Larval stages of the Antarctic dragonfish Akarotaxis nudiceps (Waite, 1916), with comments on the larvae of the morphologically similar species Prionodraco evansii Regan 1914 (Notothenioidei: Bathydraconidae).

The notothenioid family Bathydraconidae is a poorly understood family of fishes endemic to the Southern Ocean. There is especially little information on Akarotaxis nudiceps, one of the deepest-dwelling and least fecund bathydraconid species. Using genetic and morphological data, we document and describe the larval stages of this unique species, offer a novel characteristic to distinguish it from the morphologically similar bathydraconid Prionodraco evansii and use the sampling locations to infer a possible spawning area of A. nudiceps along the western Antarctic Peninsula. These results provide important baseline information for locating, identifying and studying the biology of A. nudiceps, an important component of the Southern Ocean ecosystem.

High level of genetic connectivity in a deep-water reef fish, Caulolatilus microps.

The life-history characteristics of blueline tilefish make them particularly vulnerable to overfishing. Although North Carolina, U.S.A. was previously considered to be the northern extent of the range of C. microps, concentrations have recently been discovered in Virginia and Maryland, with reports as far north as Montauk, New York. Attempts to manage the fishery have been hampered by a lack of information about whether the U.S. East Coast includes multiple stocks. To assess the appropriateness of alternate management options, we used 25 variable microsatellite loci and sequencing of the mitochondrial (mt)DNA control region (CR) to evaluate the genetic structure of 490 C. microps sampled from across the U.S. East Coast range. Pairwise comparisons of genetic differentiation among collection locations based on both nuclear microsatellite and mtCR sequence data were all low and non significant. No significant autocorrelation was observed across multiple distance classes, consistent with widespread dispersal., Although the assumed sedentary nature of adult C. microps suggests population structuring, the genetic data were consistent with the presence of sufficient gene flow to prevent the accumulation of significant genetic differences and supports management of C. microps as a single stock along the U.S. East Coast.

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

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

Low levels of sibship encourage use of larvae in western Atlantic bluefin tuna abundance estimation by close-kin mark-recapture.

Globally, tunas are among the most valuable fish stocks, but are also inherently difficult to monitor and assess. Samples of larvae of Western Atlantic bluefin tuna Thunnus thynnus (Linnaeus, 1758) from standardized annual surveys in the northern Gulf of Mexico provide a potential source of "offspring" for close-kin mark-recapture (CKMR) estimates of abundance. However, the spatial patchiness and highly skewed numbers of larvae per tow suggest sampled larvae may come from a small number of parents, compromising the precision of CKMR. We used high throughput genomic profiling to study sibship within and among larval tows from the 2016 standardized Gulf-wide survey compared to targeted sampling carried out in 2017. Full- and half-siblings were found within both years, with 12% of 156 samples in 2016 and 56% of 317 samples in 2017 having at least one sibling. There were also two pairs of cross cohort half-siblings. Targeted sampling increased the number of larvae collected per sampling event but resulted in a higher proportion of siblings. The combined effective sample size across both years was about 75% of the nominal size, indicating that Gulf of Mexico larval collections could be a suitable source of juveniles for CKMR in Western Atlantic bluefin tuna.

Comparative transcriptomics of spotted seatrout (Cynoscion nebulosus) populations to cold and heat stress.

Resilience to climate change depends on a species' adaptive potential and phenotypic plasticity. The latter can enhance survival of individual organisms during short periods of extreme environmental perturbations, allowing genetic adaptation to take place over generations. Along the U.S. East Coast, estuarine-dependent spotted seatrout (Cynoscion nebulosus) populations span a steep temperature gradient that provides an ideal opportunity to explore the molecular basis of phenotypic plasticity. Genetically distinct spotted seatrout sampled from a northern and a southern population were exposed to acute cold and heat stress (5 biological replicates in each treatment and control group), and their transcriptomic responses were compared using RNA-sequencing (RNA-seq). The southern population showed a larger transcriptomic response to acute cold stress, whereas the northern population showed a larger transcriptomic response to acute heat stress compared with their respective population controls. Shared transcripts showing significant differences in expression levels were predominantly enriched in pathways that included metabolism, transcriptional regulation, and immune response. In response to heat stress, only the northern population significantly upregulated genes in the apoptosis pathway, which could suggest greater vulnerability to future heat waves in this population as compared to the southern population. Genes showing population-specific patterns of expression, including hpt, acot, hspa5, and hsc71, are candidates for future studies aiming to monitor intraspecific differences in temperature stress responses in spotted seatrout. Our findings contribute to the current understanding of phenotypic plasticity and provide a basis for predicting the response of a eurythermal fish species to future extreme temperatures.

World phylogeography and male-mediated gene flow in the sandbar shark, Carcharhinus plumbeus.

The sandbar shark, Carcharhinus plumbeus, is a large, cosmopolitan, coastal species. Females are thought to show philopatry to nursery grounds while males potentially migrate long distances, creating an opportunity for male-mediated gene flow that may lead to discordance in patterns revealed by mitochondrial DNA (mtDNA) and nuclear markers. While this dynamic has been investigated in elasmobranchs over small spatial scales, it has not been examined at a global level. We examined patterns of historical phylogeography and contemporary gene flow by genotyping 329 individuals from nine locations throughout the species' range at eight nuclear microsatellite markers and sequencing the complete mtDNA control region. Pairwise comparisons often resulted in fixation indices and divergence estimates of greater magnitude using mtDNA sequence data than microsatellite data. In addition, multiple methods of estimation suggested fewer populations based on microsatellite loci than on mtDNA sequence data. Coalescent analyses suggest divergence and restricted migration among Hawaii, Taiwan, eastern and western Australia using mtDNA sequence data and no divergence and high migration rates, between Taiwan and both Australian sites using microsatellite data. Evidence of secondary contact was detected between several localities and appears to be discreet in time rather than continuous. Collectively, these data suggest complex spatial/temporal relationships between shark populations that may feature pulses of female dispersal and more continuous male-mediated gene flow.

Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin (Kajikia audax), a broadly distributed and highly migratory pelagic species.

Genomic methodologies offer unprecedented opportunities for statistically robust studies of species broadly distributed in environments conducive to high gene flow, providing valuable information for wildlife conservation and management. Here, we sequence restriction site-associated DNA to characterize genome-wide single nucleotide polymorphisms (SNPs) in a broadly distributed and highly migratory large pelagic fish, striped marlin (Kajikia audax). Assessment of over 4,000 SNPs resolved spatiotemporal patterns of genetic connectivity throughout the species range in the Pacific and, for the first time, Indian oceans. Individual-based cluster analyses identified six genetically distinct populations corresponding with the western Indian, eastern Indian, western South Pacific, and eastern central Pacific oceans, as well as two populations in the North Pacific Ocean (F ST = 0.0137-0.0819). F ST outlier analyses identified a subset of SNPs (n = 59) putatively under the influence of natural selection and capable of resolving populations separated by comparatively high degrees of genetic differentiation. Temporal collections available for some regions demonstrated the stability of allele frequencies over three to five generations of striped marlin. Relative migration rates reflected lower levels of genetic connectivity between Indian Ocean populations (m R ≤ 0.37) compared with most populations in the Pacific Ocean (m R ≥ 0.57) and highlight the importance of the western South Pacific in facilitating gene flow between ocean basins. Collectively, our results provide novel insights into rangewide population structure for striped marlin and highlight substantial inconsistencies between genetically distinct populations and stocks currently recognized for fisheries management. More broadly, we demonstrate that species capable of long-distance dispersal in environments lacking obvious physical barriers to movement can display substantial population subdivision that persists over multiple generations and that may be facilitated by both neutral and adaptive processes. Importantly, surveys of genome-wide markers enable inference of population-level relationships using sample sizes practical for large pelagic fishes of conservation concern.

Plasticity in Standard and Maximum Aerobic Metabolic Rates in Two Populations of an Estuarine Dependent Teleost, Spotted Seatrout (Cynoscion nebulosus).

We studied the effects of metabolic cold adaptation (MCA) in two populations of a eurythermal species, spotted seatrout (Cynoscion nebulosus) along the U.S. East Coast. Fish were captured from their natural environment and acclimated at control temperatures 15 °C or 20 °C. Their oxygen consumption rates, a proxy for metabolic rates, were measured using intermittent flow respirometry during acute temperature decrease or increase (2.5 °C per hour). Mass-specific standard metabolic rates (SMR) were higher in fish from the northern population across an ecologically relevant temperature gradient (5 °C to 30 °C). SMR were up to 37% higher in the northern population at 25 °C and maximum metabolic rates (MMR) were up to 20% higher at 20 °C. We found evidence of active metabolic compensation in the southern population from 5 °C to 15 °C (Q10 < 2), but not in the northern population. Taken together, our results indicate differences in metabolic plasticity between the northern and southern populations of spotted seatrout and provide a mechanistic basis for predicting population-specific responses to climate change.

World without borders-genetic population structure of a highly migratory marine predator, the blue shark (Prionace glauca).

Highly migratory, cosmopolitan oceanic sharks often exhibit complex movement patterns influenced by ontogeny, reproduction, and feeding. These elusive species are particularly challenging to population genetic studies, as representative samples suitable for inferring genetic structure are difficult to obtain. Our study provides insights into the genetic population structure one of the most abundant and wide-ranging oceanic shark species, the blue shark Prionace glauca, by sampling the least mobile component of the populations, i.e., young-of-year and small juveniles (<2 year; N = 348 individuals), at three reported nursery areas, namely, western Iberia, Azores, and South Africa. Samples were collected in two different time periods (2002-2008 and 2012-2015) and were screened at 12 nuclear microsatellites and at a 899-bp fragment of the mitochondrial control region. Our results show temporally stable genetic homogeneity among the three Atlantic nurseries at both nuclear and mitochondrial markers, suggesting basin-wide panmixia. In addition, comparison of mtDNA CR sequences from Atlantic and Indo-Pacific locations also indicated genetic homogeneity and unrestricted female-mediated gene flow between ocean basins. These results are discussed in light of the species' life history and ecology, but suggest that blue shark populations may be connected by gene flow at the global scale. The implications of the present findings to the management of this important fisheries resource are also discussed.

Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2011-31 January 2012.

This article documents the addition of 473 microsatellite marker loci and 71 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross-tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.

Genetic identity of YOY bluefin tuna from the eastern and western Atlantic spawning areas.

We used 320 young-of-the-year (YOY) specimens of the highly migratory and overfished Atlantic bluefin tuna, Thunnus thynnus, Linnaeus 1758, to evaluate the hypothesis that Atlantic bluefin tuna comprises 2 stocks with spawning grounds in the Gulf of Mexico and in the Mediterranean Sea. Significant genetic differentiation at 8 nuclear microsatellite loci (F(ST) = 0.0059, P = 0.0005) and at the mitochondrial control region (Phi(ST) = 0.0129, P = 0.0139) was detected among YOY Atlantic bluefin tuna captured on spawning grounds in the Gulf of Mexico (n = 40) versus the western (n = 255) and eastern (n = 25) basins of the Mediterranean Sea. The genetic divergence among spawning populations, combined with the extensive trans-Atlantic movements reported for juvenile and adult Atlantic bluefin tuna, indicates a high degree of spawning site fidelity. Recognition of genetically distinct populations necessitates independent management of Atlantic bluefin tuna on spawning grounds and warrants evaluation of the level of mixing of populations on feeding grounds. The genetic pattern might not have been detected unless juvenile specimens or actively spawning adults had been sampled.

Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea.

Genetic variation was surveyed at nine microsatellite loci and the mitochondrial control region (868 bp) to test for the presence of genetic stock structure in young-of-the-year Atlantic bluefin tuna (Thunnus thynnus thynnus) from the Mediterranean Sea. Bluefin tuna were sampled over a period of 5 years from the Balearic and Tyrrhenian seas in the western basin of the Mediterranean Sea, and from the southern Ionian Sea in the eastern basin of the Mediterranean Sea. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences revealed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for both microsatellite markers and mitochondrial control region sequences (FST=0.0023, P=0.038 and PhiST=0.0233, P=0.000, respectively). Significant genetic differentiation between the Tyrrhenian and Ionian collections was found for both microsatellite and mitochondrial markers (FST=0.0087, P=0.015 and PhiST=0.0367, P=0.030, respectively). These results suggest the possibility of a genetically discrete population in the eastern basin of the Mediterranean Sea.