Genetic signatures of intermediate divergence: Population history of Old and New World Holarctic ravens (Corvus corax)

Molecular Ecology

Volumn 15, Issue 3, 2006, Pages 795-808

  Omland, Kevin E ^a   Baker, Jason M ^b   Peters, Jeffrey L ^a,c  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^b INDIANA UNIVERSITY   (United States)

^c University of Alaska   (United States)

Author keywords

Coalescent methods; Corvus corax; Intermediate polyphyly; phylogeography; reciprocal monophyly; speciation

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; COMPARATIVE STUDY; CROW; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; REGULATOR GENE;

ANIMALS; CROWS; DNA, MITOCHONDRIAL; GEOGRAPHY; HAPLOTYPES; LOCUS CONTROL REGION; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

CORVUS CORAX;

EID: 33644779643     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2005.02827.x     Document Type: Article

References (56)

1. Avise JC 2000 Phylogeography: The History and Formation of Species Harvard University Press Cambridge, Massachusetts
2. Avise JC 2004 Molecular Markers, Natural History and Evolution 2nd edn Sinauer Associates Sunderland, Massachusetts
3. Baker JM López-Medrano E Navarro-Sigüenza AG Rojas-Soto OR Omland KE 2003 Recent speciation in the Orchard Oriole group: divergence of Icterus spurius spurius and Icterus spurius fuertesi Auk 120 848 859
4. Baker JM Omland KE 2006 Canary Island ravens (Corvus corax tingitanus) have distinct mtDNA Ibis in press
5. Ballard JWO Kreitman M 1995 Is mitochondrial DNA a strictly neutral marker? Trends in Ecology & Evolution 10 485 488
6. Bandelt H Forster P Rohl A 1999 Median joining networks for inferring intraspecific phylogenies Molecular Biology and Evolution 16 37 48
7. Bremer K 1992 Ancestral areas: a cladistic reinterpretation of the center of origin concept Systematic Biology 44 255 259
8. Castelloe J Templeton AR 1994 Root probabilities for intraspecific gene trees under neutral coalescent theory Molecular Phylogenetics and Evolution 3 102 113
9. Davis JI 1996 Phylogenetics, molecular variation and species concepts Bioscience 46 502 511
10. Del Hoyo J Elliott A Sargatal J 2004 Handbook of Birds of the World Lynx Editions Barcelona, Spain
11. Donoghue MD 1985 A critique of the biological species concept and recommendations for a phylogenetic alternative Bryologist 88 172 181
12. Drovetski S Zink R Rohwer S et al. 2004 Complex biogeographic history of a Holarctic passerine Proceedings of the Royal Society of LondonSeries B, Biological Sciences 271 545 551
13. Encalada SE Lahanas PN Bjorndal KA et al. 1996 Phylogeography and population structure of the Atlantic and Mediterranean green turtle Chelonia mydas: a mitochondrial DNA control region sequence assessment Molecular Ecology 5 473 484
14. Excoffier L Smouse PE Quattro JM 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data Genetics 131 479 491
15. Feldman CR Omland KE 2005 Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, CO1, and intron 7 of the β-fibrinogen gene in avian molecular systematics Zoologica Scripta 34 145 156
16. Fleischer RC McIntosh CE Tarr CL 1998 Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates Molecular Ecology 7 533 545
17. 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
18. Hare M 2001 Prospects for nuclear gene phylogeography Trends in Ecology & Evolution 16 700 706
19. Hare MP Cipriano F Palumbi SR 2002 Genetic evidence on the demography of speciation in allopatric dolphin species Evolution 56 804 816
20. Harrison RG 1991 Molecular changes at speciation Annual Review of Ecology and Systematics 22 281 308
21. Hasegawa M Kishino H Yano T 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA Journal of Molecular Evolution 22 160 174
22. Hebert PD Stoeckle MY Zemlak TS Francis CM 2004 Identification of birds through DNA barcodes Public Library of Science Biology 2 e312
23. Hennig W 1966 Phylogenetic Systematics University of Illinois Press Urbana, Illinois
24. Hey J 2005 On the number of New World founders: a population genetic portrait of the peopling of the Americas Public Library of Science Biology 3 e193
25. Hey J Nielsen R 2004 Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis Genetics 167 747 760
26. Hudson RR 1990 Gene genealogies and the coalescent process Oxford Surveys in Evolutionary Biology 7 1 44
27. Hudson RR Turelli M 2003 Stochasticity overrules the 'three-times rule': genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA Evolution 57 182 190
28. Knowles LL 2004 The burgeoning field of statistical phylogeography Journal of Evolutionary Biology 17 1 10
29. Lambert DM Ritchie PA Millar CD et al. 2002 Rates of evolution in ancient DNA from Adélie penguins Science 295 2270 2273
30. Lovette IJ 2004 Mitochondrial dating and mixed support for the '2% rule' in birds Auk 121 1 6
31. McCracken KG Johnson WP Sheldon FH 2001 Molecular population genetics, phylogeography, and conservation biology of the mottled duck (Anas fulvigula) Conservation Genetics 2 87 102
32. Moritz C 1994 Applications of mitochondrial DNA analysis in conservation: a critical review Molecular Ecology 3 401 411
33. Neigel JE Avise JC 1986 Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation In Evolutionary Processes and Theory (eds Nevo E Karlin S pp 515 534 Academic Press New York
34. Omland KE Tarr CL Boarman WI Marzluff JM Fleischer RC 2000 Cryptic genetic variation and paraphyly in ravens Proceedings of the Royal Society of LondonSeries B, Biological Sciences 267 2475 2482
35. Peters JL Gretes W Omland KE 2005 Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method Molecular Ecology 14 3407 3418
36. Posada D Crandall KA 1998 modeltest: testing the model of DNA substitution Bioinformatics 14 817 818
37. 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
38. Rand DM 2001 The units of selection on mitochondrial DNA Annual Review of Ecology and Systematics 32 415 448
39. Rieseberg LH Burke JM 2001 The biological reality of species: gene flow, selection, and collective evolution Taxon 50 47 67
40. Ronquist F 1997 Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography Systematic Biology 46 195 203
41. Rosenberg NA Nordborg M 2002 Genealogical trees, coalescent theory and the analysis of genetic polymorphisms Nature Reviews Genetics 3 380 390
42. Schneider S Keuffer J-M Roessli D Excoffier L 2000 arlequin: A software package for population genetics Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva Geneva, Switzerland.
43. Shields GF Wilson AC 1989 Calibration of mitochondrial DNA evolution in geese Journal of Molecular Evolution 24 212 217
44. Shimodaira H Hasegawa M 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference Molecular Biology and Evolution 16 1114 1116
45. Simpson GG 1944 Tempo and Mode in Evolution Columbia University Press New York
46. Swofford DL 2002 paup *: Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.0 Sinauer Associates Sunderland, Massachusetts
47. Templeton AR 1998 Nested clade analysis of phylogeographic data: testing hypotheses about gene flow and population history Molecular Ecology 7 381 397
48. Vaurie C 1959 Birds of the Palearctic Fauna Vol. 1 Witherby London
49. Wenink GW Baker AJ Rosner H Tilanus MGJ 1996 Global mitochondrial DNA phylogeography of Holarctic breeding Dunlins (Calidris alpha) Evolution 50 318 330
50. Wiens JJ 2004 What is speciation and how should we study it? American Naturalist 163 914 923
51. Wiens JJ Servedio MR 2000 Species delimitation in systematics: inferring diagnostic differences between species Proceedings of the Royal Society of LondonSeries B, Biological Sciences 267 631 636
52. Wiley EO 1981 Phylogenetics: the Theory and Practice of Phylogenetic Systematics John Wiley & Sons New York
53. Zink RM 2004 The role of subspecies in obscuring avian biological diversity and misleading conservation policy Proceedings of the Royal Society of LondonSeries B, Biological Sciences 271 561 564
54. Zink RM Blackwell-Rago RC 2000 Species limits and recent population history in the curve-billed thrasher Condor 102 881 886
55. Zink RM McKitrick MC 1995 The debate over species concepts and its implications for ornithology Auk 112 701 719
56. Zink RM Rohwer S Andreev AV Dittmann DL 1995 Trans-Beringia comparisons of mitochondrial DNA differentiation in birds Condor 97 639 649