Genetic response to climatic change: Insights from ancient DNA and phylochronology

PLoS Biology

Volumn 2, Issue 10, 2004, Pages

  Hadly, Elizabeth A ^a   Ramakrishnan, Uma ^a   Chan, Yvonne L ^a   Van Tuinen, Marcel ^a   O'Keefe, Kim ^a   Spaeth, Paula A ^a   Conroy, Chris J ^b  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLIMATE; DATA ANALYSIS; ECOLOGY; GENE FLOW; GENETIC ANALYSIS; GENETIC MODEL; GENETIC VARIABILITY; HOLOCENE; LIFE HISTORY; MAMMAL; NONHUMAN; PHYLOGEOGRAPHY; POPULATION RESEARCH; SPECIES IDENTIFICATION; ANIMAL; ARVICOLINAE; BIOLOGICAL MODEL; CHEMISTRY; ENVIRONMENT; EVOLUTION; FOSSIL; GENETICS; GEOGRAPHY; GREENHOUSE EFFECT; HAPLOTYPE; MOLECULAR GENETICS; PHYLOGENY; POPULATION DENSITY; POPULATION GENETICS; TIME;

MAMMALIA; MICROTUS; MICROTUS MONTANUS; THOMOMYS TALPOIDES;

DNA;

ANIMALS; ARVICOLINAE; CLIMATE; DNA; ECOLOGY; ENVIRONMENT; EVOLUTION; FOSSILS; GENETICS, POPULATION; GEOGRAPHY; GREENHOUSE EFFECT; HAPLOTYPES; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; POPULATION DENSITY; TIME FACTORS; VARIATION (GENETICS);

EID: 8844251536     PISSN: 15449173     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pbio.0020290     Document Type: Article

References (46)

1. Andreassen HP, Ims RA (2001) Dispersal in patchy vole populations: Role of patch configuration, density dependence, and demography. Ecology 82: 2911-2926.
2. Avise JC (2000) Phylogeography: The history and formation of species. Cambridge: Harvard University Press. 447 p.
3. Bjørnstadt ON, Grenfell BT (2001) Noisy clockwork: Time series analysis of population fluctuation in animals. Science 293: 638-643.
4. Clement M, Posada D, Crandall K (2000) TCS: A computer program to estimate gene genealogies. Mol Ecol 9: 1657-1660.
5. Cody ML (1968) On methods of resource division in grassland bird communities. Am Nat 102: 107-147.
6. Conroy CJ, Cook JA (1999) MtDNA evidence for repeated pulses of speciation within arvicoline and murid rodents. J Mammal Evol 6: 221-245.
7. Conroy CJ, Cook JA (2000) Phylogeography of Microtus longicaudus a postglacial colonizer. Mol Ecol 9: 165-175.
8. Consuegra S, García de Leániz C, Serdio A, González Morales M, Straus LG (2002) Mitochondrial DNA variation in Pleistocene and modern Atlantic salmon from the Iberian glacial refugium. Mol Ecol 11: 2037-2048.
9. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307-1320.
10. Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG (2003) Measurably evolving populations. Trends Ecol Evol 18: 481-488.
11. Ewens WJ (1972) Sampling theory of selectively neutral alleles. Theor Popul Biol 3: 87-112.
12. Excoffier L, Novembre J, Schneider S (2000) SIMCOAL: A general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J Hered 91: 506-509.
13. Frankham R (1996) Relationship of genetic variation to population size in wildlife. Conserv Biol 10: 1500-1508.
14. Hadly EA (1996) Influence of late-Holocene climate on northern Rocky Mountain mammals. Quaternary Res 46: 298-310.
15. Hadly EA (1997) Evolutionary and ecological response of pocket gophers (Thomomys talpoides) to late-Holocene climatic change. Biol J Linn Soc Lond 60: 277-296.
16. Hadly EA (1999) Fidelity of terrestrial vertebrate fossils to a modern ecosystem. Palaeogeogr Palaeoclimatol Palaeoecol 149: 389-409.
17. Hadly EA, Maurer BA (2001) Spatial and temporal patterns of species diversity in montane mammal communities of western North America. Evol Ecol Res 3: 477-486.
18. Hadly EA, Kohn MH, Leonard JA, Wayne RK (1998) A genetic record of population isolation in pocket gophers during Holocene climatic change. Proc Natl Acad Sci U S A 95: 6893-6896.
19. Hadly EA, van Tuinen M, Chan Y, Heiman K (2003) Ancient DNA evidence of prolonged population persistence with negligible genetic diversity in an endemic tuco-tuco (Ctenomys sociabilis). J Mammal 84: 403-417.
20. Hofreiter M, Capelli MC, Krings M, Waits L, Conard N, et al. (2002) Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late Pleistocene cave bears. Mol Biol Evol 19: 1244-1250.
21. Irwin DM, Kocher TD, Wilson AC (1991) Evolution of the cytochrome-b gene of mammals. J Mol Evol 32: 128-144.
22. Jaarola M, Searle JB (2002) Phylogeography of field voles (Microtus agrestis) in Eurasia inferred from mitochondrial DNA sequences. Mol Ecol 11: 2613-2621.
23. Jaarola M, Tegelström H (1996) Mitochondrial DNA variation in the field vole (Microtus agrestis) Regional population structure and colonization history. Evolution 50: 2073-2085.
24. Jenkins HO (1948) A population study of the meadow mice (Microtus) in three Sierra Nevada meadows. Proc Calif Acad Sci 26: 43-67.
25. Kalinowski ST, Waples RS (2002) Relationship of effective to census size in fluctuating populations. Conserv Biol 16: 129-136.
26. Lambert DM, Ritchie PA, Millar CD, Holland B, Drummond AJ, et al. (2002) Rates of evolution in ancient DNA from Adélie penguins. Science 295: 2270-2273.
27. Leonard JA, Wayne RK, Cooper A (2000) Population genetics of ice age brown bears. Proc Natl Acad Sci U S A 97: 1651-1654.
28. Lessa EP, Cook JA, Patton JL (2003) Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proc Natl Acad Sci U S A 100: 10331-10334.
29. Lidicker WZ (1985) Dispersal. In: Tamarin RH, editor. Biology of the new world Microtus Special Publication no. 8 Lawrence, Kansas: American Society of Mammalogists. pp 420-454.
30. Moritz C, Dowling TE, Brown WM (1987) Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Annu Rev Ecol Syst 18: 269-292.
31. Orlando L, Bonjean D, Bocherens H, Thenot A, Argant A, et al. (2002) Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Mol Biol Evol 19: 1920-1933.
32. Paxinos EE, James HF, Olson SL, Ballou JD, Leonard JA, et al. (2002) Prehistoric decline of genetic diversity in the nene. Science 296: 1827-1827.
33. Pergams ORW, Barnes WM, Nyberg D (2003) Rapid change in mouse mitochondrial DNA. Nature 423: 397.
34. Plante Y, Boag PT, White BN (1989) Microgeographic variation in mitochondrial-DNA of meadow voles (Microtus pennsylvanicus) in relation to population density. Evolution 43: 1522-1537.
35. Porder SJ, Paytan A, Hadly EA (2003) Mapping the origin of faunal assemblages using strontium isotopes. Paleobiology 29: 196-203.
36. Rodrigo AG, Felsenstein J (1999) Coalescent approaches to HIV-1 population genetics. In: Crandall KA, editor. The evolution of HIV Baltimore: Johns Hopkins University Press. pp 233-272.
37. Root TL, Price JT, Hall KR, Schneider SH, Rosenzweig C, et al. (2003) Fingerprints of global warming on animals and plants. Nature 421: 57-60.
38. Schneider S, Roessli D, Excoffier L (2000) Arlequin: A software for population genetics data analysis. Version 2.000. Geneva: University of Geneva.
39. Slatkin M (1994) An exact test for neutrality based on the Ewens sampling distribution. Genet Res 64: 71-74.
40. Slatkin M (1996) A correction to the exact test based on the Ewens sampling distribution. Genet Res 68: 259-260.
41. Soon W, Baliunas S (2003) Proxy climatic and environmental changes of the past 1,000 years. Climate Res 23: 89-110.
42. Storz JF, Beaumont MA (2002) Testing for genetic evidence of population expansion and contraction: An empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution 56: 154-166.
43. Storz JF, Ramakrishnan U, Alberts SC (2002) Genetic effective size of a wild primate population: Influence of current and historical demography. Evolution 56: 817-829.
44. Sullivan TP, Sullivan DS, Hogue EJ (2003) Demography of montane voles in old field and orchard habitats in southern British Columbia. Northwest Sci 77: 228-236.
45. Verts BJ, Carraway LN (1999) Thomomys talpoides. Mammal Spec 618: 1-11.
46. Yang Z, Yoder AD (1999) Estimation of the transition/transversion rate bias and species sampling. J Mol Evol 48: 274-283.