Evolution of Hypervariable Microsatellites in Apomictic Polyploid Lineages of Ranunculus carpaticola: Directional Bias at Dinucleotide Loci

Abstract

Microsatellites are widely used in genetic and evolutionary analyses, but their own evolution is far from simple. The mechanisms maintaining the mutational patterns of simple repeats and the typical stable allele-frequency distributions are still poorly understood. Asexual lineages may provide particularly informative models for the indirect study of microsatellite evolution, because their genomes act as complete linkage groups, with mutations being the only source of genetic variation. Here, we study the direction of accumulated dinucleotide microsatellite mutations in wild asexual lineages of hexaploid Ranunculus carpaticola. Whereas the overall number of contractions is not significantly different from that of expansions, the within-locus frequency of contractions, but not of expansions, significantly increases with allele length. Moreover, within-locus polymorphism is positively correlated with allele length, but this relationship is due solely to the influence of contraction mutations. Such asymmetries may explain length constraints generally observed with microsatellites and are consistent with stable, bell-shaped allelefrequency distributions. Although apomictic and allohexaploid, the R. carpaticola lineages show mutational patterns resembling the trends observed in a broad range of organisms, including sexuals and diploids, suggesting that, even if not of germline origin, the mutations in these apomicts may be the consequence of similar mechanisms.

Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10

“…The mutation rates were estimated to be more than three-fold higher in the longest compared with the smallest allele classes in the two swallow populations (Figure 3). Higher mutation rates for longer repeated regions have been reported in a number of previous studies [5,10,11,30,32,36,38,39,43-46]. The higher mutability in longer alleles can be explained by stabilization patterns concerning the mismatch-repair system, which may be less effective and as a result generate a relatively large probability for insertion of slippage events if the repeated region is sufficiently long, as suggested by Wierdl et al [32].…”

On the origin and evolution of apomixis in Boechera

“…Additionally, heterozygosity in apomictic lineages will increase over time as a function of the number of mutations accumulated post divergence (especially at SSR and other highly mutable loci) (Paun and Hörandl 2006); therefore, we expect generally elevated levels of heterozygosity in apomictic individuals relative to the ancestral, sexual lineages.…”

Eight microsatellite markers for the bulbous buttercup Ranunculus bulbosus (Ranunculaceae)

“…Out of seven R. nodifl orus L . markers ( Noel et al, 2005 ), three R. carpaticola Soó markers ( Paun and Hörandl, 2006 ), and 15 de novo designed primer pairs based on R. carpaticola microsatellite sequences released in GenBank ( Paun and Hörandl, 2006 ), no markers proved to reliably amplify in R. bulbosus. Species-specifi c nuclear simple sequence repeat (SSR) primers were subsequently isolated from genomic DNA of R. bulbosus using the two approaches described below.…”