Abstract
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.
Highlights
Demographic factors shape baseline genetic variability within and between populations and can obscure detection of molecular evolution signatures and identification of adaptive alleles [1,2]
Demographic factors include population structure, effective population size changes and gene flow between populations, all of which can dramatically impact the levels of genetic diversity across the entire genome [1,3]
The use of multiple unlinked loci is commonly employed in population genetic studies to capture the levels of genetic diversity which have been shaped by the demographic history of that population [4,5,6,7,8,9]
Summary
Demographic factors shape baseline genetic variability within and between populations and can obscure detection of molecular evolution signatures and identification of adaptive alleles [1,2]. The use of multiple unlinked loci is commonly employed in population genetic studies to capture the levels of genetic diversity which have been shaped by the demographic history of that population [4,5,6,7,8,9] This approach has been widely accepted, the extent to which demography can shape genetic variability at coding genes across the genome has not been well tested in naturally occurring populations, but see [6,8,10]. This is most likely due to the lack of natural populations in which demography can be separated from other processes, such as selection and adaptation as well as lack of extensive sampling focused on attributes specific to alternative demographic histories rather than tests for evidence of adaptive evolution in candidate genes
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