Effective population size (Ne) is a key parameter of population genetics. However, Ne remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient FIS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Neestimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies.

Visual observations were collected using video from a remotely operated vehicle (ROV) for a number of deep-water species on the continental slope of the Bay of Biscay, Northeast Atlantic. Relative trawl availability was defined as the ratio of population density estimates from a scientific bottom-trawl survey to those derived from visual strip transects. Several natural and reaction behaviour variables were explored to explain between-species variation in relative trawl availability. The variable with most explanatory power was spatial dispersion, with aggregating species showing lower relative availability than those that were randomly or uniformly distributed. This variable was also strongly correlated with ROV density estimates (aggregated species had the highest densities). Mean distance off the ground and mean body length of a species were positively related to relative trawl availability. In contrast, the way different species reacted to the ROV did not appear to be correlated with relative trawl availability. KEY WORDS: Remotely operated vehicle · ROV · Catchability · Spatial distribution · Continental slopeResale or republication not permitted without written consent of the publisher

Most deep-water fish species are long-lived, slow growing and have low reproductive capacity. These stocks are highly vulnerable to exploitation and can be rapidly depleted with recovery being very slow, often taking decades. In the Northeast Atlantic, a diversity of deep-water fisheries exists for a variety of finfish and shellfish species. The major characteristics of these fisheries are described and the available fisheries, biological and life history data are reviewed. Surplus production and DeLury models are the principal methods currently used in assessing the stocks, although agebased methods, stock reduction models and life history models are likely to be used once sufficient biological data become available. Most of the deep-water fisheries in the Northeast Atlantic have been completely unregulated; the latest stock assessments indicate that nearly all exploited deepwater species are being harvested "outside safe biological limits" and that immediate reductions in catches are needed to avoid stock depletion. Various approaches for managing deep-water fisheries resources are discussed, including the need to harmonize conservation and enforcement measures across management jurisdictions for straddling stocks.

Sex-determination systems greatly vary between taxa and are generally classified as genetic, including monogenic or polygenic, or environmental. Genetic-based sex-determination systems have been characterized for a wide range of taxa, including plants

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