Signatures of demography and recombination at coding genes in naturally-distributed populations of Arabidopsis lyrata subsp. petraea

Demography impacts the observed standing level of genetic diversity present in populations. Distinguishing the relative impacts of demography from selection requires a baseline of expressed gene variation in naturally occurring populations. Six nuclear genes were sequenced to estimate the patterns a...

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Published in:PloS one 2013-03, Vol.8 (3), p.e58916-e58916
Main Authors: Vigueira, Cynthia C, Rauh, Brad, Mitchell-Olds, Thomas, Lawton-Rauh, Amy L
Format: Article
Language:English
Subjects:
Arabidopsis
Arabidopsis - genetics
Arabidopsis thaliana
Bayes Theorem
Bayesian analysis
Biochemistry
Biodiversity
Bioinformatics
Biology
Demographics
Demography
Deoxyribonucleic acid
Divergence
DNA
Ecology
Estimates
Europe
Evolution & development
Evolution, Molecular
Genes
Genes, Plant
Genetic diversity
Genetic Variation
Genetics, Population
Genomes
Geography
Glaciation
Glaciology
Haplotypes
Integrated software
Microsatellites
Molecular biology
Mutation
Pleistocene
Population biology
Population bottleneck
Population Density
Population genetics
Population number
Populations
Quantitative Trait Loci
Recombination
Recombination, Genetic
Refugia
Signatures
Studies
Transposons
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description Demography impacts the observed standing level of genetic diversity present in populations. Distinguishing the relative impacts of demography from selection requires a baseline of expressed gene variation in naturally occurring populations. Six nuclear genes were sequenced to estimate the patterns and levels of genetic diversity in natural Arabidopsis lyrata subsp. petraea populations that differ in demographic histories since the Pleistocene. As expected, northern European populations have genetic signatures of a strong population bottleneck likely due to glaciation during the Pleistocene. Levels of diversity in the northern populations are about half of that in central European populations. Bayesian estimates of historical population size changes indicate that central European populations also have signatures of population size change since the last glacial maxima, suggesting that these populations are not as stable as previously thought. Time since divergence amongst northern European populations is higher than amongst central European populations, suggesting that the northern European populations were established before the Pleistocene and survived glaciation in small separated refugia. Estimates of demography based on expressed genes are complementary to estimates based on microsatellites and transposable elements, elucidating temporal shifts in population dynamics and confirming the importance of marker selection for tests of demography.
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Distinguishing the relative impacts of demography from selection requires a baseline of expressed gene variation in naturally occurring populations. Six nuclear genes were sequenced to estimate the patterns and levels of genetic diversity in natural Arabidopsis lyrata subsp. petraea populations that differ in demographic histories since the Pleistocene. As expected, northern European populations have genetic signatures of a strong population bottleneck likely due to glaciation during the Pleistocene. Levels of diversity in the northern populations are about half of that in central European populations. Bayesian estimates of historical population size changes indicate that central European populations also have signatures of population size change since the last glacial maxima, suggesting that these populations are not as stable as previously thought. Time since divergence amongst northern European populations is higher than amongst central European populations, suggesting that the northern European populations were established before the Pleistocene and survived glaciation in small separated refugia. 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subjects Arabidopsis
Arabidopsis - genetics
Arabidopsis thaliana
Bayes Theorem
Bayesian analysis
Biochemistry
Biodiversity
Bioinformatics
Biology
Demographics
Demography
Deoxyribonucleic acid
Divergence
DNA
Ecology
Estimates
Europe
Evolution & development
Evolution, Molecular
Genes
Genes, Plant
Genetic diversity
Genetic Variation
Genetics, Population
Genomes
Geography
Glaciation
Glaciology
Haplotypes
Integrated software
Microsatellites
Molecular biology
Mutation
Pleistocene
Population biology
Population bottleneck
Population Density
Population genetics
Population number
Populations
Quantitative Trait Loci
Recombination
Recombination, Genetic
Refugia
Signatures
Studies
Transposons
title Signatures of demography and recombination at coding genes in naturally-distributed populations of Arabidopsis lyrata subsp. petraea
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