An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex

Molecular Ecology

Volumn 22, Issue 19, 2013, Pages 4943-4957

  McKay, Bailey D ^a   Mays Jr , Herman L ^b   Wu, Yuchun ^c   Li, Hui ^c   Yao, Cheng Te ^d   Nishiumi, Isao ^e   Zou, Fasheng ^c  

^a UNIVERSITY OF MINNESOTA   (United States)

^b Cincinnati Museum Center   (United States)

^c Guangdong Academy of Sciences   (China)

^d ENDEMIC SPECIES RESEARCH INSTITUTE   (Taiwan)

^e DEPARTMENT OF BOTANY   (Japan)

Author keywords

Bayesian Phylogenetics and Phylogeography; lineage delimitation; population aggregation analysis; Pycnonotus sinensis; Pycnonotus taivanus; species delimitation

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BAYESIAN PHYLOGENETICS AND PHYLOGEOGRAPHY; BIOLOGICAL MODEL; FEATHER; GENETICS; INTRON; LINEAGE DELIMITATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION AGGREGATION ANALYSIS; POPULATION GENETICS; PYCNONOTUS SINENSIS; PYCNONOTUS TAIVANUS; SONGBIRD; SPECIES DELIMITATION; SPECIES DIFFERENTIATION; TAIWAN;

BAYESIAN PHYLOGENETICS AND PHYLOGEOGRAPHY; LINEAGE DELIMITATION; POPULATION AGGREGATION ANALYSIS; PYCNONOTUS SINENSIS; PYCNONOTUS TAIVANUS; SPECIES DELIMITATION;

ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; FEATHERS; GENETIC SPECIATION; GENETICS, POPULATION; INTRONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PASSERIFORMES; PHYLOGENY; PHYLOGEOGRAPHY; TAIWAN;

EID: 84884838878     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12446     Document Type: Article

References (64)

1. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
2. Avise JC, Ball R, (1990) Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surveys in Evolutionary Biology, 7, 45-67.
3. Backström N, Fagerberg S, Ellegren H, (2008) Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome. Molecular Ecology, 17, 964-980.
4. Barrett CF, Freudenstein JV, (2011) An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Molecular Ecology, 20, 2771-2786.
5. Bauer AM, Parham JF, Brown RM, et al,. (2011) Availability of new Bayesian-delimited gecko names and the importance of character-based species descriptions. Proceedings of the Royal Society of London, Series B: Biological Sciences, 278, 490-492.
6. Birdlife International (2008) Pycnonotus taivanus. In: IUCN 2010. IUCN Red List of Threatened Species. Version 2010.4. [Internet]. Available from http://www.iucnredlist.org.
7. Brower AVZ, (1999) Delimitation of phylogenetic species with DNA sequences: a critique of Davis and Nixon's population aggregation analysis. Systematic Biology, 48, 199-213.
8. Bruen TC, Philippe H, Bryant D, (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics, 172, 2665-2681.
9. Camargo A, Morando M, Avila LJ, Sites JW Jr, (2012) Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution, 66, 2834-2849.
10. Clement M, Posada D, Crandall KA, (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
11. Cracraft J, (1983) Species concepts and speciation analysis. Current Ornithology, 1, 159-187.
12. Darriba D, Taboada GL, Doallo R, Posada D, (2012) JModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772.
13. Davis JI, Nixon KC, (1992) Populations, genetic variation, and the delimitation of phylogenetic species. Systematic Biology, 41, 421-435.
14. DeSalle R, Egan MG, Siddall M, (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360, 1905-1916.
15. Drovetski SV, Zink RM, Rohwer S, et al,. (2004) Complex biogeographic history of a Holarctic passerine. Proceedings of the Royal Society of London, Series B: Biological Sciences, 271, 545-551.
16. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
17. Drummond AJ, Ashton B, Buxton S, et al,. (2010) Geneious v5.1. Available from http://www.geneious.com.
18. Ence DD, Carstens BC, (2010) SpedeSTEM: a rapid and accurate method for species delimitation. Molecular Ecology Resources, 11, 473-480.
19. Fishpool L, Tobias J, (2005) Family Pycnonotidae (Bulbuls). In: Handbook of the Birds of the World (eds, del Hoyo J, Elliott A, Christie D,), pp. 124-250. Lynx Edicions, Barcelona, Spain.
20. Frost DR, Kluge AG, (1994) A consideration of epistemology in systematic biology, with special reference to species. Cladistics, 10, 259-294.
21. Fujita MK, Leaché AD, (2011) A coalescent perspective on delimiting and naming species: a reply to Bauer et al. Proceedings of the Royal Society of London, Series B: Biological Sciences, 278, 493-495.
22. Fujita MK, Leaché AD, Burbrink FT, McGuire JA, Moritz C, (2012) Coalescent-based species delimitation in integrative taxonomy. Trends in Ecology & Evolution, 27, 480-488.
23. Funk DJ, Omland KE, (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics, 34, 397-423.
24. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
25. Heled J, Drummond AJ, (2010) Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570-580.
26. Hey J, (2009) On the arbitrary identification of real species. In: Speciation and Patterns of Diversity (eds, Butlin RK, Bridle J, Schuluter D,), pp. 15-28. Cambridge University Press, Cambridge.
27. Hey J, Pinho C, (2012) Population genetics and objectivity in species diagnosis. Evolution, 66, 1413-1429.
28. Hsu MJ, Lin YS, (1993) Morphology, sexual dimorphism and hybridization in Styan's Bulbuls Pycnontus taivanus and Chinese Bulbuls P. sinensis formosae. Acta Zoologica Taiwanica, 4, 103-111.
29. Hudson RR, Kreitman M, Aguade M, (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153-159.
30. Huson DH, Bryant D, (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23, 254-267.
31. Irwin DE, (2002) Phylogeographic breaks without geographic barriers to gene flow. Evolution, 56, 2383-2394.
32. Knowles LL, Carstens BC, (2007) Delimiting species without monophyletic gene trees. Systematic Biology, 56, 887-895.
33. Leaché AD, Fujita MK, (2010) Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proceedings of the Royal Society of London, Series B: Biological Sciences, 277, 3071-3077.
34. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
35. Mayden RL, (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. In: Species: The Units of Biodiversity (eds, Claridge MF, Dawah HA, Wilson MR,), pp. 381-424. Chapman & Hall Ltd., London.
36. McKay BD, Zink RM, (2010) The causes of mitochondrial DNA gene tree paraphyly in birds. Molecular Phylogenetics and Evolution, 54, 647-650.
37. Nelson G, Platnick N, (1981) Systematics and Biogeography: Cladistics and Vicariance. Columbia University Press, New York.
38. Nixon KC, Wheeler QD, (1990) An amplification of the phylogenetic species concept. Cladistics, 6, 211-223.
39. Oliveros CH, Moyle RG, (2010) Origin and diversification of Philippine bulbuls. Molecular Phylogenetics and Evolution, 54, 822-832.
40. O'Meara BC, (2010) New heuristic methods for joint species delimitation and species tree inference. Systematic Biology, 59, 59-73.
41. Padial JM, Miralles A, De la Riva I, Vences M, (2010) The integrative future of taxonomy. Frontiers in Zoology, 7, 16.
42. Pons J, Barraclough TG, Gomez-Zurita J, et al,. (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55, 595-609.
43. Posada D, (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
44. Price T, (2008) Speciation in Birds. Roberts and Company, Greenwood Village, Colorado.
45. de Queiroz K, (1998) The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. In: Endless Forms: Species and Speciation (eds, Howard DJ, Berlocher SH,), pp. 57-75. Oxford University Press, New York.
46. de Queiroz K, (2007) Species concepts and species delimitation. Systematic Biology, 56, 879-886.
47. Rambaut A, Drummond AJ, (2007) Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer.
48. Rannala B, Yang Z, (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164, 1645-1656.
49. Reid NM, Carstens BC, (2012) Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology, 12, 196.
50. Schlick-Steiner BC, Steiner FM, Seifert B, Stauffer C, Christian E, Crozier RH, (2010) Integrative taxonomy: a multisource approach to exploring biodiversity. Annual Review of Entomology, 55, 421-438.
51. Sites JW Jr, Marshall JC, (2003) Delimiting species: a Renaissance issue in systematic biology. Trends in Ecology & Evolution, 18, 462-470.
52. Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP, (1999) Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution, 12, 105-114.
53. 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.
54. Swofford DL, (2003) PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
55. Uly JAC, Moyle RG, Filardi CE, Cheviron ZA, (2009) Difference in plumage color used in species recognition between incipient species is linked to a single amino acid substitution in the melanocortin-1 receptor. The American Naturalist, 174, 244-254.
56. Wiens JJ, (2007) Species delimitation: new approaches for discovering diversity. Systematic Biology, 56, 875-878.
57. Wiens JJ, Servedio MR, (2000) Species delimitation in systematics: inferring diagnostic differences between species. Proceedings of the Royal Society of London, Series B: Biological Sciences, 267, 631-636.
58. Will KW, Mishler BD, Wheeler QD, (2005) The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology, 54, 844-851.
59. Xing XY, Alström P, Yang XJ, Lei FM, (2013) Recent northward range expansion promotes song evolution in a passerine bird, the Light-vented Bulbul. Journal of Evolutionary Biology, 26, 867-877.
60. Yamasaki T, (2006) Taxonomic status of populations of the Light-vented Bulbul Pycnonotus sinensis (Gmelin, 1789) (Passeriformes: Pycnonotidae) in Taiwan and the southern Ryukyus. Zoological Studies, 45, 168-179.
61. Yang Z, Rannala B, (2010) Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America, 107, 9264-9269.
62. Zhang C, Zhang D-X, Zhu T, Ziheng Y, (2011) Evaluation of a Bayesian coalescent method of species delimitation. Systematic Biology, 60, 747-761.
63. Zink RM, (1996) Species concepts, speciation, and sexual selection. Journal of Avian Biology, 27, 1-6.
64. Zink RM, Barrowclough GF, (2008) Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17, 2107-2121.