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ABSTRACT Across the tree of life, many organisms are able to reproduce clonally, via vegetative spread, budding or parthenogenesis. In population genetic analyses of clonally reproducing organisms, it is common practice to retain only a single representative per multilocus genotype. Though this practice of clone correction is widespread, the theoretical justification behind it has been very little studied. Here, I use individual‐based simulations to study the effect of clone correction on the estimation of the genetic summary statistics HO, HS, FIS, FST, F′′ST and Dest. The simulations follow the standard finite island model, consisting of a set of populations connected by gene flow, but with a variable rate of sexual versus asexual reproduction. The results of the simulations show that by itself, the inclusion of replicated genotypes does not lead to a deviation in the values of the summary statistics, except when the rate of sexual reproduction is less than about one in thousand. However, clone correction can introduce a strong deviation in the values of most of the statistics, when compared to a scenario of full sexual reproduction. For HS and FIS, this deviation can be informative about the process of asexual reproduction, but for FST, F′′ST and Dest, clone correction can lead to incorrect conclusions. I therefore argue that clone correction is not strictly necessary, but can in some cases be insightful. However, when clone correction is applied, it is imperative that results for both the corrected and uncorrected data are presented. [ABSTRACT FROM AUTHOR]

Abstract: The increasing use of exotic and hybrid poplar species in forestry and the lack of genetic barriers between most poplar species may present a risk to the genetic integrity [...]

Understanding the impact of historical and demographic processes on genetic variation is essential for devising conservation strategies and predicting responses to climate change. Recolonization after Pleistocene glaciations is expected to leave distinct genetic signatures, characterised by lower genetic diversity in previously glaciated regions. Populations' positions within species ranges also shape genetic variation, following the central‐marginal paradigm dictating that peripheral populations are depauperate, sparse and isolated. However, the general applicability of these patterns and relative importance of historical and demographic factors remains unknown. Here, we analysed the distribution of genetic variation in 91 native species of North American plants by coupling microsatellite data and species distribution modelling. We tested the contributions of historical climatic shifts and the central‐marginal hypothesis on genetic diversity and structure on the whole data set and across subsets based on taxonomic groups and growth forms. Decreased diversity was found with increased distance from potential glacial refugia, coinciding with the expected make‐up of postglacially colonised localities. At the range periphery, lower genetic diversity, higher inbreeding levels and genetic differentiation were reported, following the assumptions of the central‐marginal hypothesis. History and demography were found to have approximately equal importance in shaping genetic variation. [ABSTRACT FROM AUTHOR]

Abstract Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and association genetic studies of adaptation and growth in Picea taxa. The putative QTNs identified will be tested for associations in natural populations, with potential applications in molecular breeding and gene conservation programs. QTLs mapping consistently across years and environments could also be the most important targets for breeding, because they represent genomic regions that may be least affected by G × E interactions.

A method to estimate a standardized measure of population differentiation based on the analysis of molecular variance framework is described. The advantage of this method is that it can be expanded to include different hierarchical levels in the tested population structure.

Many species suffer from anthropogenic habitat fragmentation. The resulting small and isolated populations are more prone to extinction due to, amongst others, genetic erosion, inbreeding depression and Allee-effects. Genetic rescue can help mitigate such problems, but might result in outbreeding depression. We evaluated offspring fitness after selfing and outcrossing within and among three very small and isolated remnant populations of the heterostylous plant Primula vulgaris. We used greenhouse-grown offspring from these populations to test several fitness components. One population was fixed for the pin-morph, and was outcrossed with another population in the field to obtain seeds. Genetic diversity of parent and offspring populations was studied using microsatellites. Morph and population-specific heterosis, inbreeding and outbreeding depression were observed for fruit and seed set, seed weight and cumulative fitness. Highest fitness was observed in the field-outcrossed F1-population, which also showed outbreeding depression following subsequent between-population (back)crossing. Despite outbreeding depression, fitness was still relatively high. Inbreeding coefficients indicated that the offspring were more inbred than their parent populations. Offspring heterozygosity and inbreeding coefficients correlated with observed fitness. One population is evolving homostyly, showing a thrum morph with an elongated style and high autonomous fruit and seed set. This has important implications for conservation strategies such as genetic rescue, as the mating system will be altered by the introduction of homostyles. [ABSTRACT FROM AUTHOR]