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

From rivers to ocean basins : quantifying sex‚ÄövÑv´specific connectivity in sharks

Globally, elasmobranch populations (sharks and rays) are declining due to increasing anthropogenic and climate pressures. Genetic connectivity between elasmobranch populations is crucial to ensure their persistence and sustain the ecological integrity of ecosystems. Consequently, knowledge on connectivity is important to inform the conservation and management of threatened or commercially important species. Genetic connectivity implies gene flow among discrete populations occurring via the dispersal of individuals outside their population of origin, followed by reproduction ‚ÄövÑvÆ a process that can be biased between sexes (known as sex-biased dispersal or SBD). Male-biased dispersal (MBD) patterns have been observed for some elasmobranchs, yet the extent of SBD in this group is currently unknown. Knowledge of SBD is often lacking due to technical limitations. Detecting SBD relies on knowledge of reproductive isolation (i.e. population structure) and the appropriate genetic and analytical tools. With improved genetic tools, SBD can be inferred directly with individual-based (e.g. population assignment testing) and population-based (e.g. spatial autocorrelation) approaches, or indirectly, with population-level metrics (e.g. comparing markers with sex-specific inheritance, termed 'mixed-marker'). However, these methods contain many prerequisites and assumptions; for example, the need for discrete populations that have reached genetic drift ‚Äö- gene flow equilibrium. To overcome these caveats, two novel methods have been proposed that warrant testing in elasmobranchs. To evaluate historical SBD (>1,000 generations in the past), the first method contrasts the population diversity and/or structure from genetic markers located on sex chromosomes with that from mitochondrial DNA (mtDNA) or autosomal DNA (auDNA) markers. The second approach looks at the spatial distribution of closely related individuals (i.e. close-kin) to investigate reproductive dispersal over a contemporary timescale (i.e. a single generation). To date, 90 studies on 50 elasmobranch species have allowed inference of SBD. Most studies tested SBD using a mixed-marker approach, and specifically by comparing mtDNA to auDNA markers. Male-biased dispersal was observed in 25 of the 50 studied species, yet no distinct patterns that explained the presence of MBD emerged. Regarding the remaining species, symmetric gene flow was found across both females and males. While this could suggest equal female and male dispersal, this observation may be obscured by several confounding factors: (i) the characteristics of dispersal (e.g. rate and distance), (ii) the analysis method (e.g. power of genetic markers), and (iii) the experimental design (e.g. sample size and spatial scope). These factors are discussed in detail throughout this thesis. This thesis uses novel genomic approaches (such as nuclear single nucleotide polymorphisms, or SNPs, and mitochondrial genomes) to provide insights into the patterns of (i) population structure, (ii) sex-chromosome systems, and (iii) SBD in elasmobranchs. My thesis focuses on three shark species that allow me to identify dispersal patterns based on life history, local ecology, population size and different seascape features: the Northern River Shark, Glyphis garricki; the School Shark, Galeorhinus galeus; and the Bull Shark, Carcharhinus leucas. Specifically, I first examine the current knowledge of population structure and SBD in elasmobranchs, and the tools that are commonly used ('General Introduction'). Secondly, I investigate population structure in the three study species using genomic and close-kin methods. The School Shark and Bull Shark studies are considered separate data chapters (Chapters 1-2), while the Northern River Shark population study was published separately from my thesis, yet the results are be summarised. Thirdly, I further analyse the thousands of SNP markers to identify signals of sex-chromosome systems in my three study species and an additional 18 species with publicly available datasets (Chapters 3-4). To accomplish this, I develop a new analytical approach in the R environment to investigate the presence of sex-linked markers (SLMs). After I identify these SLMs and the spatial scale of population structure, I quantify the amount of sex-specific connectivity between populations (Chapters 5-6). Explicitly, I contrast the auDNA to mtDNA and SLMs to detect signals of long-term dispersal. Where adult sharks were available, I also look at signals of direct, contemporary (intra-generational) dispersal by assigning individuals back to their population of origin. A close-kin framework was expanded to quantify contemporary (inter-generational) philopatry and SBD. Population structure was found at both broad (Bull Shark) and fine (Northern River Shark) spatial scales. Yet, no signals of population structure were detected for School Sharks between Tasmania and New Zealand. These results allowed me to discuss potential ecological drivers of population structure, such as biogeographical barriers, population sizes and philopatric behaviours. I also discussed how different confounding variables could obscure signals of structure (e.g. sampling bias with sex, life-stage, or family member, and inappropriate time and spatial scale of sampling). I further demonstrated that 19 out of the 21 studied elasmobranch species contain X and Y chromosomes (overall 3,297 X-linked and 78 Y-linked markers), using the R function I developed for the 'radiator' package. The SLMs can be employed to contrast autosomal SNPs and mitochondrial genome data to investigate SBD. Given the broad taxonomic range in my results, I discussed how the XX/XY sex-chromosome system in elasmobranchs may have evolved from ancestral autosomes. This hypothesis is supported by the large number of highly conserved SLMs (n = 710) within the order of Carcharhiniformes. The Y-linked markers also allowed me to develop a rapid PCR-based test to identify the genetic sex of White Shark (Carcharodon carcharias) samples, which has direct management applications. Lastly, I found supporting evidence of MBD in the Northern River Shark and the Bull Shark; whereas the lack of population structure for the School Shark did not allow further investigation of SBD. Specifically, for the Northern River Shark, the kinship approach showed a slight bias towards male dispersal (63 % of the dispersal was attributed to males), whereas SNPs and mtDNA demonstrated strong philopatric signals and no SBD. The Bull Shark kinship results revealed a stronger signal of MBD (100 %), yet only few kin pairs were found. Therefore, this result needs to be verified with larger sample sizes. However, at an intra-ocean-basin scale, the mixed-marker approach (including X-linked markers) suggested female philopatry for the Bull Shark. My final discussion synthesised the dispersal patterns observed from my three study species and examines the potential ecological and evolutionary drivers for these patterns. I critically compared the genetic and analytical approaches for the detection of population structure and SBD. I concluded that genomic tools have improved the resolution of population connectivity analyses, although sampling biases can have a substantial effect, and that the close-kin approach will prove a valuable tool to assess dispersal at very fine spatial and temporal scales. Overall, the potential implications of these quantitative findings for management were highlighted and future work is proposed

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 152C. 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 ΦST values 0.92–0.98, FST values 0.036–0.059). Mitochondrial DNA indicated significant population structuring between PNG and east Australia (ΦST=0.102), but nuclear markers suggested connectivity between these geographically close regions (FST=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.</jats:p

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

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 ΦST values 0.92–0.98, FST values 0.036–0.059). Mitochondrial DNA indicated significant population structuring between PNG and east Australia (ΦST = 0.102), but nuclear markers suggested connectivity between these geographically close regions (FST = 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.</p

How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores

Tropical reefs are highly diverse ecosystems, and reliable biomonitoring, through diet metabarcoding, is needed to understand present and future trophic relationships in this changing habitat. Several studies have assessed the reliability and effectiveness of single molecular markers; however, a cross-marker validation has rarely been performed. This study identified crucial properties for 12S rDNA, 16S rDNA and COI metabarcoding in tropical-reef piscivores (Plectropomus spp.). In addition, three new versatile primer sets for 16S were designed in silico for metabarcoding of reef fish. Results showed that COI was overall better at recovering true diversity because of a well-supported database. Second, optimal 16S amplicon sizes ranged between 160 and 440 base pairs for full diversity recovery, with increased species detection for the 270-base pairs region. Finally, blocking of predator-specific COI sequences was not equally effective in all host species, potentially introducing bias when diet compositions are directly compared. In conclusion, this novel study showed that marker success for prey identification is highly dependent on the reference database, taxonomic scope, DNA quality, amplicon length and sequencing platform. Results suggest that COI, complemented with 16S, yields the best outcome for diet metabarcoding in reef piscivores. Findings in this paper are relevant to other piscivores and other metabarcoding applications.</p

Accounting for kin sampling reveals genetic connectivity in Tasmanian and New Zealand school sharks, Galeorhinus galeus

Fishing represents a major problem for conservation of chondrichthyans, with a quarter of all species being overexploited. School sharks, Galeorhinus galeus, are targeted by commercial fisheries in Australia and New Zealand. The Australian stock has been depleted to below 20% of its virgin biomass, and the species is recorded as Conservation Dependent within Australia. Individuals are known to move between both countries, but it is disputed whether the stocks are reproductively linked. Accurate and unbiased determination of stock and population connectivity is crucial to inform effective management. In this study, we assess the genetic composition and population connectivity between Australian and New Zealand school sharks using genome‐wide SNPs, while accounting for non‐random kin sampling. Between 2009 and 2013, 88 neonate and juvenile individuals from Tasmanian and New Zealand nurseries were collected and genotyped. Neutral loci were analyzed to detect fine‐scale signals of reproductive connectivity. Seven full‐sibling groups were identified and removed for unbiased analysis. Based on 6,587 neutral SNPs, pairwise genetic differentiation from Tasmanian and New Zealand neonates was non‐significant (FST = 0.0003, CI95 = [−0.0002, 0.0009], p = 0.1163; Dest = 0.0006 ± 0.0002). This pattern was supported by clustering results. In conclusion, we show a significant effect of non‐random sampling of kin and identify fine‐scale reproductive connectivity between Australian and New Zealand school sharks. </p

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