Comparative Historical Demography of Migratory and Nonmigratory Birds from the Caribbean Island of Hispaniola

Evolutionary Biology

Volumn 39, Issue 3, 2012, Pages 400-414

  Fahey, Anna L ^a   Ricklefs, Robert E ^b   Latta, Steven C ^c   DeWoody, J Andrew ^d  

^a PURDUE UNIVERSITY   (United States)

^b UNIVERSITY OF MISSOURI ST LOUIS   (United States)

^c National Aviary   (United States)

^d PURDUE UNIVERSITY   (United States)

Author keywords

Avian evolution; Fu and Li's D and F; Migration; Mismatch distribution; Mitochondrial DNA; Tajima's D

Indexed keywords

AVES;

EID: 84865569648     PISSN: 00713260     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11692-012-9164-9     Document Type: Article

References (58)

1. Amos, W., Flint, J., & Xu, X. (2008). Heterozygosity increases microsatellite mutation rate, linking it to demographic history. BMC Genetics, 9, 72.
2. Avise, J. C. (1992). Molecular population structure and the biogeographic history of a regional fauna: A case history with lessons for conservation biology. Oikos, 63, 62-76.
3. Avise, J. C. (2000). Phylogeography. Cambridge, MA: Harvard University Press.
4. Avise, J. C., & Walker, D. (1998). Pleistocene phylogeographic effects on avian populations and the speciation process. Proceedings of the Royal Society of London Series B-Biological Sciences, 265, 457-463.
5. Bellemain, E., Bermingham, E., & Ricklefs, R. E. (2008). The dynamic evolutionary history of the bananaquit (Coereba flaveola) in the Caribbean revealed by a multigene analysis. BMC Evolutionary Biology, 8, 240.
6. Bellemain, E., Gaggiotti, O., Fahey, A. & Ricklefs, R. E. (2012). Demographic history and genetic diversity in the West Indian Coereba flaveola populations. Genetica, in revision.
7. Bonatti, E., & Gartner, S., Jr. (1973). Caribbean climate during Pleistocene ice ages. Nature, 244, 563-565.
8. Bos, D. H., Gopurenko, D., Williams, R. N., & DeWoody, J. A. (2008). Inferring population history and demography using microsatellites, mitochondrial DNA, and major histocompatibility complex (MHC) genes. Evolution, 62, 1458-1468.
9. Clement, M., Posada, D., & Crandall, K. (2000). TCS: A computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1660.
10. Curtis, J. H., Brenner, M., & Hodell, D. A. (2001). Climate change in the circum-Caribbean (Late Pleistocene to Present) and implications for regional biogeography. In C. A. Woods & F. E. Sergile (Eds.), Biogeography of the West Indies. Patterns and Perspectives (pp. 35-54). Boca Raton, FL: CRC Press.
11. Eo, S. H., & DeWoody, J. A. (2010). Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles. Proceeding of the Royal Society B-Biological Sciences, 277, 3587-3592.
12. Eo, S. H., Doyle, J. M., & DeWoody, J. A. (2011). Genetic diversity in birds is associated with body mass and habitat type. Journal of Zoology (London), 283, 220-226.
13. Excoffier, L., Laval, L. G., & Schneider, S. (2005). Arlequin ver. 3. 0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1, 47-50.
14. Felsenstein, J. (1992). Estimating effective population size from samples of sequences: Inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genetical Research, 59, 139-147.
15. Fu, Y. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
16. Fu, Y., & Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics, 133, 693-709.
17. Harpending, H. C., Sherry, A. R., Rogers, A. R., & Stoneking, M. (1993). Genetic structure of ancient human populations. Current Anthropology, 34, 483-496.
18. Hawley, D. M., Briggs, J., Dhondt, A. A., & Lovette, I. J. (2008). Reconciling molecular signatures across markers: mitochondrial DNA confirms founder effect in invasive North American house finches (Carpodacus mexicanus). Conservation Genetics, 9, 637-643.
19. Hewitt, G. M. (1996). Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247-276.
20. Hewitt, G. M. (2000). The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
21. 14C yr record of climate and vegetation change from Haiti. Quaternary Research, 52, 159-170.
22. Hughes, A. L., & Hughes, M. K. (2007). Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Molecular Ecology, 16, 1369-1376.
23. Johnson, K. P., & Sorenson, M. D. (1998). Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND2) in the dabbling ducks (Tribe: Anatini). Molecular Phylogenetics and Evolution, 10, 82-94.
24. Lande, R., & Barrowclough, G. F. (1987). Effective population size, genetic variation, and their use in population management. In M. E. Soulé (Ed.), Viable populations for conservation. New York, NY: Cambridge University Press.
25. Latta, S. C., & Ricklefs, R. E. (2010). Prevalence patterns of avian Haemosporida on Hispaniola. Journal of Avian Biology, 41, 25-33.
26. Latta, S. C., Rimmer, C. C., & McFarland, K. P. (2003). Winter bird communities in four habitats along an elevational gradient on Hispaniola. Condor, 105, 179-197.
27. Latta, S., Rimmer, C., Keith, A., Wiley, J., Raffaele, H., McFarland, K., et al. (2006). Birds of the Dominican Republic and Haiti. Princeton, NJ: Princeton University Press.
28. Lerner, H. R. L., Johnson, J. A., Lindsay, A. R., Kiff, L. F., & Mindell, D. P. (2009). It's not too late for the harpy eagle (Harpia harpyja): high levels of genetic diversity and differentiation can fuel conservation programs. PLoS One, 4, 10.
29. Mayr, G., & Knopf, C. W. (2007). A tody (Alcediniformes: Todidae) from the early Oligocene of Germany. Auk, 124, 1294-1304.
30. McDonald, J. H., & Kreitman, M. (1991). Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 654-656.
31. McKay, B. D. (2009). Evolutionary history suggests rapid differentiation in the yellow-throated warbler Dendroica dominica. Journal of Avian Biology, 40, 181-190.
32. Merilä, J., Björklund, M., & Baker, A. J. (1997). Historical demography and present day population structure of the greenfinch, Carduelis chloris- an analysis of mtDNA control-region sequences. Evolution, 51, 946-956.
33. Mila, B., Girman, D. J., Kimura, M., & Smith, T. B. (2000). Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a North American songbird. Proceedings of the Royal Society of London Series B-Biological Sciences, 267, 1033-1040.
34. Mila, B., Smith, T. B., & Wayne, R. K. (2006). Postglacial population expansion drives the evolution of long-distance migration in a songbird. Evolution, 60, 2403-2409.
35. Mila, B., Smith, T. B., & Wayne, R. K. (2007a). Speciation and rapid phenotypic differentiation in the yellow-rumped warbler Dendroica coronata complex. Molecular Ecology, 16, 159-173.
36. Mila, B., McCormack, J. E., Castaneda, G., Wayne, R. K., & Smith, T. B. (2007b). Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco. Proceeding of the Royal Society B-Biological Sciences, 274, 2653-2660.
37. Norgate, M., Chamings, J., Pavlova, A., Bull, J. K., Murray, N. D., & Sunnucks, P. (2009). Mitochondrial DNA indicates late Pleistocene divergence of populations of Heteronympha merope, an emerging model in environmental change biology. PLoS One, 4, 11.
38. Overton, L. C., & Rhoads, D. D. (2004). Molecular phylogenetic relationships based on mitochondrial and nuclear gene sequences for the Todies (Todus, Todidae) of the Caribbean. Molecular Phylogenetics and Evolution, 32, 524-538.
39. Pielou, E. C. (1991). After the ice age. Chicago, IL: University of Chicago Press.
40. Qu, Y., Lei, F., Zhang, R., & Lu, X. (2010). Comparative phylogeography of five avian species: Implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau. Molecular Ecology, 19, 338-351.
41. Ramos-Onsins, S. E., & Rozas, J. (2002). Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092-2100.
42. Reding, D. M., Freed, L. A., Cann, R. L., & Fleischer, R. C. (2010). Spatial and temporal patterns of genetic diversity in an endangered Hawaiian honeycreeper, the Hawaii Akepa (Loxops coccineus coccineus). Conservation Genetics, 11, 225-240.
43. Ricklefs, R., & Bermingham, E. (2008a). The West Indies as a laboratory of biogeography and evolution. Philosophy Transactions of the Royal Society B-Biological Sciences, 363, 2393-2413.
44. Ricklefs, R., & Bermingham, E. (2008b). Likely human introduction of the red-legged thrush (Turdus plumbeus) to Dominica, West Indies. Auk, 125, 299-303.
45. Rogers, A. R., & Harpending, H. C. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569.
46. Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X., & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
47. Schneider, S., & Excoffier, L. (1999). Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics, 152, 1079-1089.
48. Slatkin, M., & Hudson, R. R. (1991). Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129, 555-562.
49. Sly, N. D., Townsend, A. K., Rimmer, C. C., Townsend, J. M., Latta, S., & Lovette, I. J. (2010). Phylogeography and conservation genetics of the Hispaniolan endemic Palm-Tanagers (Aves: Phaenicophilus). Conservation Genetics, 11, 2121-2129.
50. Sly, N. D., Townsend, A. K., Rimmer, C. C., Townsend, J. M., Latta, S. C. & Lovette, I. J. (2011). Ancient islands and modern invasions: Disparate phylogeographic histories among Hispaniola's endemic birds. Molecular Ecology, 20, 5012-5024.
51. Sorenson, M. D. (2003). Avian mtDNA primers. http://people. bu. edu/msoren/primers. html.
52. Sorenson, M. D., Ast, J. C., Dimcheff, D. E., Yuri, T., & Mindell, D. P. (1999). Primers for PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution, 12, 105-114.
53. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
54. Townsend, A. K., Rimmer, C. C., Latta, S. C., & Lovette, I. J. (2007). Ancient differentiation in the single-island avian radiation of endemic Hispaniolan Chat-Tanagers (Aves: Calyptophilus). Molecular Ecology, 16, 3634-3642.
55. Walker, D., & Avise, J. C. (1998). Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern United States. Annual Review of Ecology, Evolution, and Systematics, 29, 23-58.
56. Zimmerman, J. L. (1998). Migration of Birds. Circular 16. Fish and Wildlife Service, U. S. Department of the Interior.
57. Zink, R. M., & Barrowclough, G. F. (2008). Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17, 2107-2121.
58. Zink, R. M., Drovetski, S. V., & Rohwer, S. (2006). Selective neutrality of mitochondrial ND2 sequences, phylogeography and species limits in Sitta europaea. Molecular Phylogenetics and Evolution, 40, 679-686.