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.

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.

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.

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.

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.

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.

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.