The 'New Wave' in plant demographic inference: More loci and more individuals

Molecular Ecology

Volumn 19, Issue 6, 2010, Pages 1075-1078

  Lascoux, Martin ^a,b   Petit, Remy J ^c,d  

^a UPPSALA UNIVERSITY   (Sweden)

^b MAX PLANCK INSTITUTE   (Germany)

^c UMR 1202 BIOGECO   (France)

^d UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

Forest tree; Instruct; Lamarc; Populus; Sampling strategy; SNP; Structure

Indexed keywords

PLANT DNA;

ARTICLE; ASPEN; BAYES THEOREM; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DNA SEQUENCE; GENE FLOW; GENE FREQUENCY; GENETIC VARIABILITY; GENETICS; NORTH AMERICA; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

BAYES THEOREM; CLUSTER ANALYSIS; DNA, PLANT; GENE FLOW; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; MODELS, GENETIC; NORTH AMERICA; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULUS; SEQUENCE ANALYSIS, DNA;

POPULUS;

EID: 77950223612     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04547.x     Document Type: Article

References (26)

1. Adams A, Hudson RR (2004) Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics, 168, 1699-1712.
2. Ahmed S, Compton SG, Butlin RK, Gilmartin PM (2009) Windborne insects mediate directional pollen transfer between desert fig trees 160 kilometers apart. Proceedings of the National Academy of Sciences, USA, 106, 20342-20346.
3. Alsos IG, Eidesen PB, Ehrich D, et al. (2007) Frequent long-distance plant colonization in the changing Arctic. Science, 316, 1606-1609.
4. Chen J, Källman T, Gyllenstrand N, Lascoux M (2009) New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict. Heredity, 104, 3-14.
5. Evano 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.
6. Excoffier L, Ray N (2008) Surfing during population expansions promotes genetic revolutions and strucuration. Trends in Ecology and Evolution, 23, 347-351.
7. Excoffier L, Foll M, Petit RJ (2009) Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and Systematics, 40, 481-501.
8. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
9. 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.
10. Guillot G, Leblois R, Coulon A, Frantz AC (2009) Statistical methods in spatial genetics. Molecular Ecology, 18, 4734-4756.
11. Heuertz M, De Paoli E, Källman T, et al. (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce (Picea abies (L.) Karst). Genetics, 174, 2095-2105.
12. Ingvarsson P (2008) Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics, 180, 329-340.
13. Keller SR, Olson MS, Silim S, Schroeder W, Tiffin P (2010) Genomic diversity, population structure, and migration following rapid range expansion in the Balsam Poplar, Populus balsamifera. Molecular Ecology, 19, 1212-1226.
14. Kuhner MK (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22, 768-770.
15. Lagercrantz U, Ryman N (1990) Genetic structure of Norway Spruce (Picea abies): concordance of morphological and allozymic variation. Evolution, 44, 38-53.
16. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, et al. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science, 319, 1100-1104.
17. Petit RJ, Hampe A (2006) Some evolutionary consequences of being a tree. Annual Review of Ecology, Evolution, and Systematics, 37, 187-214.
18. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
19. Pritchard J, Wen X, Falush D (2009). Documentation for structure software: Version 2.3. http://pritch.bsd.uchicago.edu/structure. html.
20. Pyhäjärvi T, García-Gil MR, Knürr T, Mikkonen M, Wachowiak W, Savolainen O (2007) Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics, 177, 1713-1724.
21. Ratmann O, Andrieu C, Wiuf C, Richardson S (2009) Model criticism based on likelihood-free inference, with an application to protein network evolution. Proceedings of the National Academy of Sciences, USA, 106, 10576-10578.
22. Setakis E, Stirnadel H, Balding DJ (2006) Logistic regression protects against population structure in genetic association studies. Genome Research, 16, 290-296.
23. Spiegelhalter DJ, Best NG, Carlin BP, Van der LindeA (2002) Bayesian measures of model complexity and fit (with Discussion). Journal of the Royal Statistical Society, Series B, 64, 583-616.
24. Wakeley J (2003) Inferences about the structure and history of populations: coalescents and intraspecific phylogeography. In: The Evolution of Population Biology (eds Singh Rama, Uyenoyama Marcy). pp. 193-215, Cambridge University Press, Cambridge.
25. Wakeley J (2008) Coalescent theory. An introduction. Roberts & Co, Publishers, Greenwood Village, CO.
26. Wheeler NC, Guries RP (1982) Population structure, genic diversity, and morphological variation in Pinus contorta Dougl. Canadian Journal of Forest Research, 12, 595-606.