Nuclear and mitochondrial DNA reveal contrasting evolutionary processes in populations of deer mice (Peromyscus maniculatus)

Molecular Ecology

Volumn 18, Issue 24, 2009, Pages 5115-5125

  Yang, Dou Shuan ^a   Kenagy, G J ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Cytonuclear discordance; Environmental history; MtDNA; Peromyscus maniculatus; Phylogeography; Population genetics

Indexed keywords

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; DNA SEQUENCE; GENE FLOW; GENETIC DRIFT; GENETICS; HAPLOTYPE; MOLECULAR EVOLUTION; NORTH AMERICA; PEROMYSCUS; PHYLOGENY; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS;

ANIMALS; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC DRIFT; GENETICS, POPULATION; HAPLOTYPES; MICROSATELLITE REPEATS; NORTH AMERICA; PEROMYSCUS; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA;

PEROMYSCUS; PEROMYSCUS MANICULATUS;

EID: 71549132287     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04399.x     Document Type: Article

References (44)

1. Arbogast BS (1999) Mitochondrial DNA phylogeography of the New World flying squirrels (Glaucomys): implications for Pleistocene biogeography. Journal of Mammalogy, 80, 142 155.
2. Avise JC, Lansman RA, Shade RO (1979a) The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. I. Population structure and evolution in the genus Peromyscus. Genetics, 92, 279 295.
3. Avise JC, Smith MH, Selander RK (1979b) Biochemical polymorphism and systematics in the genus Peromyscus VII. Geographic differentiation in members of the Truei and Maniculatus species groups. Journal of Mammalogy, 60, 177 192.
4. Brunsfeld S, Sullivan J, Soltis DE, Soltis PS (2001) Comparative Phylogeography of Northwestern North America: a Synthesis. Blackwell Publishing, Willston, Vermont.
5. Carstens BC, Richards CL (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution, 61, 1439 1454.
6. Delcourt P, Delcourt HR (1993) Paleoclimates, paleovegetation and paleofloras during the late Quarternary. In : Flora of North America (ed. committee FoNAe pp. 71 94. Oxford University Press, New York.
7. Demboski JR, Cook JA (2001) Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North America. Molecular Ecology, 10, 1227 1240.
8. Di Candia MR, Routman EJ (2007) Cytonuclear discordance across a leopard frog contact zone. Molecular Phylogenetics and Evolution, 45, 564 575.
9. Dragoo JW, Lackey JA, Moore KE et al. (2006) Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses. Journal of General Virology, 87, 1997 2003.
10. Egger B, Koblmuller S, Sturmbauer C, Sefc K (2007) Nuclear and mitochondrial data reveal different evolutionary processes in the Lake Tanganyika cichlid genus Tropheus. BMC Evolutionary Biology, 7, 137.
11. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611 2620.
12. Frontier S (1976) Étude de la decroissance des valeurs propres dans une analyze en composantes principales: comparison avec le modèle de baton brisé. Journal of Experimental Marine Biology and Ecology, 25, 67 75.
13. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
14. Goios A, Pereira Ls, Bogue M, Macaulay V, Amorim AN (2007) MtDNA phylogeny and evolution of laboratory mouse strains. Genome Research, 17, 293 298.
15. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696 704.
16. Haine E, Martin J, Cook J (2006) Deep mtDNA divergences indicate cryptic species in a fig-pollinating wasp. BMC Evolutionary Biology, 6, 83.
17. Hall ER (1981) The Mammals of North America. John Wiley And Sons, New York.
18. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America, 101, 14812 14817.
19. Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnaean Society, 58, 247 276.
20. King JA (1968) Biology of Peromyscus (Rodentia), 1st edn. The American Society of Mammalogists, Stillwater, Oklahoma.
21. Kocher TD, Thomas WK, Meyer A et al. (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America, 86, 6196 6200.
22. Kocher TD, Conroy JA, McKaye KR, Stauffer JR (1993) Similar morphologies of Cichlid fish in Lakes Tanganyika and Malawi are due to convergence. Molecular Phylogenetics and Evolution, 2, 158 165.
23. Lanave C, Preparata G, Sacone C, Serio G (1984) A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution, 20, 86 93.
24. Lansman RA, Avise JC, Aquadro CF, Shapira JF, Daniel SW (1983) Extensive genetic variation in mitochondrial DNA'S among geographic populations of the deer mouse, Peromyscus maniculatus. Evolution, 37, 1 16.
25. Leaché AD, Cole CJ (2007) Hybridization between multiple fence lizard lineages in an ecotone: locally discordant variation in mitochondrial DNA, chromosomes, and morphology. Molecular Ecology, 16, 1035 1054.
26. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209 220.
27. Miller MP, Bellinger MR, Forsman ED, Haig SM (2006) Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudus) in the Pacific Northwestern United States. Molecular Ecology, 15, 145 159.
28. Mullen LM, Hirschmann RJ, Prince KL et al. (2006) Sixty polymorphic microsatellite markers for the oldfield mouse developed in Peromyscus polionotus and Peromyscus maniculatus. Molecular Ecology Notes, 6, 36 40.
29. Mullis K, Faloona F (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology, 155, 335 350.
30. Nylander J (2004) mrmodeltest 2.2. Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
31. Oksanen J, Kindt R, Legendre P et al. (2008) Vegan: Community Ecology Package. R package version 1.15-1.
32. Peakall R, Smouse PE (2006) genalex6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295.
33. Pielou E (1992) After the Ice Age: The Return of Life to Glaciated North America. University of Chicago Press, Chicago.
34. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959.
35. R Development Core Team (2008) r: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
36. Roca AL, Georgiadis N, O'Brien SJ (2005) Cytonuclear genomic dissociation in African elephant species. Nature genetics, 37, 96 100.
37. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552 569.
38. Ronquist F, Huelsenbeck JP (2003) mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574.
39. Smouse PE, Long JC, Sokal RR (1986) Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic Zoology, 35, 627 632.
40. Soltis DE, Gitzendanner MA, Strenge DD, Soltis PS (1997) Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Systematics and Evolution, 206, 353 373.
41. Swofford D (2002) paup*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
42. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585 595.
43. Wilcox TP, Hugg L, Zeh JA, Zeh DW (1997) Mitochondrial DNA sequencing reveals extreme genetic differentiation in a cryptic species complex of Neotropical pseudoscorpions. Molecular Phylogenetics and Evolution, 7, 208 216.
44. Zheng X, Arbogast BS, Kenagy GJ (2003) Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest. Molecular Ecology, 12, 711 724.