Asymmetric oceanographic processes mediate connectivity and population genetic structure, as revealed by RADseq, in a highly dispersive marine invertebrate (Parastichopus californicus)

Highly structured populations of copepods at risk to deep-sea mining: Integration of genomic data with demogenetic and biophysical modelling

Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where hard substrate is available. Despite the increasing interest in seafloor massive sulphides exploitation, there have been no population genomic studies conducted on vent meiofauna, which are known to contribute over 50% to metazoan biodiversity at vents. To bridge this knowledge gap, restriction-site-associated DNA sequencing, specifically 2b-RADseq, was used to retrieve thousands of genome-wide single-nucleotide polymorphisms (SNPs) from abundant populations of the vent-obligate copepod Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate population structure, demographic histories and genotype-environment associations at a basin scale. Genetic analyses also helped to evaluate the suitability of tailored larval dispersal models and the parameterization of life-history traits that better fit the population patterns observed in the genomic dataset for the target organism. Highly structured populations were observed on both spatial and temporal scales, with divergence of populations between the north, mid, and south of the basin estimated to have occurred after the creation of the major transform fault dividing the Australian and the Niuafo'ou tectonic plate (350 kya), with relatively recent secondary contact events (<20 kya). Larval dispersal models were able to predict the high levels of structure and the highly asymmetric northward low-level gene flow observed in the genomic data. These results differ from most studies conducted on megafauna in the region, elucidating the need to incorporate smaller size when considering site prospecting for deep-sea exploitation of seafloor massive sulphides, and the creation of area-based management tools to protect areas at risk of local extinction, should mining occur.

Seascape genomics of the pink abalone (Haliotis corrugata): An insight into a cross-border species in the northeast Pacific coast

Seascape genomics gives insight into the geographic and environmental factors shaping local adaptations. It improves the understanding of the potential effects of climate change, which is relevant to provide the basis for the international management of fishery resources. The pink abalone (Haliotis corrugata) is distributed from California, United States to Baja California Sur, Mexico, exposed to a latitudinal environmental gradient in the California Current System. Management of the pink abalone contrasts between Mexico and the United States; Mexico has an active fishery organized in four administrative areas, while the United States has kept the fishery in permanent closure since 1996. However, the impact of environmental factors on genetic variation along the species distribution remains unknown, and understanding this relationship is crucial for effective spatial management strategies. This study aims to investigate the neutral and adaptive genomic structure of H. corrugata. A total of 203 samples from 13 locations were processed using ddRADseq, and covering the species' distribution. Overall, 2,231 neutral, nine potentially adaptive and three genomic-environmental association loci were detected. The neutral structure identified two groups: 1) California, United States and 2) Baja California Peninsula, México. In addition, the adaptive structure analysis also detected two groups with genetic divergence observed at Punta Eugenia. Notably, the seawater temperature significantly correlated with the northern group (temperate) and the southern (warmer) group. This study is a valuable foundation for future research and conservation initiatives, emphasizing the importance of considering neutral and adaptive genetic factors when developing management strategies for marine species.

Rare, long-distance dispersal underpins genetic connectivity in the pink sea fan, Eunicella verrucosa

Characterizing patterns of genetic connectivity in marine species is of critical importance given the anthropogenic pressures placed on the marine environment. For sessile species, population connectivity can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries and currents. This study combines restriction-site associated DNA sequencing (RADseq) and passive particle dispersal modelling to delineate patterns of population connectivity in the pink sea fan, Eunicella verrucosa, a temperate octocoral. Individuals were sampled from 20 sites covering most of the species' northeast Atlantic range, and a site in the northwest Mediterranean Sea to inform on connectivity across the Atlantic-Mediterranean transition. Using 7510 neutral SNPs, a geographic cline of genetic clusters was detected, partitioning into Ireland, Britain, France, Spain (Atlantic), and Portugal and Spain (Mediterranean). Evidence of significant inbreeding was detected at all sites, a finding not detected in a previous study of this species based on microsatellite loci. Genetic connectivity was characterized by an isolation by distance pattern (IBD) (r 2 = 0.78, p < 0.001), which persisted across the Mediterranean-Atlantic boundary. In contrast, exploration of ancestral population assignment using the program ADMIXTURE indicated genetic partitioning across the Bay of Biscay, which we suggest represents a natural break in the species' range, possibly linked to a lack of suitable habitat. As the pelagic larval duration (PLD) is unknown, passive particle dispersal simulations were run for 14 and 21 days. For both modelled PLDs, inter-annual variations in particle trajectories suggested that in a long-lived, sessile species, range-wide IBD is driven by rare, longer dispersal events that act to maintain gene flow. These results suggest that oceanographic patterns may facilitate range-wide stepping-stone genetic connectivity in E. verrucosa and highlight that both oceanography and natural breaks in a species' range should be considered in the designation of ecologically coherent MPA networks.

Multidisciplinary estimates of connectivity and population structure suggest the use of multiple units for the conservation and management of meagre, Argyrosomus regius

Information on population structure and connectivity of targeted species is key for proper implementation of spatial conservation measures. We used a combination of genomics, biophysical modelling, and biotelemetry to infer the population structure and connectivity of Atlantic meagre, an important fisheries resource throughout its distribution. Genetic samples from previously identified Atlantic spawning locations (Gironde, Tejo, Guadalquivir, Banc d'Arguin) and two additional regions (Algarve and Senegal) were analysed using genome-wide SNP-genotyping and mitochondrial DNA analyses. Biophysical models were conducted to investigate larval dispersal and connectivity from the known Atlantic spawning locations. Additionally, thirteen fish were double-tagged with biotelemetry transmitters off the Algarve (Portugal) to assess movement patterns and connectivity of adult individuals. This multidisciplinary approach provided a robust overview of meagre population structure and connectivity in the Atlantic. Nuclear SNP-genotyping showed a clear differentiation between the European and African populations, with significant isolation of the few known Atlantic spawning sites. The limited level of connectivity between these subpopulations is potentially driven by adults, capable of wide-ranging movements and connecting sites 500 km apart, as evidenced by tagging studies, whilst larval dispersal inferred by modelling is much more limited (average of 52 km; 95% of connectivity events up to 174 km). Our results show sufficient evidence of population structure, particularly between Africa and Europe but also within Europe, for the meagre to be managed as separate stocks. Additionally, considering the low degree of larvae connectivity, the implementation of marine protected areas in key spawning sites could be crucial towards species sustainability.

Population genomic and biophysical modeling show different patterns of population connectivity in the spiny lobster Jasus frontalis inhabiting oceanic islands

Knowledge about connectivity between populations is essential for the fisheries management of commercial species. The lobster Jasus frontalis inhabits two oceanic island groups, the Juan Fernández Archipelago and the Desventuradas Islands, separated by 800 km. Since this species is primarily exploited in the Juan Fernández Archipelago, knowledge of the connectivity patterns among islands is foundational for species management. Here, we used variability at single-nucleotide polymorphisms (SNPs) and individual-based modeling (IBM) to estimate the genetic structure and connectivity between J. frontalis populations in these island groups. The variability at 9090 SNPs suggests two genetic populations, one in the Juan Fernández Archipelago and one in the Desventuradas Islands. Furthermore, IBM suggests an asymmetric connectivity pattern, with particles moving from the Juan Fernández Archipelago to the Desventuradas Islands but not vice versa. Since the IBM analysis suggests asymmetric larval movement between the islands, and the genetic analysis indicates isolation between the Juan Fernández Archipelago and the Desventuradas Islands, larval retention mechanisms such as small-scale oceanographic processes or behavior could hinder larval movement between islands. This study highlights the importance of using more than one methodology to estimate population connectivity.

Riverscape community genomics: A comparative analytical approach to identify common drivers of spatial structure

Genetic differentiation among local groups of individuals, that is, genetic β-diversity, is a key component of population persistence related to connectivity and isolation. However, most genetic investigations of natural populations focus on a single species, overlooking opportunities for multispecies conservation plans to benefit entire communities in an ecosystem. We present an approach to evaluate genetic β-diversity within and among many species and demonstrate how this riverscape community genomics approach can be applied to identify common drivers of genetic structure. Our study evaluated genetic β-diversity in 31 co-distributed native stream fishes sampled from 75 sites across the White River Basin (Ozarks, USA) using SNP genotyping (ddRAD). Despite variance among species in the degree of genetic divergence, general spatial patterns were identified corresponding to river network architecture. Most species (N = 24) were partitioned into discrete subpopulations (K = 2-7). We used partial redundancy analysis to compare species-specific genetic β-diversity across four models of genetic structure: Isolation by distance (IBD), isolation by barrier (IBB), isolation by stream hierarchy (IBH), and isolation by environment (IBE). A significant proportion of intraspecific genetic variation was explained by IBH (x̄ = 62%), with the remaining models generally redundant. We found evidence for consistent spatial modularity in that gene flow is higher within rather than between hierarchical units (i.e., catchments, watersheds, basins), supporting the generalization of the stream hierarchy model. We discuss our conclusions regarding conservation and management and identify the 8-digit hydrologic unit (HUC) as the most relevant spatial scale for managing genetic diversity across riverine networks.

Fine-scale population structure of the northern hard clam (Mercenaria mercenaria) revealed by genome-wide SNP markers

Aquaculture is growing rapidly worldwide, and sustainability is dependent on an understanding of current genetic variation and levels of connectivity among populations. Genetic data are essential to mitigate the genetic and ecological impacts of aquaculture on wild populations and guard against unintended human-induced loss of intraspecific diversity in aquacultured lines. Impacts of disregarding genetics can include loss of diversity within and between populations and disruption of local adaptation patterns, which can lead to a decrease in fitness. The northern hard clam, Mercenaria mercenaria (Linnaeus, 1758), is an economically valuable aquaculture species along the North American Atlantic and Gulf coasts. Hard clams have a pelagic larval phase that allows for dispersal, but the level of genetic connectivity among geographic areas is not well understood. To better inform the establishment of site-appropriate aquaculture brood stocks, this study used DArTseq™ genotyping by sequencing to characterize the genetic stock structure of wild clams sampled along the east coast of North America and document genetic diversity within populations. Samples were collected from 15 locations from Prince Edward Island, Canada, to South Carolina, USA. Stringent data filtering resulted in 4960 single nucleotide polymorphisms from 448 individuals. Five genetic breaks separating six genetically distinct populations were identified: Canada, Maine, Massachusetts, Mid-Atlantic, Chesapeake Bay, and the Carolinas (F ST 0.003-0.046; p < 0.0001). This is the first study to assess population genetic structure of this economically important hard clam along a large portion of its native range with high-resolution genomic markers, enabling identification of previously unrecognized population structure. Results of this study not only broaden insight into the factors shaping the current distribution of M. mercenaria but also reveal the genetic population dynamics of a species with a long pelagic larval dispersal period along the North American Atlantic and Gulf coasts.

Dispersive currents explain patterns of population connectivity in an ecologically and economically important fish

How to identify the drivers of population connectivity remains a fundamental question in ecology and evolution. Answering this question can be challenging in aquatic environments where dynamic lake and ocean currents coupled with high levels of dispersal and gene flow can decrease the utility of modern population genetic tools. To address this challenge, we used RAD-Seq to genotype 959 yellow perch (Perca flavescens), a species with an ~40-day pelagic larval duration (PLD), collected from 20 sites circumscribing Lake Michigan. We also developed a novel, integrative approach that couples detailed biophysical models with eco-genetic agent-based models to generate "predictive" values of genetic differentiation. By comparing predictive and empirical values of genetic differentiation, we estimated the relative contributions for known drivers of population connectivity (e.g., currents, behavior, PLD). For the main basin populations (i.e., the largest contiguous portion of the lake), we found that high gene flow led to low overall levels of genetic differentiation among populations (F _ST = 0.003). By far the best predictors of genetic differentiation were connectivity matrices that were derived from periods of time when there were strong and highly dispersive currents. Thus, these highly dispersive currents are driving the patterns of population connectivity in the main basin. We also found that populations from the northern and southern main basin are slightly divergent from one another, while those from Green Bay and the main basin are highly divergent (F _ST = 0.11). By integrating biophysical and eco-genetic models with genome-wide data, we illustrate that the drivers of population connectivity can be identified in high gene flow systems.

Out to sea: ocean currents and patterns of asymmetric gene flow in an intertidal fish species

Passive dispersal via wind or ocean currents can drive asymmetric gene flow, which influences patterns of genetic variation and the capacity of populations to evolve in response to environmental change. The mangrove rivulus fish (Kryptolebias marmoratus), hereafter "rivulus," is an intertidal fish species restricted to the highly fragmented New World mangrove forests of Central America, the Caribbean, the Bahamas, and Florida. Mangrove patches are biological islands with dramatic differences in both abiotic and biotic conditions compared to adjacent habitat. Over 1,000 individual rivulus across 17 populations throughout its range were genotyped at 32 highly polymorphic microsatellites. Range-wide population genetic structure was evaluated with five complementary approaches that found eight distinct population clusters. However, an analysis of molecular variance indicated significant population genetic structure among regions, populations within regions, sampling locations within populations, and individuals within sampling locations, indicating that rivulus has both broad- and fine-scale genetic differentiation. Integrating range-wide genetic data with biophysical modeling based on 10 years of ocean current data showed that ocean currents and the distance between populations over water drive gene flow patterns on broad scales. Directional migration estimates suggested some significant asymmetries in gene flow that also were mediated by ocean currents and distance. Specifically, populations in the center of the range (Florida Keys) were identified as sinks that received migrants (and alleles) from other populations but failed to export individuals. These populations thus harbor genetic variation, perhaps even from extirpated populations across the range, but ocean currents and complex arrangements of landmasses might prevent the distribution of that genetic variation elsewhere. Hence, the inherent asymmetry of ocean currents shown to impact both genetic differentiation and directional migration rates may be responsible for the complex distribution of genetic variation across the range and observed patterns of metapopulation structure.

The role of oceanic currents in the dispersal and connectivity of the mangrove Rhizophora mangle on the Southwest Atlantic region

Dispersal is a crucial mechanism to living beings, allowing them to reach new resources such that populations and species can occupy new environments. However, directly observing the dispersal mechanisms of widespread species can be costly or even impractical, which is the case for mangrove trees. The influence of ocean currents on mangrove dispersal is increasingly evident; however, few studies mechanistically relate the patterns of population distribution with the dispersal by oceanic currents under an integrated framework. Here, we evaluate the role of oceanic currents on connectivity of Rhizophora mangle along the Southwest Atlantic. We inferred population genetic structure and migration rates, simulated the displacement of propagules and tested our hypotheses with Mantel tests and redundancy analysis. We observed populations structured in two major groups, north and south, which is corroborated by other studies with Rhizophora and other coastal plants. Inferred recent migration rates do not indicate ongoing gene flow between sites. Conversely, long-term migration rates were low across groups and contrasting dispersal patterns within each one, which is consistent with long-distance dispersal events. Our hypothesis tests suggest that both isolation by distance and isolation by oceanography (derived from the oceanic currents) can explain the neutral genetic variation of R. mangle in the region. Our findings expand current knowledge of mangrove connectivity and highlight how the association of molecular methods with oceanographic simulations improve the interpretation of the dispersal process. This integrative approach is a cost- and time-efficient strategy to include dispersal and connectivity data into marine protected areas planning and management.

Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges

The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.

Heat stress does not induce wasting symptoms in the giant California sea cucumber (Apostichopus californicus)

Oceanic heatwaves have significant impacts on disease dynamics in marine ecosystems. Following an extreme heatwave in Nanoose Bay, British Columbia, Canada, a severe sea cucumber wasting event occurred that resulted in the mass mortality of Apostichopus californicus. Here, we sought to determine if heat stress in isolation could trigger wasting symptoms in A. californicus. We exposed sea cucumbers to (i) a simulated marine heatwave (22 °C), (ii) an elevated temperature treatment (17 °C), or (iii) control conditions (12 °C). We measured the presence of skin lesions, mortality, posture maintenance, antipredator defences, spawning, and organ evisceration during the 79-hour thermal exposure, as well as 7-days post-exposure. Both the 22 °C and 17 °C treatments elicited stress responses where individuals exhibited a reduced ability to maintain posture and an increase in stress spawning. The 22 °C heatwave was particularly stressful, as it was the only treatment where mortality was observed. However, none of the treatments induced wasting symptoms as observed in the Nanoose Bay event. This study provides evidence that sea cucumber wasting may not be triggered by heat stress in isolation, leaving the cause of the mass mortality event observed in Nanoose unknown.

Isolation-by-distance and isolation-by-oceanography in Maroon Anemonefish (Amphiprion biaculeatus)

Obtaining dispersal estimates for a species is key to understanding local adaptation and population dynamics and to implementing conservation actions. Genetic isolation-by-distance (IBD) patterns can be used for estimating dispersal, and these patterns are especially useful for marine species in which few other methods are available. In this study, we genotyped coral reef fish (Amphiprion biaculeatus) at 16 microsatellite loci across eight sites across 210 km in the central Philippines to generate fine-scale estimates of dispersal. All sites except for one followed IBD patterns. Using IBD theory, we estimated a larval dispersal kernel spread of 8.9 km (95% confidence interval of 2.3-18.4 km). Genetic distance to the remaining site correlated strongly with the inverse probability of larval dispersal from an oceanographic model. Ocean currents were a better explanation for genetic distance at large spatial extents (sites greater than 150 km apart), while geographic distance remained the best explanation for spatial extents less than 150 km. Our study demonstrates the utility of combining IBD patterns with oceanographic simulations to understand connectivity in marine environments and to guide marine conservation strategies.

Population structure and adaptive differentiation in the sea cucumber Apostichopus californicus and implications for spatial resource management

A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species' range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driving two patterns of differentiation: isolation-by-distance and a latitudinal gradient of differentiation. Notably, we found detectable population differences among collection sites within the Salish Sea (pairwise FST = 0.001-0.006). Using FST outlier detection and gene-environment association, we identified 10.2% of total SNPs as putatively adaptive. Environmental variables (e.g., temperature, salinity) from the sea surface were more correlated with genetic variation than those same variables measured near the benthos, suggesting that selection on pelagic larvae may drive adaptive differentiation to a greater degree than selection on adults. Our results were consistent with previous estimates of and patterns in population structure for this species in other extents of the range. Additionally, we found that patterns of neutral and adaptive differentiation co-varied, suggesting that adaptive barriers may limit dispersal. Our study provides guidance to decision-makers regarding the designation of management units for A. californicus and adds to the growing body of literature identifying genetic population differentiation in marine species despite large, nominally connected populations.

Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography

Background

High levels of standing genomic variation in wide-ranging marine species may enhance prospects for their long-term persistence. Patterns of connectivity and adaptation in such species are often thought to be influenced by spatial factors, environmental heterogeneity, and oceanographic and geomorphological features. Population-level studies that analytically integrate genome-wide data with environmental information (i.e., seascape genomics) have the potential to inform the spatial distribution of adaptive diversity in wide-ranging marine species, such as many marine mammals. We assessed genotype-environment associations (GEAs) in 214 common dolphins (Delphinus delphis) along > 3000 km of the southern coast of Australia.

Results

We identified 747 candidate adaptive SNPs out of a filtered panel of 17,327 SNPs, and five putatively locally-adapted populations with high levels of standing genomic variation were disclosed along environmentally heterogeneous coasts. Current velocity, sea surface temperature, salinity, and primary productivity were the key environmental variables associated with genomic variation. These environmental variables are in turn related to three main oceanographic phenomena that are likely affecting the dispersal of common dolphins: (1) regional oceanographic circulation, (2) localised and seasonal upwellings, and (3) seasonal on-shelf circulation in protected coastal habitats. Signals of selection at exonic gene regions suggest that adaptive divergence is related to important metabolic traits.

Conclusion

To the best of our knowledge, this represents the first seascape genomics study for common dolphins (genus Delphinus). Information from the associations between populations and their environment can assist population management in forecasting the adaptive capacity of common dolphins to climate change and other anthropogenic impacts.

Genomic basis for early-life mortality in sharpsnout seabream

Mortality at early life stages of fishes is common in nature and can be shaped by stochastic and selective processes. Selective mortality has rarely been assessed in natural conditions but can now be studied by combining genomic data with information on different life stages that realates to fitness. Here we investigate selective mortality between settlers and six-month survivors of the sharpsnout seabream by genotype-phenotype/environmental association studies in three localities along a geographic gradient. We gathered information on 105 individuals at 85,031 SNPs, obtained from individual based 2b-RAD libraries, as well as 9 phenotypic and environmental variables derived from individual otolith readings. We found common signals across localities for potential selection, such as lower survival rates for individuals hatching earlier, growing faster and experiencing higher temperatures during their planktonic phase. We identified 122 loci with parallel significant association to phenotypic and environmental variables. Importantly, one of these loci mapped to the exonic region of the il20rb, a gene involved in immune response, in the phylogenetically closest reference genome, showing parallel frequency changes in non-synonymous mutations in the three studied populations. Further temporal assessments are needed to understand how polymorphisms that are key to selective mortality are maintained.

Spatial coalescent connectivity through multi-generation dispersal modelling predicts gene flow across marine phyla

Gene flow governs the contemporary spatial structure and dynamic of populations as well as their long-term evolution. For species that disperse using atmospheric or oceanic flows, biophysical models allow predicting the migratory component of gene flow, which facilitates the interpretation of broad-scale spatial structure inferred from observed allele frequencies among populations. However, frequent mismatches between dispersal estimates and observed genetic diversity prevent an operational synthesis for eco-evolutionary projections. Here we use an extensive compilation of 58 population genetic studies of 47 phylogenetically divergent marine sedentary species over the Mediterranean basin to assess how genetic differentiation is predicted by Isolation-By-Distance, single-generation dispersal and multi-generation dispersal models. Unlike previous approaches, the latter unveil explicit parents-to-offspring links (filial connectivity) and implicit links among siblings from a common ancestor (coalescent connectivity). We find that almost 70 % of observed variance in genetic differentiation is explained by coalescent connectivity over multiple generations, significantly outperforming other models. Our results offer great promises to untangle the eco-evolutionary forces that shape sedentary population structure and to anticipate climate-driven redistributions, altogether improving spatial conservation planning.

Spatial and temporal stability in the genetic structure of a marine crab despite a biogeographic break

Elucidating the processes responsible for maintaining the population connectivity of marine benthic species mediated by larval dispersal remains a fundamental question in marine ecology and fishery management. Understanding these processes becomes particularly important in areas with a biogeographic break and unidirectional water movement along the sides of the break. Based on variability at 4209 single-nucleotide polymorphisms in 234 individuals, we determine the genetic structure, temporal genetic stability, and gene flow among populations of the commercially important mola rock crab Metacarcinus edwardsii in a system in southern Chile with a biogeographic break at latitude 42°S. Specimens were collected at eight sites within its geographic distribution, with collection at four of these sites was performed twice. Using population genetic approaches, we found no evidence of geographic or temporal population differentiation. Similarly, we found no evidence of an effect on gene flow of the biogeographic break caused by the the West Wind Drift Current. Moreover, migration analyses supported gene flow among all sites but at different rates for different pairs of sites. Overall, our findings indicate that M. edwardsii comprises a single large population with high levels of gene flow among sites separated by over 1700 km and demonstrate temporal stability in its genetic structure.

Fisheries genomics of snapper ( Chrysophrys auratus ) along the west Australian coast

The efficacy of fisheries management strategies depends on stock assessment and management actions being carried out at appropriate spatial scales. This requires understanding of spatial and temporal population structure and connectivity, which is challenging in weakly structured and highly connected marine populations. We carried out a population genomics study of the heavily exploited snapper (Chrysophrys auratus) along ~2600 km of the Australian coastline, with a focus on Western Australia (WA). We used 10,903 filtered SNPs in 341 individuals from eight sampling locations to characterize population structure and connectivity in snapper across WA and to assess if current spatial scales of stock assessment and management agree with evidence from population genomics. Our dataset also enabled us to investigate temporal stability in population structure as well as connectivity between WA and its nearest, eastern jurisdictional neighbour. As expected for a species influenced by the extensive ocean boundary current in the region, low genetic differentiation and high connectivity were uncovered across WA. However, we did detect strong isolation by distance and genetic discontinuities in the mid‐west and south‐east. The discontinuities correlate with boundaries between biogeographic regions, influenced by on‐shelf oceanography, and the sites of important spawning aggregations. We also detected temporal instability in genetic structure at one of our sites, possibly due to interannual variability in recruitment in adjacent regions. Our results partly contrast with the current spatial management of snapper in WA, indicating the likely benefits of a review. This study supports the value of population genomic surveys in informing the management of weakly structured and wide‐ranging marine fishery resources.

Population structure of lake whitefish (Coregonus clupeaformis) from the Mississippian lineage in North America

The lake whitefish ( Coregonus clupeaformis) is a commercially valuable freshwater species with a broad distribution in North America. Some phylogeographic work has been done on this species, but little is known about genetic population subdivision among populations of the widely dispersed Mississippian lineage. We used 3,173 single nucleotide polymorphisms in 508 lake whitefish from 22 different lakes to examine population structure across central Canada and the United States. Bayesian clustering, ordination, and fixation indices identified population subdivision that largely reflected geographic distance and hydrological connectivity, with greater differentiation between lakes that are farther apart. Population subdivision was hierarchical, with greater differentiation between Canadian provinces and less differentiation based on river basins within provincial boundaries. Interestingly, isolation by distance alone was not sufficient to account for all of the observed genetic differentiation among populations. We conclude that important components of lake whitefish genetic diversity are present at different spatial scales, and that populations within the Mississippian lineage have differentiated widely across their range.

Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments

Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations from contrasting environments along a latitudinal gradient (54.9-63.6°N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, probably reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.

Whole-genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

The genomic era continues to revolutionize our understanding of the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long-standing questions about the evolution of biodiversity largely unexplored. Here, we used whole-genome sequencing (WGS) datasets to survey species diversity in the kelp genus Alaria, compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia, A. praelonga, A. crispa, A. marginata, and A. esculenta), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single-nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high-quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria, which we hypothesize represents the synonymized taxon A. grandifolia. The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A. praelonga, A. crispa, and putative A. grandifolia, and between some lineages of the A. marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and biodiversity beyond amplicon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria. We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.

High levels of connectivity over large distances in the diadematid sea urchin Centrostephanus sylviae

Most benthic marine invertebrates with sedentary benthic adult phases have planktonic larvae that permit connectivity between geographically isolated populations. Planktonic larval duration and oceanographic processes are vital to connecting populations of species inhabiting remote and distant islands. In the present study, we analyzed the population genetic structure of the sea urchin Centrostephanus sylviae, which inhabits only the Juan Fernández Archipelago and the Desventuradas islands, separated by more than 800 km. For 92 individuals collected from Robinson Crusoe and Selkirk Islands (Juan Fernández Archipelago) and San Ambrosio Island (Desventuradas Islands), 7,067 single nucleotide polymorphisms (SNPs) were obtained. The results did not show a spatial genetic structure for C. sylviae; relative high migration rates were revealed between the islands. An analysis of the water circulation pattern in the area described a predominant northward water flow with periods of inverted flow, suggesting that larvae could move in both directions. Overall, this evidence suggests that C. sylviae comprises a single large population composed of individuals separated by more than 800 km.

Hierarchical genetic structure and implications for conservation of the world's largest salmonid, Hucho taimen

Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.

Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity

Adaptation across environmental gradients has been demonstrated in numerous systems with extensive dispersal, despite high gene flow and consequently low genetic structure. The speed and mechanisms by which such adaptation occurs remain poorly resolved, but are critical to understanding species spread and persistence in a changing world. Here, we investigate these mechanisms in the European green crab Carcinus maenas, a globally distributed invader. We focus on a northwestern Pacific population that spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1500 km, we examine genetic structure using 9376 single nucleotide polymorphisms (SNPs). We find high connectivity among five locations, with significant structure between these locations and an enclosed lagoon with limited connectivity to the coast. Among the five highly connected locations, the only structure observed was a cline driven by a handful of SNPs strongly associated with latitude and winter temperature. These SNPs are almost exclusively found in a large cluster of genes in strong linkage disequilibrium that was previously identified as a candidate for cold tolerance adaptation in this species. This region may represent a balanced polymorphism that evolved to promote rapid adaptation in variable environments despite high gene flow, and which now contributes to successful invasion and spread in a novel environment. This research suggests an answer to the paradox of genetically depauperate yet successful invaders: populations may be able to adapt via a few variants of large effect despite low overall diversity.

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

BACKGROUND

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.

RESULTS

In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.

CONCLUSIONS

Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea

Connectivity of marine populations is shaped by complex interactions between biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications for the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST  = 0.0057, p < .001) and a subset of 1,643 putatively neutral SNP markers (FST  = 0.0042, p < .001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation ( R adj 2  = 0.133, p = .035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (N e < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST  = 0.2390, p < .001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea ( R adj 2  = 0.692-0.763; p < .050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly dispersive marine species, and provides information useful for spatial management of the fishery resource.

The impact of aquaculture on the genetics and distribution of the onuphid annelid Diopatra biscayensis

AIM

Evolutionary history of natural populations can be confounded by human intervention such as the case of decorator worm species Diopatra (Onuphidae), which have a history of being transported through anthropogenic activities. Because they build tubes and act as ecosystem engineers, they can have a large impact on the overall ecosystem in which they occur. One conspicuous member, Diopatra biscayensis, which was only described in 2012, has a fragmented distribution that includes the Bay of Biscay and the Normanno-Breton Gulf in the English Channel. This study explores the origin of these worms in the Normanno-Breton region, which has been debated to either be the result of a historic range contraction from a relic continuous population or a more recent introduction.

LOCATION

Northeastern Atlantic, the Bay of Biscay, and the Normanno-Breton Gulf.

METHODS

We utilized a RAD-tag-based SNP approach to create a reduced genomic data set to recover fine-scale population structure and infer which hypothesis best describes the D. biscayensis biogeographic distribution. The reduced genomic data set was used to calculate standard genetic diversities and genetic differentiation statistics, and utilized various clustering analyses, including PCAs, DAPC, and admixture.

RESULTS

Clustering analyses were consistent with D. biscayensis as a single population spanning the Bay of Biscay to the Normanno-Breton Gulf in the English Channel, although unexpected genetic substructure was recovered from Arcachon Bay, in the middle of its geographic range. Consistent with a hypothesized introduction, the isolated Sainte-Anne locality in the Normanno-Breton Gulf was recovered to be a subset of the diversity found in the rest of the Bay of Biscay.

MAIN CONCLUSIONS

These results are congruent with previous simulations that did not support connectivity from the Bay of Biscay to the Normanno-Breton Gulf by natural dispersal. These genomic findings, with support from previous climatic studies, further support the hypothesis that D. biscayensis phylogeographic connectivity is the result of introductions, likely through the regions' rich shellfish aquaculture, and not of a historically held range contraction.

Incorporating putatively neutral and adaptive genomic data into marine conservation planning

The availability of genomic data for an increasing number of species makes it possible to incorporate evolutionary processes into conservation plans. Recent studies show how genetic data can inform spatial conservation prioritization (SCP), but they focus on metrics of diversity and distinctness derived primarily from neutral genetic data sets. Identifying adaptive genetic markers can provide important information regarding the capacity for populations to adapt to environmental change. Yet, the effect of including metrics based on adaptive genomic data into SCP in comparison to more widely used neutral genetic metrics has not been explored. We used existing genomic data on a commercially exploited species, the giant California sea cucumber (Parastichopus californicus), to perform SCP for the coastal region of British Columbia (BC), Canada. Using a RAD-seq data set for 717 P. californicus individuals across 24 sampling locations, we identified putatively adaptive (i.e., candidate) single nucleotide polymorphisms (SNPs) based on genotype-environment associations with seafloor temperature. We calculated various metrics for both neutral and candidate SNPs and compared SCP outcomes with independent metrics and combinations of metrics. Priority areas varied depending on whether neutral or candidate SNPs were used and on the specific metric used. For example, targeting sites with a high frequency of warm-temperature-associated alleles to support persistence under future warming prioritized areas in the southern coastal region. In contrast, targeting sites with high expected heterozygosity at candidate loci to support persistence under future environmental uncertainty prioritized areas in the north. When combining metrics, all scenarios generated intermediate solutions, protecting sites that span latitudinal and thermal gradients. Our results demonstrate that distinguishing between neutral and adaptive markers can affect conservation solutions and emphasize the importance of defining objectives when choosing among various genomic metrics for SCP.

Population genomics and history of speciation reveal fishery management gaps in two related redfish species (Sebastes mentella and Sebastes fasciatus)

Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.

Population Genomic Analyses of the Sea Urchin Echinometra sp. EZ across an Extreme Environmental Gradient

Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E sp. EZ's life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was among the highest recorded for an echinoderm at 4.5%. We recovered 918 high-quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.

Gene flow in the Antarctic bivalve Aequiyoldia eightsii (Jay, 1839) suggests a role for the Antarctic Peninsula Coastal Current in larval dispersal

The Antarctic Circumpolar Current (ACC) dominates the open-ocean circulation of the Southern Ocean, and both isolates and connects the Southern Ocean biodiversity. However, the impact on biological processes of other Southern Ocean currents is less clear. Adjacent to the West Antarctic Peninsula (WAP), the ACC flows offshore in a northeastward direction, whereas the Antarctic Peninsula Coastal Current (APCC) follows a complex circulation pattern along the coast, with topographically influenced deflections depending on the area. Using genomic data, we estimated genetic structure and migration rates between populations of the benthic bivalve Aequiyoldia eightsii from the shallows of southern South America and the WAP to test the role of the ACC and the APCC in its dispersal. We found strong genetic structure across the ACC (between southern South America and Antarctica) and moderate structure between populations of the WAP. Migration rates along the WAP were consistent with the APCC being important for species dispersal. Along with supporting current knowledge about ocean circulation models at the WAP, migration from the tip of the Antarctic Peninsula to the Bellingshausen Sea highlights the complexities of Southern Ocean circulation. This study provides novel biological evidence of a role of the APCC as a driver of species dispersal and highlights the power of genomic data for aiding in the understanding of the influence of complex oceanographic processes in shaping the population structure of marine species.

Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multimodelling approach

Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine-scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April-September), factoring in larval duration and interannual variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean F ST = 0.021) within a relatively fine spatial scale in the north-west Atlantic. Environmental association analysis indicates that oceanographic currents and geographic proximity explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperature extremes. These results fill an important knowledge gap in the management of a commercially important and overexploited species, bringing us closer to understanding the role of larval dispersal in connecting populations at a fine geographic scale.

Seascape genomics reveals population isolation in the reef-building honeycomb worm, Sabellaria alveolata (L.)

BACKGROUND

Under the threat of climate change populations can disperse, acclimatise or evolve in order to avoid fitness loss. In light of this, it is important to understand neutral gene flow patterns as a measure of dispersal potential, but also adaptive genetic variation as a measure of evolutionary potential. In order to assess genetic variation and how this relates to environment in the honeycomb worm (Sabellaria alveolata (L.)), a reef-building polychaete that supports high biodiversity, we carried out RAD sequencing using individuals from along its complete latitudinal range. Patterns of neutral population genetic structure were compared to larval dispersal as predicted by ocean circulation modelling, and outlier analyses and genotype-environment association tests were used to attempt to identify loci under selection in relation to local temperature data.

RESULTS

We genotyped 482 filtered SNPs, from 68 individuals across nine sites, 27 of which were identified as outliers using BAYESCAN and ARLEQUIN. All outlier loci were potentially under balancing selection, despite previous evidence of local adaptation in the system. Limited gene flow was observed among reef-sites (FST = 0.28 ± 0.10), in line with the low dispersal potential identified by the larval dispersal models. The North Atlantic reef emerged as a distinct population and this was linked to high local larval retention and the effect of the North Atlantic Current on dispersal.

CONCLUSIONS

As an isolated population, with limited potential for natural genetic or demographic augmentation from other reefs, the North Atlantic site warrants conservation attention in order to preserve not only this species, but above all the crucial functional ecological roles that are associated with their bioconstructions. Our study highlights the utility of using seascape genomics to identify populations of conservation concern.

Limited Genetic Connectivity Among Sargassum horneri (Phaeophyceae) Populations in the Chinese Marginal Seas Despite Their high Dispersal Capacity

Sargassum horneri is a habitat-forming species in the Northwest Pacific and an important contributor to seaweed rafts. In this study, 131 benthic samples and 156 floating samples were collected in the Yellow Sea and East China Sea (ECS) to test the effects of seaweed rafts on population structure and connectivity. Our results revealed high levels of genetic diversity in both benthic and floating samples based on concatenated mitochondrial markers (rpl5-rps3, rnl-atp9, and cob-cox2). Phylogenetic analyses consistently supported the existence of two lineages (lineages I and II), with divergence dating to c. 0.692 Mya (95% HPD: 0.255-1.841 Mya), indicating that long-term isolation may have occurred during the mid-Pleistocene (0.126-0.781 Mya). Extended Bayesian skyline plots demonstrated a constant population size over time in lineage I and slight demographic expansion in lineage II. Both lineages were found in each marginal sea (including both benthic and floating samples), but PCoA, FST , and AMOVA analyses consistently revealed deep genetic variation between regions. Highly structured phylogeographic pattern supports limited genetic connectivity between regions. IMA analyses demonstrated that asymmetric gene flow between benthic populations in the North Yellow Sea (NYS) and ECS was extremely low (ECS→NYS, 2Nm = 0.6), implying that high dispersal capacity cannot be assumed to lead to widespread population connectivity, even without dispersal barriers. In addition, there were only a few shared haplotypes between benthic and floating samples, suggesting the existence of hidden donors for the floating masses in the Chinese marginal seas.

Mining whole genome sequence data to efficiently attribute individuals to source populations

Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that efficiently mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.

Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

Ocean circulation driving macro-algal rafting is believed to serve as an important mode of dispersal for many marine organisms, leading to predictions on population-level genetic connectivity and the directionality of effective dispersal. Here, we use genome-wide single nucleotide polymorphism data to investigate whether gene flow directionality in two seahorses (Hippocampus) and three pipefishes (Syngnathus) follows the predominant ocean circulation patterns in the Gulf of Mexico and northwestern Atlantic. In addition, we explore whether gene flow magnitudes are predicted by traits related to active dispersal ability and habitat preference. We inferred demographic histories of these co-distributed syngnathid species, and coalescent model-based estimates indicate that gene flow directionality is in agreement with ocean circulation data that predicts eastward and northward macro-algal transport. However, the magnitude to which ocean currents influence this pattern appears strongly dependent on the species-specific traits related to rafting propensity and habitat preferences. Higher levels of gene flow and stronger directionality are observed in Hippocampus erectus, Syngnathus floridae and Syngnathus louisianae, which closely associated with the pelagic macro-algae Sargassum spp., compared to Hippocampus zosterae and the Syngnathus scovelli/Syngnathus fuscus sister-species pair, which prefer near shore habitats and are weakly associated with pelagic Sargassum. This study highlights how the combination of population genomic inference together with ocean circulation data can help explain patterns of population structure and diversity in marine ecosystems.

Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico

Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While evolutionary divergence occurs through DNA sequence differences among populations, plastic divergence among populations may be generated by changes in the epigenome. Here, we present the results of a genome-wide comparison of DNA methylation patterns and genetic structure among four populations of Eastern oyster (Crassostrea virginica) in the northern Gulf of Mexico. We used a combination of restriction site-associated DNA sequencing (RADseq) and reduced representation bisulfite sequencing (RRBS) to explore population structure, gene-wide averages of F ST, and DNA methylation differences between oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low F ST (0.02) across the freshwater boundary of the Mississippi river, a finding that may reflect recent efforts to restore oyster stock populations. Divergence between populations in CpG methylation was greater than for divergence in F ST, likely reflecting environmental effects on DNA methylation patterns. Assessment of CpG methylation patterns across all populations identified that only 26% of methylated DNA was intergenic; and, only 17% of all differentially methylated regions (DMRs) were within these same regions. DMRs within gene bodies between sites were associated with genes known to be involved in DNA damage repair, ion transport, and reproductive timing. Finally, when assessing the correlation between genomic variation and DNA methylation between these populations, we observed population-specific DNA methylation profiles that were not directly associated with single nucleotide polymorphisms or broader gene-body mean F ST trends. Our results suggest that C. virginica may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.

Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high-throughput genotyping approaches

Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.

Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs

In the open ocean without terrain boundaries, marine invertebrates with pelagic larvae can migrate long distances using ocean currents, suggesting reduced genetic diversification. Contrary to this assumption, however, genetic differentiation is often observed in marine invertebrates. In the present study, we sought to explain how population structure is established in the western Pacific Ocean, where the strong Kuroshio Current maintains high levels of gene flow from south to north, presumably promoting genetic homogeneity. We determined the population structure of the pearl oyster, Pinctada fucata, in the Indo-Pacific Ocean using genome-wide genotyping data from multiple sampling localities. Cluster analysis showed that the western Pacific population is distinct from that of the Indian Ocean, and that it is divided into northern (Japanese mainland) and southern (Nansei Islands, China, and Cambodia) populations. Genetic differentiation of P. fucata can be explained by geographic barriers in the Indian Ocean and a local lagoon, and by environmental gradients of sea surface temperature (SST) and oxygen concentration in the western Pacific. A genome scan showed evidence of adaptive evolution in genomic loci, possibly associated with changes in environmental factors, including SST and oxygen concentration. Furthermore, Bayesian simulation demonstrated that the past population expansion and division are congruent with ocean warming after the last glacial period. It is highly likely that the environmental gradient forms a genetic barrier that diversifies P. fucata populations in the western Pacific. This hypothesis helps to explain genetic differentiation and possible speciation of marine invertebrates.

Seascape genetics of the stalked kelp Pterygophora californica and comparative population genetics in the Santa Barbara Channel

We conducted a population genetic analysis of the stalked kelp, Pterygophora californica, in the Santa Barbara Channel, California, USA. The results were compared with previous work on the genetic differentiation of giant kelp, Macrocystis pyrifera, in the same region. These two sympatric kelps not only share many life history and dispersal characteristics but also differ in that dislodged P. californica does not produce floating rafts with buoyant fertile sporophytes, commonly observed for M. pyrifera. We used a comparative population genetic approach with these two species to test the hypothesis that the ability to produce floating rafts increases the genetic connectivity among kelp patches in the Santa Barbara Channel. We quantified the association of habitat continuity and oceanographic distance with the genetic differentiation observed in stalked kelp, like previously conducted for giant kelp. We compared both overall (across all patches) and pairwise (between patches) genetic differentiation. We found that oceanographic transit time, habitat continuity, and geographic distance were all associated with genetic connectivity in P. californica, supporting similar previous findings for M. pyrifera. Controlling for differences in heterozygosity between kelp species using Jost's DEST , we showed that global differentiation and pairwise differentiation were similar among patches between the two kelp species, indicating that they have similar dispersal capabilities despite their differences in rafting ability. These results suggest that rafting sporophytes do not play a significant role in effective dispersal of M. pyrifera at ecologically relevant spatial and temporal scales.

How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish

Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth, as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these “simple” methodological decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) a larger number of loci at low sequencing depth based on a 9mer (library A); and (2) fewer loci at higher sequencing depth based on a 10mer (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (F_ST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters, largely due to retention of more loci in analyses. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for F_ST and ADMIXTURE, but not DAPC. When detecting fine population differentiation, the population map influenced the number of loci and missing data, which generated artefacts in all downstream analyses tested. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library construction and bioinformatics parameters can have important impacts on the interpretation of population subdivision. Although potentially more costly on a per-locus basis, early investment in striking a balance between the number of loci and sequencing effort is well worth the reduced genomic coverage for population genetics studies. More conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation. Overall, we recommend that researchers approach “simple” methodological decisions with caution, especially when working on non-model species for the first time.

Choosing the right home: settlement responses by larvae of six sea urchin species align with hydrodynamic traits of their contrasting adult habitats

Ocean organisms as diverse as seaweeds and sea cucumbers exhibit life cycles in which dispersal occurs primarily via microscopic larvae or spores, with adults exhibiting limited or even no dispersal. In benthic animals, the larval stage concludes with irreversible settlement into the benthos. The decision of where and when to settle is thus one of substantial import. Prior work has shown that settlement in two shoreline echinoids (a sea urchin and a sand dollar) is unexpectedly sensitive to an environmental feature (intense fluid turbulence) that can be considered as a signal to larvae of their arrival in the neighbourhood of the hydrodynamically energetic habitats in which these taxa live as adults. Here, we used a comparative approach to explore the evolution of turbulence responsiveness in late-stage echinoid larvae. We examined three pairs of closely related sea urchins that differ in the energetic exposure of their adult habitats and found that larval responsiveness to turbulence was more pronounced in urchins that settle in more hydrodynamically exposed locations. These results raise the possibility that evolutionary differences in larval responsiveness to environmental indicators of appropriate adult habitat might reinforce or even provide a mechanism for vicariance in the ocean.

Ocean currents and the population genetic signature of fish migrations

Animal migrations are a fascinating and global phenomenon, yet they are often difficult to study and sometimes poorly understood. Here, we build on classic ecological theory by hypothesizing that some enigmatic spawning migrations across coastal marine habitats can be inferred from the population genetic signature of larval dispersal by ocean currents. We test this assumption by integrating spatially realistic simulations of alternative spawning migration routes, associated patterns of larval dispersal, and associated variation in the population genetic structure of eastern Australian sea mullet (Mugil cephalus). We then use simulation results to assess the implications of alternative spawning destinations for larval replenishment, and we contrast simulated against measured population genetic variation. Both analyses suggest that the spawning migrations of M. cephalus in eastern Australia are likely to be localized (approximately 100 km along the shore), and that spawning is likely to occur in inshore waters. Our conclusions are supported by multiple lines of evidence available through independent studies, but they challenge the more traditional assumption of a single, long-distance migration event with subsequent offshore spawning in the East Australian Current. More generally, our study operationalizes classic theory on the relationship between fish migrations, ocean currents, and reproductive success. However, rather than confirming the traditionally assumed adaptation of migratory behavior to dominant ocean current flow, our findings support the concept of a genetically measurable link between fish migrations and local oceanographic conditions, specifically water temperature and coastal retention of larvae. We believe that future studies using similar approaches for high resolution and spatially realistic ecological-genetic scenario testing can help rapidly advance our understanding of key ecological processes in many other marine species.

Little evidence of adaptation potential to ocean acidification in sea urchins living in "Future Ocean" conditions at a CO2 vent

Ocean acidification (OA) can be detrimental to calcifying marine organisms, with stunting of invertebrate larval development one of the most consistent responses. Effects are usually measured by short-term, within-generation exposure, an approach that does not consider the potential for adaptation. We examined the genetic response to OA of larvae of the tropical sea urchin Echinometra sp. C. raised on coral reefs that were either influenced by CO2 vents (pH ~ 7.9, future OA condition) or nonvent control reefs (pH 8.2). We assembled a high quality de novo transcriptome of Echinometra embryos (8 hr) and pluteus larvae (48 hr) and identified 68,056 SNPs. We tested for outlier SNPs and functional enrichment in embryos and larvae raised from adults from the control or vent sites. Generally, highest F ST values in embryos were observed between sites (intrinsic adaptation, most representative of the gene pool in the spawned populations). This comparison also had the highest number of outlier loci (40). In the other comparisons, classical adaptation (comparing larvae with adults from the control transplanted to either the control or vent conditions) and reverse adaptation (larvae from the vent site returned to the vent or explanted at the control), we only observed modest numbers of outlier SNPs (6-19) and only enrichment in two functional pathways. Most of the outliers detected were silent substitutions without adaptive potential. We conclude that there is little evidence of realized adaptation potential during early development, while some potential (albeit relatively low) exists in the intrinsic gene pool after more than one generation of exposure.