Range wide versus local patterns of genetic diversity in hornbeam (Carpinus betulus L.)

Coart, Els; Glabeke, Sabine Van; Petit, Rémy J.; Bockstaele, Erik Van; Roldán‐Ruiz, Isabel

doi:10.1007/s10592-004-7833-7

Cited by 121 publications

(107 citation statements)

References 27 publications

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“…This kind of spatial pattern is generally found in tree species (e.g. Tollefsrud et al 2009;Grivet et al 2009), although such studies often require large spatial scales (Comps et al 2001;Coart et al 2005). This is because trees are often characterised by wide distribution, high potential for gene flow and strong human impact, including forest management and translocation of seed material (Petit and Hampe 2006).…”

Section: Discussionmentioning

confidence: 98%

“…For example, in many European trees the geographic distribution of genetic diversity reflects the process of postglacial recolonisation (Comps et al 2001;Coart et al 2005;Tollefsrud et al 2009;Grivet et al 2009). In consequence, genetic diversity tends to decrease with the distance from refugia (generally northwards), even if no sharp differences in a species' current density can be found.…”

Section: Discussionmentioning

confidence: 99%

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Population at the edge: increased divergence but not inbreeding towards northern range limit in Acer campestre

Chybicki

Waldon‐Rudzionek

Meyza

2014

Tree Genetics & Genomes

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Ecological conditions shape natural distribution of plants. Populations are denser in optimal habitats but become more fragmented in the areas of suboptimal environmental conditions. Usually, fragmentation increases towards the limits of species distribution. Fragmented populations are often characterised by decreased genetic variation, and this effect is frequent in peripheral populations, mostly due to the reduced effective population size. Interestingly, the genetic consequences of fragmentation seem to be relatively weak in forest trees. Using microsatellite markers, we assessed the impact of population fragmentation on the genetic structure of a European tree species Acer campestre. Within the study area, this medium-size wind-dispersed and insect-pollinated tree reveals a gradual decrease in population density towards the northern range limit. Over the distance of 150 km, we detected the significant decrease in allelic richness, heterozygosity as well as an increase in the rate of population divergence along with latitude. On the other hand, we failed to show that the observed patterns of genetic structure result from the variation in population densities. Moreover, inbreeding levels revealed no association with both density and geographic location, suggesting that pollen limitation does not occur, even at the range margin. As we showed that there is no difference in a dispersal scale between low-and highdensity populations in the study species, we argue that the genetic structure is a result of postglacial recolonization. However, unlike many other forest trees, A. campestre showed the sharp latitudinal genetic pattern at a very restricted spatial scale. Limited dispersal and high fragmentation are likely the reasons.

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Population at the edge: increased divergence but not inbreeding towards northern range limit in Acer campestre

Chybicki

Waldon‐Rudzionek

Meyza

2014

Tree Genetics & Genomes

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“…Intrapopulation genetic diversity of each species was measured from all loci in each data set as band richness after rarefaction to n¼29, Br(29), and percentage of polymorphic loci at 1% level for a standardized sample size, PLP1%(29), calculated using Aflpdiv 1.1 (Coart et al, 2005). Band richness is the average number of band-present phenotypes expected at each AFLP locus in each population in a specified sample size (Coart et al, 2005). Expected heterozygosity, H e , was estimated using AFLP-SURV 1.0 (Vekemans et al, 2002) using the Bayesian method with non-uniform prior for allele frequency estimation and assuming Hardy-Weinberg equilibrium.…”

Section: Genetic Diversity and Population Structure Comparisonsmentioning

confidence: 99%

Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters

Zhang

Hare

2012

Heredity

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Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified fragment length polymorphisms (AFLPs) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by comparing results across a nested series of data sets with mean mismatch errors of 0, 1, 2, 3, 4 and 44%. Artifactual population structure was diagnosed in high-error data sets and we assessed the low-error point at which expected population substructure signal was lost. In both species, we identified substructure patterns deemed to be inaccurate at average mismatch error rates p2 and 44%. In the species comparison, the optimum data sets showed higher gene flow for the brooding oyster with more oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but our results suggest that important signal may be lost in the pursuit of 'acceptable' error levels and our procedures provide a general method for empirically exploring these tradeoffs.

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“…AFLP data were analyzed first using AFLPDiv version 1.1 (available at http://www.pierroton. inra.fr/genetics/labo/Software/Aflpdiv; Coart et al 2005) to compute the percentage of polymorphic loci (PLP) and the number of phenotypes Br (or 'band richness') expected at each 'locus' (=scored AFLP fragment) in each population after rarefaction to the smallest sample size (12 in this case) (see El Mousadik and Petit 1996). A locus is considered polymorphic at the 1% level if 1.01 \ Br \ 1.99.…”

Section: Diversity Analysesmentioning

confidence: 99%

Assessment of the domestication state of ackee (Blighia sapida K.D. Koenig) in Benin based on AFLP and microsatellite markers

et al. 2010

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Ackee (Blighia sapida) is a native multipurpose species important for the livelihoods of the rural populations in Benin. Trees are found in natural forests or are managed by farmers in different traditional agroforestry systems. Genetic variation at amplified fragment length polymorphism (AFLP) markers, four nuclear microsatellites (nSSRs) and one chloroplast microsatellite (cpSSR) were investigated in 279 individuals from six wild and eight cultivated populations from Benin. The AFLP data revealed moderate levels of diversity of ackee in Benin (mean diversity values are proportion of polymorphic loci = 52.8% and Nei's gene diversity = 0.157, for 375 AFLP fragments). The mean diversity values based on nSSR-markers are expected heterozygosity = 0.286, allelic richness = 2.77. Genetic variation of wild and cultivated populations did not differ markedly. AMOVA revealed that only 7.3 and 5.2% of the variation was partitioned among populations for nSSR-and AFLP-markers, respectively. A Mantel test based on these both markertypes revealed significant correlations between population pairwise geographic distance and genetic differentiation. Differentiation among cultivated populations was higher than among wild populations. The only polymorphic chloroplast microsatellite marker (ccmp7) showed three haplotypes. Cultivated populations from northeastern Benin were fixed on one haplotype which was not observed elsewhere indicating a different origin of these populations possibly from neighboring Nigeria. Farmer-led domestication had an impact on the spatial distribution of genetic variation but did not result in significant losses of diversity within populations. Measures to conserve genetic resources of ackee in each of the three main bioclimatic zones in Benin are proposed.

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Range wide versus local patterns of genetic diversity in hornbeam (Carpinus betulus L.)

Cited by 121 publications

References 27 publications

Population at the edge: increased divergence but not inbreeding towards northern range limit in Acer campestre

Population at the edge: increased divergence but not inbreeding towards northern range limit in Acer campestre

Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters

Assessment of the domestication state of ackee (Blighia sapida K.D. Koenig) in Benin based on AFLP and microsatellite markers

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