Marc Rius

Most genetic data come from contemporary populations, leaving historical changes in within-species variation poorly documented. Sedimentary ancient DNA ( seda DNA) offers an opportunity to recover historical sequence variation, but its potential to reconstruct temporal changes in within-species composition remains underexplored. Here, we analysed dated sediment cores from eight Atlantic and Mediterranean coastal wetlands using COI and 18S metabarcoding, treating amplicon sequence variants as putative haplotypes. Across native, non-indigenous and cryptogenic taxa, accumulated haplotype diversity and geographic sharing varied markedly among species and markers, without consistently distinguishing species status. Temporal reconstructions revealed that accumulated haplotype networks combined distinct sets of variants detected across historical periods. Broader analyses of 18S data further showed substantial variation in haplotype composition among periods, sites and taxa. By resolving the temporal and spatial distributions of within-species sequence variants, our findings demonstrate how sedimentary DNA archives can uncover historical dimensions of biodiversity obscured by time-aggregated analyses, establishing a foundation for historical metaphylogeography.

Coastal wetlands have undergone centuries of anthropogenic modification, yet their long-term biodiversity trajectories remain poorly understood because ecological monitoring rarely extends beyond recent decades. Sedimentary ancient DNA ( seda DNA) offers a historical perspective for evaluating how biodiversity patterns vary across environmental contexts and timescales. We combined COI and 18S seda DNA metabarcoding with ²¹⁰Pb and radiocarbon chronologies, sediment geochemistry and stable-isotope records from eight coastal wetlands across four regions of the Iberian Peninsula. We reconstructed changes in eukaryotic amplicon sequence variant (ASV) richness and taxonomic composition and examined their relationships with an Anthropogenic Enrichment Index (AEI) based on ten elements potentially associated with human activities. Richness-AEI relationships differed among sediment records and genetic markers. Higher enrichment was associated with lower richness for both markers in one Cádiz record, whereas COI richness increased with enrichment in the Ebro Delta. However, after accounting for calendar time, only the positive association in the Ebro Delta remained statistically significant, indicating that several initial relationships were partly explained by shared temporal trends. Exploratory rolling correlations further suggested that the direction of richness-enrichment associations varied across historical periods within individual records. Taxonomic profiles differed between markers and wetlands, while community composition was strongly differentiated among sediment records, highlighting ecological variation not captured by richness alone. Multiproxy changes also followed locally specific configurations rather than a common regional trajectory. Together, these findings show that long-term relationships between sedimentary enrichment and biodiversity are context-dependent and sensitive to the temporal perspective considered. Integrating molecular, geochemical and isotopic records can therefore improve the historical interpretation of biodiversity change and inform conservation approaches that account for taxonomic composition, environmental history and locally appropriate reference conditions.

Contemporary climate change is reshaping marine ecosystems worldwide. Thus, understanding how population connectivity and local adaptation interact with contemporary climate change is critical for predicting ecosystem resilience and recovery. Here, we investigated the genomic signatures of two sympatric intertidal gastropods with low-dispersive early life-history stages, Phorcus articulatus and Phorcus turbinatus, across a contemporary climate change hotspot, the Mediterranean Sea. We generated genotyping-by-sequencing data from 336 Mediterranean specimens to unravel connectivity patterns across the Mediterranean and to identify environmentally associated genomic variation. Lagrangian particle-tracking simulations revealed strong short-term larval retention and basin-scale isolation. Accordingly, our genomic data showed a pronounced east-west population structure, with P. articulatus showing stronger population differentiation than P. turbinatus. However, we found unexpected genetic affinities among several distant localities, indicating recent human-mediated connectivity, most likely via maritime transport. We also found contrasting genomic architectures and different adaptive responses. Specifically, genotype-environment association analyses identified ∼600 high-quality SNPs potentially under selection. These loci showed limited overlap between species, suggesting divergent evolutionary strategies to overcome similar environmental pressures: P. articulatus showed evidence of local adaptation driven only by temperature, whereas P. turbinatus displayed adaptive associations involving temperature and salinity. Our results suggest that P. turbinatus will be more resilient to future climatic conditions than P. articulatus, given its higher population connectivity and capacity to adapt to multiple stressors. These findings highlight the importance of conducting studies that include both comparative population genomics and oceanographic modelling to understand how evolutionary dynamics are shaped by contemporary climate change across species ranges.

Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine‐scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals integrate ecological information through depositional and burial processes, yet are commonly inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S) using a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained > 70% of the variation in beta diversity, indicating that among‐site spatial and stratigraphic differences were the dominant drivers of community composition. PERMANOVA likewise identified non‐significant effects of biological replication. Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than those associated with biological replication or site identity, indicating a limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within‐site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may provide little additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedimentary DNA metabarcoding datasets.

Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals integrate ecological information through depositional and burial processes, yet are commonly inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S) using a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained >70% of the variation in beta diversity, indicating that among-site spatial and stratigraphic differences were the dominant drivers of community composition. PERMANOVA likewise identified non-significant effects of biological replication. Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than those associated with biological replication or site identity, indicating a limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may provide little additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedimentary DNA metabarcoding datasets.

Aim: Uncovering the drivers that shape biodiversity patterns is critical to understanding ecological and evolutionary dynamics. Despite evidence that biodiversity is influenced by processes at different spatial scales, little is known about the role of fine‐scale oceanographic processes on the structure of marine communities. Here we evaluated how fine‐scale oceanographic processes influence marine biodiversity patterns around the Galápagos Islands, with a focus on understanding the role of local current dynamics in structuring nektonic communities. Location: The Galápagos Archipelago, eastern tropical Pacific Ocean. Methods: We combined high‐resolution ocean modelling with 12S environmental DNA (eDNA) metabarcoding targeting teleost and elasmobranch species. Community composition across sites was analysed in relation to Lagrangian particle‐tracking metrics, environmental variables, and spatial distance. When standard Lagrangian connectivity metrics failed to explain biodiversity variation, we developed a novel metric quantifying cumulative seawater flow resistance between geographic sites. Results: Significant differences in eDNA‐based community structure were detected across the archipelago's heterogeneous seascape. Traditional Lagrangian particle‐tracking metrics provided limited explanatory power for observed beta diversity. In contrast, the newly developed seawater flow resistance metric accounted for a substantial proportion of community dissimilarity, comparable to key abiotic factors such as temperature and geographic distance. Main Conclusions: The introduction of a cumulative flow resistance metric reveals that fine‐scale oceanographic processes can shape biodiversity patterns to a previously underappreciated extent. We found that marine community composition around the Galápagos Islands is strongly influenced by local hydrodynamic variability. In addition, our findings highlight the need to integrate local current dynamics into ecological and biogeographic frameworks, particularly where subtle environmental shifts may have pronounced community‐level effects.

Understanding how anthropogenic pressures shape ecosystems over time is crucial for managing both biodiversity and bioinvasion risk. Despite recent research efforts focussing on temporal community changes as a result of human impacts, little is known about such changes over periods exceeding a century. Here, we reconstructed long-term community changes and non-indigenous species (NIS) dynamics by using sedimentary ancient DNA (sedaDNA) metabarcoding and geochemical analysis of sediment cores samples collected from a temperate estuary (Southampton Water, southern British Isles) subject to significant human impacts for centuries. We detected 73 species of Metazoa and Plantae and classified them by their status (native, cryptogenic and NIS). Our results revealed sporadic detection of NIS (both failed and continuously successful NIS introductions) throughout the entire sedimentary record. Notably, some NIS were detected as early as the 18 ^th century, indicating the presence of NIS introductions in pre-industrial times. We found a continuous overall decline in native species richness since the 19 ^th century. In addition, we found distinct peaks in copper and zinc concentrations reflecting recent periods of intensified industrial and port activity, highlighting the role of human activities in shaping biodiversity patterns and NIS dynamics. Our findings demonstrate how metabarcoding of sedaDNA archives can reveal trends in the distribution of NIS and wider biodiversity over centuries. The integrated approach used here provides new insights into biodiversity changes through time, unravels key information for biodiversity conservation management and biosecurity policy, and shows the potential that sedaDNA metabarcoding has for investigating intrinsic attributes of NIS introductions.

Tropicalisation is rapidly restructuring marine communities globally. Despite extensive research in subtidal habitats, the extent of tropicalisation and its impact on rocky intertidal communities remains poorly understood. Here we integrated contemporary field surveys with genetic barcoding, historic surveys, museum collections, and fossil records to document changes in the rocky shore gastropod communities along 8 degrees of latitude (approximately 3,120 km of coastline) of the Baja California Peninsula. We detected poleward range expansions of 30 tropical and subtropical species, and trailing-edge retractions of 13 temperate species, with some range shifts occurring across long-standing biogeographic boundaries. Fossil evidence reveals that several range-extending species previously occupied latitudes beyond their modern distributions during Pleistocene warm periods, suggesting that contemporary expansions echo historical responses to climatic warming, albeit under accelerated rates. Using Lottia gigantea as a case study, we demonstrated early range retractions can be marked by shifts in size-frequency distributions demonstrating declines in abundance, and loss of small individuals suggestive of reduced recruitment. We showed that rocky intertidal systems are sensitive to climate-driven range shifts, and highlighted the importance of integrating historical, palaeontological and contemporary data to detect early ecological and evolutionary consequences of tropicalisation. Continued monitoring combined with molecular approaches is crucial for predicting and managing biodiversity responses under ongoing climate change.

Aim: Tropicalisation and other climate‐induced range shifts are rapidly restructuring global biodiversity patterns. The detection of range shifts is often complex and requires big‐data approaches. Environmental DNA (eDNA) monitoring is emerging as a powerful method for assessing biodiversity changes at unprecedented spatial and temporal resolutions. While eDNA‐based methodologies continue to evolve, the impacts of species traits and eDNA dynamics are rarely measured, though they likely affect our eDNA data interpretation. Here we combine diverse methodologies to better understand processes affecting eDNA data and to elucidate how eDNA dispersal influences the interpretation of eDNA results in a tropicalisation context. Location: Baja California Peninsula, Mexico. Methods: We combined semi‐quantitative field surveys with eDNA sampling, quantitative PCR assays of different amplicon sizes, assessment of spawning period, and oceanographic modelling. We used as a model system the range‐retracting, marine gastropod Tegula gallina , which we sampled across a region that is experiencing tropicalisation. Results: We detected eDNA of T. gallina across both its current range (i.e., occupied region) and > 250 km beyond the species' range limit (i.e., unoccupied regions). Shorter amplicons were detected more consistently than larger targeted fragments across the unoccupied regions. Tegula gallina was likely spawning at the time of eDNA collection, and oceanographic modelling revealed possible transport of eDNA (and early life‐history stages) beyond the species' range limit. Main Conclusions: Our study reveals that eDNA signals can be detected over substantial spatial scales, which can likely be explained by the interaction among spawning period, larval dispersal, and eDNA dispersal. The varying detection sensitivity of the different amplicon sizes may be due to eDNA decay during transport. Our results highlight the need for integrative approaches combining eDNA detection, life‐history traits, field surveys of living organisms, and modelling to uncover the full potential of eDNA data, especially for ecological and conservation applications.

Studying the early stages of the introduction of non-indigenous species (NIS) is crucial as it allows immediate management actions aimed at preventing NIS spread at a time when these actions are more likely to be effective. Recent species introductions present unique opportunities to study key aspects of the invasion process. However, comprehensive information on how and when NIS are first introduced remains rare. We assessed the characteristics of the introduction of a member of the widespread Pyura stolonifera species group (Chordata, Tunicata) in Europe. These ascidians are important bioengineer species that can attain amongst the highest benthic biomass per surface area ever reported. We collected introduced individuals on the coast of the northwestern Iberian Peninsula, an area with high shipping traffic and one of the world’s most important mussel farming regions. The specimens were analysed using taxonomic and genetic tools. Both field surveys and taxonomic analysis showed that one of the African members of the species group, Pyura herdmani, has recently been introduced to Europe and, although it does not yet form the large aggregates found in the native range, it is already well-established. Genetic data revealed that only the northwest African lineage of P. herdmani has been introduced to Europe. Considering the low dispersal capabilities of the early life-history stages of P. herdmani, the introduction of this species into Europe can only be explained via human mediated transport of NIS. In order to prevent any detrimental effects on both native biota and/or economically-important anthropogenic activities, regular monitoring of recent NIS introductions is urgently required.