Ocean currents help explain population genetic structure

Does depth divide? Variable genetic connectivity patterns among shallow and mesophotic Montastraea cavernosa coral populations across the Gulf of Mexico and western Caribbean

Despite general declines in coral reef ecosystems in the tropical western Atlantic, some reefs, including mesophotic reefs (30-150 m), are hypothesized to function as coral refugia due to their relative isolation from anthropogenic stressors. Understanding the connectivity dynamics among these putative refugia and more degraded reefs is critical to develop effective management strategies that promote coral metapopulation persistence and recovery. This study presents a geographically broad assessment of shallow (<30 m) and mesophotic (>30 m) connectivity dynamics of the depth-generalist coral species Montastraea cavernosa. Over 750 coral genets were collected across the Northwest and Southern Gulf of Mexico, Florida, Cuba, and Belize, and ~5000 SNP loci were generated to quantify high-resolution genetic structure and connectivity among these populations. Generally, shallow and mesophotic populations demonstrated higher connectivity to distant populations within the same depth zone than to adjacent populations across depth zones. However, exceptions to this pattern include the Northwest Gulf of Mexico and the Florida Keys which exhibited relatively high vertical genetic connectivity. Furthermore, estimates of recent gene flow emphasize that mesophotic M. cavernosa populations are not significant sources for their local shallow counterparts, except for the Northwest Gulf of Mexico populations. Location-based differences in vertical connectivity are likely a result of diverse oceanographic and environmental conditions that may drive variation in gene flow and depth-dependent selection. These results highlight the need to evaluate connectivity dynamics and refugia potential of mesophotic coral species on a population-by-population basis and to identify stepping-stone populations that warrant incorporation in future international management approaches.

Determining the most recent common ancestor in a finite linear habitat with asymmetric dispersal

Many species that are birthed in one location and become reproductive in another location can be treated as if in a one-dimensional habitat where dispersal is biased downstream. One example of such is planktonic larvae that disperse in coastal oceans, rivers, and streams. In these habitats, the dynamics of the dispersal are dominated by the movement of offspring in one direction and the distance between parents and offspring in the other direction does not matter. We study an idealized species with non-overlapping generations in a finite linear habitat that has no larval input from outside of the habitat and is therefore isolated from other populations. The most non-realistic assumption that we make is that there are non-overlapping generations, and this is an assumption to be considered in future work. We find that a biased dispersal in the habitat reduces the average time to the most recent common ancestor and causes the average location of the most recent common ancestor to move from the center of the habitat to the upstream edge of the habitat. Due to the decrease in the time to the most recent common ancestor and the shift of the average location to the upstream edge, the effective population size (Ne) no longer depends on the census size and is dependent on the dispersal statistics. We determine the average time and location of the most recent common ancestor as a function of the larval dispersal statistics. The location of the most recent common ancestor becomes independent of the length of the habitat and is only dependent on the location of the upstream edge and the larval dispersal statistics.

Reduced genetic diversity and restricted gene flow of broadcast-spawning coral Galaxea fascicularis in the South China Sea reveals potential degradation under environmental change

Under the dual effects of climate change and anthropogenic activities, coral reefs in the South China Sea (SCS) are at serious risk of degradation. Galaxea fascicularis is a widely distributed species in the SCS, and the study of its genetics, survival, and adaptability is conducive to further understanding the future characteristics of coral reefs in the SCS. In this study, 146 G. fascicularis samples were selected from 9 survey stations across 12 latitudes in the SCS, and 8 pairs of microsatellite markers were used to characterize their genetic diversity and structure. The results showed moderate genetic diversity index values (Ar = 3.444-4.147, He = 0.634-0.782, Ho = 0.367-0.586). The AMOVA results and pairwise FST values showed a moderate level of genetic differentiation (ΦST = 0.119, P < 0.05) among G. fascicularis populations in the SCS, whereas its genetic structure showed high genetic differentiation (FST = 0.062-0.225) among relatively high-latitude populations (n = 3) and low genetic differentiation (FST = 0.012-0.064) in low-latitude populations (n = 6). The living environment of relatively high-latitude populations is disturbed by high-intensity human activities, leading to the specialization of local populations. Mantel test results showed a significant positive correlation between genetic differentiation among G. fascicularis populations and sea surface temperature (SST) variance (R2 = 0.4885; Mantel test, p = 0.010 < 0.05) in addition to geographical distance (R2 = 0.1134; Mantel, test p = 0.040 < 0.05), indicating that SST and geographical isolation were primary factors affecting the genetic structure of this species in the SCS. The lower genetic diversity and limited gene flow of G. fascicularis indicate limited genetic adaptation, and corresponding vulnerability may be more pronounced under future environmental changes. These findings provide a theoretical basis for the conservation and restoration of coral reefs in the SCS.

Phytoplankton diversity explained by connectivity across a mesoscale frontal system in the open ocean

Phytoplankton community composition is important in establishing ecosystem structure and function. Intuitively, we recognize that water movements must be important for modifying spatial gradients and plankton diversity. However, identifying boundaries and exchange between habitats in the open ocean is not straightforward. Here, we use the abundance of nine phytoplankton species closely sampled in a mesoscale frontal system in the northeastern North Sea as a proxy for community composition and explore the relationship between phytoplankton biogeography and transport patterns. Subsurface community distributions could be related to modeled patterns in water movement. A methodology for analyzing pelagic diversity that includes a representation of plankton community composition and an Eulerian connectivity tracer was developed, and the relative importance of connectivity and geographical distance for phytoplankton species composition analyzed. The connectivity tracer identifies timescales and dispersal barriers in the open ocean. Connectivity was found to be superior in explaining pelagic plankton diversity and found to be a prerequisite for understanding the pelagic phytoplankton composition. This approach is a valuable tool for establishing the link between ocean transports, ecosystem structure and biodiversity and for informing the placement of marine protected areas.

Ocean connectivity and habitat characteristics predict population genetic structure of seagrass in an extreme tropical setting

Understanding patterns of gene flow and processes driving genetic differentiation is important for a broad range of conservation practices. In marine organisms, genetic differentiation among populations is influenced by a range of spatial, oceanographic, and environmental factors that are attributed to the seascape. The relative influences of these factors may vary in different locations and can be measured using seascape genetic approaches. Here, we applied a seascape genetic approach to populations of the seagrass, Thalassia hemprichii, at a fine spatial scale (~80 km) in the Kimberley coast, western Australia, a complex seascape with strong, multidirectional currents greatly influenced by extreme tidal ranges (up to 11 m, the world's largest tropical tides). We incorporated genetic data from a panel of 16 microsatellite markers, overwater distance, oceanographic data derived from predicted passive dispersal on a 2 km-resolution hydrodynamic model, and habitat characteristics from each meadow sampled. We detected significant spatial genetic structure and asymmetric gene flow, in which meadows 12-14 km apart were less connected than ones 30-50 km apart. This pattern was explained by oceanographic connectivity and differences in habitat characteristics, suggesting a combined scenario of dispersal limitation and facilitation by ocean current with local adaptation. Our findings add to the growing evidence for the key role of seascape attributes in driving spatial patterns of gene flow. Despite the potential for long-distance dispersal, there was significant genetic structuring over small spatial scales implicating dispersal and recruitment bottlenecks and highlighting the importance of implementing local-scale conservation and management measures.

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.

Reconstructing the colonization history of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Northwestern Australia

Bottlenose dolphins (Tursiops spp.) are found in waters around Australia, with T. truncatus typically occupying deeper, more oceanic habitat, while T. aduncus occur in shallower, coastal waters. Little is known about the colonization history of T. aduncus along the Western Australian coastline; however, it has been hypothesized that extant populations are the result of an expansion along the coastline originating from a source in the north of Australia. To investigate the history of coastal T. aduncus populations in the area, we generated a genomic SNP dataset using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach. The resulting dataset consisted of 103,201 biallelic SNPs for 112 individuals which were sampled from eleven coastal and two offshore sites between Shark Bay and Cygnet Bay, Western Australia. Our population genomic analyses showed a pattern consistent with the proposed source in the north with significant isolation by distance along the coastline, as well as a reduction in genomic diversity measures along the coastline with Shark Bay showing the most pronounced reduction. Our demographic analysis indicated that the expansion of T. aduncus along the coastline began around the last glacial maximum and progressed southwards with the Shark Bay population being founded only 13 kya. Our results are in line with coastal colonization histories inferred for Tursiops globally, highlighting the ability of delphinids to rapidly colonize novel coastal niches as habitat is released during glacial cycle-related global sea level and temperature changes.

Genetic Diversity and Structure Revealed by Genomic Microsatellite Markers of Mytilus unguiculatus in the Coast of China Sea

The hard-shelled mussel Mytilus unguiculatus plays an important role in mussel aquaculture in China due to its characteristic and nutritive value. In this study, 10 microsatellite loci are used to study the genetic diversity and genetic structure of seven location populations of M. unguiculatus in coastal areas of China. The results of amplification and genotyping show that the observed heterozygosity (H_o) and the expected heterozygosity (H_e) are 0.61~0.71 and 0.72~0.83, respectively. M. unguiculatus has high genetic diversity. The inbreeding index (F_IS) of M. unguiculatus is significantly positive (F_IS: 0.14~0.19), indicating that inbreeding might exist within populations. The genetic structure of M. unguiculatus is weak within populations from the East China Sea All results showed that genetic differences existed between the Qingdao population from the Yellow Sea and other populations from the East China Sea. It does not detect a population bottleneck event or expansion event in the populations. The results from this study can be used to provide important insights in genetic management units and sustainable utilization of M. unguiculatus resources and provide a better understand of genetic structure of marine bivalve with similar planktonic larval stage in the China Sea.

Genomic assessment of larval odyssey: self-recruitment and biased settlement in the Hawaiian surgeonfish Acanthurus triostegus sandvicensis

The gap between spawning and settlement location of marine fishes, where the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches provide some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, the authors applied this method to the endemic Hawaiian convict tang (Acanthurus triostegus sandvicensis), a surgeonfish with a long pelagic larval stage of c. 54-77 days. They collected 606 adults and 607 juveniles from 23 locations around the island of O'ahu, Hawai'i. Based on 399 single nucleotide polymorphisms, the authors assigned 68 of these juveniles back to a parent (11.2% assignment rate). Each side of the island showed significant population differentiation, with higher levels in the west and north. The west and north sides of the island also had little evidence of recruitment, which may be due to westerly currents in the region or an artefact of uneven sampling. In contrast, the majority of juveniles (94%) sampled along the eastern shore originated on that side of the island, primarily within semi-enclosed Kāne'ohe Bay. Nearly half of the juveniles assigned to parents were found in the southern part of Kāne'ohe Bay, with local settlement likely facilitated by extended water residence time. Several instances of self-recruitment, when juveniles return to their natal location, were observed along the eastern and southern shores. Cumulatively, these findings indicate that most dispersal is between adjacent regions on the eastern and southern shores. Regional management efforts for Acanthurus triostegus and possibly other reef fishes will be effective only with collaboration among adjacent coastal communities, consistent with the traditional moku system of native Hawaiian resource management.

Cross-Hemispheric Genetic Diversity and Spatial Genetic Structure of Callinectes sapidus Reovirus 1 (CsRV1)

The movement of viruses in aquatic systems is rarely studied over large geographic scales. Oceanic currents, host migration, latitude-based variation in climate, and resulting changes in host life history are all potential drivers of virus connectivity, adaptation, and genetic structure. To expand our understanding of the genetic diversity of Callinectes sapidus reovirus 1 (CsRV1) across a broad spatial and host life history range of its blue crab host (Callinectes sapidus), we obtained 22 complete and 96 partial genomic sequences for CsRV1 strains from the US Atlantic coast, Gulf of Mexico, Caribbean Sea, and the Atlantic coast of South America. Phylogenetic analyses of CsRV1 genomes revealed that virus genotypes were divided into four major genogroups consistent with their host geographic origins. However, some CsRV1 sequences from the US mid-Atlantic shared high genetic similarity with the Gulf of Mexico genotypes, suggesting potential human-mediated movement of CsRV1 between the US mid-Atlantic and Gulf coasts. This study advances our understanding of how climate, coastal geography, host life history, and human activity drive patterns of genetic structure and diversity of viruses in marine animals and contributes to the capacity to infer broadscale host population connectivity in marine ecosystems from virus population genetic data.

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.

The role of genomic signatures of directional selection and demographic history in the population structure of a marine teleost with high gene flow

Recent studies have uncovered patterns of genomic divergence in marine teleosts where panmixia due to high gene flow has been the general paradigm. These signatures of divergent selection are often impacted by structural variants, acting as "supergenes" facilitating local adaptation. The highly dispersing European plaice (Pleuronectes platessa)-in which putative structural variants (i.e., inversions) have been identified-has successfully colonized the brackish water ecosystem of the Baltic Sea. Thus, the species represents an ideal opportunity to investigate how the interplay of gene flow, structural variants, natural selection, past demographic history, and gene flow impacts on population (sub)structuring in marine systems. Here, we report on the generation of an annotated draft plaice genome assembly in combination with population sequencing data-following the salinity gradient from the Baltic Sea into the North Sea together with samples from Icelandic waters-to illuminate genome-wide patterns of divergence. Neutral markers pointed at large-scale panmixia across the European continental shelf associated with high gene flow and a common postglacial colonization history of shelf populations. However, based on genome-wide outlier loci, we uncovered signatures of population substructuring among the European continental shelf populations, i.e., suggesting signs of ongoing selection. Genome-wide selection analyses (xp-EHH) and the identification of genes within genomic regions of recent selective sweeps-overlapping with the outlier loci-suggest that these represent the signs of divergent selection. Our findings provide support for genomic divergence driven by local adaptation in the face of high gene flow and elucidate the relative importance of demographic history versus adaptive divergence in shaping the contemporary population genetic structure of a marine teleost. The role of the putative inversion(s) in the substructuring-and potentially ongoing adaptation-was seemingly not substantial.

Molecular Evolutionary Growth of Ultralong Semiconducting Double-Walled Carbon Nanotubes

The self-assembling preparation accompanied with template auto-catalysis loop and the ability to gather energy, induces the appearance of chirality and entropy reduction in biotic systems. However, an abiotic system with biotic characteristics is of great significance but still missing. Here, it is demonstrated that the molecular evolution is characteristic of ultralong carbon nanotube preparation, revealing the advantage of chiral assembly through template auto-catalysis growth, stepwise-enriched chirality distribution with decreasing entropy, and environmental effects on the evolutionary growth. Specifically, the defective and metallic nanotubes perform inferiority to semiconducting counterparts, among of which the ones with double walls and specific chirality (n, m) are more predominant due to molecular coevolution. An explicit evolutionary trend for tailoring certain layer chirality is presented toward perfect near-(2n, n)-containing semiconducting double-walled nanotubes. These findings extend our conceptual understanding for the template auto-catalysis assembly of abiotic carbon nanotubes, and provide an inspiration for preparing chiral materials with kinetic stability by evolutionary growth.

Spatial and temporal variation of genetic diversity and genetic differentiation in Daphnia galeata populations in four large reservoirs in southern China

Daphnia galeata is a common and dominant species in warmer waters, and has a strong top-down effect on both phytoplankton and bacteria. The knowledge of its temporal and spatial patterns of genetic diversity is fundamental in understanding its population dynamics and potential ecological function in ecosystems. Its population genetics have been investigated at regional scales but few within regions or at smaller spatial scales. Here, we examined the fine-scale spatial genetic variation of D. galeata within four large, deep reservoirs in wet and dry seasons and the six-year variation of genetic diversity in one of the reservoirs by using cytochrome c oxidase subunit I and microsatellites (simple sequence repeat). Our study shows that fine-scale spatial genetic variation commonly occurred within the reservoirs, indicating strong environmental selection at least in the two of reservoirs with strong longitudinal gradients. Since the environmental gradients established in the dry season was largely reduced in the wet season, the fine-scale spatial genetic variation was much higher in the dry season. The dynamics of local genetic diversity did not follow the theoretical pattern of rapid erosion but peaked in mid or mid-late growth season. The local genetic diversity of D. galeata appears to be shaped and maintained not only by recruitment from resting egg banks but also by gene flow within reservoirs. The temporal and fine-scale genetic variation within a water body suggests that it is necessary to pay attention to sampling periods and locations of a given water body in regional studies.

Phylogenetic evidence of the re-evolution of planktotrophy in Australian periwinkles

The mode of development of marine invertebrates has major effects on dispersal and population structure. Species without a feeding larval stage (direct developers) are generally more genetically subdivided than species with planktotrophic (swimming and feeding) development. Evidence of the re-evolution of planktotrophy from a direct-developing ancestor has been accumulating within marine invertebrates. However, it remains unclear whether such evolutionary transitions are rare or common. The Bembicium genus (Gastropoda: Littorinidae) provides an additional opportunity to examine the re-evolution of planktotrophy. The genus includes two species with planktotrophic development (Bembicium auratum and Bembicium nanum) and three species with direct development (Bembicium vittatum, Bembicium melanostoma and Bembicium flavescens). Phylogenetic analyses based on sequences of two mitochondrial markers (COI and 16S rRNA) and one nuclear marker (ANT) provide evidence for a switch from direct development back to planktotrophy. Also, pairwise genetic distances between haplotypes reveal that the two planktotrophic species have greater genetic diversity (at the species level) than the direct developers, and the three direct-developing species are genetically structured based on geographical distance. Our study adds to growing evidence for the re-evolution of planktotrophy and suggests that the genetic basis for a switch between modes of development might be simple in marine snails.

Genome‐wide SNPs of vegetable leafminer, Liriomyza sativae : insights into the recent Australian invasion

Liriomyza sativae, the vegetable leafminer, is an important agricultural pest originally from the Americas, which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country near the Torres Strait, which provides a possible pathway for pests to enter Australia and evade biosecurity efforts. Here, we assessed genetic variation in L. sativae based on genome‐wide single nucleotide polymorphisms (SNPs) generated by double digest restriction‐site‐associated DNA sequencing (ddRAD‐seq), aiming to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our fineRADstructure results and principal component analysis suggest Australian mainland populations were genetically close to populations from the Torres Strait, whereas populations from Asia, Africa, and Papua New Guinea (PNG) were more distantly related. Hawaiian populations were genetically distinct from all other populations of L. sativae included in our study. Admixture analyses further revealed that L. sativae from the Torres Strait may have genetic variation originating from multiple sources including Indonesia and PNG, and which has now spread to the Australian mainland. The L. sativae lineages from Asia and Africa appear closely related. Isolation‐by‐distance (IBD) was found at a broad global scale, but not within small regions, suggesting that human‐mediated factors likely contribute to the local spread of this pest. Overall, our findings suggest that an exotic Liriomyza pest invaded Australia through the Indo‐Papuan conduit, highlighting the importance of biosecurity programs aimed at restricting the movement of pests and diseases through this corridor.

IIb-RAD-sequencing coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice (Lepeophtheirus salmonis)

The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between subpopulations must be studied to monitor louse species and enhance targeted control measures. We have used IIb-RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19,428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish the differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection was also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.

High-throughput SNPs dataset reveal restricted population connectivity of marine gastropod within the narrow distribution range of peripheral oceanic islands

Molecular studies based on the high resolution genetic markers help us to grasp the factor shaping the genetic structure of marine organisms. Ecological factors linking to life history traits have often explained the process of genetic structuring in open and connectable oceanic environments. Besides, population genetic divergence can be affected by fragmented habitat, oceanic current, and past geographical events. In the present study, we demonstrated the genetic differentiation of marine gastropod Monodonta sp. within a narrow range of peripheral oceanic islands, the Ogasawara Islands. Genetic analyses were performed not only with a mitochondrial DNA marker but also with a high-throughput SNPs dataset obtained by ddRAD-seq. The results of the mtDNA analyses did not show genetic divergence among populations, while the SNPs dataset detected population genetic differentiation. Population demographic analyses and gene flow estimation suggested that the genetic structure was formed by sea level fluctuation associated with the past climatic change and regulated by temporal oceanographic conditions. These findings provide important insights into population genetic patterns in open and connectable environments.

Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas

Most marine invertebrates disperse during a planktonic larval stage that may drift for weeks with ocean currents. A challenge for larvae of coastal species is to return to coastal nursery habitats. Shore crab (Carcinus maenas L.) larvae are known to show tidal rhythmicity in vertical migration in tidal areas and circadian rhythmicity in microtidal areas, which seems to increase successful coastal settlement. We studied genome‐wide differentiation based on 24,000 single nucleotide polymorphisms of 12 native populations of shore crab sampled from a large tidal amplitude gradient from macrotidal (~8 m) to microtidal (~0.2 m). Dispersal and recruitment success of larvae was assessed with a Lagrangian biophysical model, which showed a strong effect of larval behaviour on long‐term connectivity, and dispersal barriers that partly coincided with different tidal environments. The genetic population structure showed a subdivision of the samples into three clusters, which represent micro‐, meso‐ and macrotidal areas. The genetic differentiation was mostly driven by 0.5% outlier loci, which showed strong allelic clines located at the limits between the three tidal areas. Demographic modelling suggested that the two genetic barriers have different origins. Differential gene expression of two clock genes (cyc and pdp1) further highlighted phenotypic differences among genetic clusters that are potentially linked to the differences in larval behaviour. Taken together, our seascape genomic study suggests that tidal regime acts as a strong selection force on shore crab population structure, consistent with larval behaviour affecting dispersal and recruitment success.

Right out of the gate: the genomics of Lessepsian invaders in the vicinity of the Suez Canal

Marine organisms that enter the Mediterranean from the Red Sea via the Suez Canal are known as Lessepsian bioinvaders. In general, genetic studies of Lessepsian fishes have shown little structure between Red Sea and Mediterranean populations. Yet notable exceptions suggest the importance of life-history factors that may influence patterns of spatial genetic variation. In this study, by sampling two invasive fishes with different life histories (the rabbitfish Siganus rivulatus and the filefish Stephanolepis diaspros), we looked at evidence of population structure and selection at the boundary between the Red Sea and the Mediterranean (the Suez Canal), using thousands of molecular markers. Results illustrate two divergent patterns of genetic patterns, with little genetic structure in S. rivulatus and strong population structure in S. diaspros, even at such small spatial scale. We discuss differences in ecological characteristics between the two species to account for such differences. In addition, we report that in the face of both high (S. rivulatus) and low (S. diaspros) gene flow, loci under selection were uncovered, and some protein coding genes were identified as being involved with osmoregulation, which seems to be an important feature of individuals crossing the salinity-variable Suez Canal. The presence of genes under selection in populations near the Suez Canal supports the idea that selection may be active and essential for successful invasions right out of the gate.

Comparing the genetic diversity and population structure of sister marine snails having contrasting habitat specificity

BACKGROUND

To grasp the processes of spatial genetic structuring in open and connectable marine environments is the principal study goal in molecular biological studies. Comparative seascape genetics using multiple species are a powerful approach to understand the physical geographic and oceanographic effects on genetic variation. Besides, species-specific ecological traits such as dispersal abilities and habitat specificity are important factors for spatial genetic structuring.

METHODS AND RESULTS

We focused on the sister marine snail species Tegula kusairo and T. xanthostigma around the Japanese mainland, which have contrasting habitat specificities for wave strength. Tegula kusairo only inhabits sheltered coastal environments, while T. xanthostigma is found mainly on wave-exposed rocky shores facing the open sea. We estimated their genetic diversity indices and levels of population differentiation based on mtDNA. We found that the genetic diversity of T. kusairo was lower than that of T. xanthostigma, while their level of population genetic differentiation was higher than that of T. xanthostigma. Namely, the species specific to weak wave environments had a higher level of population genetic differentiation than the species specific to strong wave action.

CONCLUSION

Ecological traits linked not only to dispersal abilities but also to habitat specificity can influence genetic variation in a pair of closely related sister species distributed in the same seascape.

Individual-based eco-evolutionary models for understanding adaptation in changing seas

As climate change threatens species' persistence, predicting the potential for species to adapt to rapidly changing environments is imperative for the development of effective conservation strategies. Eco-evolutionary individual-based models (IBMs) can be useful tools for achieving this objective. We performed a literature review to identify studies that apply these tools in marine systems. Our survey suggested that this is an emerging area of research fuelled in part by developments in modelling frameworks that allow simulation of increasingly complex ecological, genetic and demographic processes. The studies we identified illustrate the promise of this approach and advance our understanding of the capacity for adaptation to outpace climate change. These studies also identify limitations of current models and opportunities for further development. We discuss three main topics that emerged across studies: (i) effects of genetic architecture and non-genetic responses on adaptive potential; (ii) capacity for gene flow to facilitate rapid adaptation; and (iii) impacts of multiple stressors on persistence. Finally, we demonstrate the approach using simple simulations and provide a framework for users to explore eco-evolutionary IBMs as tools for understanding adaptation in changing seas.

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.

Combining genotypic and phenotypic variation in a geospatial framework to identify sources of mussels in northern New Zealand

The New Zealand green-lipped mussel aquaculture industry is largely dependent on the supply of young mussels that wash up on Ninety Mile Beach (so-called Kaitaia spat), which are collected and trucked to aquaculture farms. The locations of source populations of Kaitaia spat are unknown and this lack of knowledge represents a major problem because spat supply may be irregular. We combined genotypic (microsatellite) and phenotypic (shell geochemistry) data in a geospatial framework to determine if this new approach can help identify source populations of mussels collected from two spat-collecting and four non-spat-collecting sites further south. Genetic analyses resolved differentiated clusters (mostly three clusters), but no obvious source populations. Shell geochemistry analyses resolved six differentiated clusters, as did the combined genotypic and phenotypic data. Analyses revealed high levels of spatial and temporal variability in the geochemistry signal. Whilst we have not been able to identify the source site(s) of Kaitaia spat our analyses indicate that geospatial testing using combined genotypic and phenotypic data is a powerful approach. Next steps should employ analyses of single nucleotide polymorphism markers with shell geochemistry and in conjunction with high resolution physical oceanographic modelling to resolve the longstanding question of the origin of Kaitaia spat.

Identification of dispersal barriers for a colonising seagrass using seascape genetic analysis

Seagrasses are important habitats providing many ecological services. Most species have broad distributions with maximum dispersal distances of 100's of kms, however there is limited understanding of dispersal distances of colonising species like Halodule uninervis. It commonly grows in disturbed environments and could disperse to other meadows via clonal fragments. Effective conservation management requires greater understanding of genetic structure, dispersal barriers, and connectivity timescales to predict recovery following disturbance. Despite fragment viability of up to 28 days in a congenera, this theory remains untested in situ. Using 80 neutral single nucleotide polymorphisms, we investigated genetic diversity, gene flow patterns and structure among 15 populations of H. uninervis along 2000 km of Western Australian coastline. These data were combined with a multi-generational oceanographic dispersal model and a barrier dispersal analysis to identify dispersal barriers and determine which fragment dispersal duration (FDD) and timescale over which stepping-stone connectivity occurred, best matched the observed genetic structure. The 2-7 day FDD best matched the genetic structure with 4-12 clusters, with barriers to dispersal that persisted for up to 100 years. Modelling suggested greater fragmentation of metapopulations towards the southern edge of the species distribution, but genetic diversity did not decline. Several long-term boundaries were identified even with fragment viability of up to 28 days. This suggests H. uninervis dispersal is spatially limited by factors like oceanographic features and habitat continuity which may limit dispersal of this species. This study reiterates that potential dispersal does not equal realised dispersal, and management scales of 10's of kilometers are required to maintain existing meadows. Recruitment from distances further than this scale are unlikely to aid recovery after extreme disturbance events, particularly towards the range edge of H. uninervis distribution.

Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation

Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.

Species boundaries and phylogeographic patterns in new species of Nannoniscus (Janiroidea: Nannoniscidae) from the equatorial Pacific nodule province inferred from mtDNA and morphology

Spatial patterns of genetic variation (based on COI and 16S mtDNA) for morphologically similar species in the isopod genus Nannoniscus G.O. Sars. 1870 were examined that occur broadly across the Clarion Clipperton Fracture Zone (CCZ). Samples were obtained from five different licence areas as well as an Area of Particular Environmental Interest (APEI-6) with sites located at various distances (a few to several hundred kilometres) from one another. Applying three different species delimitation (SD) methods (sGMYC, mPTP and ABGD) of the molecular data, we could distinguish between four and 12 different molecular taxonomic operational units (MOTUs). Morphological analyses could confirm five distinct phenotypic clades that represent species new to science and are described here: Nannoniscus brenkei sp. nov., Nannoniscus hilario sp. nov., Nannoniscus magdae sp. nov., Nannoniscus menoti sp. nov. and Nannoniscus pedro sp. nov. Despite the assumed limited dispersal capacity of Nannoniscus species, we found haplotypes of two species to be geographically widespread (up to &gt; 1400 km apart), as opposed to several divergent clades occurring in close vicinity or even sympatry. Geographic distance appeared to explain the phylogeographic structure of Nannoniscus species to some extent, although oceanographic features and level of environmental heterogeneity were probably equally important.

Temperature reduces fish dispersal as larvae grow faster to their settlement size

As species struggle to cope with rising ocean temperatures, temperate marine assemblages are facing major reorganization. Many benthic species have a brief but critical period dispersing through the plankton, when they are particularly susceptible to variations in temperature. Impacts of rising temperatures can thus ripple through the population with community-wide consequences. However, responses are highly species-specific, making it difficult to discern assemblage-wide patterns in the life histories of different fish species. Here, we evaluate the responses to temperature in the early life histories of several fish species using otolith reconstructive techniques. We also assess the consequences of future warming scenarios to this assemblage. We sampled recent settlers of nine common species across a temperature gradient in the Mediterranean Sea and obtained environmental data for each individual. Using otolith microstructure, we measured early life traits including pelagic larval duration (PLD), growth rate, settlement size, hatching and settlement dates. We used a GLM framework to examine how environmental variables influenced early life-history parameters. We show that increasing temperature results in considerable reduction in the dispersal potential of temperate fish. We find a nearly universal, assemblage-wide decline in pelagic larval duration (PLD) of between 10% and 25%. This was because, with increasing temperature, larvae grew quicker to their settlement size. Settlement size itself was less affected by temperature and appears to be an ontogenetically fixed process. Given current estimates of ocean warming, there could be an assemblage-wide reduction in larval dispersal of up to 50 km across the Mediterranean, reducing connectivity and potentially isolating populations as waters warm.

Pleistocene Ice Ages Created New Evolutionary Lineages, but Limited Speciation in Northeast Pacific Winged Kelp

The extent that Pleistocene climate variability promoted speciation has been much debated. Here, we surveyed genetic markers in winged kelp Alaria in the Gulf of Alaska, Northeast Pacific Ocean to understand how paleoclimates may have influenced diversity in this kelp. The study included wide geographic sampling over 2800 km and large sample sizes compared to previous studies of this kelp. Mitochondrial 5'-COI (664 bp), plastid rbcL-3' (740 bp) and 8 microsatellite markers in 16 populations resolved 5 well-defined lineages. COI-rbcL haplotypes were distributed chaotically among populations around the Gulf of Alaska. Principal Coordinates Analysis of microsatellite genotypes grouped plants largely by organellar lineage instead of geography, indicating reproductive isolation among lineages. However, microsatellite markers detected hybrids at 3 sites where lineages co-occurred. Local adaptation on various time scales may be responsible for some genetic differences between populations located along wave-energy and salinity gradients, but the chaotic pattern of variability over hundreds of kilometers is likely due to isolations in northern refugia during Pleistocene ice ages. The range of divergences between populations indicates that episodic glaciations led to the creation of new lineages, but population turnover (local extinctions and recolonizations) limited the formation of new species in the Northeastern Pacific Ocean.

Nuclear microsatellites reveal population genetic structuring and fine-scale pattern of hybridization in the Japanese mantis shrimp Oratosquilla oratoria

The interplay between historical and contemporary processes can produce complex patterns of genetic differentiation in the marine realm. Recent mitochondrial and nuclear sequence analyses revealed cryptic speciation in the Japanese mantis shrimp Oratosquilla oratoria. Herein, we applied nuclear microsatellite markers to examine patterns and causes of genetic differentiation in this morphotaxon. Population structure analyses revealed two genetically divergent and geographically structured clades in O. oratoria, one dominating the temperate zone of the Northwestern (NW) Pacific and the other occurring in the subtropical and tropical waters where are influenced by the Kuroshio Current. Two sympatric zones, one around the Changjiang Estuary in China coast and the other in the northern Japan Sea, were demonstrated to be hybrid zones where introgressive hybridization occurred asymmetrically. The interaction between historical climate shifts and contemporary factors (e.g., freshwater discharge, temperature gradient and isolation by distance) may contribute to the present-day genetic architecture in the Japanese mantis shrimp. Range shift induced by climate changes and oceanographic factors may promote hybridization and gene flow between the O. oratoria complex. Our results provide insights into the interacting mechanisms that give rise to diversification and speciation of coastal species in the NW Pacific.

Investigation of mechanisms underlying chaotic genetic patchiness in the intertidal marbled crab Pachygrapsus marmoratus (Brachyura: Grapsidae) across the Ligurian Sea

Background

Studies on marine community dynamics and population structures are limited by the lack of exhaustive knowledge on the larval dispersal component of connectivity. Genetic data represents a powerful tool in understanding such processes in the marine realm. When dealing with dispersion and connectivity in marine ecosystems, many evidences show patterns of genetic structure that cannot be explained by any clear geographic trend and may show temporal instability. This scenario is usually referred to as chaotic genetic patchiness, whose driving mechanisms are recognized to be selection, temporal shifts in local population dynamics, sweepstakes reproductive success and collective dispersal.

In this study we focused on the marbled crab Pachygrapsus marmoratus that inhabits the rocky shores of the Mediterranean Sea, Black Sea and East Atlantic Ocean, and disperses through planktonic larvae for about 1 month. P. marmoratus exhibits unexpectedly low connectivity levels at local scale, although well-defined phylogeographic patterns across the species’ distribution range were described. This has been explained as an effect of subtle geographic barriers or due to sweepstake reproductive success. In order to verify a chaotic genetic patchiness scenario, and to explore mechanisms underlying it, we planned our investigation within the Ligurian Sea, an isolated basin of the western Mediterranean Sea, and we genotyped 321 individuals at 11 microsatellite loci.

Results

We recorded genetic heterogeneity among our Ligurian Sea samples with the occurrence of genetic clusters not matching the original populations and a slight inter-population divergence, with the geographically most distant populations being the genetically most similar ones. Moreover, individuals from each site were assigned to all the genetic clusters. We also recorded evidences of self-recruitment and a higher than expected within-site kinship.

Conclusions

Overall, our results suggest that the chaotic genetic patchiness we found in P. marmoratus Ligurian Sea populations is the result of a combination of differences in reproductive success, en masse larval dispersion and local larval retention. This study defines P. marmoratus as an example of marine spawner whose genetic pool is not homogenous at population level, but rather split in a chaotic mosaic of slightly differentiated genetic patches derived from complex and dynamic ecological processes.

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.

Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species

Background

Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species.

Methods

White seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (N_e), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary N_e.

Results

For mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and the sand smelt. Haplotype networks revealed deep genealogies, with various levels of diversification. The shanny revealed a smaller N_e/generation when compared to the other species, which, in turn, revealed no evidence of genetic drift for most study periods. These results highlight the fact that temporal variations in genetic pool composition should be considered when evaluating the population structure of fish species with long distance dispersal, which are more vulnerable to recruitment fluctuations.

Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate

Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral Millepora cf. platyphylla. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 27,000 m² of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with a minimum of 8% of sexual propagules produced locally. Assigned offspring often settled at <10 m from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal versus nonclonal genotypes. Interhabitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit nearby on the reef (more than 40% settled at <30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.

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.

Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea

Sandeels are an ecologically important group of fishes; they are a key part of the food chain serving as food for marine mammals, seabirds and fish. Sandeels are further targeted by a large industrial fishery, which has led to concern about ecosystem effects. In the North Sea, the lesser sandeel Ammodytes marinus is by far the most prevalent species of sandeel in the fishery. Management of sandeel in the North Sea plus the Kattegat is currently divided into seven geographical areas, based on subtle differences in demography, population dynamics and results from simulations of larval dispersal. However, little is known about the underlying genetic population structure. In this study, we used 2,522 SNPs derived from restriction site-associated DNA sequencing (RADseq) typed in 429 fish representing four main sandeel management areas. Our main results showed (a) a lack of a clear spatially defined genetic structure across the majority of genetic markers and (b) the existence of a group of at least 13 SNPs under strong linkage disequilibrium which together separate North Sea sandeel into three haplotype clusters, suggestive of one or more structural variants in the genome. Analyses of the spatial distribution of these putative structural variants suggest at least partial reproductive isolation of sandeel in the western management area along the Scottish coast, supporting a separate management. Our results highlight the importance of the application of a large number of markers to be able to detect weak patterns of differentiation. This study contributes to increasing the genetic knowledge of this important exploited species, and results can be used to improve our understanding of population dynamics and stock structure.

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.

A novel integrative approach elucidates fine-scale dispersal patchiness in marine populations

Dispersal is one of the main determining factors of population structure. In the marine habitat, well-connected populations with large numbers of reproducing individuals are common but even so population structure can exist on a small-scale. Variation in dispersal patterns between populations or over time is often associated to geographic distance or changing oceanographic barriers. Consequently, detecting structure and variation in dispersal on a fine-scale within marine populations still remains a challenge. Here we propose and use a novel approach of combining a clustering model, early-life history trait information from fish otoliths, spatial coordinates and genetic markers to detect very fine-scale dispersal patterns. We collected 1573 individuals (946 adults and 627 juveniles) of the black-faced blenny across a small-scale (2 km) coastline as well as at a larger-scale area (<50 kms). A total of 178 single nucleotide polymorphism markers were used to evaluate relatedness patterns within this well-connected population. In our clustering models we categorized SHORT-range dispersers to be potential local recruits based on their high relatedness within and low relatedness towards other spatial clusters. Local retention and/or dispersal of this potential local recruitment varied across the 2 km coastline with higher frequency of SHORT-range dispersers towards the southwest of the area for adults. An inverse pattern was found for juveniles, showing an increase of SHORT-range dispersers towards the northeast. As we rule out selective movement and mortality from one year to the next, this pattern reveals a complex but not full genetic mixing, and variability in coastal circulation is most likely the main driver of this fine-scale chaotic genetic patchiness within this otherwise homogeneous population. When focusing on the patterns within one recruitment season, we found large differences in temperatures (from approx. 17 °C to 25 °C) as well as pelagic larval duration (PLD) for juveniles from the beginning of the season and the end of the season. We were able to detect fine-scale differences in LONG-range juvenile dispersers, representing distant migrants, depending on whether they were born at the beginning of the season with a longer PLD, or at the end of the reproductive season. The ability to detect such fine-scale dispersal patchiness will aid in our understanding of the underlying mechanisms of population structuring and chaotic patchiness in a wide range of species even with high potential dispersal abilities.

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

Marine populations are typically characterized by weak genetic differentiation due to the potential for long-distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the coast of North America in the northeastern Pacific Ocean. Then, we tested two hypotheses regarding spatial processes influencing population structure: (i) isolation by distance (IBD: genetic structure is explained by geographic distance) and (ii) isolation by resistance (IBR: genetic structure is driven by ocean circulation). Using RADseq, we genotyped 717 individuals from 24 sampling locations across 2,719 neutral SNPs to assess the degree of population differentiation and integrated estimates of genetic variation with inferred connectivity probabilities from a biophysical model of larval dispersal mediated by ocean currents. We identified two clusters separating north and south regions, as well as significant, albeit weak, substructure within regions (F_ST  = 0.002, p = .001). After modelling the asymmetric nature of ocean currents, we demonstrated that local oceanography (IBR) was a better predictor of genetic variation (R²  = .49) than geographic distance (IBD) (R²  = .18), and directional processes played an important role in shaping fine-scale structure. Our study contributes to the growing body of literature identifying significant population structure in marine systems and has important implications for the spatial management of P. californicus and other exploited marine species.

Maintenance of a Genetic Cline in the Barnacle Balanus glandula

The barnacle Balanus glandula is a broadly distributed species in the temperate northeastern Pacific that is notable for a robust genetic cline between about 36° and 40° N latitude. Prior work established the evolutionary origins of this pattern and proposed that it is maintained by environmental selection. In recent years, "climate velocity" studies in marine habitats have shown dramatic distributional shifts for many species as they track their preferred temperature range in a warming ocean. We re-sampled B. glandula across its entire geographic range to determine whether there has been any shift in this genetic distribution, a development signaling that temperature or other climate factors are maintaining this genetic cline. Additionally, we asked whether the spatially distributed mitochondrial lineages also vary in reproductive output with latitude, using location as a proxy for temperature and other coastal environmental factors. Here we show that although the distribution of the genetic cline has not appreciably changed, there is a notable association of decreased reproductive output at lower latitudes of the distribution in the "northern" lineage of B. glandula.

Dwarf brooder versus giant broadcaster: combining genetic and reproductive data to unravel cryptic diversity in an Antarctic brittle star

Poecilogony, or multiple developmental modes in a single species, is exceedingly rare. Several species described as poecilogenous were later demonstrated to be multiple (cryptic) species with a different developmental mode. The Southern Ocean is known to harbor a high proportion of brooders (Thorson's Rule) but with an increasing number of counter examples over recent years. Here we evaluated poecilogony vs. crypticism in the brittle star Astrotoma agassizii across the Southern Ocean. This species was initially described from South America as a brooder before some pelagic stages were identified in Antarctica. Reproductive and mitochondrial data were combined to unravel geographic and genetic variation of developmental modes. Our results indicate that A. agassizii is composed of seven well-supported and deeply divergent clades (I: Antarctica and South Georgia; II: South Georgia and Sub-Antarctic locations including Kerguelen, Patagonian shelf, and New Zealand; III-VI-VII: Patagonian shelf, IV-V: South Georgia). Two of these clades demonstrated strong size dimorphism when in sympatry and can be linked to differing developmental modes (Clade V: dwarf brooder vs. Clade I: giant broadcaster). Based on their restricted geographic distributions and on previous studies, it is likely that Clades III-VI-VII are brooders. Clade II is composed of different morphological species, A. agassizii and A. drachi, the latter originally used as the outgroup. By integrating morphology, reproductive, and molecular data we conclude that the variation identified in A. agassizii is best described as crypticism rather than poecilogony.