Genomic signatures of environmental selection despite near-panmixia in summer flounder

Complex patterns of genetic population structure in the mouthbrooding marine catfish, Bagre marinus, in the Gulf of Mexico and U.S. Atlantic

Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish (Bagre marinus, Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics to generate neutral and non-neutral SNP data sets. Because genomic resources are lacking for ariids, linkage disequilibrium network analysis was used to examine patterns of putatively adaptive variation. Finally, historical demographic parameters were estimated from site frequency spectra. The results show four differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2) northeastern, (3) northwestern, and (4) southern Gulf of Mexico. The non-neutral data presented two contrasting signals of structure, one due to increases in diversity moving west to east and north to south, and another to increased heterozygosity in the Atlantic. Demographic analysis suggested that recently reduced long-term effective population size in the Atlantic is likely an important driver of patterns of genetic variation and is consistent with a known reduction in population size potentially due to an epizootic. Overall, patterns of genetic variation resemble that of other fishes that use the same estuarine habitats as nurseries, regardless of the presence/absence of a larval phase, supporting the idea that adult/juvenile behavior and habitat are important predictors of contemporary patterns of genetic structure.

Local adaptation with gene flow in a highly dispersive shark

Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.

Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales

Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and has direct implications for the spatial scales of management. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach employing mitochondrial control region sequences and 4339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units-the Atlantic, eastern Gulf, and western Gulf-that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighbouring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.

Genetic decline and recovery of a demographically rebuilt fishery species

The demographic history of a population is important for conservation and evolution, but this history is unknown for many populations. Methods that use genomic data have been developed to infer demography, but they can be challenging to implement and interpret, particularly for large populations. Thus, understanding if and when genetic estimates of demography correspond to true population history is important for assessing the performance of these genetic methods. Here, we used double-digest restriction-site associated DNA (ddRAD) sequencing data from archived collections of larval summer flounder (Paralichthys dentatus, n = 279) from three cohorts (1994-1995, 1997-1998 and 2008-2009) along the U.S. East coast to examine how contemporary effective population size and genetic diversity responded to changes in abundance in a natural population. Despite little to no detectable change in genetic diversity, coalescent-based demographic modelling from site frequency spectra revealed that summer flounder effective population size declined dramatically in the early 1980s. The timing and direction of change corresponded well with the observed decline in spawning stock census abundance in the late 1980s from independent fish surveys. Census abundance subsequently recovered and achieved the prebottleneck size. Effective population size also grew following the bottleneck. Our results for summer flounder demonstrate that genetic sampling and site frequency spectra can be useful for detecting population dynamics, even in species with large effective sizes.

Genetic Population Structure of Summer Flounder Paralichthys dentatus using Microsatellite DNA Analysis

Summer flounder Paralichthys dentatus supports one of the most valuable commercial and recreational fisheries along the Atlantic Coast of the U.S. However, in recent decades the management of this species has proven to be one of the most contentious for any exploited marine resource in the region. A coastwide catch quota is imposed annually for summer flounder of which 60% is allocated to the commercial fishery and 40% to the recreational fishery. The allocation is further divided among the individual coastal states from North Carolina to Massachusetts based on their landings in the 1980s. This process, based on political jurisdictions, does not consider the species' biological stock structure. Previous genetic studies (allozyme, mtDNA, and SNPs) provided contradictory results regarding the possible population structure of summer. To address this issue, we used DNA microsatellite analysis at 9 loci to define the coastwide population structure of summer flounder. In total, 1,182 specimens were analyzed from 18 collection sites. Most collections were from the continental shelf during the fall-winter spawning season. These were supplemented with additional samples from inshore waters from North Carolina to Florida, and inshore sites which support significant recreational fisheries at Nantucket Shoals, Massachusetts and Fire Island, New York. The overall level of genetic differentiation in pairwise comparison between collections was very low, mean F ST = 0.001. There was no evidence of genetic differentiation between collections from north and south of Cape Hatteras. Our microsatellite results are consistent with an earlier SNP study which failed to find significant allelic heterogeneity among coastwide collections of summer flounder. However, a subset of pairwise F ST comparisons between some collections proved statistically significant. Furthermore, in STRUCTURE analysis we found evidence of two genetic clusters within the species' northern landings area, however, this finding was not supported by DPAC analysis. We conclude that summer flounder most likely constitute a single population along their entire Atlantic Coast distribution.

Genomic Stock Structure of the Marine Teleost Tarakihi (Nemadactylus macropterus) Provides Evidence of Potential Fine-Scale Adaptation and a Temperature-Associated Cline Amid Panmixia

Tarakihi (Nemadactylus macropterus) is an important fishery species with widespread distribution around New Zealand and off the southern coasts of Australia. However, little is known about whether the populations are locally adapted or genetically structured. To address this, we conducted whole-genome resequencing of 175 tarakihi from around New Zealand and Tasmania (Australia) to obtain a dataset of 7.5 million genome-wide and high-quality single nucleotide polymorphisms (SNPs). Variant filtering, FST-outlier analysis, and redundancy analysis (RDA) were used to evaluate population structure, adaptive structure, and locus-environment associations. A weak but significant level of neutral genetic differentiation was found between tarakihi from New Zealand and Tasmania (FST = 0.0054–0.0073, P ≤ 0.05), supporting the existence of at least two separate reproductive stocks. No clustering was detected among the New Zealand populations (ΦST < 0.001, P = 0.77). Outlier-based, presumably adaptive variation suggests fine-scale adaptive structure between locations around central New Zealand off the east (Wairarapa, Cape Campbell, and Hawke’s Bay) and the west coast (Tasman Bay/Golden Bay and Upper West Coast of South Island). Allele frequencies from 55 loci were associated with at least one of six environmental variables, of which 47 correlated strongly with yearly mean water temperature. Although genes associated with these loci are linked to various functions, the most common functions were integral components of membrane and cilium assembly. Projection of the RDA indicates the existence of a latitudinal temperature cline. Our work provides the first genomic insights supporting panmixia of tarakihi in New Zealand and evidence of a genomic cline that appears to be driven by the temperature gradients, together providing crucial information to inform the stock assessment of this species, and to widen the insights of the ecological drivers of adaptive variation in a marine species.

Climate differently influences the genomic patterns of two sympatric marine fish species

Climate influences population genetic variation in marine species. Capturing these impacts remains challenging for marine fishes which disperse over large geographical scales spanning steep environmental gradients. It requires the extensive spatial sampling of individuals or populations, representative of seascape heterogeneity, combined with a set of highly informative molecular markers capable of revealing climatic-associated genetic variations. We explored how space, dispersal and environment shape the genomic patterns of two sympatric fish species in the Mediterranean Sea, which ranks among the oceanic basins most affected by climate change and human pressure. We hypothesized that the population structure and climate-associated genomic signatures of selection would be stronger in the less mobile species, as restricted gene flow tends to facilitate the fixation of locally adapted alleles. To test our hypothesis, we genotyped two species with contrasting dispersal abilities: the white seabream Diplodus sargus and the striped red mullet Mullus surmuletus. We collected 823 individuals and used genotyping by sequencing (GBS) to detect 8,206 single nucleotide polymorphisms (SNPs) for the seabream and 2,794 for the mullet. For each species, we identified highly differentiated genomic regions (i.e. outliers) and disentangled the relative contribution of space, dispersal and environmental variables (climate, marine primary productivity) on the outliers' genetic structure to test the prevalence of gene flow and local adaptation. We observed contrasting patterns of gene flow and adaptive genetic variation between the two species. The seabream showed a distinct Alboran sea population and panmixia across the Mediterranean Sea. The mullet revealed additional differentiation within the Mediterranean Sea that was significantly correlated to summer and winter temperatures, as well as marine primary productivity. Functional annotation of the climate-associated outlier SNPs then identified candidate genes involved in heat tolerance that could be examined to further predict species' responses to climate change. Our results illustrate the key steps of a comparative seascape genomics study aiming to unravel the evolutionary processes at play in marine species, to better anticipate their response to climate change. Defining population adaptation capacities and environmental niches can then serve to incorporate evolutionary processes into species conservation planning.

Disentangling complex genomic signals to understand population structure of an exploited, estuarine-dependent flatfish

Interpreting contemporary patterns of population structure requires an understanding of the interactions among microevolutionary forces and past demographic events. Here, 4,122 SNP-containing loci were used to assess structure in southern flounder (Paralichthys lethostigma) sampled across its range in the US Atlantic Ocean (Atlantic) and Gulf of Mexico (Gulf) and relationships among components of genomic variation and spatial and environmental variables were assessed across estuarine population samples in the Gulf. While hierarchical amova revealed significant heterogeneity within and between the Atlantic and Gulf, pairwise comparisons between samples within ocean basins demonstrated that all significant heterogeneity occurred within the Gulf. The distribution of Tajima's D estimated at a genome-wide scale differed significantly from equilibrium in all estuaries, with more negative values occurring in the Gulf. Components of genomic variation were significantly associated with environmental variables describing individual estuaries, and environment explained a larger component of variation than spatial proximity. Overall, results suggest that there is genetic spatial autocorrelation caused by shared larval sources for proximal nurseries (migration/drift), but that it is modified by environmentally driven differentiation (selection). This leads to conflicting signals in different parts of the genome and creates patterns of divergence that do not correspond to paradigms of strong local directional selection.

Madrepora oculata forms large frameworks in hypoxic waters off Angola (SE Atlantic)

This study aims to map the occurrence and distribution of Madrepora oculata and to quantify density and colony sizes across recently discovered coral mounds off Angola. Despite the fact that the Angolan populations of M. oculata thrive under extreme hypoxic conditions within the local oxygen minimum zone, they reveal colonies with remarkable heights of up to 1250 mm—which are the tallest colonies ever recorded for this species—and average densities of 0.53 ± 0.37 (SD) colonies m⁻². This is particularly noteworthy as these values are comparable to those documented in areas without any oxygen constraints. The results of this study show that the distribution pattern documented for M. oculata appear to be linked to the specific regional environmental conditions off Angola, which have been recorded in the direct vicinity of the thriving coral community. Additionally, an estimated average colony age of 95 ± 76 (SD) years (total estimated age range: 16–369 years) indicates relatively old M. oculata populations colonizing the Angolan coral mounds. Finally, the characteristics of the Angolan populations are benchmarked and discussed in the light of the existing knowledge on M. oculata gained from the North Atlantic and Mediterranean Sea.

Genomic signatures of spatially divergent selection at clownfish range margins

Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.

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.

Restricted dispersal in a sea of gene flow

How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels of genetic structure at large spatial scales (hundreds of kilometres). Yet this result, typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous sampling strategy along 950 km of coast in the northwestern Mediterranean Sea to address this question in four species. In line with expectations, we observe weak genetic structure at a large spatial scale. Nevertheless, our continuous sampling strategy uncovers a pattern of isolation by distance at small spatial scales (few tens of kilometres) in two species. Individual-based simulations indicate that this signal is an expected signature of restricted dispersal. At the other extreme of the connectivity spectrum, two pairs of individuals that are closely related genetically were found more than 290 km apart, indicating long-distance dispersal. Such a combination of restricted dispersal with rare long-distance dispersal events is supported by a high-resolution biophysical model of larval dispersal in the study area, and we posit that it may be common in marine species. Our results bridge population genetic studies with direct dispersal studies and have implications for the design of marine reserve networks.

Ecological adaptation in European eels is based on phenotypic plasticity

The relative role of genetic adaptation and phenotypic plasticity is of fundamental importance in evolutionary ecology [M. J. West-Eberhard, Proc. Natl. Acad. Sci. U.S.A. 102 (suppl. 1), 6543-6549 (2005)]. European eels have a complex life cycle, including transitions between life stages across ecological conditions in the Sargasso Sea, where spawning occurs, and those in brackish and freshwater bodies from northern Europe to northern Africa. Whether continental eel populations consist of locally adapted and genetically distinct populations or comprise a single panmictic population has received conflicting support. Here we use whole-genome sequencing and show that European eels belong to one panmictic population. A complete lack of geographical genetic differentiation is demonstrated. We postulate that this is possible because the most critical life stages-spawning and embryonic development-take place under near-identical conditions in the Sargasso Sea. We further show that within-generation selection, which has recently been proposed as a mechanism for genetic adaptation in eels, can only marginally change allele frequencies between cohorts of eels from different geographic regions. Our results strongly indicate plasticity as the predominant mechanism for how eels respond to diverse environmental conditions during postlarval stages, ultimately solving a long-standing question for a classically enigmatic species.

Rapid Adaptation to Temperature via a Potential Genomic Island of Divergence in the Invasive Green Crab, Carcinus maenas

Widespread species often adapt easily to novel conditions – both those found in new habitats and those generated by climate change. However, rapid adaptation may be hindered in the marine realm, where long-distance dispersal and consequently high gene flow are predicted to limit potential for local adaptation. Here, we use a highly dispersive invasive marine crab to test the nature and speed of adaptation to temperature in the sea. Using single nucleotide polymorphisms (SNPs) generated from cardiac transcriptome sequencing, we characterized six populations of the European green crab (Carcinus maenas) located across parallel thermal gradients in their native and invasive ranges. We compared SNP frequencies with local temperatures and previously generated data on cardiac heat and cold tolerance to identify candidate markers associated with population-level differences in thermal physiology. Of 10,790 SNPs, 104 were identified as frequency outliers, a signal that was strongly driven by association with temperature and/or cold tolerance. Seventy-two of these outlier markers, representing 28 different genes, were in a cluster of SNPs identified as a potential inversion polymorphism using linkage disequilibrium network analysis. This SNP cluster was unique in the data set, which was otherwise characterized by low levels of linkage disequilibrium, and markers in this cluster showed a significant enrichment of coding substitutions relative to the full SNP set. These 72 outlier SNPs appear to be transmitted as a unit, and represent a putative genomic island of divergence which varied in frequency with organismal cold tolerance. This relationship was strikingly similar across both native and invasive populations, all of which showed a very strong correlation with cold tolerance (R2 = 0.96 over all six populations). Notably, three of these populations have diverged recently (&lt;100 years) and show little to no neutral divergence, suggesting that this genomic region may be responding to temperature on a relatively short time scale. This relationship indicates adaptation to temperature based on the action of a putative genomic island of divergence, perhaps partially explaining the extraordinary invasive ability of this species.

Genomic signals found using RNA sequencing show signatures of selection and subtle population differentiation in walleye (Sander vitreus) in a large freshwater ecosystem

RNA sequencing is an effective approach for studying aquatic species yielding both physiological and genomic data. However, its population genetic applications are not well-characterized. We investigate this possible role for RNA sequencing for population genomics in Lake Winnipeg, Manitoba, Canada, walleye (Sander vitreus). Lake Winnipeg walleye represent the largest component of the second-largest freshwater fishery in Canada. In the present study, large female walleye were sampled via nonlethal gill biopsy over two years at three spawning sites representing a latitudinal gradient in the lake. Genetic variation from sequenced mRNA was analyzed for neutral and adaptive markers to investigate population structure and possible adaptive variation. We find low population divergence (F ST = 0.0095), possible northward gene flow, and outlier loci that vary latitudinally in transcripts associated with cell membrane proteins and cytoskeletal function. These results indicate that Lake Winnipeg walleye may be effectively managed as a single demographically connected metapopulation with contributing subpopulations and suggest genomic differences possibly underlying observed phenotypic differences. Despite its high cost relative to other genotyping methods, RNA sequencing data can yield physiological in addition to genetic information discussed here. We therefore argue that it is useful for addressing diverse molecular questions in the conservation of freshwater species.

Genotyping-by-sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes

Effective resource management depends on our ability to partition diversity into biologically meaningful units. Recent evolutionary divergence, however, can often lead to ambiguity in morphological and genetic differentiation, complicating the delineation of valid conservation units. Such is the case with the "coregonine problem," where recent postglacial radiations of coregonines into lacustrine habitats resulted in the evolution of numerous species flocks, often with ambiguous taxonomy. The application of genomics methods is beginning to shed light on this problem and the evolutionary mechanisms underlying divergence in these ecologically and economically important fishes. Here, we used restriction site-associated DNA (RAD) sequencing to examine genetic diversity and differentiation among sympatric forms in the Coregonus artedi complex in the Apostle Islands of Lake Superior, the largest lake in the Laurentian Great Lakes. Using 29,068 SNPs, we were able to clearly distinguish among the three most common forms for the first time, as well as identify putative hybrids and potentially misidentified specimens. Population assignment rates for these forms using our RAD data were 93%-100% with the only mis-assignments arising from putative hybrids, an improvement from 62% to 77% using microsatellites. Estimates of pairwise differentiation (F ST: 0.045-0.056) were large given the detection of hybrids, suggesting that reduced fitness of hybrid individuals may be a potential mechanism for the maintenance of differentiation. We also used a newly built C. artedi linkage map to look for islands of genetic divergence among forms and found widespread differentiation across the genome, a pattern indicative of long-term drift, suggesting that these forms have been reproductively isolated for a substantial amount of time. The results of this study provide valuable information that can be applied to develop well-informed management strategies and stress the importance of re-evaluating conservation units with genomic tools to ensure they accurately reflect species diversity.

Using multiple natural tags provides evidence for extensive larval dispersal across space and through time in summer flounder

Dispersal sets the fundamental scales of ecological and evolutionary dynamics and has important implications for population persistence. Patterns of marine dispersal remain poorly understood, partly because dispersal may vary through time and often homogenizes allele frequencies. However, combining multiple types of natural tags can provide more precise dispersal estimates, and biological collections can help to reconstruct dispersal patterns through time. We used single nucleotide polymorphism genotypes and otolith core microchemistry from archived collections of larval summer flounder (Paralichthys dentatus, n = 411) captured between 1989 and 2012 at five locations along the US East coast to reconstruct dispersal patterns through time. Neither genotypes nor otolith microchemistry alone were sufficient to identify the source of larval fish. However, microchemistry identified clusters of larvae (n = 3-33 larvae per cluster) that originated in the same location, and genetic assignment of clusters could be made with substantially more confidence. We found that most larvae probably originated near a biogeographical break (Cape Hatteras) and that larvae were transported in both directions across this break. Larval sources did not shift north through time, despite the northward shift of adult populations in recent decades. Our novel approach demonstrates that summer flounder dispersal is widespread throughout their range, on both intra- and intergenerational timescales, and may be a particularly important process for synchronizing population dynamics and maintaining genetic diversity during an era of rapid environmental change. Broadly, our results reveal the value of archived collections and of combining multiple natural tags to understand the magnitude and directionality of dispersal in species with extensive gene flow.

Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine-scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open-sourced research on the population structure of O. lurida.

High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coral Porites lobata (Dana, 1846)

Spatial heterogeneity in environmental characteristics can drive adaptive differentiation when contrasting environments exert divergent selection pressures. This environmental and genetic heterogeneity can substantially influence population and community resilience to disturbance events. Here, we investigated corals from the highly variable back reef habitats of Ofu Island in American Samoa that thrive in thermal conditions known to elicit widespread bleaching and mortality elsewhere. To investigate the relative importance of acclimation vs. site of origin in shaping previously observed differences in coral tolerance limits in Ofu, specimens of the common Indo-Pacific coral Porites lobata (Dana, 1846) from locations with differing levels of thermal variability were acclimated to low and high thermal variation in controlled common garden aquaria. Overall, there were minimal effects of the acclimation exposure. Corals native to the site with the highest level of daily variability grew fastest, regardless of acclimation treatment. When exposed to lethal thermal stress, corals native to both variable sites contained elevated levels of heat shock proteins and maintained photosynthetic performance for 1-2 days longer than corals from the stable environment. Despite being separated by&lt;5 km, there was significant genetic differentiation among coral colonies (FST=0.206, p&lt;0.0001; nuclear ribosomal DNA), while Symbiodiniaceae were all Cladocopium sp. (ITS-type C15). Our study demonstrates consistent signatures of adaptation in growth and stress resistance in corals from naturally thermally variable habitats, suggesting that differences in the amount of thermal variability may be an important contributor to adaptive differentiation in reef building corals.