A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae)

Molecular Phylogenetics and Evolution

Volumn 67, Issue 3, 2013, Pages 578-588

  Fuchs, Jérôme ^a,b,c   Pons, Jean Marc ^a   Liu, Liang ^d   Ericson, Per G P ^e   Couloux, Arnaud ^f   Pasquet, Eric ^a  

^a MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF GEORGIA   (United States)

^e SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^f CENTRE NATIONAL DE SÉQUENÇAGE   (France)

Author keywords

Campephilus; Gene tree; Hybridization; Introgression; Phylogeny; Species tree

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIRD; CLASSIFICATION; GENE LOCUS; GENETICS; HYBRIDIZATION; MOLECULAR EVOLUTION; MULTILOCUS SEQUENCE TYPING; PHYLOGENY;

ANIMALS; BIRDS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC LOCI; HYBRIDIZATION, GENETIC; MULTILOCUS SEQUENCE TYPING; PHYLOGENY;

AVES; BLYTHIPICUS; CAMPEPHILUS; CHRYSOCOLAPTES; MELANERPES; PICIDAE; REINWARDTIPICUS; SPHYRAPICUS;

EID: 84876159291     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.02.014     Document Type: Article

References (65)

1. Ballard J.W.O., Whitlock M.C. The incomplete natural history of mitochondria. Mol. Ecol. 2004, 2004(13):729-744.
2. Bensasson D., Zhang D., Hartl D.L., Hewitt G.M. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol. Evol. 2001, 2001(16):314-321.
3. Benz B.W., Robbins M.R., Peterson A.T. Evolutionary history of woodpeckers and allies (Aves: Picidae): placing key taxa on the phylogenetic tree. Mol. Phylogenet. Evol. 2006, 40:389-399.
4. Borge T., Lindroos K., Nadvornik P., Syvänen A.C., Sætre G.-P. Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post-zygotic barriers to gene exchange. J. Evol. Biol. 2005, 18:1416-1424.
5. Borge T., Webster M.T., Andersson G., Sætre G.-P. Contrasting patterns of polymorphism and divergence on the Z chromosome and autosomes in two Ficedula flycatcher species. Genetics 2005, 171:1861-1873.
6. Bossu CM, Near TJ: Gene trees reveal repeated instances of mitochondrial DNA introgression in orangethroat darters (Percidae: Etheostoma). Syst Biol 58: 114-129.
7. Boucher Y., Douady C.J., Papke R.T., Walsh D.A., Boudreau M.E., Nesbø C.L., Case R.J., Doolittle W.F. Lateral gene transfer and the origins of prokaryotic groups. Annu. Rev. Genet. 2003, 37:283-328.
8. Brown J.M., Lemmon A.R. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol. 2007, 56:643-665.
9. Brown J.W., Rest J.S., Garcia-Moreno J., Sorenson M.D., Mindell D.P. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biol. 2008, 6:6.
10. Coyne J.A., Charlesworth B., Orr H.A. Haldane's rule revisited. Evolution 1991, 45:1710-1714.
11. Currat M., Ruedi M., Petit R.J., Excoffier L. The hidden size of invasions: massive intogression by local genes. Evolution 2008, 62:1908-1920.
12. Degnan J.H., Rosenberg N.A. Discordance of species trees with their most likely gene trees. PLoS Genet. 2006, 2:e68.
13. Delport W., Poon A.F., Frost S.D.V., Kosakovsky Pond S.L. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 2010, 26:2455-2457.
14. Doolittle R.F. Fibrinogen and fibrin. Annu. Rev. Biochem. 1984, 53:195-229.
15. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:e88.
16. Drummond A.J., Nicholls G.K., Rodrigo A.G., Solomon W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 2002, 161:1307-1320.
17. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
18. Ericson P.G.P., Anderson C.L., Britton T., Elzanowski A., Johansson U.S., Källersjo M., Ohlson J.I., Parsons T.J., Zuccon D., Mayr G. Diversification of Neoaves: integration of molecular data and fossils. Biol. Lett. 2006, 2:543-547.
19. Fain M.G., Houde P. Parallel radiations in the primary clades of birds. Evolution 2004, 58:2558-2573.
20. Felsenstein J. Alternative methods of phylogenetic inference and their interrelationship. Syst. Zool. 1979, 28:49-62.
21. Felsenstein J, 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
22. Fleischer R.C., Kirchman J.J., Dumbacher J.P., Bevier L., Dove C., Rotzel N.C., Edwards S.V., Lammertink M., Miglia K.J., Moore W.S. Mid-pleistocene divergence of Cuban and North American ivory-billed woodpeckers. Biol. Lett. 2006, 2:466-469.
23. Fuchs J., Ohlson J.I., Ericson P.G.P., Pasquet E. Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae). J. Avian Biol. 2006, 37:487-496.
24. Fuchs J., Ohlson J.I., Ericson P.G.P., Pasquet E. Synchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data. Zool. Scr. 2007, 36:11-25.
25. Fuchs J., Pons J.-M., Ericson P.G.P., Bonillo C., Couloux A., Pasquet E. Molecular support for a rapid cladogenesis of the woodpecker clade Malarpicini, with further insights into the genus Picus (Piciformes: Picinae). Mol. Phylogenet. Evol. 2008, 48:34-46.
26. Funk D.J., Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Syst. 2002, 34:397-423.
27. Gibb G.C., Kardailsky O., Kimball R.T., Braun E.L., Penny D. Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol. Biol. Evol. 2007, 24:269-280.
28. Hackett S.J., Kimball R.T., Reddy S., Bowie R.C.K., Braun E.L., Braun M.J., Chojnowski J.L., Cox W.A., Han K.-L., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Sheldon F.H., Steadman D.W., Witt C.C., Yuri T. A phylogenomic study of birds reveals their evolutionary history. Science 2008, 320:1763-1768.
29. Ho S.Y.W. Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol. 2007, 38:409-414.
30. Holder M.T., Anderson J.A., Holloway A.K. Difficulties in detecting hybridization. Syst. Biol. 2001, 50:978-982.
31. Huelsenbeck JP, Ronquist F, 2003. MrBayes: A Program for the Bayesian Inference of Phylogeny. Version 3.1.2. http://mrbayes.scs.fsu.edu/index.php.
32. Jeffreys H. The Theory of Probability (3e) 1961, Oxford.
33. Jeffroy O., Brinkmann H., Delsuc F., Philippe H. Phylogenomics: the beginning of incongruence?. Trends Genet. 2006, 22:225-231.
34. Kosakovsky Pond S.L., Posada D., Gravenor M.B., Woelk C.H., Frost S.D.W. Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol. 2006, 23:1891-1901.
35. Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
36. Landan G., Graur D. Heads or tails? A simple reliability check for multiple sequence alignments. Mol. Biol. Evol. 2007, 24:1380-1383.
37. Liu L., Yu L. Phybase: an R package for species tree analysis. Bioinformatics 2010, 26:962-963.
38. Liu L., Yu L., Edwards S.V. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10:302.
39. Mallet J., Beltrán M., Neukirchen W., Linares M. Natural hybridization in heliconiine butterflies: the species boundary as a continuum. BMC Evol. Biol. 2007, 7:28.
40. Melo-Ferreira J., Boursot P., Suchentrunk F., Ferrand N., Alves P.C. Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia. Mol. Ecol. 2005, 14:2459-2464.
41. Milne I., Lindner D., Bayer M., Husmeier D., McGuire G., Marshall D.F., Wright F. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 2009, 25:126-127.
42. Mindell D.P., Sorenson M.D., Dimcheff D.E. An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Mol. Biol. Evol. 1998, 15:1568-1571.
43. Moran N.A., Jarvik T. Lateral transfer of genes from gungi underlies carotenoid production in aphids. Science 2010, 328:624-627.
44. Morgan-Richards M., Trewick S.A., Bartosch-Harlid A., Kardialsky O., Phillips M.J., McLenachan P.A., Penny D. Bird evolution: testing the metaves clade with six new mitochondrial genomes. BMC Evol. Biol. 2008, 8:20.
45. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 2004, 53:47-67.
46. Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5:568-583.
47. Petit R.J., Excoffier L. Gene flow and species delimitation. Trends Ecol. Evol. 2009, 24:386-393.
48. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
49. Price T.D., Bouvier M.M. The evolution of F1 postzygotic incompatibilities in birds. Evolution 2002, 56:2083-2089.
50. Prychitko T.M., Moore W.S. The utility of DNA sequences of an intron from the beta-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae). Mol. Phylogenet. Evol. 1997, 8(193):204.
51. Putman A.S., Scriber M., Andolfatto P. Discordant divergence time among Z-chromosome regions between two ecologically distinct swallowtail butterfly species. Evolution 2007, 61:912-927.
52. Rambaut, A., 2007. Se-Al v2.0a11. http://tree.bio.ed.ac.uk/software/seal.
53. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4 http://tree.bio.ed.ac.uk/software/tracer/.
54. Rokas A., Caroll S.B. Bushes in the tree of life. PLoS Biol. 2006, 4:e352.
55. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
56. Ropiquet A., Hassanin A. Hybrid origin of the Pliocene ancestor of wild goats. Mol. Phylogenet. Evol. 2006, 41:395-404.
57. Sæther S.A., Sætre G.P., Borge T., Wiley C., Svedin N., Andersson G., Veen T., Haavie J., Servedio M.R., BureŠ S., Král M., Hjernquist M.B., Gustafsson L., Träff J., Qvarnström A. Sex chromosome-linked species recognition and evolution of reproductive isolation in flycatchers. Science 2007, 318:95-97.
58. Short, L.L., 1982. Woodpeckers of the World. Delaware Museum of Natural History: Greenville, Delaware.
59. Spinks P.Q., Shaffer B.H. Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization. Syst. Biol. 2009, 58:1-20.
60. Stamatakis A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
61. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst. Biol. 2008, 75:758-771.
62. Swierczewski E.V., Raikow R.J. Hind limb morphology, phylogeny, and classification of the Piciformes. Auk 1981, 98:466-480.
63. Takahata N., Slatkin M. Mitochondrial gene flow. Proc. Natl. Acad. Sci. USA 1984, 81:1764-1767.
64. Webb D.M., Moore W.S. A phylogenetic analysis of woodpeckers and their allies using 12S, Cyt b, and COI nucleotide sequences (class Aves; order Piciformes). Mol. Phylogenet. Evol. 2005, 36:233-248.
65. Zhang A.B., Sota T. Nuclear gene sequences resolve species phylogeny and mitochondrial introgression in Leptocarabus beetles showing trans-species polymorphisms. Mol. Phylogenet. Evol. 2007, 45:534-546.