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 irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their ...genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer's 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control.
Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons.
Tested building-loci pipelines for selection of SNP panels seem to have low influence on population genetics inference across the diverse case-study scenarios here studied. However, preliminary trials with different bioinformatic pipelines are suggested to evaluate their influence on population parameters according with the specific goals of each study.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
The existence of strong genetic structure is expected in species with limited ability to disperse and philopatric behaviour. These life-history traits are found in many small benthic ...elasmobranchs, such as in the small-spotted catshark (Scyliorhinus canicula). However, no evidence of genetic structure was found across its northeastern Atlantic (NEA) range using traditional molecular markers. Here, fine-scale genetic differentiation was detected between the British Isles and southern Iberia using 2674 single nucleotide polymorphism loci generated using 2b-restriction site-associated DNA (2b-RAD). Geographical distance and historical demography were two major drivers shaping the distribution of genetic diversity of S. canicula along the NEA. Significant positive spatial autocorrelation of allelic frequencies was detected, with genetic differentiation generally increasing with geographical distance. However, marked genetic divergence of the Celtic Sea and South Portugal collections from their closest neighbours resulted in geographically constrained genetic breaks south of the British Isles and off southwestern Iberia. Historical demographic reconstruction of population pairs across these genetic breaks suggested a scenario of historical isolation before secondary contact, probably related to distinct northern and southern glacial refugia. These results provide new insights into the population structure of S. canicula along the NEA and serve as a reference for benthic elasmobranchs with similar distribution ranges.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of ...the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date.
In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed.
Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.
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•In recent years recurrent bivalve mass mortalities considerably increased around the world.•Criticalities affecting clam stocks in different sites within the Venice lagoon have been characterized.•Microbiota and gene expression profiling allowed the identification of seasonal- and site-specific environmental stressors.•Identification of molecular mechanisms adopted by Manila clam to cope with stressors
Extreme events like Marine Heatwaves (MHWs) are becoming more intense, severe, and frequent, threatening benthic communities, specifically bivalves. However, the consequences of non-lethal MHWs on ...animals are still poorly understood. Here, we exposed the Manila clam Ruditapes philippinarum to non-lethal MHW for 30 days and provided an integrative view of its effects. Our result indicated that albeit non-lethal, MHW reduced clam's energy reserves (by reducing their hepato-somatic index), triggered antioxidant defenses (particularly in males), impaired reproduction (via the production of smaller oocytes in females), triggered dysbiosis in the digestive gland microbiota and altered animals' behaviour (by impacting their burying capacity) and filtration rate. Such effects were seen also at RNA-seq (i.e. many down-regulated genes belonged to reproduction) and metabolome level. Interestingly, negative effects were more pronounced in males than in females. Our results show that MHWs influence animal physiology at multiple levels, likely impacting its fitness and its ecosystem services.
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•Consequences of Marine Heatwaves (MHW) on benthic species are still mostly unknown.•We exposed Manila clams Ruditapes philippinarum to MHW predicted by 2050.•MHW altered reproduction, behaviour, energy reserves and caused dysbiosis.•Results suggest a reduced fitness despite MHW did not reach lethal temperatures.•Climate change prediction models should account for such non-lethal impacts.
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
Background The Atlantic mackerel, Scomber scombrus (Linnaeus, 1758) is a commercially valuable migratory pelagic fish inhabiting the northern Atlantic Ocean and the Mediterranean Sea. Given its ...highly migratory behaviour for feeding and spawning, several studies have been conducted to assess differentiation among spawning components to better define management units, as well as to investigate possible adaptations to comprehend and predict recent range expansion northwards. Methods Here, a high-quality genome of S. scombrus was sequenced and annotated, as an increasing number of population genetic studies have proven the relevance of reference genomes to investigate genomic markers/regions potentially linked to differences at finer scale. Such reference genome was used to map Restriction-site-associated sequencing (RAD-seq) reads for SNP discovery and genotyping in more than 500 samples distributed along the species range. The resulting genotyping tables have been used to perform connectivity and adaptation analyses. Results The assembly of the reference genome for S. scombrus resulted in a high-quality genome of 741 Mb. Our population genetic results show that the Atlantic mackerel consist of three previously known genetically isolated units (Northwest Atlantic, Northeast Atlantic, Mediterranean), and provide no evidence for genetically distinct spawning components within the Northwest or Northeast Atlantic. Conclusions Therefore, our findings resolved previous uncertainties by confirming the absence of genetically isolated spawning components in each side of the northern Atlantic, thus rejecting homing behaviour and the need to redefine management boundaries in this species. In addition, no further genetic signs of ongoing adaptation were detected in this species.
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