Pablo Saenz-Agudelo

Characterizing open ocean biodiversity at basin scales remains challenging due to sparse sampling and limited opportunities to validate satellite‐derived estimates of plankton community composition. Through the Citizens of the Sea initiative, we deployed standardized environmental DNA (eDNA) sampling kits on 27 sailing vessels during the 2024 Pacific Rally circumnavigating between New Zealand, Tonga, and Fiji, generating 728 surface ocean eDNA samples across 1.5 million km ² . Using three complementary metabarcoding markers (bacterial 16S rRNA, eukaryotic 18S rRNA and metazoan Cytochrome Oxidase I genes), and following rigorous bioinformatic quality control, we obtained 31,177 unique Amplicon Sequence Variants (ASVs), providing the first high‐resolution plankton biodiversity assessment of this understudied region. After accounting for human‐derived variation, all metabarcoding markers revealed clear latitudinal patterns in alpha diversity and community composition. ASV richness increased significantly with sea‐surface temperature and community turnover was strongly correlated with gradients in temperature and chlorophyll‐a. Comparisons between eDNA‐inferred phytoplankton functional groups and satellite‐based estimates showed moderate agreement for prokaryote‐dominated communities ( R ² = 0.27) but a weak correlation for eukaryotic phytoplankton ( R ² < 0.15), reflecting functional‐type‐specific mismatches between molecular and remote sensing approaches. Our results reinforce that citizen science fleets can generate high‐quality oceanographic eDNA datasets at scales unattainable by research expeditions, while demonstrating the strong potential of these initiatives to bridge molecular observations with satellite‐derived assessments and improve our understanding of open ocean plankton biodiversity.

Caulerpa seaweeds reproduce clonally via fragmentation, but sporadic sexual reproduction is also posited to be a common feature of their life cycles. Sexual reproduction of Caulerpa seaweeds is understudied, with evidence of gametogenesis reported for Caulerpa species and only one prior record from gametogenesis through to new juvenile plants (for Caulerpa racemosa ). In this study, laboratory experiments were conducted to observe and document the process of sexual reproduction in Caulerpa parvifolia and test the effect of light stress as an environmental trigger of gametogenesis. Sexual reproduction was observed via holocarpic production of male and female gametes from monoecious individuals. Gametes were released en masse from papillae and fused in the water column to form zygotes, which settled, expanded into spherical bodies, and elongated into primary germ tubes. By 35 days post spawning, these germ tubes had become juveniles comprising a stolon bearing fronds and rhizoids. Sexual reproduction was triggered by light levels that exceed the optima for C. parvifolia , supporting a hypothesis that stochastic environmental stressors may trigger gametogenesis. These findings add to the fundamental knowledge of reproduction in the genus Caulerpa and provide specific insights to help inform the management of invasive C. parvifolia populations.

Background: Environmental DNA (eDNA) has revolutionized biodiversity monitoring by enabling species detection from microbes to megafauna without direct observation or capture. Yet most marine eDNA collection systems remain expensive and labor-intensive, limiting their deployment at scale or by non-specialists. To address these challenges, we developed TorpeDNA, a compact, low-cost, and user-friendly eDNA sampler designed to operate under diverse marine conditions, including high-speed towing and citizen-science use. This proof-of-concept study evaluates its performance, scalability, and limitations across three contrasting marine environments encompassing different trophic levels, taxa, and user contexts. Methods: Three case studies were conducted. (1) In Northern Brittany (France), TorpeDNA (20 µm filters) was compared with large-capacity filtration capsule (0.45 µm) for characterising eukaryotic and vertebrates’ communities using metabarcoding. (2) Along the French Atlantic coast, TorpeDNA was benchmarked against serial laboratory filtration (10–0.45 µm fraction) to assess bacterial assemblages near aquaculture and wastewater gradients. (3) In the South-West Pacific, TorpeDNA was deployed aboard a Citizens of the Sea vessel to sample open-ocean plankton communities from microbes to vertebrates along a 2,000 km transect between Aotearoa-New Zealand and Fiji. Results: Across all studies, TorpeDNA generated biodiversity profiles broadly comparable to those from fine-pore or serial filtration methods. However, some notable differences were observed between methods, largely attributable to the different filter pore sizes and water volumes processed, which influenced the preferential capture or exclusion of host-associated or sediment-bound microbes, larger plankton forms, and/or rare taxa. TorpeDNA effectively recovered dominant microbial, phytoplankton, and zooplankton assemblages, reproducing known ecological and biogeographic gradients, from temperate to tropical plankton turnover and coastal-to-offshore transitions. Vertebrate DNA detection was limited in both methods, likely reflecting low natural eDNA concentrations, insufficient water volume processed, or marker inefficiency and highlighting the need for further optimization of sampling duration, flow rate, and assay sensitivity. Conclusion: TorpeDNA achieves a practical balance between usability, versatility across trophic levels, and integration across spatial and methodological scales. Its robust, low-cost design and compatibility with different filter types and standard molecular workflows make it scalable across platforms, from small to large research vessels to citizen-science initiatives and offering a fit-for-purpose tool for global, inclusive, and scalable ocean biodiversity sampling.

In Mazzaella laminarioides , a red alga commonly encountered along Chilean rocky coasts, three genetic lineages, named North, Center, and South and presenting distinct levels of genetic divergence, have been previously described based on organellar sequences. However, the coarse sampling strategy and the type of molecular markers used limited the understanding of where, when and how the lineages interact. Here we present the results obtained for six nuclear microsatellites and the mitochondrial COI acquired for 29 localities positioned between the 28°S and the 43°S, allowing us for the first time to study precisely the position of the contact zones between the three lineages. We also tested for signals potentially related to introgression between lineages using phylogenetic network reconstruction and sequences of eight nuclear loci. Our results show that the three genetic lineages of M. laminarioides already represent highly genetically isolated sibling species. Indeed, the level of admixture estimated with STRUCTURE detected only a few introgressed individuals even when lineages are located a few kilometers apart. The transition zone detected between North and Center corresponds to a more or less continuous rocky platform of only 5 km in length located at 32°48’S. Contrastingly, a mosaic of Center and South sampling sites is observed in an area extending over some 225 km between 37°S and 38°S; generating three transition zones between these two lineages, all centered on sandy beaches. We propose that a complex history of earthquakes, coastal uplift, and subsequent recolonization events is at the origin of this Center and South mosaic. We propose that these results reflect the contrasting levels of reproductive isolation that have been established between the lineages. The split between North and Center/South lineages being much older than the Center South one, intrinsic barriers may have already developed between North and Center while the limitation of gene flow between Center and South still mostly relies on extrinsic barriers.

Biogeographic breaks represent crucial ecological junctures where species encounter novel environments that challenge their physiological limits and influence evolutionary trajectories. Two biogeographic breaks delineate distinct environmental regimes along the Chilean coastline on the Southeastern Pacific. In particular, the equatorward break, situated around 30° S–32° S, marks a transition from semi‐permanent upwelling to seasonal and intermittent upwelling poleward. The environmental break maintains a heterogeneous landscape for all coastal species along the region. Marine invertebrates, particularly intertidal ectothermic species such as limpets of the Scurria genus, exhibit diverse physiological responses to variation in the thermal environment. We characterized the physiological performance of five Scurria limpet species by measuring metabolic rate (oxygen consumption) and heart rate, together with buoyant weight as a proxy of shell calcification, under a standardized acclimation design under controlled laboratory conditions in individuals sourced from four locations spanning 17° of latitude, including the 30° S–32° S biogeographic break. We tested if the observed geographic variation in phenotypic traits was associated with differences in sea surface temperature, geographic location, and population genetic structure. Our findings indicate that the observed variation in metabolic traits among localities does not follow a latitudinal trend or mirror the biogeographic origin of the populations. We found no evidence supporting the role of latitudinal metabolic compensation or local adaptation in metabolism in explaining the distribution of limpets. However, significant differences in these traits among locations were observed, varying among species between sites but showing little to no correlation with the documented genetic structure.

In Mazzaella laminarioides , a red alga commonly found along Chilean rocky coasts, three genetic lineages, named North, Center, and South, have been previously described based on organellar sequences, presenting distinct levels of genetic divergence. However, the coarse sampling strategy and the type of molecular markers used limited the understanding of where, when, and how the lineages interact. Here we present the results obtained for six nuclear microsatellites and mitochondrial COI acquired for 29 localities positioned between the 28°S and the 43°S, allowing us the first time to study precisely the position of the contact zones between the three lineages. We also tested for signals potentially related to introgression between lineages using phylogenetic network reconstruction and sequences of eight nuclear loci. Our results show that the three genetic lineages of M. laminarioides already represents highly genetically isolated sibling species. Indeed, the level of admixture estimated with STRUCTURE detected only a few introgressed individuals, even when lineages are located a few kilometers apart. The transition zone detected between North and Center corresponds to a more or less continuous rocky platform of only 5km in length located at 32°48’S. Contrastingly, a mosaic of Center-South sampling sites is observed in an area extending over some 225 kilometers between 37°S and 38°S, generating three transition zones between these two lineages, all centered on sandy beaches. We propose that a complex history of earthquakes, coastal uplift, and subsequent recolonization events is at the origin of this Center and South mosaic. We propose that these results reflect the contrasting levels of reproductive isolation that have been established between the lineages. The split between the North and Center/South lineages being much older than the Center-South one, intrinsic barriers may have already developed between North and Center, while the limitation of gene flow between Center and South still largely relies on extrinsic barriers.

Understanding the drivers of heterogeneous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganisation 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 maintains the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterised by high recombination rate variation among the populations of S. viridula . These results challenge traditional 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.

Decades of research in population genetics have revealed that genetic divergence between populations and species is not uniformly distributed throughout the genome but rather exhibits a high degree of heterogeneity. Two main conceptual models—allopatric divergence and divergence with gene flow—have been proposed to explain this variability under natural selection. Here, we investigate patterns of genomic divergence in three marine limpet species, Scurria scurra, Scurria araucana, and Scurria ceciliana, across two major biogeographic breaks (30–34°S and 41–43°S). Genomic divergence varied among species, even between the two sympatric species S. scurra and S. araucana, which exhibited heterogeneous divergence patterns across the 30–34°S range. In S. ceciliana, the southernmost species (41–43°S), divergence was shaped by a combination of allopatric divergence and divergence with gene flow. This was unexpected given that its evolutionary history suggests past isolation in glacial refugia, which would have limited gene flow. However, the observed genomic divergence indicates that genetic exchange occurred between populations, challenging previous assumptions about its evolutionary dynamics. Divergence patterns appear species-specific, with few shared genomic regions, though more similarities were found among the sister species S. scurra and S. araucana. In highly divergent regions, genes associated with lipid metabolism were identified in S. scurra and S. araucana, whereas genes related to oxidative stress response and mitochondrial functions were found in S. ceciliana. These findings suggest that genomic divergence is not entirely stochastic but may be shaped by different selective pressures in each species, potentially reflecting adaptation to distinct ecological conditions.

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 species 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 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 valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.

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.