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We analyze multi-scalar social, economic, and policy dynamics of shark fin production and consumption through Hong Kong, the world's leading shark fin entrepôt, and U.S. Mid-Atlantic artisanal fisheries in New Jersey (NJ), a U.S. state that enacted a shark-fin retail ban in 2021. Trade statistics point to a rise in shark fin circulation to Hong Kong in recent years supplied through global pathways of production. Global discourses of overconsumption and shark finning in Asia have shaped U.S. state environmental policies banning shark fin retail. However, interviews with shark fin retailers and consumers in Hong Kong point not to undifferentiated Asian consumption, but instead indicate gendered, classed, and intergenerational dynamics that undergird consumption and bear on production elsewhere. New Jersey fisheries, once an exporter to Hong Kong, enacted a state-wide shark fin retail ban in response to global defaunation and anxieties related to Asian fishing and consumption practices. Interviews and focus group discussions illustrate how the ban has resulted in a practice artisanal fishers call "reverse shark-finning," i.e., the discarding of fins post-landing. Moreover, local regulations neglect artisanal fishers' knowledge and capability to identify shark species at sea. The findings show how the totalizing ban diminishes economic returns but does not reduce total shark catches in the artisanal sector. To test fishers' knowledge at sea, the study uses a mitochondrial DNA barcoding method on post-landing shark fins (n = 47) to compare genetic identification with fishers' visual species identification. The findings illustrate artisanal fishers' knowledge is sufficient to accurately identify the shark species they catch. These findings are significant for environmental policies, biodiversity conservation, and global-local relations of production and consumption. We argue that more targeted efforts that take socioeconomic dynamics into account are needed to affect consumption, while more holistic policies that examine impacts rather than blanket bans may be more effective on the production and conservation side. Ecologically sustainable and socioeconomically sound shark conservation practices, therefore, require multi-scalar interdisciplinary and dialectical analyses of social, economic, and policy dynamics. [ABSTRACT FROM AUTHOR]

Over the past few decades, there has been an explosion in the amount of publicly available sequencing data. This opens new opportunities for combining data sets to achieve unprecedented sample sizes, spatial coverage or temporal replication in population genomic studies. However, a common concern is that nonbiological differences between data sets may generate patterns of variation in the data that can confound real biological patterns, a problem known as batch effects. In this paper, we compare two batches of low‐coverage whole genome sequencing (lcWGS) data generated from the same populations of Atlantic cod (Gadus morhua). First, we show that with a "batch‐effect‐naive" bioinformatic pipeline, batch effects systematically biased our genetic diversity estimates, population structure inference and selection scans. We then demonstrate that these batch effects resulted from multiple technical differences between our data sets, including the sequencing chemistry (four‐channel vs. two‐channel), sequencing run, read type (single‐end vs. paired‐end), read length (125 vs. 150 bp), DNA degradation level (degraded vs. well preserved) and sequencing depth (0.8× vs. 0.3× on average). Lastly, we illustrate that a set of simple bioinformatic strategies (such as different read trimming and single nucleotide polymorphism filtering) can be used to detect batch effects in our data and substantially mitigate their impact. We conclude that combining data sets remains a powerful approach as long as batch effects are explicitly accounted for. We focus on lcWGS data in this paper, which may be particularly vulnerable to certain causes of batch effects, but many of our conclusions also apply to other sequencing strategies. see also the Perspective by ‐ Claire Mérot [ABSTRACT FROM AUTHOR]

Worldwide, many commercial fish stocks have experienced dramatic declines due to overfishing. Such fisheries-induced population reductions could potentially erode the genetic diversity of marine fish populations. Based on analyses of DNA extracted from archived and contemporary samples, this paper compares the genetic variability at nine microsatellite loci in a Canadian population of Atlantic cod (Gadus morhua) over 80 years, spanning from before the fishery intensified to now when the population is at historically low abundance. Extensively validated genetic data from the temporally spaced samples were used to estimate the effective population size. Over the period, we observed no loss of either heterozygosity or allelic diversity. Several of the estimation methods applied could not distinguish the effective population size from infinity, and the lower 95% confidence limit on estimates was generally >500, suggesting that the effective population size is probably considerably larger than this. Hence, it appears that the southern Gulf of St. Lawrence cod stock has maintained genetic variability to sustain future evolution despite a dramatic population decline Resume: A lechelle globale, plusieurs stocks commerciaux de poissons ont connu des declins spectaculaires a` cause de la surpeche. De telles reductions demographiques dues a` la peche pourraient potentiellement diminuer la diversite gene-tique des populations de poissons marins. Sappuyant sur des analyses d'ADN faites sur des echantillons archives et contemporains, notre etude compare la variabilite genetique a` neuf locus microsatellites dans une population canadienne de morues franches (Gadus morhua) sur une periode de 80 ans couvrant le temps d'avant l'intensification de la peche jusqua maintenant alors que la population connait une abondance historiquement basse. Des donnees genetiques solidement validees provenant d'echantillons etales dans le temps ont servi a estimer la taille effective de la population. Durant cette periode, nous n'observons de perte ni d'heterozygotie, ni de diversite allelique. Plusieurs des methodes d'estimation utiliseesne peuvent pas distinguer la taille effective de la population de l'infini et la limite inferieure de l'intervalle de confiance de 95 % des estimations est generalement >500, ce qui laisse croire que la taille effective est probablement beaucoup plus elevee que ce nombre. Il apparait donc que le stock de morues du sud du golfe du Saint-Laurent a conserve la variabilite genetique necessaire pour assurer son evolution future, malgre son declin demographique spectaculaire. [Traduit par la Redaction], Introduction In recent years many commercial fish stocks have declined dramatically as a result of overfishing (Hutchings and Reynolds 2004; Worm et al. 2006). A growing body of literature has [...]

Today most population genomic studies of nonmodel organisms either sequence a subset of the genome deeply in each individual or sequence pools of unlabelled individuals. With a step-by-step workflow, we illustrate how low-coverage whole-genome sequencing of hundreds of individually barcoded samples is now a practical alternative strategy for obtaining genomewide data on a population scale. We used a highly efficient protocol to generate high-quality libraries for ~6.5 USD from each of 876 Atlantic silversides (a teleost fish with a genome size ~730 Mb) that we sequenced to 1-4× genome coverage. In the absence of a reference genome, we developed a bioinformatic pipeline for mapping the genomic reads to a de novo assembled reference transcriptome. This provides an 'in silico' method for exome capture that avoids the complexities and expenses of using wet chemistry for target isolation. Using novel tools for analysis of low-coverage data, we extracted population allele frequencies, individual genotype likelihoods and polymorphism data for 2 504 335 SNPs across the exome for the 876 fish. To illustrate the use of the resulting data, we present a preliminary analysis of geographical patterns in the exome data and a comparison of complete mitochondrial genome sequences for each individual (constructed from the low-coverage data) that show population colonization patterns along the US east coast. With a total cost per sample of less than 50 USD (including sequencing) and ability to prepare 96 libraries in only 5 h, our approach adds a viable new option to the population genomics toolbox. [ABSTRACT FROM AUTHOR]

High-throughput sequencing technologies are currently revolutionizing the field of biology and medicine, yet bioinformatic challenges in analysing very large data sets have slowed the adoption of these technologies by the community of population biologists. We introduce the 'Simple Fool's Guide to Population Genomics via RNA-seq' ( SFG), a document intended to serve as an easy-to-follow protocol, walking a user through one example of high-throughput sequencing data analysis of nonmodel organisms. It is by no means an exhaustive protocol, but rather serves as an introduction to the bioinformatic methods used in population genomics, enabling a user to gain familiarity with basic analysis steps. The SFG consists of two parts. This document summarizes the steps needed and lays out the basic themes for each and a simple approach to follow. The second document is the full SFG, publicly available at http://sfg.stanford.edu, that includes detailed protocols for data processing and analysis, along with a repository of custom-made scripts and sample files. Steps included in the SFG range from tissue collection to de novo assembly, blast annotation, alignment, gene expression, functional enrichment, SNP detection, principal components and FST outlier analyses. Although the technical aspects of population genomics are changing very quickly, our hope is that this document will help population biologists with little to no background in high-throughput sequencing and bioinformatics to more quickly adopt these new techniques. [ABSTRACT FROM AUTHOR]

Collections of historical tissue samples from fish (e.g. scales and otoliths) stored in museums and fisheries institutions are precious sources of DNA for conducting retrospective genetic analysis. However, in some cases, only external tags used for documentation of spatial dynamics of fish populations have been preserved. Here, we test the usefulness of fish tags as a source of DNA for genetic analysis. We extract DNA from historical tags from cod collected in Greenlandic waters between 1950 and 1968. We show that the quantity and quality of DNA recovered from tags is comparable to DNA from archived otoliths from the same individuals. Surprisingly, levels of cross-contamination do not seem to be significantly higher in DNA from external (tag) than internal (otolith) sources. Our study therefore demonstrates that historical tags can be a highly valuable source of DNA for retrospective genetic analysis of fish., (© 2013 John Wiley & Sons Ltd.)