Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana - PubMed (original) (raw)

Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana

Kirsten Bomblies et al. PLoS Genet. 2010.

Abstract

As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local "outcrossing hotspots" appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Map of collection sites in Tübingen area.

Sub-region names are indicated and color-coded to match colors used in cluster diagrams in Figure 3 and Figure 5.

Figure 2

Figure 2. Diagram of haplotype block identity and recombination patterns in several rural stands.

The columns represent the five chromosomes of A. thaliana, and each line represents an individual plant. Haplotypes are color-coded to indicate regions of allele identity within populations. Yellow indicates regions where putative parents were identical and recombination breakpoints were ambiguous. Plants from Ergenzingen (Erg) are shown in the order in which they were found. For other populations, individuals are ordered by similarity. “*” in the right hand column indicates first-generation outcrossed progeny (pollination event in spring 2007). “+” in the right hand column indicates a later-generation outcrossed descendant or homozygous individual with a clearly recombinant genotype.

Figure 3

Figure 3. Non-parametric clustering of non-redundant Tübingen area multi-locus genotypes.

(A) Cladogram of 324 non-redundant genotypes from the Tübingen area using 436 SNP markers. Branch colors indicate sub-region of origin as indicated in Figure 1. Red dotted lines indicate cutoffs for K = 2 and K = 5 clusters. Colored circles designate individual clusters. (B) Maps showing distribution of K = 2 and K = 5 clusters. Circles are approximately proportional to population size and are color-coded as indicated by the colored circles on the cladogram in (A).

Figure 4

Figure 4. Box plots showing association of genetic diversity and effective outcrossing with site type.

(A) Population genetic diversity (H e) in rural versus urban stands. (B) Estimated outcrossing (calculated from F IS) in rural versus urban stands. P-values are from Mann-Whitney U-tests comparing rural versus urban sites.

Figure 5

Figure 5. Clustering of 2007 and 2008 genotypes.

Nonparametric clustering of 88 non-redundant (within stand and year) 2007 genotypes and 100 non-redundant 2008 genotypes using data from 133 SNP markers. Branches are color-coded by sub-region of origin as described for Figure 2. Samples in red are from 2008, samples in blue from 2007.

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