Syst. Biol. 56 (2007) 879-886
3. Hajibabaei M., et al. DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 968-971
4. Hebert P.D.N., et al. Identification of birds through DNA barcodes. PLoS Biol. 2 (2004) e312
5. Tavares E., and Baker A. Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evol. Biol. 8 (2008) 81
6. Monaghan M.T., et al. DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360 (2005) 1925-1933
7. Rubinoff D., et al. A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification. J. Hered. 97 (2006) 581-594
8. Morjan C.L., and Rieseberg L.H. How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles. Mol. Ecol. 13 (2004) 1341-1356
9. Rieseberg L.H., and Burke J.M. The biological reality of species: gene flow, selection, and collective evolution. Taxon 50 (2001) 47-67
10. Greenwood P.J. Mating systems, philopatry and dispersal in birds and mammals. Anim. Behav. 28 (1980) 1140-1162
11. Vähä J.-P., and Primmer C.R. Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol. Ecol. 15 (2006) 63-72
12. Currat M., et al. The hidden side of invasions: massive introgression by local genes. Evolution Int. J. Org. Evolution 62 (2008) 1908-1920
13. Currat M., and Excoffier L. Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol. 2 (2004) e421
14. Lawson Handley L., and Perrin N. Advances in our understanding of mammalian sex-biased dispersal. Mol. Ecol. 16 (2007) 1559-1578
15. Clarke A.L., et al. Sex biases in avian dispersal: a reappraisal. Oikos 79 (1997) 429-438
16. Palumbi S., et al. Predicting nuclear gene coalescence from mitochondrial DNA: the three-times rule. Evolution Int. J. Org. Evolution 55 (2001) 859-868
17. Petit R.J., et al. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol. Ecol. 14 (2005) 689-701
18. Rieseberg L.H., et al. Molecular marker incongruence in plant hybrid zones and phylogenetic trees. Acta Bot. Neerl. 45 (1996) 243-262
19. Dumolin-Lapègue S., et al. Are chloroplast and mitochondrial DNA variation species independent in oaks?. Evolution Int. J. Org. Evolution 53 (1999) 1406-1413
20. McKinnon G.E., et al. Chloroplast sharing in the Tasmanian eucalypts. Evolution Int. J. Org. Evolution 55 (2001) 703-711
21. Wolf P.G., and Sipes S.D. Species-independent, geographical structuring of chloroplast DNA haplotypes in a montane herb Ipomopsis (Polemoniaceae). Mol. Ecol. 6 (1997) 283-291
22. Petit R.J., and Vendramin G.G. Plant phylogeography based on organelle genes: an introduction. In: Weiss S., and Ferrand N. (Eds). Phylogeography of the Southern European Refugia (2002), Springer 23-97
23. Du F., et al. More introgression with less gene flow: chloroplast versus mitochondrial DNA in the Picea asperata complex in China, and comparison with other conifers. Mol. Ecol. 18 (2009) 1396-1407
24. Haldane J. Sex ratio and unisexual sterility in hybrid animals. J. Genet. 12 (1922) 101-109
25. Cathey J.C., et al. Introgressive hybridization and nonconcordant evolutionary history of maternal and paternal lineages in North American deer. Evolution Int. J. Org. Evolution 52 (1998) 1224-1229
26. Dod B., et al. Counterselection on sex-chromosomes in the Mus musculus European hybrid zone. J. Evol. Biol. 6 (1993) 529-546
27. Funk D.J., and Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34 (2003) 397-423
28. Hoelzer G.A. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees revisited. Evolution Int. J. Org. Evolution 51 (1997) 622-626
29. Wright S. Isolation by distance. Genetics 28 (1943) 114-138
30. Buggs R.J.A. Empirical study of hybrid zone movement. Heredity 99 (2007) 301-312
31. Bonhomme M., et al. Assessing natural introgression in two biomedical model species, the Rhesus macaque (Macaca mulatta) and the long-tailed macaque (Macaca fascicularis). J. Hered. 100 (2008) 158-169
32. Hamada Y., et al. Morphological and body color variation in Thai Macaca fascicularis fascicularis north and south of the Isthmus of Kra. Int. J. Primatol. 29 (2008) 1271-1294
33. Tosi A., et al. Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys. Evolution Int. J. Org. Evolution 57 (2003) 1419-1435
34. Mossman C., and Waser P. Genetic detection of sex-biased dispersal. Mol. Ecol. 8 (1999) 1063-1067
35. Meier R., et al. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 55 (2006) 715-728
36. Trewick S. DNA barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). Cladistics 24 (2008) 240-254
37. Little D., and Stevenson D. A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 23 (2007) 1-21
38. Berthier P., et al. Recurrent replacement of mtDNA and cryptic hybridization between two sibling bat species Myotis myotis and Myotis blythii. Proc. R. Soc. Lond. B Biol. Sci. 273 (2006) 3101-3109
39. Duminil J., et al. Blind population genetics survey of tropical rainforest trees. Mol. Ecol. 15 (2006) 3505-3513
40. Rieseberg L.H., et al. Integration of populations and differentiation of species. New Phytol. 161 (2004) 59-69
41. Lexer C., et al. Shared alleles in sympatric oaks: recurrent gene flow is a more parsimonious explanation than ancestral polymorphism. Mol. Ecol. 15 (2006) 2007-2012
42. Beurton P. How is a species kept together?. Biol. Philos. 10 (1995) 181-196
43. Rubinoff D. Utility of mitochondrial DNA barcodes in species conservation. Conserv. Biol. 20 (2006) 1026-1033
44. Rieseberg L.H., et al. The nature of plant species. Nature 440 (2006) 524-527
45. Fitzpatrick B.M., et al. Distinctiveness in the face of gene flow: hybridization between specialist and generalist gartersnakes. Mol. Ecol. 17 (2008) 4107-4117
46. Strasburg J., and Rieseberg L. Molecular demographic history of the annual sunflowers Helianthus annuus and H. petiolaris-large effective population sizes and rates of long-term gene flow. Evolution Int. J. Org. Evolution 62 (2008) 1936-1950
47. Martínez-Cruz B., and Godoy J.A. Genetic evidence for a recent divergence and subsequent gene flow between Spanish and Eastern imperial eagles. BMC Evol. Biol. 7 (2007) 170
48. Helbig A.J., et al. Genetic differentiation and hybridization between greater and lesser spotted eagles (Accipitriformes: Aquila clanga. A. pomarina). J. Ornithol. 146 (2005) 226-234
49. Sætre G.-P., et al. Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers. Mol. Ecol. 10 (2001) 737-749
50. Secondi J., et al. Spreading introgression in the wake of a moving contact zone. Mol. Ecol. 15 (2006) 2463-2475
51. Crochet P.A., et al. Genetic differentiation at nuclear and mitochondrial loci among large white-headed gulls: sex-biased interspecific gene flow?. Evolution Int. J. Org. Evolution 57 (2003) 2865-2878
52. Brumfield R.T., et al. Evolutionary implications of divergent clines in an avian (Manacus: Aves) hybrid zone. Evolution Int. J. Org. Evolution 55 (2001) 2070-2087
53. Carling M.D., and 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 Int. J. Org. Evolution 62 (2008) 2600-2615
54. Helbig A.J., et al. Male-biased gene flow across an avian hybrid zone: evidence from mitochondrial and microsatellite DNA. J. Evol. Biol. 14 (2001) 277-287
55. Bensch S., et al. Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers. Mol. Ecol. 15 (2006) 161-171
56. Vallender R., et al. Complex hybridization dynamics between golden-winged and blue-winged warblers (Vermivora chrysoptera and Vermivora pinus) revealed by AFLP, microsatellite, intron and mtDNA markers. Mol. Ecol. 16 (2007) 2017-2029
57. Won Y.J., and Hey J. Divergence population genetics of chimpanzees. Mol. Biol. Evol. 22 (2005) 297-307
58. Bull V., et al. Polyphyly and gene flow between non-sibling Heliconius species. BMC Biol. 4 (2006) 11
59. Morgan-Richards M., and Wallis G.P. A comparison of five hybrid zones of the weta Hemideina thoracica (Orthoptera: Anostostomatidae): degree of cytogenetic differentiation fails to predict zone width. Evolution Int. J. Org. Evolution 57 (2003) 849-861
60. Mullen S.P., et al. Hybrid zone origins, species boundaries, and the evolution of wing-pattern diversity in a polytypic species complex of North American admiral butterflies (Nymphalidae: Limenitis). Evolution Int. J. Org. Evolution 62 (2008) 1400-1417
61. Abe T.A., et al. Mitochondrial introgression is restricted relative to nuclear markers in a water strider (Hemiptera: Gerridae) hybrid zone. Can. J. Zool. 83 (2005) 432-444
62. Cianchi R., et al. Differential patterns of hybridization and introgression between the swallowtails Papilio machaon and P. hospiton from Sardinia and Corsica islands (Lepidoptera, Papilionidae). Mol. Ecol. 12 (2003) 1461-1471
63. Peters J.L., et al. Nuclear loci and coalescent methods support ancient hybridization as cause of mitochondrial paraphyly between gadwall and falcated duck (Anas spp.). Evolution Int. J. Org. Evolution 61 (2007) 1992-2006
64. Pidancier N., et al. Evolutionary history of the genus Capra (Mammalia, Artiodactyla): discordance between mitochondrial DNA and Y-chromosome phylogenies. Mol. Phylogenet. Evol. 40 (2006) 739-749
65. Iwasa M.A., and Suzuki H. Intra- and interspecific genetic complexities of two Eothenomys species in Honshu. Japan. Zoolog. Sci. 20 (2003) 1305-1313
66. Alves P.C., et al. Ancient introgression of Lepus timidus mtDNA into L. granatensis and L. europaeus in the Iberian Peninsula. Mol. Phylogenet. Evol. 27 (2003) 70-80
67. Roca A.L., et al. Cytonuclear genomic dissociation in African elephant species. Nat. Genet. 37 (2005) 96-100
68. Evans B.J., et al. Diversification of Sulawesi macaque monkeys: decoupled evolution of mitochondrial and autosomal DNA. Evolution Int. J. Org. Evolution 57 (2003) 1931-1946
69. Geraldes A., et al. Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula. Mol. Ecol. 17 (2008) 4489-4499
70. Balloux F., et al. Microsatellites can be misleading: an empirical and simulation study. Evolution Int. J. Org. Evolution 54 (2000) 1414-1422
71. Ermakov O.A., et al. A search for Y-chromosomal species-specific markers and their use for hybridization analysis in ground squirrels (Spermophilus: Rodentia, Sciuridae). Russ. J. Genet. 42 (2006) 429-438
72. Ermakov O.A., et al. A molecular genetic study of hybridization in four species of ground squirrels (Spermophilus: Rodentia, Sciuridae). Russ. J. Genet. 38 (2002) 796-809
73. Good J.M., et al. Ancient hybridization and mitochondrial capture between two species of chipmunks. Mol. Ecol. 17 (2008) 1313-1327
74. Jordal B.H., et al. Apparent 'sympatric' speciation in ecologically similar herbivorous beetles facilitated by multiple colonizations of an island. Mol. Ecol. 15 (2006) 2935-2947
75. Sota T. Radiation and reticulation: extensive introgressive hybridization in the carabid beetles Ohomopterus inferred from mitochondrial gene genealogy. Popul. Ecol. 44 (2002) 145-156
76. Narita S., et al. Genetic structure of sibling butterfly species affected by Wolbachia infection sweep: evolutionary and biogeographical implications. Mol. Ecol. 15 (2006) 1095-1108
77. Schmidt B.C., and Sperling F.A.H. Widespread decoupling of mtDNA variation and species integrity in Grammia tiger moths (Lepidoptera: Noctuidae). Syst. Entomol. 33 (2008) 613-634
78. Gompert Z., et al. Identifying units for conservation using molecular systematics: the cautionary tale of the Karner blue butterfly. Mol. Ecol. 15 (2006) 1759-1768
79. Hayashi F., et al. Disturbed population genetics: suspected introgressive hybridization between two Mnais damselfly species (Odonata). Zoolog. Sci. 22 (2005) 869-881
80. Linnen C.R., and Farrell B.D. Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies. Evolution Int. J. Org. Evolution 61 (2007) 1417-1438
81. Mayr E. Systematics and the Origin of Species (1942), Columbia University Press
82. Mayr E. Animal Species and Evolution (1963), Harvard University Press
83. Ehrlich P.R., and Raven P.H. Differentiation of populations. Science 165 (1969) 1228-1232
84. Levin D., and Kerster H. Gene flow in seed plants. Evol. Biol. 7 (1974) 138-220
85. Hoelzer, G.A. et al. (2008) Isolation-by-distance and outbreeding depression are sufficient to drive parapatric speciation in the absence of environmental influences. PLoS Comp. Biol. 4, e1000126
86. Mallet J. Species, concepts of. In: Levin S. (Ed). Encyclopedia of Biodiversity (2001), Academic Press 427-440
87. Barker M.J. The empirical inadequacy of species cohesion by gene flow. Philos. Sci. 74 (2007) 654-665
88. Stebbins G. Variation and Evolution in Plants (1950), Columbia University Press
89. Hewitt G. Postglacial distribution and species substructure: lessons from pollen, insects and hybrid zones. In: Lees D., and Edwards D. (Eds). Evolutionary Patterns and Processes (1993), Academic Press 97-123
90. Hubbs C.L. Hybridization between fish species in nature. Syst. Zool. 4 (1955) 1-20
91. Klopfstein S., et al. The fate of mutations surfing on the wave of a range expansion. Mol. Biol. Evol. 23 (2006) 482-490