Identifying shared genetic structure patterns among pacific northwest forest taxa: Insights from use of visualization tools and computer simulations

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Miller, Mark P ^a,b   Haig, Susan M ^b  

^a UTAH STATE UNIVERSITY   (United States)

^b FOREST AND RANGELAND ECOSYSTEM SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARBORIMUS LONGICAUDUS; ARTICLE; COMPUTER SIMULATION; CONTROLLED STUDY; GENE IDENTIFICATION; GENETIC CORRELATION; GENETIC DISTANCE; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HAPLOTYPE; INTERSPECIFIC COMPETITION; MOLECULAR PHYLOGENY; NONHUMAN; OWL; PHYLOGEOGRAPHY; PINUS MONTICOLA; RHYACOTRITON VARIEGATUS; SALAMANDER; SPECIES COMPARISON; SPECIES CONSERVATION; SPECIES DIFFERENCE; SPECIES DISTRIBUTION; SPECIES HABITAT; STRIX OCCIDENTALIS CAURINA; STRUCTURE ANALYSIS; UNITED STATES; VOLE; WHITE PINE; ANIMAL; BIODIVERSITY; TREE;

ARBORIMUS LONGICAUDUS; PINUS MONTICOLA; RHYACOTRITON VARIEGATUS; STRIX OCCIDENTALIS CAURINA;

ANIMALS; BIODIVERSITY; COMPUTER SIMULATION; NORTHWESTERN UNITED STATES; TREES;

EID: 78149419610     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013683     Document Type: Article

References (63)

1. Excoffier L, Heckel G (2006) computer programs for population genetics data analysis: a survival guide. Nat Rev Genet 7: 745-758.
2. Fu YX (1997) Statistical tests of neutrality against population growth, hitchhiking and background selection. Genetics 147: 915-925.
3. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
4. Tajima F (1989a) The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
5. Tajima F (1989b) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
6. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22: 1185-1192.
7. Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol 13: 853-864.
8. Ray N, Currat M, Excoffier L (2003) Intra-deme molecular diversity in spatially expanding populations. Mol Biol Evol 20: 76-86.
9. Schneider S, Excoffier L (1999) Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA. Genetics 152: 1079-1089.
10. Templeton AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol Ecol 7: 381-397.
11. Garrick RC, Dyer RJ, Beheregaray LB, Sunnucks P (2008) Babies and Bathwater: a comment on the premature obituary for nested clade phylogeo-graphic analysis. Mol Ecol 17: 1401-1403.
12. Knowles LL, Maddison WP (2002) Statistical phylogeography. Mol Ecol 11: 2623-2635.
13. Panchal M, Beaumont MA (2007) The automation and evaluation of nested clade phylogeographic analysis. Evolution 61: 1466-1480.
14. Petit RJ (2008a) The coup de grace for the nested clade phylogeographic analysis? Mol Ecol 17: 516-518.
15. Petit RJ (2008b) On the falsifiablilty of the nested clade phylogeographic analysis method. Mol Ecol 17: 1404.
16. Petit RJ, Grivet D (2002) Optimal randomization strategies when testing the existence of a phylogeographic structure. Genetics 161: 469-471.
17. Templeton AR (2002) ''Optimal'' randomization strategies when testing the existence of a phylogeographic structure: A reply to Petit and Grivet. Genetics 161: 473-475.
18. Templeton AR (2008) Nested clade analysis: an extensively validated method for strong phylogeographic inference. Mol Ecol 17: 1877-1880.
19. Fagundes NJR, Ray N, Beaumont M, Neuenschwander S, Salzano FM, et al. (2007) Statistical evaluation of alternate models of human evolution. Proc Natl Acad Sci USA 104: 17614-17619.
20. Lemey P, Rambaut A, Drummond AJ, Suchard MA (2009) Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol 5(9): e1000520. doi:10.1371/journal.pcbi.1000520.
21. Templeton AR (2009) Statistical hypothesis testing in intraspecific phylogeog-raphy: NCPA versus ABC. Mol Ecol 18: 319-331.
22. Nielsen R, Beaumont MA (2009) Statistical inferences in phylogeography. Mol Ecol 18: 1034-1047.
23. Miller MP (2005) Alleles In Space: Computer software for the joint analysis of interindividual spatial and genetic information. J Hered 96: 722-724.
24. Miller MP, Bellinger MR, Forsman ED, Haig SM (2006a) 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. Mol Ecol 15: 145-159.
25. Haig SM, Mullins TD, Forsman ED (2004) Subspecific relationships and genetic structure in the spotted owl. Conserv Genet 5: 683-705.
26. Funk WC, Forsman ED, Mullins TD, Haig SM (2008) Introgression and dispersal among spotted owl (Strix occidentalis) subspecies. Evol Appl 1: 161-171.
27. Steinhoff RJ, Joyce DG, Fins S (1983) Isozyme variation in Pinus monticola. Can J Forest Res 13: 1122-1132.
28. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
29. Miller MP, Haig SM, Wagner RS (2006b) Phylogeography and spatial genetic structure of the Southern torrent salamander: Implications for conservation and management. J Hered 97: 561-570.
30. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18: 189-197.
31. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219-1228.
32. Manni F, Gue ́rard E, Heyer E (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by ''Mon-monier's algorithm''. Hum Biol 76: 173-190.
33. Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43: 1349-1368.
34. Hartl DL, Clark AG (1989) Principles of Population Genetics. Sunderland: Sinauer Associates, Inc. 682 p.
35. Austerlitz F, Smouse PE (2001) Two-generation analysis of pollen flow across a landscape. II. Relation between Wft, pollen dispersal and interfemale distance. Genetics 157: 851-857.
36. Wright, S (1946) Isolation by distance under diverse systems of mating. Genetics 31: 39-59.
37. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
38. Sokal RR, Oden NL (1978) Spatial autocorrelation analysis in biology. 2. Some biological implications and four applications of evolutionary and ecological interest. Biol J Linn Soc 10: 229-249.
39. Chen C, Durand E, Forbes F, Francois O (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol Notes 7: 747-756.
40. Crida A, Manel S (2007) WOMBSOFT: an R package that implements the Wombling method to identify genetic boundary. Mol Ecol Notes 7: 588-591.
41. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11: 2571-2581.
42. Guillot G, Estoup A, Mortier F, Cosson JF (2005) A spatial statistical model for landscape genetics. Genetics 170: 1261-1280.
43. Manel S, Berthoud F, Bellemain E, Gaudeul M, Luikart G, et al. (2007) A new individual-based spatial approach for identifying genetic discontinuities in natural populations. Mol Ecol 16: 2031-2043.
44. Vandergast AG, Hathaway SA, Fisher RN, Boys J, Bohonak AJ (2008) Are hotspots of evolutionary potential adequately protected in southern California? Biol Conserv 141: 1648-1664.
45. Brunsfeld SJ, Sullivan J, Soltis DE, Soltis PS (2001) Comparative phylogeog-raphy of northwestern North America: a synthesis. In: Silvertown J, Antonovics J, eds. Integrating ecology and evolution in a spatial context. Oxford: Blackwell Science Ltd. pp 319-339.
46. Nielson M, Lohman K, Sullivan J (2001) Phylogeography of the tailed frog (Ascaphus truei): Implications for the biogeography of the Pacific Northwest. Evolution 55: 147-160.
47. Soltis DE, Gitzendanner MA, Strenge DD, Soltis PE (1997) Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Syst Evol 206: 353-373.
48. Wilke T, Duncan N (2004) Phylogeographical patterns in the American Pacific Northwest: lessons from the arionid slug Prophysaon coeruleum. Molecular Ecology 13: 2303-2315.
49. Irwin DE (2002) Phylogeographic breaks without geographic barriers to gene flow. Evolution 56: 2383-2394.
50. Excoffier L, Ray N (2008) Surfing during population expansion promotes genetic revolutions and structuration. Trends Ecol Evol 23: 347-351.
51. Burns KJ, Barhoum DN (2006) Population-level history of the wrentit (Chamaea fasciata): Implications for comparative phylogeogrphy in the California Floristic Province. Mol Phylogenet Evol 38: 117-129.
52. Johnson JA (2008) Recent range expansion and divergence among North American prairie grouse. J Hered 99: 165-173.
53. Míla B, McCormac JE, Castaneda G, Wayne RK, Smith TB (2007) Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco. P Roy Soc B-Biol Sci 274: 2653-2660.
54. Martin PR, McKay JK (2004) Latitudinal variation in genetic divergence of populations and the potential for future speciation. Evolution 58: 938-945.
55. Graham RT (2004) Western White Pine. In: Burns RM, Honkala BH, eds. Silvics of North America. Washington D.C. United States Department of Agriculture Handbook 654.: United States Department of Agriculture. pp 775-796.
56. Andersen BG, Borns HWJ (1994) The ice age world: an introduction to Quaternary history and research with emphasis on North America and Northern Europe during the last 2.5 million years. Copenhagen: Scandinavian University Press. 208 p.
57. Bonnicksen TM (2000) America's ancient forests: from the ice age to the age of discovery. New York: John Wiley & Sons, Inc. 608 p.
58. US Fish and Wildlife Service. (1990) Determination of threatened status for the northern spotted owl. Federal Register 55: 26114-26194.
59. USDA Forest Service and USDI Bureau of Land Management (2000) Final supplemental environmental impact statement for amendment to the survey and manage, protection buffer, and other mitigation measures, standards and guides. Vol. 1. Portland: USDA Forest Service and USDI Bureau of Land Management. 516 p.
60. U.S. Fish and Wildlife Service (2000) 12-month finding for a petition to list the southern torrent salamander in California as endangered or threatened. Federal Register 65: 35951.
61. Cushman SA, McKelvey KS, Hayden J, Schwartz MK (2006) Gene flow in complex landscapes: Testing multiple hypotheses with causal modeling. Am Nat 168: 486-499.
62. Balkenhol N, Gugerli F, Cushman SA, Waits LP, Coulon A, et al. (2007) Identifying future research needs in landscape genetics: where to from here? Landscape Ecol 24: 455-463.
63. Epperson BK, McRae BH, Scribner K, Cushman SA, Rosenburg MS, et al. (2010) Utility of computer simulations in landscape genetics. Molecular Ecology 19: 3549-3564.