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SUMMARY: We developed loco-pipe, a Snakemake pipeline that seamlessly streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data. loco-pipe is highly automated, easily customizable, massively parallelized, and thus is a valuable tool for both new and experienced users of lcWGS. AVAILABILITY AND IMPLEMENTATION: loco-pipe is published under the GPLv3. It is freely available on GitHub (github.com/sudmantlab/loco-pipe) and archived on Zenodo (doi.org/10.5281/zenodo.10425920).

Blooms of Alexandrium catenella threaten to disrupt subsistence, recreational, and commercial shellfish harvest in Alaska, as the paralytic shellfish toxins (PSTs) produced pose a serious public health risk and can lead to costly shutdowns for shellfish farmers. Current methods of PST detection in the region range from monitoring programs utilizing net tows to detect A. catenella to direct shellfish tissue testing via mouse bioassay (MBA) for commercial aquaculture harvest, as well as various optional testing methods for subsistence and recreational harvesters. The efficacy and feasibility of these methods vary, and they have not been directly compared in Southeast Alaska. In this study, we sought to assess and compare A. catenella and PST early detection methods to determine which can provide the most effective and accurate warning of A. catenella blooms or PST events. We found microscope counts to be variable and prone to missing lower numbers of A. catenella, which may be indicative of bloom formation. However, quantitative polymerase chain reaction (qPCR) significantly correlated with microscope counts and was able to effectively detect even low numbers of A. catenella on all sampling days. Paralytic shellfish toxin concentrations measured by enzyme‐linked immunosorbent assay and MBA significantly correlated with each other, qPCR, and some microscope counts. These results show that qPCR is an effective tool for both monitoring A. catenella and serving as a proxy for PSTs. Further work is needed to refine qPCR protocols in this system to provide bloom warnings on an actionable timescale for the aquaculture industry and other shellfish harvesters. Integr Environ Assess Manag 2024;20:2189–2202. © 2024 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Key Points: The species‐specific quantitative polymerase chain reaction (qPCR) assay effectively detects Alexandrium catenella at numbers too low for other methods.A threshold of ~90 000 000 A. catenella qPCR copies per liter may indicate elevated paralytic shellfish toxins in Pacific oysters.Microscope counts of A. catenella cells are variable and miss low quantities.Enzyme‐linked immunosorbent assays detect elevated paralytic shellfish toxins, and correlate with approved testing methods. [ABSTRACT FROM AUTHOR]

Sloth bears are non‐carnivorous yet they attack more people than any other bear. They often stand up and charge explosively if a person mistakenly gets too close. Here, we argue that their aggression toward humans is an extension of their behavior toward tigers, which are their only natural predator. Interactions between sloth bears and tigers have not previously been studied because scientists have rarely observed such events. We collected and examined 43 videos or photo documentations of sloth bear–tiger interactions posted on the internet or social media from 2011 to 2023, mainly by tourists visiting tiger parks in India. We observed that sloth bears were most likely to stand up and charge if they first became aware of the tiger at close range (<3 m away). This aggressive–defensive strategy, intended to dissuade the tiger from attacking, appeared to be successful, in that 86% of interactions ended with no contact, whereas four (9%) culminated in the bear's death. We propose that a myrmecophagous diet led to this species' aggressive behavior: (1) their long, blunt front claws, well adapted for digging termites and ants, hamper their ability to climb trees for escape, and (2) they walk with their head down focused on scents underground, and make considerable noise digging and blowing soil, enabling tigers to approach quite closely without being detected. Sloth bears have coexisted with tigers or other (now extinct) large felid predators for their entire evolutionary history. Whereas their aggressive behavior has served them well for millions of years, more recently, people's fear of and retaliation against sloth bears represents a major threat to their survival. Understanding how sloth bears react to tigers provides guidance for reducing attacks on humans, thereby contributing to sloth bear conservation. Our investigation was made possible by passive citizen scientists, who unknowingly collected valuable data. [ABSTRACT FROM AUTHOR]

Strain performance evaluations are vital for developing successful fishery management and restoration strategies. Here, we utilized genotypes from 36 microsatellites to investigate hatchery strain contribution to collections of naturally produced lake trout (Salvelinus namaycush) sampled across Lake Michigan. Strain composition varied by area, with recoveries of Seneca Lake strain exceeding expectations based on stocking records in northern Lake Michigan but performing similarly to other strains in southern Lake Michigan. Interstrain hybrids were present at moderate frequencies similar to expectations based on simulations, suggesting that strains are interbreeding randomly. We hypothesize that the superior performance of the Seneca Lake strain in northern Lake Michigan is partially due to adaptive advantages that facilitate increased survival in areas with high mortality from sea lamprey (Petromyzon marinus) predation, such as northern Lake Michigan. However, when this selective pressure is lessened, the Seneca Lake strain performs similarly to other strains. Our study demonstrates that strain performance can vary across small spatial scales and illustrates the importance of conducting thorough strain evaluations to inform management and conservation. Les evaluations de la performance de lignees sont d'importance vitale pour l'elaboration de strategies efficaces de gestion et de retablissement des ressources halieutiques. Nous utilisons les genotypes etablis a partir de 36 microsatellites pour examiner la contribution de lignees issues d'ecloseries a des collections de truites de lac (Salvelinus namaycush) produites naturellement prelevees a la grandeur du lac Michigan. La composition des lignees varie selon la region, les taux de recuperation de truites de la lignee du lac Seneca depassant les predictions basees sur les registres d'empoissonnement dans le nord du lac Michigan, alors que ces taux sont semblables a ceux d'autres lignees dans le sud du lac Michigan. Des hybrides issus du croisement de lignees sont presents a des frequences moderees semblables aux frequences predites sur la base de simulations, ce qui indiquerait que le croisement de lignees est aleatoire. Nous postulons que la meilleure performance de la lignee du lac Seneca dans le nord du lac Michigan decoule en partie d'avantages adaptatifs facilitant une survie accrue dans des secteurs de forte mortalite associee a la predation par les lamproies (Petromyzon marinus), tels que le nord du lac Michigan. Quand ces pressions de selection sont reduites, la performance de la lignee du lac Seneca est toutefois semblable a celles d'autres lignees. L'etude demontre que la performance de lignees peut varier sur de courtes distances et souligne l'importance de realiser des evaluations exhaustives des lignees pour appuyer les decisions concernant la gestion et la conservation. [Traduit par la Redaction], Introduction Attempting to rebuild collapsed or extirpated fish populations through stocking of hatchery-reared individuals is a common practice, but the short- and long-term success of this approach is highly variable [...]

Harvest in walleye Sander vitreus fisheries is size‐selective and could influence phenotypic traits of spawners; however, contributions of individual spawners to recruitment are unknown. We used parentage analyses using single nucleotide polymorphisms to test whether parental traits were related to the probability of offspring survival in Escanaba Lake, Wisconsin. From 2017 to 2020, 1339 adults and 1138 juveniles were genotyped and 66% of the offspring were assigned to at least one parent. Logistic regression indicated the probability of reproductive success (survival of age‐0 to first fall) was positively (but weakly) related to total length and growth rate in females, but not age. No traits analyzed were related to reproductive success for males. Our analysis identified the model with the predictors' growth rate and year for females and the models with year and age and year for males as the most likely models to explain variation in reproductive success. Our findings indicate that interannual variation (i.e., environmental conditions) likely plays a key role in determining the probability of reproductive success in this population and provide limited support that female age, length, and growth rate influence recruitment. [ABSTRACT FROM AUTHOR]

Natural-origin steelhead trout (Oncorhynchus mykiss (Walbaum, 1792)) in the Pacific Northwest, USA, are threatened by a number of factors including habitat destruction, disease, decline in marine survival, and a potential erosion of genetic viability due to introgression from hatchery strains. Our major goal was to use a recently developed SNP array containing ~57 000 SNPs to identify a subset of SNPs that differentiate hatchery and natural-origin populations. We analyzed 35 765 polymorphic SNPs in nine populations of steelhead trout sampled from Puget Sound, Washington, USA. We then conducted two outlier tests and found 360 loci that were candidates for divergent selection between hatchery and natural-origin populations (mean [F.sub.CT] = 0.29, maximum = 0.65) and 595 SNPs that were candidates for selection among natural- origin populations (mean [F.sub.ST] = 0.25, maximum = 0.51). Comparisons with a linkage map revealed that two chromosomes (Omy05 and Omy25) contained significantly more outliers than other chromosomes, suggesting that regions on Omy05 and Omy25 may be of adaptive significance. Our results highlight several advantages of the 57 000 SNP array as a tool for population and conservation genomics studies. Les truites arc-en-ciel (Oncorhynchus mykiss (Walbaum, 1792)) anadromes d'origine naturelle dans la region du Pacific Northwest (Etats-Unis) sont menacees par divers facteurs dont la destruction d'habitats, les maladies, la baisse de la survie en mer et une erosion possible de la viabilite genetique decoulant de l'introgression de souches issues d'alevinieres. Notre objectif principal consistait a utiliser une puce contenant ~57 000 SNP mise au point recemment pour cerner un sous-ensemble de SNP qui differencient les populations issues d'alevinieres des populations d'origine naturelle. Nous avons analyse 35 765 SNP polymorphiques dans neuf populations de truites arc-en-ciel anadromes echantillonnees dans le Puget Sound (Washington, Etats-Unis). Nous avons ensuite realise deux tests pour detecter les regions aberrantes et trouve 360 sites qui sont des candidats pour une selection divergente entre les populations issues d'alevinieres et d'origine naturelle ([F.sub.CT] moyen = 0,29, max = 0,65) et 595 SNP qui sont des candidats pour une selection au sein de populations d'origine naturelle ([F.sub.CT] moyen = 0,25, max = 0,51). Des comparaisons avec une carte de filiation revelent que deux chromosomes (Omy05 et Omy25) contiennent significativement plus de regions aberrantes que les autres chromosomes, ce qui porte a croire que des regions sur Omy05 et Omy25 pourraient etre importantes pour l'adaptation. Nos resultats font ressortir plusieurs avantages de la puce a 57 000 SNP comme outil pour les etudes de genomique des populations et de la conservation. [Traduit par la Redaction], Introduction Many steelhead trout (Oncorhynchus mykiss (Walbaum, 1792)) populations in the Pacific Northwest, USA, are at a fraction of their historic numbers even after more than 70 years of conservation [...]

Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from recombination and thus be selected for, but few studies have tested it with empirical data. Here, we used restriction site‐associated sequencing to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We used four differentiation‐based outlier tests and three genotype–environment association analyses to define neutral single nucleotide polymorphisms (SNPs) and outlier SNPs that were putatively under selection. We then examined the distribution of outlier SNPs along the genome and investigated whether these SNPs were found in genomic islands of differentiation and inversions. We found that gene flow varied among species, and outlier SNPs were clustered more tightly in species with higher gene flow. The two species with the highest overall FST (0.0303–0.0720) and therefore lowest gene flow showed little evidence of clusters of outlier SNPs, with outlier SNPs in these species spreading uniformly across the genome. In contrast, nearly all outlier SNPs in the species with the lowest FST (0.0003) were found in a single large putative inversion. Two other species with intermediate gene flow (FST ~ 0.0025–0.0050) also showed clustered genomic architectures, with most islands of differentiation clustered on a few chromosomes. Our results provide important empirical evidence to support the hypothesis that increasingly clustered architecture of local adaptation is associated with high gene flow. see also the Perspective by Sara M. Schaal and Sara J. Smith [ABSTRACT FROM AUTHOR]

Genetic stock identification (GSI), an important tool for fisheries management that relies upon the ability to differentiate stocks of interest, can be difficult when populations are closely related. Here we genotyped 11850 single-nucleotide polymorphisms (SNPs) from existing DNA sequence data available in five closely related populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. We then converted a subset of 96 of these SNPs displaying high differentiation into high-throughput genotyping assays. These 96 SNPs (RAD96) and 191 SNPs developed previously (CTC191) were screened in 28 populations from western Alaska. Regional assignment power was evaluated for five different SNP panels, including a panel containing the 96 SNPs with the highest [F.sub.ST] across the CTC191 and RAD96 panels ([F.sub.ST]96). Assignment tests indicated that SNPs in the RAD96 were more useful for GSI than those in the CTC191 and that increasing the number of reporting groups in western Alaska from one to three was feasible with the [F.sub.ST]96. Our approach represents an efficient way to discover SNPs for GSI and should be applicable to other populations and species. Resume: L'identification genetique des stocks (IGS), un important outil de gestion des peches reposant sur la capacite de distinguer des stocks d'interet, peut etre difficile si les populations sont etroitement reliees. Nous avons genotype 11850 polymorphismes mononucleotidiques (SNPs) tires de donnees de sequences d'ADN disponibles pour cinq populations etroitement reliees de saumon quinnat (Oncorhynchus tshawytscha) de l'ouest de l'Alaska. Nous avons ensuite converti un sous-ensemble de 96 de ces SNP presentant une forte differentiation en des tests de genotypage de haute capacite. Ces 96 SNP (RAD96) et 191 SNP etablis precedemment (CTC191) ont fait l'objet d'un criblage dans 28 populations de l'ouest de l'Alaska. La puissance d'affection regionale a ete evaluee pour cinq panels de SNP distincts dont un panel contenant les 96 SNP presentant les [F.sub.ST] les plus eleves des panels CTC191 et RAD96 ([F.sub.ST]96). Les tests d'affectation ont indique que les SNP du RAD96 etaient plus utiles pour l'IGS que ceux du CTC191 et qu'une augmentation d'un a trois du nombre de groupes pouvant etre distingues dans l'ouest de l'Alaska etait possible avec le [F.sub.ST]96. Notre approche constitue une maniere efficace de cerner des SNP pour l'IGS et devrait pouvoir s'appliquer a d'autres populations et especes. [Traduit par la Redaction], Introduction Genetic tools have been used to document biodiversity and to manage wild populations for over four decades (Utter 2004; Waples et al. 2008). These techniques are particularly applicable to [...]

Inferences made from molecular data support regional stock assessment goals by providing insights into the genetic population dynamics of enigmatic species. Population genomics metrics, such as genetic diversity and population connectivity, serve as useful proxies for species health and stability. Sleeper sharks (genus Somniosus) are ecologically important deep-sea predators, estimated to reach ages of 250 to 300 yr and taking decades to reach sexual maturity. The subgenus Somniosus (Somniosus) is comprised of 3 species: S. pacificus , S. microcephalus , and S. antarcticus. Given the life history strategy of somniosids, they are vulnerable to overfishing and population declines. Further, data to assess the stocks of these species are limited. To address this deficiency, we used the reduced representation library method Restriction-site Associated DNA sequencing (RADseq) to conduct phylogenomic and population genomics analyses, providing novel information for use in stock assessments. Our results strongly support the species status of S. microcephalus (N = 79), but recover S. antarcticus (N = 2) intermixed within the S. pacificus (N = 170) clade. Population genomics analyses reveal genetic homogeneity within S. pacificus and S. microcephalus , and estimates of effective population size were in the hundreds for both species. Kinship analysis identified 2 first-degree relative pairs within our dataset (1 within each species). Our results contribute new information for stock assessments of these uniquely long-lived species by providing the strongest molecular evidence to date for the synonymization of S. antarcticus and S. pacificus , as well as estimating population genomic metrics for each supported species within the Somniosus (Somniosus) subgenus. [ABSTRACT FROM AUTHOR]

We genotyped Chinook salmon (Oncorhynchus tshawytscha) from the Bering Sea and North Pacific Ocean for 43 single-nucleotide polymorphisms (SNPs) to investigate seasonal distribution and migration patterns. We analyzed 3563 immature fish from 22 spatiotemporal strata; composition analyses were performed using genotype data from spawning stocks spanning the species range. Substantial variation in stock composition existed among spatial and seasonal strata. We inferred patterns of seasonal migration based upon these data along with data from previous tag, scale, and parasite studies. We found that stocks from western Alaska and Yukon River overwinter on the Alaska continental shelf then travel to the middle and western Bering Sea during spring-fall. Stocks from California to Southeast Alaska were distributed in Gulf of Alaska year-round, with a substantial portion of this group migrating northward to the eastern Bering Sea during spring-fall. Proportions of Russian stocks increase when moving east to west in both the Bering Sea and North Pacific Ocean. These data can be used to better understand the impacts of fisheries and climate change on this valuable resource. Nous avons realise le genotypage de saumons quinnat (Oncorhynchus tshawytscha) de la mer de Bering et du Pacifique Nord pour 43 sites de polymorphisme mononucleotidique (SNPs) afin d'etudier la repartition saisonniere et les habitudes migratoires de ces saumons. Nous avons analyse 3563 poisons immatures issus de 22 strates spatiotemporelles; des analyses de la composition ont ete realisees a partir de donnees de genotypage pour des stocks reproducteurs recoupant toute l'aire de repartition de l'espece. Des variations importantes sur le plan de la composition des stocks des differentes strates spatiales et saisonnieres ont ete observees. Nous avons infere les habitudes de migration saisonnieres a la lumiere de ces donnees, ainsi que de donnees issues d'etudes de marquage, a l'echelle et de parasites. Nous avons constate que les stocks de l'ouest de l'Alaska et du fleuve Yukon passent l'hiver sur la plate-forme continentale de l'Alaska pour ensuite se diriger vers le milieu et l'ouest de la mer de Bering du printemps a l'automne. Des stocks provenant de la Californie au sud-est de l'Alaska sont presents dans le golfe d'Alaska a l'annee longue, une portion importante de ce groupe migrant vers le nord jusque dans la partie orientale de la mer de Bering, du printemps a l'automne. La proportion de stocks russes augmente d'est en ouest dans la mer de Bering et le Pacifique Nord. Ces donnees peuvent servir a etablir une meilleure comprehension des impacts de la peche et des changements climatiques sur cette ressource de grande valeur. [Traduit par la Redaction], Introduction Knowledge of the dynamics of migration and harvest of marine organisms is necessary to enable adequate conservation and management (Ruggerone and Goetz 2004; Welch et al. 2011). This critical [...]