Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers

Abstract

Genetic diversity and structure of 12 populations of Eryngium alpinum L. were investigated using 63 dominant amplified fragment length polymorphism (AFLP) and seven codominant microsatellite (48 alleles) markers. Within-population diversity estimates obtained with both markers were not correlated, but the microsatellite-based fixation index F is was correlated with both AFLP diversity indices (number of polymorphic bands and Nei's expected heterozygosity). Only AFLP diversity indices increased with the size of populations, although they did not significantly differ among them (Kruskall-Wallis test). The discrepancy between AFLPs and microsatellites may be explained by a better coverage of the genome with numerous AFLPs, the higher mutation rates of microsatellites or the absence of significant difference among withinpopulation diversity estimates. Genetic differentiation was higher with AFLPs (y ¼ 0.40) than with microsatellites (y ¼ 0.23), probably due to the higher polymorphism of microsatellites. Thus, we considered global qualitative patterns rather than absolute estimates to compare the performance of both types of markers. On a large geographic scale, the Mantel test and multivariate analysis showed that genetic patterns were more congruent with the spatial arrangement of populations when inferred from microsatellites than from AFLPs, suggesting higher homoplasy of AFLP markers. On a small spatial scale, AFLPs managed to discriminate individuals from neighboring populations whereas microsatellites did not (multivariate analysis), and the percentage of individuals correctly assigned to their population of origin was higher with AFLPs than with microsatellites. However, dominant AFLPs cannot be used to study heterozygosity-related topics. Thus, distinct molecular markers should be used depending on the biological question and the geographical scale investigated.

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).…”

“…Higher intrapopulation genetic diversity could be expected for microsatellites because of their higher mutation rate (Mariette et al, 2001;Gaudeul et al, 2004), but the different measures should be correlated. However, our sampling sizes were small, and selfing populations may show variable genetic diversity depending on the number of lineages sampled.…”

“…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).…”

Mesoamerican origin of the common bean ( Phaseolus vulgaris L.) is revealed by sequence data

“…Indeed, for molecular markers characterized by a higher mutation rate (SSRs compared with AFLPs), there were no (or only very small) differences in the diversities observed in the two main geographical areas, whereas there was much lower diversity in the Andes for AFLPs compared with the Mesoamerican wild P. vulgaris. Indirect estimates of the AFLP mutation rate have shown values that vary from 10 −6 to 10 −5 (34)(35)(36), whereas the SSR mutation rate is higher; it ranges from 10 −3 to 10 −4 using both indirect (34,37,38) and direct (39, 40) estimates. Thus, following the model proposed in the work by Nei et al (41) that described the effects of a bottleneck on the genetic diversity of a population at a neutral locus, the work by Rossi et al (13) suggested the occurrence of a bottleneck in the Andes before domestication.…”

Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

“…Nonetheless, the lack of concordance between AFLPs and SSRs points to some ambiguity in the pattern, which cannot be resolved using the available data. Possible reasons include the differing discriminating power of the two marker types (for example, high proportions of null alleles in SSRs lower discrimination power), or different responses to environmental selection (AFLPs are more likely to be linked to loci under selection owing to random coverage of a genome; Gaudeul et al, 2004). The distribution of clusters does not overlap with any evident ecological factor, apart from distance from a nearby lake (Mukrz).…”