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Twenty three scientists set sail on a research vessel off the eastern coast of India (14 March 2021) on a three-month-long quest to map the genomic and proteomic diversity of the Indian Ocean.

Genetic diversity can influence resilience and adaptative capacity of organisms to environmental change. Genetic diversity within populations is largely structured by reproduction, with the prevalence of asexual versus sexual reproduction often underpinning important diversity metrics that determine selection efficacy. Asexual or clonal reproduction is expected to reduce genotypic diversity and slow down adaptation through reduced selection efficacy, yet the evolutionary consequences of clonal reproduction remain unclear for many natural populations. Here, we examine the genomic consequences of sympatric sexual (haplodiplontic) and clonal morphs of the kelp Ecklonia radiata that occur interspersed on reefs in Hamelin Bay, Western Australia. Using genome-wide single nucleotide polymorphisms, we confirm significant asexual reproduction for the clonal populations, indicated by a significantly lower number of multi-locus lineages and higher intra-individual diversity patterns (individual multi-locus heterozygosity, MLH). Nevertheless, co-ancestry analysis and breeding experiments confirmed that sexual reproduction by the clonal morph and interbreeding between the two morphs is still possible, but varies among populations. One clonal population with long-term asexuality showed trends of decreased selection efficacy (increased ratio non- vs. synonymous gene diversities). Yet, all clonal populations showed distinct patterns of putative local adaptation relative to the sexual morph, possibly indicating maladaptation to local environmental conditions and high vulnerability of this unique clonal morph to environmental stress.

The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host's cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.