Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.

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.

The rate of molecular adaptation in a changing environment.

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.

Dating cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea.

The superfamily Testudinoidea is the most diverse and widely distributed clade of extant turtles. Surprisingly, despite an extensive fossil record, and increasing amount of molecular data available, the temporal origin of this group is still largely unknown. To address this issue, we used a comprehensive molecular dataset to perform phylogenetic and molecular dating analyses, as well as seven fossil constraints to calibrate the ages of the nodes in the phylogeny. The molecular dataset includes the complete mitochondrial genomes of 37 turtle species, including newly sequenced mitochondrial genomes of Phrynops hilarii, Emys orbicularis, Rhinoclemmys punctularia, and Chelonoidis nigra, and four nuclear markers. Our results revealed that the earliest divergences within crown testudinoids occurred around 95.0 Mya, in the early Late Cretaceous, earlier than previously reported, raising new questions about the historical biogeography of this group.

Short-term changes in dietary sodium intake influence sweat sodium concentration and muscle sodium content in healthy individuals.

OBJECTIVE: There is increasing evidence that sodium can be stored in the skin and muscles without being osmotically active, yet whether acute changes in dietary sodium intake alter sweat and muscle sodium content has not been investigated previously. METHODS: In a cross-over design, we assessed muscle sodium content by Na-MRI in 38 healthy normotensive volunteers (aged 33.5 ±â€Š11.1 years, 76.3% women) after 5 days of high-sodium diet (6 g of salt added to their normal diet) and 5 days of a low-sodium diet. In a subgroup of 18 participants (72.2% women) we conducted quantitative pilocarpine iontophoretic sweat collections and measured the sodium concentration in sweat. Plasma aldosterone and plasma renin activity levels were measured in all participants. RESULTS: Under high-sodium diet conditions urinary sodium excretion, muscle sodium content and sweat sodium concentration all increased significantly. Muscle sodium content (rm = 0.47, P = 0.03) and sodium sweat concentration (rm = 0.72, P < 0.001) correlated positively with salt intake as estimated by 24-h urine sodium excretion. Age, sex or the phase of the menstrual cycle did not influence muscle or sweat sodium concentrations or their changes. In contrast, plasma aldosterone levels were negatively associated with both muscle sodium (rs = -0.42, P = 0.0001) and sweat sodium content (rs = -0.52, P = 0.002). Plasma renin activity correlated negatively with sweat sodium (rs = -0.43, P = 0.012) and muscle sodium levels (rs = -0.42, P < 0.001). CONCLUSION: Muscle and sweat sodium concentrations are significantly higher on a high-salt intake in healthy male and female individuals, suggesting that muscle and sweat play a role in regulating sodium balance in humans.

Counterions in layer-by-layer films--influence of the drying process.

The amount of counterions, measured by means of X-ray photoelectron spectroscopy (XPS), in layer-by-layer (LbL) films of poly(allylamine hydrochloride) (PAH) and poly(styrene sulfonate) (PSS), prepared from solutions with various NaCl concentrations, is shown to be greatly influenced by the film drying process: a smaller amount of counterions is observed in films dried after adsorption of each layer, when compared with films that were never dried during the film preparation. This is attributed to the formation of NaCl nanocrystals during the drying process which dissolve when the film is again immersed in the next polyelectrolyte solution. The presence of bonded water molecules was confirmed in wet films indicating that the counterions near the ionic groups are immersed in a water network. The number of counterions is dependent on the amount of salt in polyelectrolyte solutions in such a way that for a concentration of 0.2 M the relative amount of counterions attains saturation for both dried and wet samples, indicating that the process which leads the aggregation of counterions near of the ionic groups is not influenced by the drying process. Moreover, it is proven for wet samples that the increase in salt concentration leads to a decrease in the number of PAH ionized groups as predicted by the Muthukumar theory [J. Chem. Phys. 120 (2004) 9343] accounting for the counterion condensation on flexible polyelectrolytes.

Phylogeography of Sardinian cave salamanders (genus Hydromantes) is mainly determined by geomorphology.

Detecting the factors that determine the interruption of gene flow between populations is key to understanding how speciation occurs. In this context, caves are an excellent system for studying processes of colonization, differentiation and speciation, since they represent discrete geographical units often with known geological histories. Here, we asked whether discontinuous calcareous areas and cave systems represent major barriers to gene flow within and among the five species of Sardinian cave salamanders (genus Hydromantes) and whether intraspecific genetic structure parallels geographic distance within and among caves. We generated mitochondrial cytochrome b gene sequences from 184 individuals representing 48 populations, and used a Bayesian phylogeographic approach to infer possible areas of cladogenesis for these species and reconstruct historical and current dispersal routes among distinct populations. Our results show deep genetic divergence within and among all Sardinian cave salamander species, which can mostly be attributed to the effects of mountains and discontinuities in major calcareous areas and cave systems acting as barriers to gene flow. While these salamander species can also occur outside caves, our results indicate that there is a very poor dispersal of these species between separate cave systems.

Counterions in poly(allylamine hydrochloride) and poly(styrene sulfonate) layer-by-layer films.

The amount of counterions in layer-by-layer (LBL) films of poly(allylamine hydrochloride) (PAH) and poly(styrene sulfonate) (PSS) has been determined with X-ray photoelectron spectroscopy (XPS) for films prepared from solutions with various NaCl concentrations. Sodium and chloride counterions are present in LBL films produced from salt solutions, which are located at the surface and in the bulk of the films. The percentage of bulk counterions increases with the ionic strength of the polyelectrolyte before reaching a constant value. The bulk sodium/sulfur percentage ratios tend to 0.8 for samples washed with pure water and for samples washed with NaCl aqueous solutions, while the bulk chlorine/nitrogen percentage ratios tend to 0.5 for the same samples. The ratio between the percentages of polyelectrolyte ionic groups lies close to unity for all samples, indicating that counterions do not contribute to charge compensation in the polyelectrolyte during the adsorption process. The presence of counterions in LBL films is explained by Manning condensation near the polyelectrolyte ionic groups, leading to inter-polyelectrolyte ionic bondings via ionic networks. It is believed that condensation leads to the formation of NaCl crystallites in these LBL films, which was confirmed by X-ray diffraction measurements.