Arabidopsis lyrata Genetics

Savolainen, Outi; Kuittinen, Helmi

doi:10.1007/978-1-4419-7118-0_12

Cited by 12 publications

(11 citation statements)

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“…Populationbased analysis with a few selected populations provided the first evidence for population genetic structure at varying geographic scales [34][35][36]. At a more local scale and focusing on different aspects of adaptation there are numerous contributions covering A. lyrata [37][38][39], and comprehensive reviews have recently been presented to summarize many more aspects [1,40]. There is very limited information regarding A. arenosa, one of the most diverse evolutionary lineages in Arabidopsis [22], with only one phylogeographic-systematic study at a broad geographic scale [19].…”

Section: Developing a Comprehensive Systematic Frameworkmentioning

confidence: 99%

Taming the wild: resolving the gene pools of non-model Arabidopsis lineages

et al. 2014

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BackgroundWild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses.ResultsBased on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins.ConclusionsOur study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0224-x) contains supplementary material, which is available to authorized users.

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Section: Developing a Comprehensive Systematic Frameworkmentioning

confidence: 99%

Taming the wild: resolving the gene pools of non-model Arabidopsis lineages

et al. 2014

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“…Indeed, the recent colonization history of A. lyrata especially in northern Europe has likely been associated with strong population bottlenecks or effective population size reduction (Mattila, Tyrmi, Pyhäjärvi, & Savolainen, 2017;Pyhäjärvi, Aalto, & Savolainen, 2012;Ross-Ibarra et al, 2008;Savolainen & Kuittinen, 2011), which is in contrast to the large and relatively stable population of C. grandiflora (Douglas et al, 2015;Slotte, Foxe, Hazzouri, & Wright, 2010;Slotte et al, 2013;St. We chose these species because they have similar mating systems (both are self-incompatible outcrossers) and genome structure, and because previous research suggests considerable differences in the demographic histories of some populations.…”

Section: Introductionmentioning

confidence: 99%

“…We chose these species because they have similar mating systems (both are self-incompatible outcrossers) and genome structure, and because previous research suggests considerable differences in the demographic histories of some populations. Indeed, the recent colonization history of A. lyrata especially in northern Europe has likely been associated with strong population bottlenecks or effective population size reduction (Mattila, Tyrmi, Pyhäjärvi, & Savolainen, 2017;Pyhäjärvi, Aalto, & Savolainen, 2012;Ross-Ibarra et al, 2008;Savolainen & Kuittinen, 2011), which is in contrast to the large and relatively stable population of C. grandiflora (Douglas et al, 2015;Slotte, Foxe, Hazzouri, & Wright, 2010;Slotte et al, 2013;St. Onge, Källman, Slotte, Lascoux, & Palmé, 2011).…”

Section: Introductionmentioning

confidence: 99%

Impact of demography on linked selection in two outcrossing Brassicaceae species

Mattila

Laenen

Horváth

et al. 2019

Ecology and Evolution

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Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.

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“…A. lyrata is becoming a model organism for studies of ecological genetics, partly because of comparisons to its close relative Arabidopsis thaliana (Koch et al 2000; Mitchell‐Olds 2001; Kuittinen et al 2004; Clauss and Koch 2006; Koch and Matschinger 2007). Genetic differentiation of A. lyrata populations has been extensively studied (e.g., Jonsell et al 1995; Clauss and Mitchell‐Olds 2006; Muller et al 2008; Ross‐Ibarra et al 2008; reviewed by Savolainen and Kuittinen 2010). Phenotypic differentiation in many potentially adaptive traits such as flowering time and trichome variation have been documented (Riihimäki and Savolainen 2004; Riihimäki et al 2005; Kivimäki et al 2007).…”

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confidence: 99%