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Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species‐rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large‐scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade‐offs during groundwater colonization. [ABSTRACT FROM AUTHOR]

Metabarcoding is often presented as an alternative identification tool to compensate for coarse taxonomic resolution and misidentification encountered with traditional morphological approaches. However, metabarcoding comes with two major impediments which slow down its adoption. First, the picking and destruction of organisms for DNA extraction are time and cost consuming and do not allow organism conservation for further evaluations. Second, current metabarcoding protocols include a PCR enrichment step which induces errors in the estimation of species diversity and relative biomasses. In this study, we first evaluated the capacity of capture enrichment to replace PCR enrichment using controlled freshwater macrozoobenthos mock communities. Then, we tested if DNA extracted from the fixative ethanol (etDNA) of the same mock communities can be used as an alternative to DNA extracted from pools of whole organisms (bulk DNA). We show that capture enrichment provides more reliable and accurate representation of species occurrences and relative biomasses in comparison with PCR enrichment for bulk DNA. While etDNA does not permit to estimate relative biomasses, etDNA and bulk DNA provide equivalent species detection rates. Thanks to its robustness to mismatches, capture enrichment is already an efficient alternative to PCR enrichment for metabarcoding and, if coupled to etDNA, is a time‐saver option in studies where presence information only is sufficient. [ABSTRACT FROM AUTHOR]

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The rate of molecular evolution varies widely among species. Life history traits (LHTs) have been proposed as a major driver of these variations. However, the relative contribution of each trait is poorly understood. Here, we test the influence of metabolic rate (MR), longevity, and generation time (GT) on the nuclear and mitochondrial synonymous substitution rates using a group of isopod species that have made multiple independent transitions to subterranean environments. Subterranean species have repeatedly evolved a lower MR, a longer lifespan and a longer GT. We assembled the nuclear transcriptomes and the mitochondrial genomes of 13 pairs of closely related isopods, each pair composed of one surface and one subterranean species. We found that subterranean species have a lower rate of nuclear synonymous substitution than surface species whereas the mitochondrial rate remained unchanged. We propose that this decoupling between nuclear and mitochondrial rates comes from different DNA replication processes in these two compartments. In isopods, the nuclear rate is probably tightly controlled by GT alone. In contrast, mitochondrial genomes appear to replicate and mutate at a rate independent of LHTs. These results are incongruent with previous studies, which were mostly devoted to vertebrates. We suggest that this incongruence can be explained by developmental differences between animal clades, with a quiescent period during female gametogenesis in mammals and birds which imposes a nuclear and mitochondrial rate coupling, as opposed to the continuous gametogenesis observed in most arthropods. [ABSTRACT FROM AUTHOR]

The hyporheic zone of rivers potentially acts as a dispersal corridor for groundwater organisms because it provides a spatially continuous interstitial habitat between isolated aquifers. Yet, the degree to which it can facilitate the movement of organisms has been hypothesized to vary in response to change in sediment regime, which determines channel morphology., In this study, we used microsatellite markers to test for a relationship between the genetic structure and diversity of the minute interstitial isopod Proasellus walteri and channel morphology along three nearby hyporheic corridors differing widely in their sediment regime. We predicted that genetic diversity would decrease and genetic structuring would increase as sediment supply-limited channels would become prominent features in the river corridor. The reason is that such channels have fewer and less suitable sedimentary habitats for migration because they lack large depositional bedforms such as gravel bars., Using genotypic data from seven microsatellite loci for a total of 713 individuals distributed among 25 demes, we found that demes had on average more alleles and were less differentiated in the river showing the most extensive alluvial deposits and shortest length of sediment supply-limited channels. Population clusters were also of greater size, reaching up to 30 km in length. The longitudinal pattern of genetic differentiation in this sediment-rich river was best explained by hydrologic distance and the longitudinal pattern of allelic richness was bell-shaped, as expected under a stepping-stone model with symmetrical migration., The length of sediment supply-channels was more important than hydrologic distance in explaining the longitudinal distribution of genetic differentiation in the two other corridors facing a sediment shortage. Allelic richness decreased monotonically upstream in the most sediment-poor river. This correlates with the expansion further downstream of sediment supply-limited channels in this river, which is likely to decrease animal movement and hence gene flow among demes., This study provides the first evidence that the degree to which the hyporheic zone facilitates the movement of groundwater organisms varies greatly among rivers of contrasted geomorphology. Extending the application of riverscape genetics across a range of interstitial taxa and geomorphic settings holds much promise for assessing the contribution of the hyporheic zone to the dispersal of groundwater organisms. [ABSTRACT FROM AUTHOR]

The field of stoichiogenomics aims at understanding the influence of nutrient limitations on the elemental composition of the genome, transcriptome, and proteome. The 20 amino acids and the 4 nt differ in the number of nutrients they contain, such as nitrogen (N). Thus, N limitation shall theoretically select for changes in the composition of proteins or RNAs through preferential use of N-poor amino acids or nucleotides, which will decrease the N-budget of an organism. While these N-saving mechanisms have been evidenced in microorganisms, they remain controversial in multicellular eukaryotes. In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower Nusage at their third codon positions. To test if this convergent compositional change was driven by natural selection, we developed a method to detect the strand-asymmetric signature that stoichiogenomic selection should leave in the substitution pattern. No such signature was evidenced, indicating that the observed stoichiogenomic-like patterns were attributable to nonadaptive processes. The absence of stoichiogenomic signal despite strong N limitation within a powerful phylogenetic framework casts doubt on the existence of stoichiogenomic mechanisms in metazoans. [ABSTRACT FROM AUTHOR]

Effective population size (Ne) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of Ne in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small Ne. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proasellus walteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for Ne estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that Ne in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small Ne. [ABSTRACT FROM AUTHOR]

Heterogeneity of hyporheic fauna is associated with geomorphological features and related vertical water exchanges. Constrictions on river floodplain are known to induce groundwater inputs and increase stygobite fauna. Two floodplain constrictions were studied in a large braided river (the Drôme River): one linked to a natural process (valley narrowing), another to an artificial river regulation (early 20th embankment). Spatial distribution of hyporheic organisms were sampled upstream and downstream of the two constrained sections, at 9 stations, 3 positions (left and right sides, centre of the braided strip), 3 replication points and at a depth of 50 cm in the river sediment. The spatial heterogeneity in community composition was higher near the banks than at the centre of the braided strip, no matter the width of the strip. The artificial constriction induced a decrease in spatial heterogeneity of the benthic fraction of the hyporheic fauna, but no changes were detected for the stygofauna. The natural valley narrowing reduced width and thickness of the alluvium and induced an inflow of groundwater resulting in an increase in stygofauna abundance. Natural floodplain narrowing linked to geology thus control the distribution of stygobite species, while artificial constrictions only modify the spatial distribution of the benthic fraction of the hyporheic fauna. Unlabelled Image • Braided channel narrowing can be natural or artificial. • Artificial narrowing induces homogenization of the benthic fraction of the hyporheos. • Natural narrowing induces upwelling of groundwater and increase in stygobite fauna. [ABSTRACT FROM AUTHOR]

Effective population size (Ne) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of Ne in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small Ne. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proasellus walteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for Ne estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that Ne in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small Ne. [ABSTRACT FROM AUTHOR]

The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical data sets. Here, we tested this hypothesis using 22 de novo transcriptomes and low-coverage genomes of asellid isopods, which represent 11 independent habitat shifts from surface water to resource-poor groundwater. We show that these habitat shifts are associated with higher transcriptome-wide [Formula: see text] After ruling out the role of positive selection and pseudogenization, we show that these transcriptome-wide [Formula: see text] increases are the consequence of a reduction in selection efficacy imposed by the smaller effective population size of subterranean species. This reduction is paralleled by an important increase in genome size (25% increase on average), an increase also confirmed in subterranean decapods and mollusks. We also control for an adaptive impact of genome size on life history traits but find no correlation between body size, or growth rate, and genome size. We show instead that the independent increases in genome size measured in subterranean isopods are the direct consequence of increasing invasion rates by repeat elements, which are less efficiently purged out by purifying selection. Contrary to selection efficacy, polymorphism is not correlated to genome size. We propose that recent demographic fluctuations and the difficulty of observing polymorphism variation in polymorphism-poor species can obfuscate the link between effective population size and genome size when polymorphism data are used alone., (© 2017 Lefébure et al.; Published by Cold Spring Harbor Laboratory Press.)

Effective population size (N e) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of N e in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small N e. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proaselluswalteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for N e estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that N e in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small N e.