Population Structure of Lethrinus Lentjan (Lethrinidae, Percoidei) Across the South China Sea and the Philippines Is Detected With Lane-Affected RADSeq Data

Southeast Asia includes the Coral Triangle, a marine biodiversity hotspot that supports important fishery resources experiencing varied threats. Patterns of speciation and population structure in the Coral Triangle have been examined to test hypotheses relating to the historical geologic processes that may have influenced this biodiversity phenomenon. This study investigates the genetic population structure of the Pink-ear Emperor Snapper, Lethrinus lentjan (Lacepède, 1802), across the Philippines and the South China Sea. The species is fished throughout the Coral Triangle by subsistence and commercial fishers and their landings have been in decline for several years, which could be indicative of depleted stocks. Six locations were sampled representing the northeastern, southeastern, central, and western Philippines, and central and southern Vietnam. This study used restriction-site associated DNA sequencing (RADSeq) to sample single nucleotide polymorphism markers from throughout the genome. Here, RADseq data is successfully used to detect structuring within the Philippines where a previous study of L. lentjan mitochondrial control region sequences did not. Genetic structure analyses revealed significant divergence along the boundaries of repeatedly isolated ocean basins, as observed in several Indo-Pacific species. Pleistocene vicariance is a suspected driving factor in lineage diversification for this species, supporting the hypothesis that the Coral Triangle is a center of origin. Before management or conservation strategies can be implemented, a stock assessment should be completed for L. lentjan, including research on its life history, ecosystem services, and metapopulation dynamics. This study also used STRUCTURE analysis to detect a strong Illumina sequencer lane effect, where the genotype of a fish is associated with the sequencer lane used to generate the data. To control and remove this lane effect, the data was parsed into two clusters, a new method for salvaging lane-affected data. It is recognized that RADSeq is prone to lane effects that can result in erroneous conclusions, and several strategies are outlined for identifying, mitigating, and avoiding them in future high-throughput RADSeq studies

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 monitorand assess. Samples of larvae of Western Atlantic bluefin tuna Thunnus thynnus (Linnaeus, 1758) fromstandardized 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 andhighly skewed numbers of larvae per tow suggest sampled larvae may come from a small number ofparents, compromising the precision of CKMR. We used high throughput genomic profiling to studysibship within and among larval tows from the 2016 standardized Gulf‑wide survey compared totargeted 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 alsotwo pairs of cross cohort half‑siblings. Targeted sampling increased the number of larvae collectedper sampling event but resulted in a higher proportion of siblings. The combined effective sample sizeacross both years was about 75% of the nominal size, indicating that Gulf of Mexico larval collectionscould be a suitable source of juveniles for CKMR in Western Atlantic bluefin tuna

Population Genetic Structure in Channeled Whelk Busycotypus canaliculatus along the U.S. Atlantic Coast

Globally, commercial fisheries for whelk (family Buccinidae) generally exhibit a boom-and-bust cycle that fuels overexploitation of resources. Channeled whelk Busycotypus canaliculatus is a commercially important species that supports a valuable fishery along the Atlantic coast of the United States. The fishery is managed at the state level, with minimum landing size varying by state. Biological studies of channeled whelk in New England and the mid-Atlantic region have indicated that females have a low probability of maturity upon entering their respective fisheries. The life history characteristics of channeled whelk, including slow growth, late maturation, and direct development paired with unsuitable minimum landing size, make this species vulnerable to overexploitation. Currently, the population genetic structure of channeled whelk is unknown, impeding the ability to appropriately inform management. This study used 2,570 single nucleotide polymorphisms to elucidate the population genetic structure of channeled whelk sampled from 10 locations ranging from Massachusetts to South Carolina. The data indicated seven genetically distinct populations across the sampled region of the U.S. Atlantic coast. Estimates of genetic divergence among populations spanned an order of magnitude (FST = 0.017–0.582), with higher levels of divergence observed when comparing populations separated by biogeographic barriers. Based on the magnitude of observed genetic differences, five regional management units are suggested. The results of this study will aid discussions among fisheries managers in Atlantic states aimed at the development of appropriate management plans. The complex population genetic structure revealed by this study underscores the need for more comprehensive sampling, including between fishing locations sampled in this study and among offshore locations, to better understand the population genetic structure of channeled whelk

Cryptic Lineages and a Population Damned to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller sub-populations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development- the Mekong River basin. Our results revealed the presence of two highly-divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal components analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically-important resources

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

Abstract 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 (FST 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