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The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a “cold-shock” protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.

Hybrid conferences are in-person events that have an online component. This type of meeting format was rare before the COVID-19 pandemic, but started to become more common recently given the asynchronous global progression of the pandemic, the uneven access to vaccines and different travel regulations among countries that led to a large proportion of participants being unable to attend conferences in person. Here we report the organization of a middle-sized (581 participants: 159 onsite, 422 online) international hybrid conference that took place in France in September 2021. We highlight particular organizational challenges inherent to this relatively new type of meeting format. Furthermore, we surveyed both in-person and online participants to better understand their conference experience and to propose improvements based on the feedback received. Finally, we compare the advantages and disadvantages of three types of conferences (onsite-only, online-only and hybrid) and suggest that hybrid events should be favored in the future because they offer the most flexibility to participants. We conclude by proposing suggestions and ways forward to maximize accessibility and inclusivity of hybrid conferences. Our study brings novel insights on the challenges and opportunities created by hybrid conferences, by reporting not only the organizing committee experience but also by considering the participants’ perspective., Frontiers in Marine Science, 9, ISSN:2296-7745

Reticulated evolution -i.e. secondary introgression/admixture between sister taxa- is increasingly recognized as a key evolutionary process that may play a role in structuring infra-specific genetic variation, and possibly promoting adaptation. Mytilus spp. is an ideal system to assess its importance, because these marine mussels form semi-isolated species that remain reproductively compatible over large time-scales. It includes three taxa that hybridize in the Northern Hemisphere (M. edulis, M. galloprovincialis and M. trossulus) and two taxa of uncertain ancestry in the Southern Hemisphere (M. platensis: South America and the Kerguelen Islands; and M. planulatus: Australasia). The Kerguelen mussels are of particular interest to investigate the potential role of admixture in enhancing micro-geographic structure, as they inhabit a small and isolated island in the Southern Ocean characterized by a highly heterogeneous environment, and genomic reticulation between Northern and Southern lineages has been suspected. Here, we extended a previous analysis by using targeted-sequencing data (51,878 SNPs) across the three Northern species and the Kerguelen population, coupled with a panel of 33 SNPs genotyped on 695 mussels across 35 sites in the Kerguelen Islands. The panel was enriched with ancestry-informative SNPs, i.e. SNPs that were more differentiated than the genomic average between Northern lineages, to evaluate whether reticulated evolution contributed to micro-geographic structure. We first showed that the Kerguelen population belongs to a divergent Southern lineage, most related to M. edulis mussels, that experienced secondary admixture with non-indigenous Northern species. We then demonstrated that the Kerguelen mussels were significantly differentiated over small spatial distance, and that this local genetic structure was associated with environmental variation and mostly revealed by ancestry-informative markers. Although local adaptation can explain the association with the environment we believe it more likely that environment variables better describe population connectivity than geographic distance. Our study highlights genetic connectivity of populations is more easily revealed by non-equilibrium secondary introgression clines at a subset of loci, while association with the environment should not be hastily advocated to support adaptation from admixture variation.

Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display a great diversity of sex-determining systems. Here, we focus on sex chromosome evolution in haplochromines, the most species-rich lineage of cichlid fishes. We investigate sex-specific signatures in the Pseudocrenilabrus philander species complex, which belongs to a haplochromine genus found in many river systems and ichthyogeographic regions in northern, eastern, central, and southern Africa. Using whole-genome sequencing and population genetic, phylogenetic, and read-coverage analyses, we show that one population of P. philander has an XX–XY sex-determining system on LG7 with a large region of suppressed recombination. However, in a second bottlenecked population, we did not find any sign of a sex chromosome. Interestingly, LG7 also carries an XX–XY system in the phylogenetically more derived Lake Malawi haplochromine cichlids. Although the genomic regions determining sex are the same in Lake Malawi cichlids and P. philander, we did not find evidence for shared ancestry, suggesting that LG7 evolved as sex chromosome at least twice in haplochromine cichlids. Hence, our work provides further evidence for the labile nature of sex determination in fishes and supports the hypothesis that the same genomic regions can repeatedly and rapidly be recruited as sex chromosomes in more distantly related lineages.

Understanding the drivers and dynamics of diversification is a central topic in evolutionary biology. Here, we investigated the dynamics of diversification in the cichlid fish Astatotilapia burtoni that diverged along a lake-stream environmental gradient. Whole-genome and morphometric analyses revealed that divergent selection was essential at the early stages of diversification, but that periods in allopatry were likely involved towards the completion of speciation. While morphological differentiation was continuous, genomic differentiation was not, as shown by two clearly separated categories of genomic differentiation. Reproductive isolation increased along a continuum of genomic divergence, with a “grey zone” of speciation at ∼0.1% net nucleotide divergence. The quantification of the extent of (non-)parallelism in nine lake-stream population pairs from four cichlid species by means of multivariate analyses revealed one parallel axis of genomic and morphological differentiation among seven lake-stream systems. Finally, we found that parallelism was higher when ancestral lake populations were more similar.

Description, African cichlid fishes reveal the dynamics of speciation and the predictability of evolution., Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.

International audience; The conspicuous Mediterranean brittle star Ophioderma longicauda (Bruzelius, 1805) has been discovered to represent a cryptic species complex, consisting of six nuclear clusters with contrasting reproductive modes (broadcast spawners and brooders). Here, O. longicauda is re-described. It is distinguished by a dark reddish-brown colouration both dorsally and on the ventral disc, and multiple tumid dorsal arm plates. One eastern Mediterranean brooding cluster is described as O. zibrowii sp. nov., characterized by a dark olive-green colour both dorsally and on the ventral disc, and single dorsal arm plates. Another brooder is described from Tunisia as O. hybrida sp. nov., with a highly variable morphology that reflects its origin by hybridization of O. longicauda and a brooder (possibly O. zibrowii sp. nov.), leaving the third brooding cluster as morphologically indistinguishable at this point and possibly conspecific with one of the others. The West-African O. guineense Greef, 1882 is resurrected as a valid species, differing morphologically from O. longicauda by predominantly single dorsal arm plates and light green or creamy white ventral side. Also from West Africa, O. africana sp. nov. is described, characterized by a dark brown colour, dorsally and ventrally, and single dorsal arm plates.

Adaptive phenotypic plasticity and fixed genotypic differences have long been considered opposing strategies in adaptation. More recently, these mechanisms have been proposed to act complementarily and under certain conditions jointly facilitate evolution, speciation, and even adaptive radiations. Here, we investigate the relative contributions of adaptive phenotypic plasticity vs. local adaptation to fitness, using an emerging model system to study early phases of adaptive divergence, the generalist cichlid fish species Astatotilapia burtoni. We tested direct fitness consequences of morphological divergence between lake and river populations in nature by performing two transplant experiments in Lake Tanganyika. In the first experiment, we used wild‐caught juvenile lake and river individuals, while in the second experiment, we used F1 crosses between lake and river fish bred in a common garden setup. By tracking the survival and growth of translocated individuals in enclosures in the lake over several weeks, we revealed local adaptation evidenced by faster growth of the wild‐caught resident population in the first experiment. On the other hand, we did not find difference in growth between different types of F1 crosses in the second experiment, suggesting a substantial contribution of adaptive phenotypic plasticity to increased immigrant fitness. Our findings highlight the value of formally comparing fitness of wild‐caught and common garden‐reared individuals and emphasize the necessity of considering adaptive phenotypic plasticity in the study of adaptive divergence.

The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including CCTα (Chaperonin Containing TCP-1 subunit α), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examinedin silicolocal protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically-corrected context and found that deep sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed byin silicoglobal protein stability analyses. This suggests that CCTα not only displays structural but also functional adaptations to deep water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as ‘cold-shock’ protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, are key metabolic deep-sea adaptations.

Xenophyophores are important megafaunal organisms in the abyssal Clarion-Clipperton Zone (CCZ; equatorial Pacific), a region hosting commercially significant deposits of polymetallic nodules. Previous studies assigned those with attached, fan-like tests to Psammina limbata, a species described from the central CCZ based on morphology. Here, we redescribe the holotype of P. limbata and then show that limbata-like morphotypes collected in the eastern CCZ include three genetically distinct species. Psammina aff. limbata is closest morphologically to P. limbata. The others are described as P. microgranulata sp. nov. and P. rotunda sp. nov. These fan-shaped species form a well-supported clade with P. tortilis sp. nov., a morphologically variable species exhibiting features typical of both Psammina and Semipsammina. A second clade containing Psammina sp. 3, and two species questionably assigned to Galatheammina branches at the base of this group. The genus Psammina includes another 9 described species for which there are no genetic data, leaving open the question of whether Psammina as a whole is monophyletic. Our study increases the number of xenophyophore species described from the eastern CCZ from 8 to 11, with a further 25 morphotypes currently undescribed. Many additional species of these giant foraminifera undoubtedly await discovery in abyssal settings.

Understanding how reproductive barriers evolve and which barriers contribute to speciation requires the examination of organismal lineages that are still in the process of diversification and the study of the full range of reproductive barriers acting at different life stages. Lake and river ecotypes of the East African cichlid fish Astatotilapia burtoni show habitat-specific adaptations, despite different levels of genetic differentiation, and thus represent an ideal model to study the evolution of reproductive barriers. To evaluate the degree of reproductive isolation between genetically divergent lake and river populations, we performed a mesocosm mating experiment in a semi-natural setting at Lake Tanganyika. We assessed reproductive isolation in the presence of male-male competition by analyzing survival and growth rates of introduced adults and their reproductive success from genetic parentage of surviving offspring. The genetically divergent river population showed reduced fitness in terms of survival, growth rate, and mating success in a lake-like environment. Hybrid offspring between different populations showed intermediate survival consistent with extrinsic postzygotic reproductive barriers. Our results suggest that both prezygotic (immigrant inviability) and postzygotic reproductive barriers contribute to divergence, and highlight the value of assessing multiple reproductive barriers acting at different stages and in natural contexts to understand speciation mechanisms.

We describe Aschemonella monile Gooday and Holzmann sp. nov. from the Clarion-Clipperton Zone (CCZ, abyssal eastern equatorial Pacific), a region characterized by commercially significant concentrations of polymetallic nodules. The new species is the most abundant xenophyophore (giant agglutinated foraminifera) in our main sampling area (12-14 degrees N; 116 degrees 30'-117 degrees 26'W). Additional specimens originate from the central CCZ, and from a third area, similar to 900 km NW of the main area, where A. monile numerically dominates the megabenthos in photographic surveys of the seafloor (average densities 1.54 individuals/m(2); peak densities > 3 individuals/m(2)). Aschemonella monile is much larger (>= 7 cm in length) than previously described species of the genus, with a test comprising an irregular sequence of self-contained, partly overlapping 'segments', creating a multichambered structure. A similar, much rarer species from the main study area, described here as Aschemonella aspera Gooday and Holzmann sp. nov., has an unsegmented test with a very rough, coarsely agglutinated wall. Genetic data suggest that A. monile is distinct from A. aspera and most closely related to a group comprising Rhizammina algaeformis and Aschemonella ramuliformis. Both new species have delicate tests that are often attached to nodule surfaces, making them particularly vulnerable to seafloor disturbances.

Xenophyophores, giant, fragile, agglutinated foraminifera (protists), are major constituents of the abyssal megafauna in the equatorial Pacific Clarion-Clipperton Zone (CCZ), a region where seabed mining of polymetallic nodules may occur in the future. As part of a baseline study of benthic communities we made extensive collections of xenophyophores in two areas (UK-1 and OMS) licensed for exploration by the International Seabed Authority. Based on test morphology, we distinguished 36 morphospecies (34 new to science) among 130 specimens. Twenty of these morphospecies yielded 184 DNA sequences, a 14-fold increase in genetic data for xenophyophores that confirms their high diversity in the eastern CCZ. A further 15 morphospecies (8 new to science) were recognised in samples from two other areas (APEI-6 and Russian exploration license area) within or adjacent to the CCZ. This large number of species confirms that the CCZ is a focal area for xenophyophore diversity. More broadly, it represents an unprecedented increase in the known global diversity of xenophyophores and suggests that many species remain undiscovered in the World's oceans. Xenophyophores are often sessile on nodules in the CCZ, making these delicate organisms particularly vulnerable to mining impacts. They can also play a crucial role in deep-sea ecosystems, providing habitat structures for meiofaunal and macrofaunal organisms and enhancing the organic content of sediments surrounding their tests. The loss of xenophyophores due to seabed mining may therefore have wider implications for the recovery of benthic communities following major human disturbances on the abyssal seafloor.

Cahill, Abigail E. ... et al.-- 15 pages, 5 figures, 4 tables, supporting information https://dx.doi.org/10.1111/mec.14389, data accessibility in GenBank (accession nos MG063882–MG064453), DataDryad https://doi.org/10.5061/dryad.dv4 mg, GitHub https://github.com/chaby/dana, Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies, Funding was provided by DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status), funded by the European Union under the 7th FRAMEWORK Programme, “The Ocean of Tomorrow” (grant agreement no. 308392), www.devotes-project.eu, and by La Faculté des Sciences de la Nature et de la Vie de l’Université Abdelhamid Ibn Badis, Mostaganem, Algeria (ZB) and the Portuguese Foundation for Science and Technology (Fundação para a Ciência e a Tecnologia; FCT; Postdoctoral grant SFRH/BPD/74400/2010; JBL). This work is a contribution to Labex OT-Med (n° ANR-11-LABX-0061) and has received funding from Excellence Initiative of Aix-Marseille University - A*MIDEX, a French “Investissements d’Avenir” programme”

International audience; Closely related species are key models to investigate mechanisms leading to reproductive isolation and early stages of diversification, also at the genomic level. The brittle star cryptic species complex Ophioderma longicauda encompasses the sympatric broadcast-spawning species C3 and the internal brooding species C5. Here, we used de novo transcriptome sequencing and assembly in two closely related species displaying contrasting reproductive modes to compare their genetic diversity and to investigate the role of natural selection in reproductive isolation. We reconstructed 20 146 and 22 123 genes for C3 and C5, respectively, and characterized a set of 12 229 orthologs. Genetic diversity was 1.5-2 times higher in C3 compared to C5, confirming that species with low parental investment display higher levels of genetic diversity. Forty-eight genes were the targets of positive diversifying selection during the evolution of the two species. Notably, two genes (NHE and TetraKCNG) are sperm-specific ion channels involved in sperm motility. Ancestral sequence reconstructions show that natural selection targeted the two genes in the brooding species. This may result from an adaptation to the novel environmental conditions surrounding sperm in the brooding species, either directly affecting sperm or via an increase in male/female conflict. This phenomenon could have promoted prezygotic reproductive isolation between C3 and C5. Finally, the sperm receptors to egg chemoattractants differed between C3 and C5 in the ligand-binding region. We propose that mechanisms of species-specific gamete recognition in brittle stars occur during sperm chemotaxis (sperm attraction towards the eggs), contrary to other marine invertebrates where prezygotic barriers to interspecific hybridization typically occur before sperm-egg fusion.

International audience; Closely related species with divergent life history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and northeastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale, we found a high genetic structure within the brooders (COI: 0.07 \textless F-ST \textless 0.65) and no polymorphism at the nuclear locus i51. In contrast, the broadcasters displayed lower genetic structure (0 \textless F-ST \textless 0.14) and were polymorphic at locus i51. At the regional scale, the multilocus analysis confirmed the contrasting genetic structure between species, with no structure in the broadcasters (global F-ST \textless 0.001) and strong structure in the brooders (global F-ST = 0.49), and revealed a higher genetic diversity in broadcasters. Our study showed that the lecithotrophic larval stage allows on average a 50-fold increase in migration rates, a 280-fold increase in effective size and a threefold to fourfold increase in genetic diversity. Our work, investigating complementary genetic markers on sympatric and syntopic taxa, highlights the strong impact of the larval phase on connectivity and genetic diversity.