Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova.

Sex strongly impacts genome evolution via recombination and segregation. In the absence of these processes, haplotypes within lineages of diploid organisms are predicted to accumulate mutations independently of each other and diverge over time. This so-called "Meselson effect" is regarded as a strong indicator of the long-term evolution under obligate asexuality. Here, we present genomic and transcriptomic data of three populations of the asexual oribatid mite species Oppiella nova and its sexual relative Oppiella subpectinata We document strikingly different patterns of haplotype divergence between the two species, strongly supporting Meselson effect-like evolution and long-term asexuality in O. nova: I) variation within individuals exceeds variation between populations in O. nova but vice versa in O. subpectinata; II) two O. nova sublineages feature a high proportion of lineage-specific heterozygous single-nucleotide polymorphisms (SNPs), indicating that haplotypes continued to diverge after lineage separation; III) the deepest split in gene trees generally separates the two haplotypes in O. nova, but populations in O. subpectinata; and IV) the topologies of the two haplotype trees match each other. Our findings provide positive evidence for the absence of canonical sex over evolutionary time in O. nova and suggest that asexual oribatid mites can escape the dead-end fate usually associated with asexual lineages.

Less effective selection leads to larger genomes.

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.

Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods.

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.

A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data.

BACKGROUND: Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same sequencing run. While different samples can be separated post sequencing using sample barcodes, the possibility of cross contamination between biological samples from different species that have been processed or sequenced in parallel has the potential to be extremely deleterious for downstream analyses. RESULTS: We present CroCo, a software package for identifying and removing such cross contaminants from assembled transcriptomes. Using multiple, recently published sequence datasets, we show that cross contamination is consistently present at varying levels in real data. Using real and simulated data, we demonstrate that CroCo detects contaminants efficiently and correctly. Using a real example from a molecular phylogenetic dataset, we show that contaminants, if not eliminated, can have a decisive, deleterious impact on downstream comparative analyses. CONCLUSIONS: Cross contamination is pervasive in new and published datasets and, if undetected, can have serious deleterious effects on downstream analyses. CroCo is a database-independent, multi-platform tool, designed for ease of use, that efficiently and accurately detects and removes cross contamination in assembled transcriptomes to avoid these problems. We suggest that the use of CroCo should become a standard cleaning step when processing multiple samples for transcriptome sequencing.

No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes.

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 N-usage 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.

A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database.

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.

Aquifer recharge by stormwater infiltration basins: Hydrological and vadose zone characteristics control the impacts of basins on groundwater chemistry and microbiology.

Stormwater infiltration systems (SIS) are designed to collect and infiltrate urban stormwater runoff into the ground for flood risk mitigation and artificial aquifer recharge. Many studies have demonstrated that infiltration practices can impact groundwater chemistry and microbiology. However, quantitative assessments of the hydrogeological factors responsible of these changes remain scarce. Thus, the present study aimed to quantitatively test whether changes of groundwater chemistry and microbiology induced by SIS were linked to two factors associated with vadose zone properties (vadose zone thickness, water transit time from surface to groundwater) and one factor associated with groundwater recharge rate (assessed by groundwater table elevation during rain events). To evaluate changes in chemistry (NO3-, PO43- and dissolved organic carbon concentrations), groundwater samples were collected in wells located in SIS-impacted and non-SIS-impacted zones during experimental periods of 10 days. During the same periods, clay beads were incubated in the same wells to measure changes of groundwater microbial biofilms (microbial biomass, dehydrogenase and hydrolytic activities) induced by SIS. Results showed that changes in PO43- supplied to groundwater during stormwater infiltration was negatively correlated with vadose zone thickness. A short water transit time from surface to groundwater increased dissolved organic carbon concentrations in the aquifer which, in turn, increased biofilm biomasses in groundwater. The groundwater recharge rate during rain events (assessed by groundwater table elevation) diluted NO3- concentrations in the aquifer but also influenced the changes of biofilm activities induced by SIS. Groundwater recharge rate during rain events probably increased the fluxes of water and dissolved organic carbon in groundwater, stimulating the activity of microbial biofilms. Overall, the present study is the first to quantify conjointly several factors and processes (water transfer, dilution, solute fluxes) that could explain the impact of stormwater infiltration on chemistry and/or microbiology in groundwater.

Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination.

Cytoplasmic male sterility (CMS) is a form of genetic conflict over sex determination that results from differences in modes of inheritance between genomic compartments.1-3 Indeed, maternally transmitted (usually mitochondrial) genes sometimes enhance their transmission by suppressing the male function in a hermaphroditic organism to the detriment of biparentally inherited nuclear genes. Therefore, these hermaphrodites become functionally female and may coexist with regular hermaphrodites in so-called gynodioecious populations.3 CMS has been known in plants since Darwin's times4 but is previously unknown in the animal kingdom.5-8 We relate the first observation of CMS in animals. It occurs in a freshwater snail population, where some individuals appear unable to sire offspring in controlled crosses and show anatomical, physiological, and behavioral characters consistent with a suppression of the male function. Male sterility is associated with a mitochondrial lineage that underwent a spectacular acceleration of DNA substitution rates, affecting the entire mitochondrial genome-this acceleration concerns both synonymous and non-synonymous substitutions and therefore results from increased mitogenome mutation rates. Consequently, mitochondrial haplotype divergence within the population is exceptionally high, matching that observed between snail taxa that diverged 475 million years ago. This result is reminiscent of similar accelerations in mitogenome evolution observed in plant clades where gynodioecy is frequent,9,10 both being consistent with arms-race evolution of genome regions implicated in CMS.11,12 Our study shows that genomic conflicts can trigger independent evolution of similar sex-determination systems in plants and animals and dramatically accelerate molecular evolution.

Convergent consequences of parthenogenesis on stick insect genomes.

The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated reference genomes for five independently evolved parthenogenetic species in the stick insect genus Timema and their closest sexual relatives. Using these references and population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, suggesting that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Parthenogenetic species did not show increased transposable element (TE) accumulation, likely because there is little TE activity in the genus. By using replicated sexual-parthenogenetic comparisons, our study reveals how the absence of sex affects genome evolution in natural populations, providing empirical support for the negative consequences of parthenogenesis as predicted by theory.

Video-based sleep detection using ocular signals under the standard conditions of the maintenance of wakefulness test in patients with sleep disorders.

OBJECTIVE: Excessive sleepiness is a physiological reaction to sleep deficiency but can also be caused by underlying medical conditions. Detecting sleep is essential in preventing accidents and for medical diagnostics. Polysomnography (PSG) is considered the gold standard for the detection of sleep. More convenient video-based methods for detecting sleepiness have recently emerged. APPROACH: The possibility of detecting sleep using video-based ocular signals will be assessed using PSG for reference. Ocular signals and EEG are recorded in parallel under the conditions of the maintenance of wakefulness test (MWT) in 30 patients with sleep disorders. MAIN RESULTS: In detecting sleep, the ocular signal percentage of eyelid closure (PERCLOS) is superior to other ocular signals, resulting in an area under the curve of 0.88. Using a PERCLOS cutoff value of 0.76, sleep is correctly detected with a sensitivity of 89%, a specificity of 76%, the sleep latency is moderately correlated to the reference (rho = 0.66, p < 0.05) and the 95% confidence interval is ±21.1 min. SIGNIFICANCE: Ocular signals can facilitate the detection of sleep under the conditions of the MWT but sleep detection should not solely rely on ocular signals. If PSG recordings are not practicable or if a signal is needed that responds relatively early in the wake/sleep transition, the use of PERCLOS for the detection of sleep is reasonable.

Effects of bioturbation by tubificid worms on biogeochemical processes, bacterial community structure and diversity in heterotrophic wetland sediments.

Bioturbation activity of tubificid worms has been recognized as a key process influencing organic matter processing and nutrient cycling in benthic aquatic ecosystems. This activity is expected to modify benthic microbial communities by affecting the physical and chemical environment in sediments. Nevertheless, quantifications of bacterial community changes associated with bioturbation in freshwater ecosystems are still lacking. The present study aimed at evaluating the impact of tubificid worms on bacterial community structure using NGS approach (16S metabarcoding) and long (6 months) laboratory experiments on four heterotrophic wetland sediments. Worm bioturbation activity significantly stimulated biogeochemical processes at the water-sediment interface but only had a marginally significant effect on bacterial community structures. Yet, bacterial diversity was consistently reduced in presence of worms. Such decrease could be associated with the stimulation of organic matter mineralization by worms, leading to a reduction of the diversity of trophic niches available for bacterial species. The slight changes in bacterial community structures induced by bioturbation did not appear to control biogeochemical processes. Thus, the stimulation of biogeochemical processes by worm bioturbation was more associated with a stimulation of the initial bacterial community than with a drastic change in bacterial communities induced by worms.

Influence of stormwater infiltration systems on the structure and the activities of groundwater biofilms: Are the effects restricted to rainy periods?

Stormwater infiltration systems (SIS) have been set up to collect and infiltrate urban stormwater runoff in order to reduce flooding and to artificially recharge aquifers. Such practices produce environmental changes in shallow groundwater ecosystems like an increase in organic matter concentrations that could drive changes in structure and functions of groundwater microbial communities. Previous works suggested that SIS influence groundwater physico-chemistry during either rainy and dry period but no study has examined the impact of SIS on groundwater microorganisms during both periods. This study aimed to fill this gap by assessing SIS impacts on groundwater quality parameters in three SIS with vadose zone thickness < 3 m during two contrasting meteorological conditions (rainy/dry periods). Physicochemical (dissolved organic carbon and nutrient concentrations) and microbial variables (biomass, dehydrogenase and hydrolytic activities, and bacterial community structure) were assessed on SIS-impacted and non-SIS-impacted zones of the aquifers for the three SIS. Using clay beads incubated in the aquifer to collect microbial biofilm, we show that SIS increased microbial activities, bacterial richness and diversity in groundwater biofilms during the rainy period but not during the dry period. In contrast, the significant differences in dissolved organic carbon and nutrient concentrations, biofilm biomass and bacterial community structures (Bray-Curtis distances, relative abundances of main bacterial orders) measured between SIS-impacted and non-SIS-impacted zones of the aquifer were comparable during the two periods. These results suggest that structural indicators of biofilm like biomass were probably controlled by long-term effects of SIS on concentrations of dissolved organic matter and nutrients whereas biofilm activities and bacterial richness were temporally stimulated by stormwater runoff infiltrations during the rainy period. This decoupling between the structural and functional responses of groundwater biofilms to stormwater infiltration practices suggests that biofilms functions were highly reactive to fluxes associated with aquifer recharge events.

Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.

Thanks to huge advances in sequencing technologies, genomic resources are increasingly being generated and shared by the scientific community. The quality of such public resources are therefore of critical importance. Errors due to contamination are particularly worrying; they are widespread, propagate across databases, and can compromise downstream analyses, especially the detection of horizontally-transferred sequences. However we still lack consistent and comprehensive assessments of contamination prevalence in public genomic data. Here we applied a standardized procedure for foreign sequence annotation to 43 published arthropod genomes from the widely used Ensembl Metazoa database. This method combines information on sequence similarity and synteny to identify contaminant and putative horizontally-transferred sequences in any genome assembly, provided that an adequate reference database is available. We uncovered considerable heterogeneity in quality among arthropod assemblies, some being devoid of contaminant sequences, whereas others included hundreds of contaminant genes. Contaminants far outnumbered horizontally-transferred genes and were a major confounder of their detection, quantification and analysis. We strongly recommend that automated standardized decontamination procedures be systematically embedded into the submission process to genomic databases.

Drowsiness or mind-wandering? Fluctuations in ocular parameters during attentional lapses.

Two independent lines of evidence suggest that drowsiness and mind-wandering share common neurocognitive processes indexed by ocular parameters (e.g., eyeblink frequency and pupil dynamics). Mind-wandering and drowsiness frequently co-occur, however, such that it remains unclear whether observed oculometric variations are related to mind-wandering, drowsiness, or a mix of both. To address this issue, we assessed fluctuations in mind-wandering and sleepiness during a sustained attention task while ocular parameters were recorded. Results showed that oculometric variations during mind-wandering were fully explained by increased sleepiness. However, mind-wandering and sleepiness had additive deleterious effects on performance that were not fully explained by ocular parameters. These findings suggest that oculometric variations during task performance reflect increased drowsiness rather than processes specifically involved in mind-wandering, and that the neurocognitive processes indexed by oculometric parameters (e.g., regulatory processes of the locus coeruleus norepinephrine system) do not fully explain how mind-wandering and sleepiness cause attentional lapses.

Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species.

A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.

Tests of a New Drowsiness Characterization and Monitoring System Based on Ocular Parameters.

Drowsiness is the intermediate state between wakefulness and sleep. It is characterized by impairments of performance, which can be very dangerous in many activities and can lead to catastrophic accidents in transportation or in industry. There is thus an obvious need for systems that are able to continuously, objectively, and automatically estimate the level of drowsiness of a person busy at a task. We have developed such a system, which is based on the physiological state of a person, and, more specifically, on the values of ocular parameters extracted from images of the eye (photooculography), and which produces a numerical level of drowsiness. In order to test our system, we compared the level of drowsiness determined by our system to two references: (1) the level of drowsiness obtained by analyzing polysomnographic signals; and (2) the performance of individuals in the accomplishment of a task. We carried out an experiment in which 24 participants were asked to perform several Psychomotor Vigilance Tests in different sleep conditions. The results show that the output of our system is well correlated with both references. We determined also the best drowsiness level threshold in order to warn individuals before they reach dangerous situations. Our system thus has significant potential for reliably quantifying the level of drowsiness of individuals accomplishing a task and, ultimately, for preventing drowsiness-related accidents.

Evaluation of the performance of an experimental somnolence quantification system in terms of reaction times and lapses.

Somnolence is known to be a major cause of various types of accidents, and ocular parameters are recognized to be reliable physiological indicators of somnolence. We have thus developed an experimental somnolence quantification system that uses images of the eye and that produces a level of somnolence on a continuous numerical scale. The aim of this paper is to show that the level of somnolence produced by our system is well related to the level of performance of subjects accomplishing three reaction-time tests in different sleep conditions. Twenty seven subjects participated in the study and images of their right eye were continuously recorded during the tests. Levels of somnolence, reaction times (RTs), and percentages of lapses were computed for each minute of test. Results show that the values of these three parameters increase significantly with sleep deprivation. We determined the best threshold on our scale of somnolence to predict lapses, and we also shown that correlations exist with some of the ocular parameters. Our somnolence quantification system has thus significant potential to predict performance decrements of subjects accomplishing a task.