Understanding the drivers of heterogenous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganization of the recombination landscape remains untested in many systems. Marine ecosystems, with their dynamic and fluid habitats, offer a compelling context to investigate genomic divergence. In this study we mapped genomic divergence and selection across recombination landscapes of parapatric marine snail sister species that we show have recently undergone secondary contact. Regions of reduced recombination were enriched for genes exhibiting signatures of negative selection, whereas regions of high recombination were associated with genes under putative positive selection. Notably, the recombination landscape of the population in parapatry of one species (Scurria viridula) differs markedly from that of the other population within this same species, highlighting the role of introgression in reshaping recombination landscapes. In the other species (Scurria zebrina), conservation of the recombination landscape and divergent selection among populations suggest trapping of beneficial allele combinations in regions of low recombination maintain the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterized by high recombination rate variation among the populations of S. viridula. These results challenge theoretical expectations of recombination evolution by showing that the causes of genomic divergence can be population- specific. This study demonstrates that recombination landscapes are key modulators of genomic divergence, with contemporary evolutionary shifts that could enable populations to adapt to distinct environments. Our findings provide new insights into the interplay between recombination, selection, and gene flow during speciation, underscoring the complexity of evolutionary trajectories in marine systems.

Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal habitats and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula, and Scurria zebrina). Comparative analysis using these genomic resources suggest that there was a large gene family contraction during the early evolutionary history of Patellogastropoda (140-170 Mya) and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be extremely valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.

The South American temperate forests have been subjected to drastic past topographic and climatic changes during the Pliocene – Pleistocene linked to Andean orogeny and glacial cycles. These changes are common drivers of genetic structure and adaptation process. Embothrium coccineum, a member of the Proteaceae family and an emblematic tree of the South American temperate forest with a distribution spanning 20° of latitude, has been strongly affected by these topographic and climatic changes. Previous studies have shown that the species presents a marked genetic structure with distinct ecotypes described; yet, little is known about their adaptive genetic responses. The main goal of this study was to investigate the effects of historical and contemporary landscape features affecting the genetic diversity and connectivity of E. coccineum throughout its natural distribution. Using more than 2000 SNPs, two genetic groups (North and Center-South) that have diverged some 2.8 million years ago were observed. The level of genetic structure was higher between populations within the North genetic group than within the Center-South group. We propose that these contrasting patterns of genetic structure are related to differences in pollinator’s assemblage and evolutionary histories between genetic groups. Moreover, we observed the existence a strong patter of isolation by environment in E. coccineum, suggesting that selection could have leaded to adaptive divergence among localities. We propose that, within the Chilean temperate forest, the patterns of genetic variation in E. coccineum reflect both a Quaternary phylogenetic imprint and the impact of selection to the strong environmental gradient.

Gracilaria chilensis is the main cultivated seaweed in Chile. The low genetic diversity observed in the Chilean population has been associated with the over-exploitation of natural beds and/or the founder effect that occurred during the post-glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. In this study, we used 2,232 SNPs to assess how the species evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over-exploitation of natural populations have influenced the genetic architecture of G. chilensis in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on G. chilensis. ABC analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over-exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of G. chilensis prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species.