Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions

Abstract

To examine the performance and information content of different marker systems, comparative assessment of population genetic diversity was undertaken in nine populations of Athyrium distentifolium using nine genomic and 10 expressed sequence tag (EST) microsatellite (SSR) loci, and 265 amplified fragment length polymorphism (AFLP) loci from two primer combinations. In range-wide comparisons (European vs. North American populations), the EST-SSR loci showed more reliable amplification and produced more easily scorable bands than genomic simple sequence repeats (SSRs). Genomic SSRs showed significantly higher levels of allelic diversity than EST-SSRs, but there was a significant correlation in the rank order of population diversities revealed by both marker types. When AFLPs, genomic SSRs, and EST-SSRs are considered, comparisons of different population diversity metrics/markers revealed a mixture of significant and nonsignificant rank-order correlations. However, no hard incongruence was detected (in no pairwise comparison of populations did different marker systems or metrics detect opposingly significant different amounts of variation). Comparable population pairwise estimates of F(ST) were obtained for all marker types, but whilst absolute values for genomic and EST-SSRs were very similar (F(ST) = 0.355 and 0.342, respectively), differentiation was consistently higher for AFLPs in pairwise and global comparisons (global AFLP F(ST) = 0.496). The two AFLP primer combinations outperformed 18 SSR loci in assignment tests and discriminatory power in phenetic cluster analyses. The results from marker comparisons on A. distentifolium are discussed in the context of the few other studies on natural plant populations comparing microsatellite and AFLP variability.

Genetic structuring in three closely related circumpolar plant species: AFLP versus microsatellite markers and high-arctic versus arctic–alpine distributions

“…So far, only a few, mostly regional studies have included direct comparison between AFLP and microsatellite variation. The results suggest that AFLPs may reveal more structure in large data sets than microsatellites (Gaudeul et al, 2004;Woodhead et al, 2005;S nsteb et al, 2007).…”

“…Thus, for large-scale intraspecific studies and for interspecific studies, AFLP may be more appropriate as molecular marker (cf. Mariette et al, 2001;Gaudeul et al, 2004;Woodhead et al, 2005;S nsteb et al, 2007).…”

Next-generation hybridization and introgression

“…This bridges the gap with the widely used candidate gene approach to functional genetics. Thirdly, the regions in which primers are designed are likely to be conserved between species, reducing the probability of null alleles, and making crossamplification and direct comparisons between species a viable option (Woodhead et al, 2005).…”

“…In addition to concerns about selection, we anticipate that EST markers are less likely to be polymorphic than anonymous markers owing to functional constraints in transcribed regions, and may contain less informative differences between the hybridizing taxa (Ellis and Burke, 2007). Woodhead et al (2005) compared genetic diversity in the fern Athyrium distentifolium using EST-SSRs, genomic SSRs and AFLPs, and all marker types showed similar rank orders of population diversity and comparable F ST values, suggesting polymorphism in EST-SSRs can often be considered effectively neutral. In a comparison of EST-SSRs and genomic SSRs in Castanea, Martin et al (2010) found no significant differences in the F ST values calculated with the two marker types, suggesting no deviation from selective neutrality.…”

A Core Set of Microsatellite Markers for Western Corn Rootworm (Coleoptera: Chrysomelidae) Population Genetics Studies

“…For example, a potentially large number of microsatellites could be developed inexpensively through mining D. v. virgifera expressed sequence tag (EST) databases (Kim et al 2008). Although EST-derived microsatellites loci are part of an expressed gene and thus may be subject to direct selection, background selection, or genetic hitchhiking (Li et al 2002), polymorphisms in EST-derived microsatellites often behave as effectively neutral markers and can provide valid information about the genetic structure of natural populations (Woodhead et al 2005, Kim et al 2008.…”