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Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.

The detection of species using environmental DNA (eDNA) relies on our capacity to identify DNA from the sampled environment. Once eDNA is released into the environment, the physical degradation of individual eDNA molecules over time directly affects our ability to detect species (eDNA decay). Therefore, interpreting eDNA data requires an explicit understanding of eDNA decay to accurately infer contemporary presence or absence of a given species in the study ecosystem. Most research to date on eDNA decay has focused on single‐species assays (predominantly quantitative PCR), and thus little is known on how eDNA decay affects the interpretation of metabarcoding datasets. Here, we used eDNA metabarcoding (targeting a section of the eukaryotic cytochrome c oxidase subunit I gene) of water samples from controlled tanks to examine eDNA decay in a wide variety of marine metazoan species. After the stocked organisms were removed from these tanks, we observed a sharp decrease in amplicon sequence variant (ASV) richness within the first 48 hours. Furthermore, there was a substantial change in beta diversity between 24 and 48 hours, and after 48 hours, most stocked species became undetectable. Interestingly, the estimated decay rate for each study species, calculated using a linear regression of reads over time, differed across organisms, with up to 2–3‐fold difference among species. Our results showed that, for marine temperate species, the most substantial change in eDNA metabarcoding detectability occurred within the first 48 h, and after that, eDNA from several taxa became undetectable. These findings inform the ecological interpretation of metabarcoding datasets and provide estimates of eDNA decay rate that are valuable for both simulation studies and the design of future ecological surveys. Ecological interpretations of eDNA metabarcoding data require an explicit understanding of eDNA decay across different study systems and species. Here, we used eDNA metabarcoding of water samples to examine eDNA decay in a wide variety of temperate marine metazoan species. We found the most substantial effects of eDNA decay on diversity occurred within 24–48 hours and showed that eDNA decay rate constants varied among the detected species.

All ontogenetic stages of a life cycle are exposed to environmental conditions so that population persistence depends on the performance of both adults and offspring. Most studies analysing the influence of abiotic conditions on species performance have focussed on adults, while studies covering early life-history stages remain rare. We investigated the responses of early stages of two widely introduced ascidians, Styela plicata and Microcosmus squamiger, to different abiotic conditions. Stressors mimicked conditions in the habitats where both species can be found in their distributional ranges and responses were related to the selection potential of their populations by analysing their genetic diversity. Four developmental stages (egg fertilisation, larval development, settlement, metamorphosis) were studied after exposure to high temperature (30°C), low salinities (26 and 22‰) and high copper concentrations (25, 50 and 100 µg/L). Although most stressors effectively led to failure of complete development (fertilisation through metamorphosis), fertilisation and larval development were the most sensitive stages. All the studied stressors affected the development of both species, though responses differed with stage and stressor. S. plicata was overall more resistant to copper, and some stages of M. squamiger to low salinities. No relationship was found between parental genetic composition and responses to stressors. We conclude that successful development can be prevented at several life-history stages, and therefore, it is essential to consider multiple stages when assessing species' abilities to tolerate stress. Moreover, we found that early development of these species cannot be completed under conditions prevailing where adults live. These populations must therefore recruit from elsewhere or reproduce during temporal windows of more benign conditions. Alternatively, novel strategies or behaviours that increase overall reproductive success might be responsible for ensuring population survival.

In recent years, new analytical tools have allowed researchers to extract historical information contained in molecular data, which has fundamentally transformed our understanding of processes ruling biological invasions. However, the use of these new analytical tools has been largely restricted to studies of terrestrial organisms despite the growing recognition that the sea contains ecosystems that are amongst the most heavily affected by biological invasions, and that marine invasion histories are often remarkably complex. Here, we studied the routes of invasion and colonisation histories of an invasive marine invertebrate Microcosmus squamiger (Ascidiacea) using microsatellite loci, mitochondrial DNA sequence data and 11 worldwide populations. Discriminant analysis of principal components, clustering methods and approximate bayesian computation (ABC) methods showed that the most likely source of the introduced populations was a single admixture event that involved populations from two genetically differentiated ancestral regions--the western and eastern coasts of Australia. The ABC analyses revealed that colonisation of the introduced range of M. squamiger consisted of a series of non-independent introductions along the coastlines of Africa, North America and Europe. Furthermore, we inferred that the sequence of colonisation across continents was in line with historical taxonomic records--first the Mediterranean Sea and South Africa from an unsampled ancestral population, followed by sequential introductions in California and, more recently, the NE Atlantic Ocean. We revealed the most likely invasion history for world populations of M. squamiger, which is broadly characterized by the presence of multiple ancestral sources and non-independent introductions within the introduced range. The results presented here illustrate the complexity of marine invasion routes and identify a cause-effect relationship between human-mediated transport and the success of widespread marine non-indigenous species, which benefit from stepping-stone invasions and admixture processes involving different sources for the spread and expansion of their range.

Over millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales. Despite the fact that large animals and microorganisms face different environmental and anthropogenic pressures, this study finds that marine biogeographic patterns are similar for organisms in different kingdoms.

Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here, we used genotyping‐by‐sequencing to study both native and introduced ranges of the amphiatlantic marine invertebrate Ciona intestinalis. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using 1,653 single nucleotide polymorphisms (SNPs) from newly collected samples (285 individuals), we first confirmed the presence of this depth‐defined genomic divergence along the Swedish coast. We then used approximate Bayesian computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e., deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonization of C. intestinalis in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonizations of C. intestinalis. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridization and by altering both colonization patterns and their ecological effects in the introduced range.

Explaining why some species are widespread, while others are not, is fundamental to biogeography, ecology, and evolutionary biology. A unique way to study evolutionary and ecological mechanisms that either limit species’ spread or facilitate range expansions is to conduct research on species that have restricted distributions. Nonindigenous species, particularly those that are highly invasive but have not yet spread beyond the introduced site, represent ideal systems to study range size changes. Here, we used species distribution modeling and genomic data to study the restricted range of a highly invasive Australian marine species, the ascidian Pyura praeputialis. This species is an aggressive space occupier in its introduced range (Chile), where it has fundamentally altered the coastal community. We found high genomic diversity in Chile, indicating high adaptive potential. In addition, genomic data clearly showed that a single region from Australia was the only donor of genotypes to the introduced range. We identified over 3,500 km of suitable habitat adjacent to its current introduced range that has so far not been occupied, and importantly species distribution models were only accurate when genomic data were considered. Our results suggest that a slight change in currents, or a change in shipping routes, may lead to an expansion of the species’ introduced range that will encompass a vast portion of the South American coast. Our study shows how the use of population genomics and species distribution modeling in combination can unravel mechanisms shaping range sizes and forecast future range shifts of invasive species.

Over the last 15 years studies on invasion genetics have provided important insights to unravel cryptic diversity, track the origin of colonizers and reveal pathways of introductions. Despite all these advances, to date little is known about how evolutionary processes influence the observed genetic patterns in marine biological invasions. Here, firstly we review the literature on invasion genetics that include samples from European seas. These seas constitute a wide array of unique water masses with diverse degrees of connectivity, and have a long history of species introductions. We found that only a small fraction of the recorded introduced species has been genetically analysed. Furthermore, most studies restrict their approach to describe patterns of cryptic diversity and genetic structure, with the underlying mechanisms involved in the invasion process being largely understudied. Secondly, we analyse how genetic, reproductive and anthropogenic traits shape genetic patterns of marine introduced species. We found that most studies reveal similar genetic diversity values in both native and introduced ranges, report evidence of multiple introductions, and show that genetic patterns in the introduced range are not explained by taxonomic group or reproductive strategy. Finally, we discuss the evolutionary implications derived from genetic patterns observed in non-indigenous species. We identify different scenarios that are determined by propagule pressure, phenotypic plasticity and pre-adaptation, and the effects of selection and genetic admixture. We conclude that there is a need for further investigations of evolutionary mechanisms that affect individual fitness and adaptation to rapid environmental change.

Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta . Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta .

Aim The relationship of population genetics with the ecology and biogeography of species may be explored by comparing phenotypically similar but ecologically different congeners with overlapping ranges. We compared genetic differentiation between two congeneric rocky intertidal gastropods across a major portion of their sympatric range. We hypothesized that the habitat generalist with high abundance and continuous distribution would exhibit comparatively less genetic differentiation than the habitat specialist with low abundance and a fragmented distribution. Location North‐east Atlantic from the north‐west Iberian Peninsula to southern British coastline. Taxon Gastropoda, Trochidae, Steromphala (formerly Gibbula). Methods Field surveys were conducted to assess the presence/absence and the abundance of Steromphala umbilicalis (generalist) and S. pennanti (specialist) at 23 localities along ~1,800 km coastline. We isolated polymorphic microsatellite markers for both species (seven loci for S. umbilicalis and eight for S. pennanti) and used these to genotype 187 S. umbilicalis and 157 S. pennanti individuals. We used standard population genetic analyses to compare patterns of genetic differentiation between species in relation to the field surveys. Results Steromphala pennanti showed a more fragmented distribution, significantly lower abundance, and greater genetic differentiation than S. umbilicalis. One S. umbilicalis population towards the north of the range (southern Britain) was genetically distinct from all other sampled populations. Steromphala pennanti showed greater genetic differentiation between three southern localities, which may be attributable to its fragmented distribution and lower abundance because of limited availability of its preferred fucoid habitat in this region. We also suggest that oceanographic currents could be associated with regional genetic structure. Main conclusions The habitat generalist showed high‐local abundances, continuous distribution and low regional genetic differentiation. We found the opposite pattern for the habitat specialist. Our study highlights the importance of considering ecological (e.g. abundance, habitat preferences) and abiotic variables (e.g. ocean currents and temperature) for understanding differences in genetic structure of sympatrically distributed congeners.