Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations

Abstract

Currently, there exists a limited knowledge on the extent of temporal variation in population genetic parameters of natural populations. Here, we study the extent of temporal variation in population genetics by genotyping 151 genome-wide SNP markers polymorphic in 466 individuals collected from nine populations of the annual plant Arabidopsis thaliana during 4 years. Populations are located along an altitudinal climatic gradient from Mediterranean to subalpine environments in NE Spain, which has been shown to influence key demographic attributes and life cycle adaptations. Genetically, A. thaliana populations were more variable across space than over time. Common multilocus genotypes were detected several years in the same population, whereas low-frequency multilocus genotypes appeared only 1 year. High-elevation populations were genetically poorer and more variable over time than low-elevation populations, which might be caused by a higher overall demographic instability at higher altitudes. Estimated effective population sizes were low but also showed a significant decreasing trend with increasing altitude, suggesting a deeper impact of genetic drift at high-elevation populations. In comparison with single-year samplings, repeated genotyping over time captured substantially higher amount of genetic variation contained in A. thaliana populations. Furthermore, repeated genotyping of populations provided novel information on the genetic properties of A. thaliana populations and allowed hypothesizing on their underlying mechanisms. Therefore, including temporal genotyping programmes into traditional population genetic studies can significantly increase our understanding of the dynamics of natural populations.

Natural Variation in Arabidopsis: From Molecular Genetics to Ecological Genomics

“…This is consistent with the view that Arabidopsis populations in the west are the oldest, with later expansion into the eastern end of its native distribution, along with recently colonized regions, such as the Alps, in the center of the range (Sharbel et al, 2000;Nordborg et al, 2005;Schmid et al, 2005;Ostrowski et al, 2006;Beck et al, 2008;Picó et al, 2008;Platt et al, 2010;Cao et al, 2011). In addition, there is also altitudinal stratification within regions, with populations from high altitude being overall less diverse than those from lower altitude (Montesinos et al, 2009;Lewandowska-Sabat et al, 2010;Gomaa et al, 2011). It has also been suggested that there is evidence for migration from east to west, accompanying the spread of agriculture (François et al, 2008); however, knowing that the Iberian Peninsula is the most diverse region, it is unclear what to make from this.…”

Association of Intron Loss with High Mutation Rate in Arabidopsis: Implications for Genome Size Evolution

“…Unfortunately, the difference in N e between A. thaliana and A. lyrata is not monotonic. Historically , A. thaliana had an N e about four times of A. lyrata ; however, its N e is now much smaller than that of A. lyrata (Lundemo et al 2009; Falahati-Anbaran et al 2011; Gomaa et al 2011). The differences in the rates of intron loss and gain between A. thaliana and A. lyrata are consistent with the difference in historical N e .…”

Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population

“…Studies that monitor genetic variability patterns over time are needed, but most monitoring efforts are restricted to a few years of sampling or single samples separated over relatively long periods of time (Nielsen et al, 1997;Heath et al, 2002;Hansen et al, 2002;Poulsen et al, 2006;Borrell et al, 2008;Hansen et al, 2009;Gomaa et al, 2011). Detailed temporal genetic studies that investigate the genetic composition over microevolutionary time scales-that is, from year to year, cohort to cohort and generation to generation-are accumulating, however (Palm et al, 2003;Dowling et al, 2005;Araki et al, 2007;Palstra et al, 2009;Osborne et al, 2010;Skrbinšek et al, 2012).…”