Crop populations in smallholder farming systems are shaped by the interaction of biological, ecological and social processes, occurring on different spatiotemporal scales. Understanding these dynamics is fundamental for the conservation of crop genetic resources. In this paper we investigated the processes involved in sorghum and pearl millet diversity dynamics on Mount Kenya. Surveys were conducted in ten sites distributed along two elevation transects and occupied by six ethnolinguistic groups. Varieties of both species grown in...

The dry forests of New Caledonia are an excep- tional ecosystem because of their numerous endemic botan- ical species and their highly diversified fauna of insects, mollusks, reptiles and birds. Unfortunately, the area of the dry forests has been significantly reduced, mainly by human activities. Ecological, phenological and genetic analysis of Ixora margaretae, a symbolic species of the sclerophyll forest, has revealed contrasting traits among natural stands. The division of the natural range and then...

Local climatic conditions likely constitute an important selective pressure on genes underlying important fitness-related traits such as flowering time and in many species flowering phenology and climatic gradients strongly covary. To test whether climate shapes genetic variation on flowering time genes and to identify candidate flowering genes involved in the adaptation to environmental heterogeneity, we used a large M. truncatula core collection to examine the association between nucleotide polymorphisms at 224 candidate genes and both...

The mating system of a species is expected to have important effects on its genetic diversity. In this paper, we explore the effects of partial selfing on the equilibrium genetic variance Vg, mutation load L and inbreeding depression δ under stabilizing selection acting on a arbitrary number n of quantitative traits coded by biallelic loci with additive effects. When the U/n ratio is low (where U is the total haploid mutation rate on selected traits)...

The evolution of extravagant sexual traits by sensory exploitation occurs if males incidentally evolve features that stimulate females owing to a pre-existing environmental response that arose in the context of natural selection. The sensory exploitation process is thus expected to leave a specific genetic imprint, a pleiotropic control of the original environmental response and the novel sexual response in females. However, females may be subsequently selected to improve their discrimination of environmental and sexual stimuli....

Biodiversity, phylogeography and population genetic studies will be revolutionized by access to large datasets thanks to next generation sequencing methods. In this study, we develop an easy and cost-effective protocol for in-solution enrichment hybridization capture of complete chloroplast genomes applicable at deep multiplexed levels. The protocol uses cheap in-house species-specific probes developed via long range PCR of the entire chloroplast. Barcoded libraries are constructed and in-solution enrichment of the chloroplasts is done using the probes....

The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission...

Cultivated plants have been molded by human-induced selection, including manipulations of the mating system in the twentieth century. How these manipulations have affected realized parameters of the mating system in freely evolving cultivated populations is of interest for optimizing the management of breeding populations, predicting the fate of escaped populations and providing material for experimental evolution studies. To produce modern varieties of sunflower (Helianthus annuus L.), self-incompatibility has been broken, recurrent generations of selfing have...

Spatio-temporal studies of hybrid zones provide an opportunity to test evolutionary hypotheses of hybrid zone maintenance and movement. We conducted a landscape genetics study on a classic hybrid zone of the south-eastern Australian frogs, Litoria ewingii and L. paraewingi. This hybrid zone has been comprehensively studied since the 1960s, providing the unique opportunity to directly assess changes in hybrid zone structure across time. We compared both mtDNA and male advertisement call data from two time...

Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that...

Plant architecture, phenology and yield components of cultivated plants have repeatedly been shaped by selection to meet human needs and adaptation to different environments. Here we assessed the genetic architecture of 24 correlated maize traits that interact during plant cycle. Overall, 336 lines were phenotyped in a network of 9 trials and genotyped with 50K single-nucleotide polymorphisms. Phenology was the main factor of differentiation between genetic groups. Then yield components distinguished dents from lower yielding...

How life-history strategies influence the evolution of populations is not well understood. Most existing models stem from the Wright-Fisher model which considers discrete generations and a fixed population size, thus not taking into account any potential consequences of overlapping generations and demographic stochasticity on allelic frequencies. We introduce an individual-based model in which both population size and genotypic frequencies at a single bi-allelic locus are emergent properties of the model. Demographic parameters can be defined...

Flowering time divergence can be a crucial component of reproductive isolation between sympatric populations but few studies have quantified its actual contribution to the reduction of gene flow. In this study, we aimed at estimating pollen-mediated gene flow between cultivated sunflower and a weedy conspecific sunflower population growing in the same field, and at quantifying how it is affected by the weeds’ flowering time. For that purpose, we extended an existing mating model by including...

The evolution of crop-related weeds may be constrained by recurrent gene flow from the crop. However, flowering time variation within weedy populations may open the way for weed adaptation by allowing some weeds to escape from this constraint. We investigated this link between phenology, gene flow and adaptation in weedy sunflower populations recently emerged in Europe from crop-wild hybridization. We studied jointly flowering phenology and genetic diversity for 15 microsatellite loci in six cultivated sunflower...

A wide range of plant lines has been propagated by farmers during crop selection and dissemination, but consequences of this crop diversification on plant-microbe interactions have been neglected. Our hypothesis was that crop evolutionary history shaped the way the resulting lines interact with soil bacteria in their rhizospheres. Here, the significance of maize diversification as a factor influencing selection of soil bacteria by seedling roots was assessed by comparing rhizobacterial community composition of inbred lines...

BACKGROUND: Flowering date in annual plants, and perception of symbiotic nitrogen-fixing rhizobium in legumes, are strongly selected traits. We asked if natural selection can be detected at key genes of the flowering and rhizobia recognition pathways in the model legume Medicago truncatula. RESULTS: We examined nucleotide variation among 57 accessions from natural populations in 53 gene fragments: 11 genes involved in flowering, 5 genes involved in nitrogen-fixing bacteria recognition, and 37 genes used as control...

Accurate estimates of heritability (h²) are necessary to assess adaptive responses of populations and evolution of fitness-related traits in changing environments. For plants, h² estimates generally rely on maternal progeny designs, assuming that offspring are either half-sibs or unrelated. However, plant mating systems often depart from half-sib assumptions, this can bias h² estimates. Here, we investigate how to accurately estimate h² in non-model species through the analysis of sibling designs with a moderate genotyping effort....

Sequencing pools of individuals rather than individuals separately reduces the costs of estimating allele frequencies at many loci in many populations. Theoretical and empirical studies show that sequencing pools comprising a limited number of individuals (typically fewer than 50) provides reliable allele frequency estimates, provided that the DNA pooling and DNA sequencing steps are carefully controlled. Unequal contributions of different individuals to the DNA pool and the mean and variance in sequencing depth both can...