Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite markers in three French Fagus sylvatica populations: (1) maximum likelihood methods that compare observed and expected homozygote frequencies in the population under the assumption of Hardy-Weinberg equilibrium and (2) direct null allele frequency estimates from progeny where parent genotypes are known. We show that null allele frequencies are high in F. sylvatica (7.0% on average with the population method, 5.1% with the progeny method), and that estimates are consistent between the two approaches, especially when the number of sampled maternal half-sib progeny arrays is large. With null allele frequencies ranging between 5% and 8% on average across loci, population genetic parameters such as genetic differentiation (F ST) may be mostly unbiased. However, using markers with such average prevalence of null alleles (up to 15% for some loci) can be seriously misleading in fine scale population studies and parentage analysi

Microgeographic adaptation and the effect of pollen flow on the adaptive potential of a temperate tree species

Recent interest for microgeographic adaptation, i.e. adaptation at spatial scales compatible with substantial amount of gene dispersal, offers to reconsider the scale at which evolution occurs (Richardson et al. 2014). Whether gene flow is constraining or facilitating local adaptation at this fine spatial scale remains an unresolved question. Too important gene flow would overwhelm the effects of natural selection and decrease local adaptation along environmental gradients. Conversely, gene flow, and particularly long-distance dispersal events, could play a major role in resupplying the genetic variation of populations and favouring the spread of beneficial alleles (Kremer et al. 2012). Hence, the high dispersal capacities of trees are often assumed to be the main process maintaining the large levels of genetic variation measured in their natural populations. However, evidences for microgeographic adaptation and the quantitative assessment of the impact of gene flow on adaptive genetic variation are still limited in most temperate trees. Here, we sampled 60 open-pollinated families of European beech (Fagus sylvatica L.) from three natural plots, spreading along a short elevation gradient (∼1.5 km) at the warm margin of this species distribution. We analysed the phenotypic and genotypic data of ∼2,300 seedlings grown in a common garden. We focused on 11 potentially adaptive traits with significant heritabilities (Gauzere et al. 2016) and tested for signature of local selection on quantitative trait differentiation. We then identified the offspring likely originating from local or distant pollen immigration events and quantified the role of gene flow in increasing locally the additive variance of traits under selection. We found a significant signal of adaptive differentiation among plots separated by less than one kilometre, with local selection acting on growth and phenological traits. We found that trees in the plots at high elevation, experiencing the lowest temperature conditions, flushed earlier and had a higher height and diameter growth in our common garden than trees from the plot at low elevation. Beech populations originating from higher longitude or elevation have also been shown to be genetically earlier in provenance tests, suggesting that these populations evolved phenological traits promoting a longer vegetation period. At this southern margin of the species, the reduced allocation to stem growth at the low elevation plot is likely an adaptive response to drought, which has previously been described by comparing marginal vs central beech populations. Consistently with theoretical expectations, our results suggest a beneficial effect of pollen dispersal by increasing the genetic diversity for these locally differentiated traits. These effects were quantitatively high, with more than twice higher genetic variance for immigrant than local offspring, although with large standard errors around estimates. Our results highlight that local selection is an important evolutionary force in natural tree populations, and provide a strong evidence that adaptive genetic differentiation can occur despite high gene flow. For the two genetically differentiated traits, our analyses suggested a beneficial effect of pollen dispersal by increasing genetic diversity after one episode of reproduction. The findings suggest that conservation and management interventions to facilitate movement of gametes along short ecological gradients would boost genetic diversity of individual tree populations, and thereby enhance their adaptive potential

Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations

Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multi-locus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene-level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes Factors over many possible phase reconstructions. Epistatic selection offers a realistic multi-locus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Over all populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a non-synonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low-elevations and northern or southern populations. Several haplotypes contained non-synonymous mutations situated in genes with known functional importance for adaptation to climatic factor

Inférer les capacités de dispersion et de migration : de l'échelle locale à l'échelle globale -

Dans le contexte actuel de changements climatiques, il est important de pouvoir connaître au mieux les capacités de migration et de déplacement des espèces. Jusqu'à présent, on utilisait des approches empiriques pour évaluer cette dynamique. Aujourd'hui, la science devient plus prédictive, utilisant des approches basées sur des modèles intégrateurs, comme celui présenté ici, le noyau de dispersion, qui décrit la répartition spatiale des graines dispersées à partir d'une source

Reliability assessment of null allele detection: inconsistencies between and within different methods

Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here we assessed five methods that indirectly detect null alleles, and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8 years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated dataset this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated dataset, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false positive and false negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false positive rate, but this approach may increase the false negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural population

Looking for local adaptation:Convergent microevolution in aleppo pine (pinus halepensis)

Finding outlier loci underlying local adaptation is challenging and is best approached by suitable sampling design and rigorous method selection. In this study, we aimed to detect outlier loci (single nucleotide polymorphisms, SNPs) at the local scale by using Aleppo pine (Pinus halepensis), a drought resistant conifer that has colonized many habitats in the Mediterranean Basin, as the model species. We used a nested sampling approach that considered replicated altitudinal gradients for three contrasting sites. We genotyped samples at 294 SNPs located in genomic regions selected to maximize outlier detection. We then applied three different statistical methodologies-Two Bayesian outlier methods and one latent factor principal component method-To identify outlier loci. No SNP was an outlier for all three methods, while eight SNPs were detected by at least two methods and 17 were detected only by one method. From the intersection of outlier SNPs, only one presented an allelic frequency pattern associated with the elevational gradient across the three sites. In a context of multiple populations under similar selective pressures, our results underline the need for careful examination of outliers detected in genomic scans before considering them as candidates for convergent adaptation

Biological Flora of the British Isles: Sorbus torminalis

1.This account presents information on all aspects of the biology of Sorbus torminalis (L.) Crantz (Wild Service-tree) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of the British Isles: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history, and conservation.2.Sorbus torminalis is an uncommon, mostly small tree (but can reach 33 m) native to lowland England and Wales, and temperate and Mediterranean regions of mainland Europe. It is the most shade-tolerant member of the genus in the British Isles and as a result it is more closely associated with woodland than any other British species. Like other British Sorbus species, however, it grows best where competition for space and sunlight is limited. Seedlings are shade tolerant but adults are only moderately so. This, combined with its low competitive ability, restricts the best growth to open areas. In shade, saplings and young adults form a sapling bank, showing reproduction and extensive growth only when released. Sorbus torminalis tolerates a wide range of soil reaction (pH 3.5-8.0) but grows best on calcareous clays and thin soils over limestone.3.Sorbus torminalis is a sexual, diploid, non-apomictic species that has hybridised with a number of other Sorbus species to form microspecies. The hermaphrodite flowers are primarily insect pollinated. Seed production is reliable only in warm years, especially at the edge of its range, although even then seed viability is low. The fruits are primarily dispersed by carnivorous mammals. Seeds display embryo dormancy but most will germinate the first spring after falling.4.This tree is very tolerant of short droughts but only moderately tolerant of frost, hence its southerly and lowland distribution. It faces no particular individual threats although the small size of most populations makes it susceptible to habitat loss and fragmentation, particularly through the loss of open coppiced areas. As a consequence it appears to be declining throughout Britain and Europe despite its wide range of historical uses and the high value of its timber. The extent to which these losses will be offset by increases due to climate change is unknown.This article is protected by copyright. All rights reserved