Retrospective genomics highlights changes in genetic composition of tiger sharks (Galeocerdo cuvier) and potential loss of a south-eastern Australia population.

Over the last century, many shark populations have declined, primarily due to overexploitation in commercial, artisanal and recreational fisheries. In addition, in some locations the use of shark control programs also has had an impact on shark numbers. Still, there is a general perception that populations of large ocean predators cover wide areas and therefore their diversity is less susceptible to local anthropogenic disturbance. Here we report on temporal genomic analyses of tiger shark (Galeocerdo cuvier) DNA samples that were collected from eastern Australia over the past century. Using Single Nucleotide Polymorphism (SNP) loci, we documented a significant change in genetic composition of tiger sharks born between ~1939 and 2015. The change was most likely due to a shift over time in the relative contribution of two well-differentiated, but hitherto cryptic populations. Our data strongly indicate a dramatic shift in the relative contribution of these two populations to the overall tiger shark abundance on the east coast of Australia, possibly associated with differences in direct or indirect exploitation rates.

The rise of genomics in snake venom research: recent advances and future perspectives.

Snake venoms represent a danger to human health, but also a gold mine of bioactive proteins that can be harnessed for drug discovery purposes. The evolution of snakes and their venom has been studied for decades, particularly via traditional morphological and basic genetic methods alongside venom proteomics. However, while the field of genomics has matured rapidly over the past 2 decades, owing to the development of next-generation sequencing technologies, snake genomics remains in its infancy. Here, we provide an overview of the state of the art in snake genomics and discuss its potential implications for studying venom evolution and toxinology. On the basis of current knowledge, gene duplication and positive selection are key mechanisms in the neofunctionalization of snake venom proteins. This makes snake venoms important evolutionary drivers that explain the remarkable venom diversification and adaptive variation observed in these reptiles. Gene duplication and neofunctionalization have also generated a large number of repeat sequences in snake genomes that pose a significant challenge to DNA sequencing, resulting in the need for substantial computational resources and longer sequencing read length for high-quality genome assembly. Fortunately, owing to constantly improving sequencing technologies and computational tools, we are now able to explore the molecular mechanisms of snake venom evolution in unprecedented detail. Such novel insights have the potential to affect the design and development of antivenoms and possibly other drugs, as well as provide new fundamental knowledge on snake biology and evolution.

Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.

Targeted sequencing is an increasingly popular next-generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.

Ancient and historical DNA in conservation policy.

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (Ne), and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.

Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea.

Sandeels are an ecologically important group of fishes; they are a key part of the food chain serving as food for marine mammals, seabirds and fish. Sandeels are further targeted by a large industrial fishery, which has led to concern about ecosystem effects. In the North Sea, the lesser sandeel Ammodytes marinus is by far the most prevalent species of sandeel in the fishery. Management of sandeel in the North Sea plus the Kattegat is currently divided into seven geographical areas, based on subtle differences in demography, population dynamics and results from simulations of larval dispersal. However, little is known about the underlying genetic population structure. In this study, we used 2,522 SNPs derived from restriction site-associated DNA sequencing (RADseq) typed in 429 fish representing four main sandeel management areas. Our main results showed (a) a lack of a clear spatially defined genetic structure across the majority of genetic markers and (b) the existence of a group of at least 13 SNPs under strong linkage disequilibrium which together separate North Sea sandeel into three haplotype clusters, suggestive of one or more structural variants in the genome. Analyses of the spatial distribution of these putative structural variants suggest at least partial reproductive isolation of sandeel in the western management area along the Scottish coast, supporting a separate management. Our results highlight the importance of the application of a large number of markers to be able to detect weak patterns of differentiation. This study contributes to increasing the genetic knowledge of this important exploited species, and results can be used to improve our understanding of population dynamics and stock structure.

Digest: Untangling the influence of soft and hard selection in experimental populations-from environment to genomics.

Gallet et al. (2018) studied the effect of two selection regimes on the maintenance of polymorphism in experimental populations. They took two strains of Escherichia coli, each resistant to a different antibiotic, evolved them in culture conditions representing "soft" or "hard" selective regimes, and measured polymorphism levels for three to five transfers. Their results supported theoretical predictions that only "soft" selection maintains polymorphism, highlighting the importance of experimental studies to understand maintenance of variation in nature.

One size fits all? Direct evidence for the heterogeneity of genetic drift throughout the genome.

Effective population size (Ne) is a central parameter in population and conservation genetics. It measures the magnitude of genetic drift, rates of accumulation of inbreeding in a population, and it conditions the efficacy of selection. It is often assumed that a single Ne can account for the evolution of genomes. However, recent work provides indirect evidence for heterogeneity in Ne throughout the genome. We study this by examining genome-wide diversity in the Danish Holstein cattle breed. Using the differences in allele frequencies over a single generation, we directly estimated Ne among autosomes and smaller windows within autosomes. We found statistically significant variation in Ne at both scales. However, no correlation was found between the detected regional variability in Ne, and proxies for the intensity of linked selection (local recombination rate, gene density), or the presence of either past strong selection or current artificial selection on traits of economic value. Our findings call for further caution regarding the wide applicability of the Ne concept for understanding quantitatively processes such as genetic drift and accumulation of consanguinity in both natural and managed populations.

Pedigree analysis for the genetic management of group-living species.

Captive breeding programs are an important tool for the conservation of endangered species. These programs are commonly managed using pedigrees containing information about the history of each individual's family, such as breeding pairs and parentage. However, there are some species that are kept in groups where it is hard to distinguish between particular individuals within the group, making it very difficult to record any information at an individual level. Currently, software and methods commonly used for registering and analyzing pedigrees to help manage populations at an individual level are not adequate for managing these group-living species. Therefore, there is a need to further develop these tools and methodologies for pedigree analysis to better manage group-living species. PMx is a program used for the management of ex situ populations in zoos and aquariums. We adapted the pedigree analysis method implemented in PMx to analyze pedigrees (records of descendant lineages) of group-living species. In addition, we developed a group pedigree data entry sheet and group2PMx, a converter program that enables group datasets to be imported into PMx. We show how pedigree analysis of a group-living species can be used for population management using the studbook of the endangered Texas blind cave salamander Eurycea rathbuni. Such analyses of the pedigree of groups can improve the management of group-living species in ex situ breeding programs. Firstly, it enables better management decisions based on more accurate genetic measures between groups, allowing for greater control of inbreeding. Secondly, it can improve the conditions in which group-living species are held by adapting husbandry practices to better reflect conditions of these species living in the wild. The use of the spreadsheet and group2PMx extends the application of PMx, allowing conservation managers and other institutions outside the zoo and aquarium community to easily import and analyze their pedigree data.