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The Anthropocene is tightly associated with a drastic loss of species worldwide and the disappearance of their key ecosystem functions. The orders Testudines (turtles and tortoises) and Crocodilia (crocodiles, alligators, and gharials) contain numerous threatened, long-lived species for which the functional diversity and potential erosion by anthropogenic impacts remains unknown. Here, we examine 259 (69%) of the existing 375 species of Testudines and Crocodilia, quantifying their life history strategies (i.e., trade-offs in survival, development, and reproduction) from open-access data on demography, ancestry, and threats. We find that the loss of functional diversity in simulated extinction scenarios of threatened species is greater than expected by chance. Moreover, the effects of unsustainable local consumption, diseases, and pollution are associated with life history strategies. In contrast, climate change, habitat disturbance, and global trade affect species independent of their life history strategy. Importantly, the loss of functional diversity for threatened species by habitat degradation is twice that for all other threats. Our findings highlight the importance of conservation programmes focused on preserving the functional diversity of life history strategies jointly with the phylogenetic representativity of these highly threatened groups.

Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. Here, we examined how genotype determines the TGP of phenotypic traits related to dispersal, a fundamental process in ecology and evolution. We used an experimental approach in Tetrahymena thermophila, a ciliate model-species, to determine if and how phenotypic changes expressed following a dispersal treatment are inherited over multiple generations. Our results show that morphological and movement traits associated with dispersal are plastic, and that these modifications are inherited over at least 35 generations. The fitness costs and benefits associated with these plastic changes are also transmitted to further generations. We highlight that the genotype modulates the expression and reversibility of transgenerational plasticity of dispersal-related traits and its fitness outcomes. Our study thus suggests that genotype-dependent TGP could play an important role in eco-evolutionary dynamics as dispersal determines gene flow and the long-term persistence of natural populations.

In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive loci to reliably infer population structure and thus more rigorously delineating biological management units in marine exploited species. Toward this end, we genotyped 14,893 single nucleotide polymorphism (SNPs) in 4,190 lobsters sampled across 96 sampling sites distributed along 1000 km in the northwest Atlantic in both Canada and the USA. As typical for most marine species, we observed a weak, albeit highly significant genetic structure. We also found that adaptive genetic variation allows detecting fine-scale population structure not resolved by neutral genetic variation alone. Using the recent genome assembly of the American lobster, we were able to map and annotate several SNPs located in functional genes potentially implicated in adaptive processes such as thermal stress response, salinity tolerance and growth metabolism pathways. Taken together, our study indicates that weak population structure in high gene flow systems can be resolved at various spatial scales, and that putatively adaptive genetic variation can substantially enhance the delineation of biological management units of marine exploited species.

Human activities and resource exploitation led to a massive decline of wild salmonid populations, consequently numerous conservation programs have been developed to supplement wild populations. However, many studies documented reduced fitness of hatchery-born relative to wild fish. Here, by using both RNA sequencing and Whole Genome Bisulfite Sequencing (WGBS), we show that of hatchery and wild born adult Coho Salmon (Oncorhynchus kisutch) originating from two previously studied river systems, early-life hatchery rearing environment induced significant and parallel gene expression differentiation is maintained until Coho come back to their natal river for reproduction. A total of 3,643 genes differentially expressed and 859 co-expressed genes were down-regulated in parallel in hatchery born fish from both rivers relative to their wild congeners. Among those genes, 26 displayed a significant relationship between gene expression and the median gene body methylation and 669 single CpG displayed a significant correlation between methylation level and the associated gene expression. The link between methylation and gene expression was weak suggesting that DNA methylation is not the only player in mediating hatchery-related expression differences. Yet, significant gene expression differentiation was observed despite 18 month spent in a common environment (i.e. the sea). Finally, the differentiation is observed in parallel in two different river system, highlighting the fact that early life environment may account for at least some of the reduced fitness of the hatchery salmon in the wild. These results illustrate the relevance and importance of considering both epigenome and transcriptome to evaluate the costs and benefits of large-scale supplementation programs.

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determinationsystems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due toan apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females)systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY andZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sexdifferences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and notlifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but agingrates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome systemon sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleteriousmutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat-rich Y/W chromosome (the “toxic Y/W effect”) couldaccelerate aging in the heterogametic sex in some vertebrate clades.

Comparative studies of mortality in the wild are necessary to understand the evolution of aging, yet ectothermic tetrapods are under-represented in this comparative landscape despite their suitability for testing evolutionary hypotheses. We provide the first comprehensive study of aging rates and longevity across tetrapod ectotherms in the wild, utilizing data from 107 populations across 77 species of reptiles and amphibians. We tested hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life contribute to aging. Controlling for phylogeny and body size, ectotherms displayed a higher diversity of aging rates than endotherms, and included many groups with negligible aging. Protective phenotypes and life-history tactics further explained macroevolutionary patterns of aging. By including ectothermic tetrapods, our comparative analyses enhance our understanding of aging evolution.