Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies.

In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity.

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Here, we show that contradictory results are to be expected when the assumption of universal pleiotropy is violated. We develop a model in which the two key parameters are the total number of traits and the mean number of traits affected by a single mutation.We derive approximations for the distribution of the fitness effect of mutations when populations are either well-adapted or away from the optimum. We also consider drift load in a well-adapted population and show that it is independent of the distribution of the fitness effect of mutations. We show that mutation accumulation experiments can only measure the effect of the mean number of traits affected by mutations, whereas drift load only provides information about the total number of traits. We discuss the plausibility of the model. K E Y W O R D S :Drift load, genetic drift, models, molecular evolution, natural selection.

The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life-history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome-wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA-seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes -a marker of the effective population size -in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels.

BackgroundThe giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles.ResultsHaving clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample.ConclusionsThese results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size.

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It is currently unclear whether the amino acid substitutions that occur during protein evolution are primarily driven by adaptation, or reflect the random accumulation of neutral changes. When estimated from genomic data, the proportion of adaptive amino acid substitutions, called α, was found to vary greatly across species, from nearly zero in humans to above 0.5 in Drosophila. These variations have been interpreted as reflecting differences in effective population size, adaptation being supposedly more efficient in large populations. Here, we investigate the influence of effective population size and other biological parameters on the rate of adaptive evolution by simulating the evolution of a coding sequence under Fisher's geometric formalism. We explicitly model recurrent environmental changes and the subsequent adaptive walks, followed by periods of stasis during which purifying selection dominates. We show that, under a variety of conditions, the effective population size has only a moderate influence on α, and an even weaker influence on the per generation rate of selective sweeps, modifying the prevalent view in current literature. The rate of environmental change and, interestingly, the dimensionality of the phenotypic space (organismal complexity) affect the adaptive rate more deeply than does the effective population size. We discuss the reasons why verbal arguments have been misleading on that subject and revisit the empirical evidence. Our results question the relevance of the "α" parameter as an indicator of the efficiency of molecular adaptation.