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The Gulf of Mexico pink shrimp, Farfantepenaeus duorarum, supports large fisheries in the United States and Mexico, with nearly 7,000 tons harvested from the region in 2016. Given the commercial importance of this species, management is critical: in 1997, the southern Gulf of Mexico pink shrimp fishery was declared collapsed and mitigation strategies went into effect, with recovery efforts lasting over a decade. Fisheries management can be informed and improved through a better understanding of how factors associated with early life history impact genetic diversity and population structure in the recruited population. Farfantepenaeus duorarum are short-lived, but highly fecund, and display high variability in recruitment patterns. To date, modeling the impacts of ecological, physical, and behavioral factors on juvenile settlement has focused on recruitment of larval individuals of F. duorarum to nursery grounds in Florida Bay. Here, we articulate testable hypotheses stemming from a recent model of larval transport and evaluate support for each with a population genomics approach, generating reduced representation library sequencing data for F. duorarum collected from seven regions around the Florida Peninsula. Our research represents the first and most molecular data-rich study of population structure in F. duorarum in the Gulf and reveals evidence of a differentiated population in the Dry Tortugas. Our approach largely validates a model of larval transport, allowing us to make management-informative inferences about the impacts of spawning location and recruitment patterns on intraspecific genetic diversity. Such inferences improve our understanding of the roles of non-genetic factors in generating and maintaining genetic diversity in a commercially important penaeid shrimp species.

Schistosomiasis persists in some Asian regions despite targeted end-game elimination measures. To determine the causes of this persistence, we performed reduced representation genome sequencing on Schistosoma japonicum miracidia collected across multiple years from transmission hotspots in Sichuan, China. We discovered strong geographic structure, suggesting that local rather than imported reservoirs are key sources of infection persistence. At the village level, parasites collected after praziquantel treatment are closely related to local pre-treatment populations. Schistosomes within villages are also highly related, suggesting that only a few parasites from a limited number of hosts drive re-infection. The close familial relationships among miracidia from different human hosts also implicates short transmission routes among humans. At the individual host level, genetic evidence indicates that multiple humans retain infections following referral for treatment. Our findings suggest that end-game schistosomiasis control measures should focus on completely extirpating local parasite reservoirs and confirming successful treatment of infected human hosts.One Sentence SummaryLocal reservoirs are the source for persistent schistosomiasis infections despite continuous efforts aimed at complete elimination.

The application of DNA barcoding represents a complementary and efficient approach to identifying specimens at all stages of their life cycle when used in combination with traditional morphological methods. Due to difficulties obtaining samples from the deep sea (> 200 m), these methods have been less frequently applied to deep-water taxa. We used DNA-barcoding techniques to enhance large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico, a region that has recently been identified as one of the world’s four most hyperdiverse ocean ecosystems. This study was conceptualized in direct response to the Deepwater Horizon Oil Spill in 2010, which identified major knowledge gaps in our understanding of deep-sea biodiversity. We employed traditional Sanger sequencing and a genomic skimming approach to target the mitochondrial ribosomal large subunit 16S and the protein-coding cytochrome oxidase subunit 1 (COI). Alongside these molecular approaches, traditional taxonomic investigations allowed for advancements in biodiversity, evolutionary relationships, cryptic species complexes, and distributional records across four abundant and common deep-pelagic orders (Amphipoda, Euphausiacea, Lophogastrida, and Decapoda). DNA barcodes were successfully obtained from 82 species for a total of 158 and 169 new 16S and COI sequences, respectively. Evidence of cryptic diversity has been found in the genera EucopiaDana, 1852 (Lophogastrida) and Allosergestes Judkins & Kensley, 2008 (Decapoda). New records for the Gulf of Mexico of species of LanceolaSay, 1818 (Amphipoda), Eupasiphae Wood-Mason in Wood-Mason & Alcock, 1893, PasiphaeaSavigny, 1816, and MeningodoraSmith, 1882 (Caridea) are presented. Preliminary results allow us to reconsider the current classification and evolutionary relationships of several lineages. The urgency to document biodiversity in the deep-pelagic is pressing against a backdrop of future threats including oil spills and deep-sea drilling.

Genomic approaches hold great promise for resolving unanswered questions about transmission patterns and responses to control efforts for schistosomiasis and other neglected tropical diseases. However, the cost of generating genomic data and the challenges associated with obtaining sufficient DNA from individual schistosome larvae (miracidia) from mammalian hosts have limited the application of genomic data for studying schistosomes and other complex macroparasites. Here, we demonstrate the feasibility of utilizing whole genome amplification and sequencing (WGS) to analyze individual archival miracidia. As an example, we sequenced whole genomes of 22 miracidia from 11 human hosts representing two villages in rural Sichuan, China, and used these data to evaluate patterns of relatedness and genetic diversity. We also down-sampled our dataset to test how lower coverage sequencing could increase the cost effectiveness of WGS while maintaining power to accurately infer relatedness. Collectively, our results illustrate that population-level WGS datasets are attainable for individual miracidia and represent a powerful tool for ultimately providing insight into overall genetic diversity, parasite relatedness, and transmission patterns for better design and evaluation of disease control efforts., Author summary Schistosomiasis is a neglected tropical disease caused by helminths within the genus Schistosoma, which affects over 200 million people globally. Here, we demonstrate the ability to obtain whole genome sequences from single S. japonicum miracidia that have been archived for years, and the promise of how these data may be used to answer major questions to understand and eventually help control schistosomiasis. To demonstrate the approach, we generated a moderate-sized dataset of 22 individual S. japonicum genomes and use these data to infer fine-scale patterns of relatedness among parasites from human hosts from two villages in Sichuan, China. We highlight how this type of genomic information may be useful for understanding the genetic variation among individual parasites with high precision, which could ultimately provide high resolution for understanding transmission pathways and inform control efforts with larger sample sizes. We also show that it is possible to use less data per individual than we obtained here, and still maintain high levels of accuracy; this would enable greater sample sizes by lowering individual sample cost. Collectively our results demonstrate that sampling genomes of individual schistosome parasites is now feasible on a population-level scale, opening new avenues for studying relatedness, tracing parasite spread, and studying parasite biology.

From its inception, population genetics has been nearly as concerned with the genetic data type—to which analyses are brought to bear—as it is with the analysis methods themselves. The field has traversed allozymes, microsatellites, segregating sites in multilocus alignments and, currently, single nucleotide polymorphisms (SNPs) generated by high‐throughput genomic sequencing methods, primarily whole genome sequencing and reduced representation library (RRL) sequencing. As each emerging data type has gained traction, it has been compared to existing methods, based on its relative ability to discern population structural complexity at increasing levels of resolution. However, this is usually done by comparing the gold standard in one data type to the gold standard in the new data type. These gold standards frequently differ in power and in sampling density, both across a genome and throughout a spatial range. In this issue of Molecular Ecology, D’Aloia et al. apply the high‐throughput approach as fully as possible to microsatellites, nuclear loci and SNPs genotyped through an RRL method; this is coupled with a spatially dense sampling scheme. Completing a battery of population genetics analyses across data types (including a series of down‐sampled data sets), the authors find that SNP data are slightly more sensitive to fine‐scale genetic structure, and the results are more resilient to down‐sampling than microsatellites and nonrepetitive nuclear loci. However, their results are far from an unqualified victory for RRL SNP data over all previous data types: the authors note that modest additions to the microsatellites and nuclear loci data sets may provide the necessary analytical power to delineate the fine‐scale genetic structuring identified by SNPs. As always, as the field begins to fully embrace the newest thing, good science reminds us that traditional data types are far from useless, especially when combined with a well‐designed sampling scheme.

Population genetics has gained popularity as a method to discover glacial refugia in terrestrial species, but has only recently been applied to the marine realm. The last glacial maxima occurred 20,000 years ago, decreasing sea levels by 120 m and exposing much of the continental shelf in the northern Gulf of Mexico, with the exception of De Soto Canyon (2100 m depth). The goal of this study was to determine whether population dynamics of the giant deep-sea isopod, Bathynomus giganteus, were better explained by habitat diversity or by the past presence of a marine glacial refugium in De Soto Canyon. To accomplish this we (1) measured genetic diversity in De Soto Canyon and adjacent regions, (2) characterized gene flow and connectivity between these regions, and (3) investigated historical changes to population size. We sequenced three mitochondrial loci (12S, 16S, and COI) from 212 individuals and also performed a next-generation sequencing pilot study using double digest Restriction site-Associated DNA sequencing. We found high genetic diversity and connectivity throughout the study regions, migration between all three regions, low population differentiation, and evidence of population expansion. This study suggests that habitat heterogeneity, rather than the presence of a glacial refugium, has had an historical effect on the population dynamics of B. giganteus.

Species of Farfantepenaeus support economically important shrimp fisheries throughout the Western Hemisphere, necessitating proper fisheries management. To be effective, species management should be informed of the potential presence of cryptic species and of the evolutionary forces driving biodiversity. This is best accomplished through a robust phylogenetic framework and evidence-based species delimitation. This study represents the first comprehensive molecular phylogeny and species delimitation analyses of shrimps belonging to the genus Farfantepenaeus. Targeting three mitochondrial genes (12S, 16S, and COI), gene trees and a phylogeny for the genus were inferred using maximum likelihood and Bayesian approaches. In general, the phylogenetic relationships inferred here largely agree with those recovered from morphological data, including the most recent designation of F. isabelae as sister to F. subtilis. Molecular divergence was found between northern and southern populations of F. brasiliensis, suggesting the existence of unrecognised subspecies. However, previous recognition of F. duorarum and F. notialis as two distinct species was not supported by this study. The phylogeny inferred here also uncovers a phylogeographic signal of latitudinal speciation in the genus. The study presented here provides valuable insight into the evolutionary history of Farfantepenaeus, improving our ability to effectively manage these economically important species.

Despite the ecological importance of deep-sea cephalopods, little is known about their genetic diversity or population dynamics. The cephalopod species Cranchia scabra, Pyroteuthis margaritifera, and Vampyroteuthis infernalis are commonly collected in midwater samples from both the Gulf of Mexico and northwestern Atlantic Ocean but, despite their common appearance in trawls and important roles in marine food webs, no genetic studies of population connectivity exist for these species. Here, Sanger sequencing of three conserved genetic loci and ddRADseq techniques were used to examine population genetic dynamics in these deep-sea species. Genetic diversity is lowest in C. scabra, which appears to be in a population growth stage, and highest in V. infernalis. Population structure was unique to V. infernalis but does not appear to be the result of ocean-basin vicariance, thus possible alternative explanations are explored, specifically environmental variation in dissolved oxygen. The genetic connectivity between these geographically disparate sites suggests these three cephalopod species could be resilient to localized environmental disturbances in the Gulf of Mexico.

Comprising over 15,000 living species, decapods (crabs, shrimp, and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (>86,000 bp) conserved across all lineages of Decapoda, eight times more molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, ‘lobster’, and ‘crab’ groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Paleozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behavior, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

Synopsis Sipuncula is a relatively small taxon with roughly 150 recognized species. Many species are geographically widespread or ‘‘cosmopolitan.’’ The pelagosphera larvae of some species are estimated to spend several months in the plankton. However, recent molecular evidence suggests that many of the ‘‘cosmopolitan’’ species actually represent species-complexes, some not even monophyletic. Herein, we present data on three sipunculan species with different developmental modes that occur both in the Sea of Japan and in the Northeast Pacific. The development of the three species—Phascolosoma agassizii, Thysanocardia nigra, and Themiste pyroides—is exceptionally well studied in both regions of the Pacific. Significant differences have been observed between the two regions with respect to egg size, developmental mode, and developmental timing. In general, eggs are larger and development slower in the Northeast Pacific when compared with the Sea of Japan. These differences have been explained as a result of phenotypic plasticity exhibited under different environmental conditions, in particular temperature, but we show that the populations of all three species are also remarkably distinct genetically and that gene flow between the two regions is extremely unlikely. In Thysanocardia nigra, we even found two very distinct genetic lineages within the same location in the Northeast Pacific. The amount of genetic divergence between populations from the Sea of Japan and those from the Northeast Pacific is not correlated with developmental mode. Themiste pyroides, the species with the most abbreviated development, actually has the least degree of genetic divergence between the regions. Analyses of molecular variance show that the majority of the observed variation in all three species is between the regions. We conclude that all three ‘‘cosmopolitan’’ species actually represent complexes of cryptic or pseudo-cryptic species. These examples demonstrate that a solid taxonomic framework based on molecular and morphological evidence is a prerequisite for evaluating relationships between dispersal capabilities, species’ ranges, and the connectivity of populations.

The annual swarming of epitokes of the eunicid polychaete Palola viridis has great cultural significance in Samoa and other Indo-Pacific locations. Palola spp. occur worldwide in warm shallow-water environments, but not all populations appear to swarm. Morphological distinctions among Palola species are subtle but, based on phylogenetic analysis of mitochondrial markers, two species groups can be distinguished, each containing numerous subclades. The objectives of this study were to determine the position of P. viridis in the phylogeny of the genus, to assess the species’ genetic distinctness and to describe P. viridis epitokes morphologically. We sequenced epitokes from Samoa (locally known as palolo) and Vanuatu (un) for two mitochondrial markers and performed phylogenetic analyses in combination with previously published sequences. The samples from Samoa and Vanuatu formed a common clade in species group B. We suggest that swarming is restricted to this species group, although probably not to a single species.