Stress related epigenetic changes may explain opportunistic success in biological invasions in Antipode mussels

Different environmental factors could induce epigenetic changes, which are likely involved in the biological invasion process. Some of these factors are driven by humans as, for example, the pollution and deliberate or accidental introductions and others are due to natural conditions such as salinity. In this study, we have analysed the relationship between different stress factors: time in the new location, pollution and salinity with the methylation changes that could be involved in the invasive species tolerance to new environments. For this purpose, we have analysed two different mussels’ species, reciprocally introduced in antipode areas: the Mediterranean blue mussel Mytilus galloprovincialis and the New Zealand pygmy mussel Xenostrobus securis, widely recognized invaders outside their native distribution ranges. The demetylathion was higher in more stressed population, supporting the idea of epigenetic is involved in plasticity process. These results can open a new management protocols, using the epigenetic signals as potential pollution monitoring tool. We could use these epigenetic marks to recognise the invasive status in a population and determine potential biopollutants

Novel multimarker comparisons address the genetic population structure of silvertip sharks (Carcharhinus albimarginatus)

The silvertip shark (Carcharhinus albimarginatus) is a reef-associated shark, with an intermittent distribution across the Indo-Pacific Ocean. Owing to global declines, the species is listed as Vulnerable under the International Union of Conservation for Nature Red List. Samples from 152 C. albimarginatus were collected from three locations: Papua New Guinea (PNG), east Australia and Seychelles. Samples were analysed using mitochondrial, microsatellite and double-digest restriction-associated DNA (ddRAD) generated single nucleotide polymorphism markers. As expected across a vast oceanic expanse, no gene flow was identified between south-west Pacific locations and Seychelles for any marker (population differentiation measured using Φ values 0.92-0.98, F values 0.036-0.059). Mitochondrial DNA indicated significant population structuring between PNG and east Australia (Φ = 0.102), but nuclear markers suggested connectivity between these geographically close regions (F = 0.000-0.001). In combination with known telemetry movements for C. albimarginatus, our results suggest stepping-stone patterns of movement between regions is likely driven by reproductive requirements. The use of three distinct marker types in this study has facilitated a powerful genetic description of the population connectivity of C. albimarginatus between the three sampled regions. Importantly, the connectivity described between PNG and east Australia should be used as a guide for managing the south-west Pacific stock of C. albimarginatus

One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark

With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close‐Kin Mark‐Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost‐efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki , a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost‐effectiveness

Original FASTQ files of: Global genetic diversity and historical demography of the Bull Shark

<p><strong>Aim</strong></p> <p>Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (N<sub>e</sub>) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high-trophic shark using population genomics and assessed our ability to detect recent bottlenecks events.</p> <p><strong>Location</strong></p> <p>Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA), Eastern Tropical Pacific (EPA)</p> <p><strong>Taxon</strong></p> <p>Carcharhinus leucas (Müller & Henle, 1839)</p> <p><strong>Methods</strong></p> <p>A <a>DArTcap</a><sup>TM</sup> approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC-RF framework coupled with coalescent simulations, to investigate within-cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with <em>fastsimcoal</em>. N<sub>e</sub> temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size.</p> <p><strong>Results</strong></p> <p>Three genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within-cluster structuring was detected. N<sub>e </sub>increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion.</p> <p><strong>Main conclusions</strong></p> <p>This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predator. N<sub>e </sub>Historical increases of N<sub>e</sub> are potentially linked to extended coastal habitat availability. The limited within-cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole genome sequencing.</p><p>Funding provided by: Laboratoire d'Excellence Corail*<br>Crossref Funder Registry ID: <br>Award Number: </p><p>Funding provided by: University of Tasmania<br>Crossref Funder Registry ID: https://ror.org/01nfmeh72<br>Award Number: </p><p>Funding provided by: CSIRO Oceans and Atmosphere<br>Crossref Funder Registry ID: https://ror.org/026nh4520<br>Award Number: </p><p>Funding provided by: Sea World Research and Rescue Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100009034<br>Award Number: </p><p>Funding provided by: Ord River Research Offset*<br>Crossref Funder Registry ID: <br>Award Number: </p><p>Funding provided by: Australian Government<br>Crossref Funder Registry ID: https://ror.org/0314h5y94<br>Award Number: </p><p>Funding provided by: DEAL, La Reunion*<br>Crossref Funder Registry ID: <br>Award Number: </p><p><strong>Sample collection and DNA extraction</strong></p> <p>A subsample of the dataset of Devloo-Delva et al. (2023) was used for this study, representing 475 <em>C. leucas</em> sampled between 1985 and 2019 from 18 locations covering its distribution (except for West Africa; Supplementary Material 1)<em>.</em> DNA was extracted with the Qiagen Blood and Tissue kit, following standard protocol (Qiagen Inc., Valencia, California, USA). After bait design and bioinformatic filtering (see following sections), the dataset comprised 16 sampling locations with at least five individuals (309 individuals; Fig. 1, Table 1) covering the WTA, IPA, and EPA. Sampling locations with mostly adults were preferentially selected to limit relatedness effects.</p> <p><strong>SNP selection for bait design</strong></p> <p>The approach used for bait design is described in Devloo-Delva et al. (2023). Briefly, a subset of 219 sample libraries were genotyped using the DArTseq<sup>TM</sup> approach (Cruz et al., 2013; Feutry et al., 2017, 2020, Supplementary material 1). From this dataset, 3,400 loci of 70 bp were randomly selected for DNA-capture bait development. The <a>DArTcap<sup>TM</sup> </a>enriched libraries were sequenced on a Illumina HiSeq 2500.</p&gt

Global genetic diversity and historical demography of the Bull Shark

Aim: Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (Ne) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high-trophic shark using population genomics and assessed our ability to detect recent bottleneck events. Location: Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA) and Eastern Tropical Pacific (EPA). Taxon: Carcharhinus leucas (Müller & Henle, 1839). Methods: A DArTcap™ approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC-RF framework coupled with coalescent simulations, to investigate within-cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with fastsimcoal. Ne temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size. Results: Three genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within-cluster structuring was detected. Ne increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion. Main Conclusions: This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predators. Ne historical increases in Ne are potentially linked to extended coastal habitat availability. The limited within-cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole-genome sequencing

Global genetic diversity and historical demography of the Bull Shark

International audienceAim: Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (Ne) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high-trophic shark using population genomics and assessed our ability to detect recent bottleneck events.Location: Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA) and Eastern Tropical Pacific (EPA).Taxon: Carcharhinus leucas (Müller & Henle, 1839).Methods: A DArTcap™ approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC-RF framework coupled with coalescent simulations, to investigate within-cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with fastsimcoal. Ne temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size.Results: Three genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within-cluster structuring was detected. Ne increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion.Main Conclusions: This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predators. Ne historical increases in Ne are potentially linked to extended coastal habitat availability. The limited within-cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole-genome sequencing

From rivers to ocean basins: the role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator

The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest