Genomic diversity, population structure, and migration following rapid range expansion in the Balsam Poplar, Populus balsamifera

Molecular Ecology

Volumn 19, Issue 6, 2010, Pages 1212-1226

  Keller, Stephen R ^a   Olson, Matthew S ^b   Salim, Silim ^c   William, Schroeder A ^c   Peter, Tiffin ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^c AGRICULTURE AND AGRI FOOD CANADA   (Canada)

Author keywords

Migration; Phylogeography; Population structure; Populus; Range expansion

Indexed keywords

PLANT DNA;

ARTICLE; ASPEN; BAYES THEOREM; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOTYPE; GEOGRAPHY; MOLECULAR EVOLUTION; NORTH AMERICA; PLANT GENOME; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

BAYES THEOREM; CLUSTER ANALYSIS; DNA, PLANT; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GENOME, PLANT; GENOTYPE; GEOGRAPHY; MODELS, GENETIC; NORTH AMERICA; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULUS; SEQUENCE ANALYSIS, DNA;

POPULUS; POPULUS BALSAMIFERA;

EID: 77950226838     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04546.x     Document Type: Article

References (69)

1. Alsos IG, Eidesen PB, Ehrich D, et al. (2007) Frequent longdistance plant colonization in the changing Arctic. Science, 316, 1606-1609.
2. Anderson LL, Hu FS, Nelson DM, Petit RJ, Paige KN (2006) Ice-age endurance: DNA evidence of a white spruce refugium in Alaska. Proceedings of the National Academy of Sciences, USA, 103, 12447-12450.
3. Arunyawat U, Stephan W, Stadler T (2007) Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes. Molecular Biology and Evolution, 24, 2310-2322.
4. Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian Computation in Population Genetics. Genetics, 162, 2025-2035.
5. Breen AL, Glenn E, Yeager A, Olson MS (2009) Nucleotide diversity among natural populations of a North American poplar (Populus balsamifera, Salicaceae). New Phytologist, 182, 763-773.
6. Burns RM, Honkala BH (1990) Silvios of North America: Volume 2. Hardwoods. United States Department of Agriculture (USDA), Forest Service, Washington, D.C.
7. Caicedo AL, Williamson SH, Hernandez RD, et al. (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. Plos Genetics, 3, 1745-1756.
8. Cavalli-Sforza LL, Menozzi P, Piazza A (1993) Demic expansions and human evolution. Science, 259, 639-646.
9. Coop G, Pickrell JK, Novembre J, et al. (2009) The role of geography in human adaptation. Plos Genetics, 5, e1000500.
10. Edmonds CA, Lillie AS, Cavalli-Sforza LL (2003) Mutations arising in the wave front of an expanding population. Proceedings of the National Academy of Sciences, USA, 101, 975-979.
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. Excoffier L, Ray N (2008) Surfing during population expansions promotes genetic revolutions and structuration. Trends in Ecology & Evolution, 23, 347-351.
13. Excoffier L, Foil M, Petit RJ (2009) Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and Systematics, 40, 481-501.
14. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1.
15. Falush D, Stephens P, Pritchard JK (2003) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
16. Francois O, Blum MGB, Jakobsson M, Rosenberg NA (2008) Demographic history of European populations of Arabidopsis thaliana. Plos Genetics, 4, e1000075, doi:1000010. 1001371/journal.pgen.1000075.
17. Gao H, Williamson S, Bustamante CD (2007) A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics, 176, 1635-1651.
18. Gilchrist EJ, Haughn GW, Ying CC, et al. (2006) Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Molecular Ecology, 15, 1367-1378.
19. Goudet J (1995) FSTAT (Version 1.2): A computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
20. Hein J, Schierup MH, Wiuf C (2005) Gene Genealogies, Variation, and Evolution. Oxford University Press, Oxford.
21. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
22. Hofer T, Ray N, Wegmann D, Excoffier L (2009) Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Annals of Human Genetics, 73, 95-108.
23. Hultén E (1937) Outline of the History of Arctic and Boreal Biota During the Quaternary Period; Their Evolution During and After the Glacial Period as Indicated by the Equiformal Progressive Areas of Present Plant Species. Bokförlags aktiebolaget Thule, Stockholm.
24. Ibrahim KM, Nichols RA, Hewitt GM (1996) Spatial patterns of genetic variation generated by different forms of dispersal during range expansion. Heredity, 77, 282-291.
25. Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilbrium within and among natural populations of European Aspen (Populus tremula L., Salicaceae). Genetics, 169, 945-953.
26. Ingvarsson PK (2008) Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics, 180, 329-340.
27. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801-1806.
28. Kalinowski ST (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes, 5, 187-189.
29. Keller SR, Sowell DR, Neiman M, Wolfe LM, Taylor DR (2009) Adaptation and colonization history affect the evolution of clines in two introduced species. New Phytologist, 183, 678-690.
30. Klopfstein S, Currat M, Excoffier L (2006) The fate of mutations surfing on the wave of a range expansion. Molecular Biology and Evolution, 23, 482-490.
31. Kuhner MK (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22, 768-770.
32. Kühner MK (2009) Coalescent genealogy samplers: windows into population history. Trends in Ecology & Evolution, 24, 86-93.
33. Li JZ, Absher DM, Tang H, et al. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science, 319, 1100-1104.
34. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
35. Manel S, Gaggiotti O, Waples RS (2005) Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology and Evolution, 20, 136-142.
36. Marth G, Schuler G, Yeh R, et al. (2003) Sequence variations in the public human genome data reflect a bottlenecked population history. Proceedings of the National Academy of Sciences, USA, 100, 376-381.
37. Moeller DA, Tenaillon MI, Tiffin P (2007) Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis). Genetics, 176, 1799-1809.
38. Neiman M, Olson M, Tiffin P (2009) Selective histories of protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates. New Phytologist, 183, 740-750.
39. Nielsen R (2005) Molecular signatures of natural selection. Annual Review of Genetics, 39, 197-218.
40. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG (2007) Recent and ongoing selection in the human genome. Nature Reviews Genetics, 8, 857-868.
41. Nielsen R, Hubisz MJ, Clark AG (2004) Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics, 168, 2373-2382.
42. Nordborg M, Hu TT, Ishino Y, et al. (2005) The Pattern of Polymorphism in Arabidopsis thaliana. PLoS Biology, 3, e196.
43. Olson MS, Robsertson AL, Takebayashi N, et al. (2010) Nucleotide diversity and linkage disequilibrium in Balsam Poplar (Populus balsamifera). New Phytologist, in press, doi: 10.1111/j.1469-8137.2009.03174.x.
44. Petit RJ, Aguinagalde I, de Beaulieu JL, et al. (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science, 300, 1563-1565.
45. Petit RJ, Bialozyt R, Garnier-Gere P, Hampe A (2004) Ecology and genetics of tree invasions: from recent introductions to Quaternary migrations. Forest Ecology and Management, 197, 117-137.
46. Price AL, Patterson NJ, Plenge RM, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics, 38, 904-909.
47. Pritchard JK, Stephens P, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
48. Provan J, Bennett KD (2008) Phylogeographic insights into cryptic glacial refugia. Trends in Ecology ¿V Evolution, 23, 564-571.
49. Ramachandran S, Deshpande O, Roseman CC, et al. (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences, USA, 102, 15942-15947.
50. Rogers AR (1995) Genetic-evidence for a Pleistocene population explosion. Evolution, 49, 608-615.
51. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138.
52. Rosenberg NA, Pritchard JK, Weber JL, et al. (2002) Genetic structure of human populations. Science, 298, 2381-2385.
53. Rosenblum EB, Novembre J (2007) Ascertainment bias in spatially structured populations: a case study in the eastern fence lizard. Journal of Heredity, 98, 331-336.
54. Ross-Ibarra J, Wright SI, Foxe JP, et al. (2008) Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS One, 3, 1-13.
55. Savolainen O, Pyhäjärvi T (2007) Genomic diversity in forest trees. Current Opinion in Plant Biology, 10, 162-167.
56. 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.
57. Spiegelhalter DJ, Best NG, Carlin BP, van der Linde A (2002) Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society, Series B, 64, 583-639.
58. Stephens M, Scheet P (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. American Journal of Human Genetics, 76, 449-462.
59. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989.
60. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology, 7, 453-464.
61. Tuskan GA, DiFazio S, Jansson S, et al. (2006) The genome of the black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313, 1596-1604.
62. Vasemagi A (2006) The adaptive hypothesis of clinal variation revisited: single-locus clines as a result of spatially restricted gene flow. Genetics, 173, 2411-2414.
63. Webb T, Bartlein PJ (1992) Global changes during the last 3 million years - climatic controls and biotic responses. Annual Review of Ecology and Systematics, 23, 141-173.
64. Whitfield CW, Behura SK, Berlocher SH, et al. (2006) Thrice out of Africa: Ancient and recent expansions of the honey bee, Apis mellifera. Science, 314, 642-645.
65. ST does not equal 1/(4Nm + 1). Heredity, 82, 117-125.
66. Widmer A, Lexer C (2001) Glacial refugia: sanctuaries for allelic richness, but not for gene diversity. Trends in Ecology & Evolution, 16, 267-269.
67. Williams JW, Shuman BN, Webb T, Bartlein PJ, Leduc PL (2004) Late-quaternary vegetation dynamics in North America: scaling from taxa to biomes. Ecological Monographs, 74, 309-334.
68. Wright SI, Bi IV, Schroeder SG, et al. (2005) The effects of artificial selection of the maize genome. Science, 308, 1310-1314.
69. Wright SI, Gaut BS (2005) Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution, 22, 506-519.