Moray eels are more common on coral reefs subject to higher human pressure in the greater Caribbean

Proximity and size of the nearest market (‘market gravity’) have been shown to have strong negative effects on coral reef fish communities that can be mitigated by the establishment of closed areas. However, moray eels are functionally unique predators that are generally not subject to targeted fishing and should therefore not directly be affected by these factors. We used baited remote underwater video systems to investigate associations between morays and anthropogenic, habitat, and ecological factors in the Caribbean region. Market gravity had a positive effect on morays, while the opposite pattern was observed in a predator group subject to exploitation (sharks). Environmental DNA analyses corroborated the positive effect of market gravity on morays. We hypothesize that the observed pattern could be the indirect result of the depletion of moray competitors and predators near humans. Environmental science; ecology; biological sciences; zoology; animals; etholog

Isolation and characterisation of 16 microsatellite loci from a widespread tropical hydrozoan, Lytocarpia brevirostris (Busk, 1852)

International audienceWe isolated and characterized 16 polymorphic microsatellite loci for Lytocarpia brevirostris (Aglaophe- niidae), a hydrozoan common in the tropical Indo-Pacific region. Four to 34 alleles per locus were detected at the Indo-Pacific scale. At the population level, observed (Ho) and expected (He) heterozygosities ranged across 0.100–0.625 and 0.097–0.597, respectively. Three markers showed significant deviation from Hardy–Weinberg equi- librium, all of them presenting null alleles. Linkage dis- equilibrium was detected in three pairs of loci among 120. These primers provide powerful tools for studying popu- lation genetic diversity and the implication of life cycle strategies on population differentiation in tropical hydro- zoans. This will be valuable for the conservation of coral reefs biodiversity and the design of marine protected areas

Isolation and characterisation of 26 microsatellite loci from a widespread tropical hydrozoan, Macrorhynchia phoenicea (Leptothecata, Aglaopheniidae), and cross-amplification in closely related species

International audienceWe isolated and characterized 26 microsatellite loci for Macrorhynchia phoenicea (Busk, 1852), a rather common tropical hydrozoan from the Indo-Pacific. The number of alleles per locus ranged from 4 to 24. The observed heterozygosity ranged from 0.000 to 0.970 and the expected heterozygosity from 0.029 to 0.833. Ten loci were at HardyeWeinberg equilibrium. No pair of loci presented linkage disequilibrium. Transferability of up to 18 loci was positive across four other Aglaopheniidae species from different genera. These loci will be used in studying reef population connectivity for these particular species at the scale of the Indo-Pacific, a promising but little explored research field

Population Structure of <i>Aetobatus narinari</i> (Myliobatiformes) Caught by the Artisanal Fishery in Northeast Brazil

In Brazil, the Whitespotted Eagle Ray Aetobatus narinari is considered data-deficient due to the scarcity of basic information on its biology, ecology, and vulnerability to capture. Despite this, the species is caught by artisanal fishing along most of the coast, especially in the northeast of Brazil. This study analyzed mitochondrial DNA data in specimens of A. narinari caught by artisanal fishing in the northeast coast of Brazil to understand their population structure. For this, 42 individuals were sequenced at three mitochondrial genes: cytochrome oxidase 1 (COI), cytochrome b (Cytb), and NADH dehydrogenase subunit 4 (ND4). Concatenated COI-Cytb-ND4 sequences yielded 14 haplotypes, with moderate haplotype diversity (h = 0.646), low nucleotide diversity (π = 0.00087), and low fixation index ΦST values, indicating no population structure. Our results suggest that there is only one population of A. narinari in the study area. Genetic studies can contribute to improving management plans in these areas, avoiding the overexploitation of this and other species

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

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

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

&lt;p&gt;&lt;strong&gt;Aim&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (N&lt;sub&gt;e&lt;/sub&gt;) 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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Location&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA), Eastern Tropical Pacific (EPA)&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Taxon&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Carcharhinus leucas (Müller &amp; Henle, 1839)&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Methods&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;A &lt;a&gt;DArTcap&lt;/a&gt;&lt;sup&gt;TM&lt;/sup&gt; 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 &lt;em&gt;fastsimcoal&lt;/em&gt;. N&lt;sub&gt;e&lt;/sub&gt; 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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Results&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;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&lt;sub&gt;e &lt;/sub&gt;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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Main conclusions&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predator. N&lt;sub&gt;e &lt;/sub&gt;Historical increases of N&lt;sub&gt;e&lt;/sub&gt; 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.&lt;/p&gt;&lt;p&gt;Funding provided by: Laboratoire d'Excellence Corail*&lt;br&gt;Crossref Funder Registry ID: &lt;br&gt;Award Number: &lt;/p&gt;&lt;p&gt;Funding provided by: University of Tasmania&lt;br&gt;Crossref Funder Registry ID: https://ror.org/01nfmeh72&lt;br&gt;Award Number: &lt;/p&gt;&lt;p&gt;Funding provided by: CSIRO Oceans and Atmosphere&lt;br&gt;Crossref Funder Registry ID: https://ror.org/026nh4520&lt;br&gt;Award Number: &lt;/p&gt;&lt;p&gt;Funding provided by: Sea World Research and Rescue Foundation&lt;br&gt;Crossref Funder Registry ID: http://dx.doi.org/10.13039/100009034&lt;br&gt;Award Number: &lt;/p&gt;&lt;p&gt;Funding provided by: Ord River Research Offset*&lt;br&gt;Crossref Funder Registry ID: &lt;br&gt;Award Number: &lt;/p&gt;&lt;p&gt;Funding provided by: Australian Government&lt;br&gt;Crossref Funder Registry ID: https://ror.org/0314h5y94&lt;br&gt;Award Number: &lt;/p&gt;&lt;p&gt;Funding provided by: DEAL, La Reunion*&lt;br&gt;Crossref Funder Registry ID: &lt;br&gt;Award Number: &lt;/p&gt;&lt;p&gt;&lt;strong&gt;Sample collection and DNA extraction&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;A subsample of the dataset of Devloo-Delva et al. (2023) was used for this study, representing 475 &lt;em&gt;C. leucas&lt;/em&gt; sampled between 1985 and 2019 from 18 locations covering its distribution (except for West Africa; Supplementary Material 1)&lt;em&gt;.&lt;/em&gt; 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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;SNP selection for bait design&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;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&lt;sup&gt;TM&lt;/sup&gt; 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 &lt;a&gt;DArTcap&lt;sup&gt;TM&lt;/sup&gt; &lt;/a&gt;enriched libraries were sequenced on a Illumina HiSeq 2500.&lt;/p&gt

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

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