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- Seascape genomics reveals limited dispersal and suggests spatially varying selection among European populations of sea lamprey (Petromyzon marinus)Publication . Baltazar-Soares, Miguel; Britton, Robert; Pinder, Adrian; Harrison, Andrew J; Nunn, Andrew; Quintella, Bernardo R.; Mateus, Catarina; Bolland, Jonathan D.; Dodd, Jamie R.; Almeida, Pedro R.; Almela, Victoria Dominguez; Andreou, DemetraSea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviors. Despite being a freshwater, free-living organism for a large part of their life cycle, its adulthood is spent as a parasite of marine vertebrates. In their native European range, while it is well-established that sea lampreys comprise a single nearly-panmictic population, few studies have further explored the evolutionary history of natural populations. Here, we performed the first genome-wide characterization of sea lamprey's genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase, with the sequencing of 186 individuals from 8 locations spanning the North Eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30,910 bi-allelic SNPs. Population genetic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the North Eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species' dispersal. Seascape genomics suggested a scenario where oxygen concentration and river runoffs impose spatially varying selection across their distribution range. Exploring associations with the abundance of potential hosts further suggested that hake and cod could also impose selective pressures, although the nature of such putative biotic interactions was unresolved. Overall, the identification of adaptive seascapes in a panmictic anadromous species could contribute to conservation practices by providing information for restoration activities to mitigate local extinctions on freshwater sites.
- Distribution of genetic diversity reveals colonization patterns and philopatry of the loggerhead sea turtles across geographic scalesPublication . Soares, Miguel Baltazar; Klein, Juliana D.; Correia, Sandra M.; Reischig, Thomas; Taxonera, Albert; Roque, Silvana Monteiro; Dos Passos, Leno; Durão, Jandira; Lomba, João Pina; Dinis, Herculano; Cameron, Sahmorie J.K.; Stiebens, Victor A.; Eizaguirre, ChristopheUnderstanding the processes that underlie the current distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, the role of colonization and dispersal events throughout a species' evolutionary history often remains elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour. Here, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boa Vista, Cabo Verde). Data analysis using hypothesis-driven population genetic models suggests the colonization of the Atlantic has occurred in two distinct waves, each corresponding to a major mtDNA lineage. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across island-specific nesting groups, despite significant genetic structure. This structure stems from female philopatric behaviours, which could further be detected by weak but significant differentiation amongst beaches separated by only a few kilometres on the island of Boa Vista. Exploring biogeographic processes at diverse geographic scales improves our understanding of the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species' evolutionary potential.
- Incorporating evolutionary based tools in cephalopod fisheries managementPublication . Sabolić, Iva; Baltazar-Soares, Miguel; Štambuk, AnamariaWith gradual decline of global finfish resources, fisheries targeting cephalopods expanded. Yet, the stock assessment and management practice are frequently lacking, and existing ones often remain poorly suited for cephalopod unique life-history. In light of increasing ecological disturbances in marine ecosystems worldwide, assessing exploited species’ status and response becomes vital for devising effective strategies that would ensure their sustainable management. There is generally scarce understanding of the way fisheries and other environmental stressors exert their combined effects on cephalopods stock dynamic and long-term resilience. To that end, evolutionary-based population studies that inform on identity, connectivity and adaptive potential of natural populations present a unique opportunity for assessing the viability of exploited cephalopod stocks. Such studies have been revolutionized in the last decade by proliferation of next generation sequencing technologies. They offer new avenues for expanding our knowledge, especially on population structure and the evolutionary responses to shifts in environmental pressures. In this paper we elaborate on how deep genomic insights into demographic and evolutionary status of fished cephalopods could improve their stock assessment and management practice. We also propose that the common octopus Octopus vulgaris would be a suitable model species to test the power of evolutionary tools to inform fishery scientists and managers on biological questions relevant for their sustainable exploitation.
- Forecasting shifts in habitat suitability across the distribution range of a temperate small pelagic fish under different scenarios of climate changePublication . Lima, André R.A.; Baltazar-Soares, Miguel; Garrido, Susana; Riveiro, I. (Isabel); Carrera, Pablo; Piecho-Santos, A. Miguel; Peck, Myron; Silva, GonçaloClimate change often leads to shifts in the distribution of small pelagic fish, likely by changing the matchmismatch dynamics between these sensitive species within their environmental optima. Using present-day habitat suitability, we projected how different scenarios of climate change (IPCC Representative Concentration Pathways 2.6, 4.5 and 8.5) may alter the large scale distribution of European sardine Sardina pilchardus (a model species) by 2050 and 2100. We evaluated the variability of species-specific environmental optima allowing a comparison between present-day and future scenarios. Regardless of the scenario, sea surface temperature and salinity and the interaction between current velocity and distance to the nearest coast were the main descriptors responsible for the main effects on sardine's distribution. Present-day and future potential “hotspots” for sardine were neritic zones (<250 km) withwater currents <0.4ms−1, where SST was between 10 and 22 °C and SSS>20 (PSU), on average.Most variability in projected shifts among climatic scenarioswas in habitats with moderate to low suitability. By the end of this century, habitat suitability was projected to increase in the Canary Islands, Iberian Peninsula, central North Sea, northern Mediterranean, and eastern Black Sea and to decrease in the Atlantic African coast, southwest Mediterranean, English Channel, northern North Sea and Western U.K. A gradual poleward-eastward shift in sardine distribution was also projected among scenarios. This shift was most pronounced in 2100 under RCP 8.5. In that scenario, sardines had a 9.6% range expansion which included waters along the entire coast of Norway up and into the White Sea. As habitat suitability is mediated by the synergic effects of climate variability and change on species fitness, it is critical to apply models with robust underlying species-habitat data that integrate knowledge on the full range of processes shaping species productivity and distribution.
- A noninvasive eDNA tool for detecting sea lamprey larvae in river sediments: Analytical validation and field testing in a low‐abundance ecosystemPublication . Baltazar-Soares; Pinder, Adrian C.; Harrison, Andrew J.; Oliver, Will; Picken, Jessica; Britton, Robert; Andreou, DemetraAnthropogenic activities are increasingly threatening aquatic biodiversity, especially anadromous species. Monitoring and conservation measures are thus required to protect, maintain and restore imperilled populations. While many species can be surveyed using traditional capture and visual census techniques, species that use riverine habitats in a less conspicuous manner, such as sea lamprey Petromyzon marinus, can be more challenging to monitor. Sea lamprey larvae (ammocoetes) can spend several years in freshwater burrowed within soft sediments, inhibiting their detection and assessment. Here, we present a qPCR assay based on the detection of environmental DNA (eDNA) to identify the presence of ammocoetes burrowed in the sediment. We present an extensively validated method that ensured both speciesspecificity of the assay as well as the capacity to detect ammocoetes when abundances are low. Experiments on burrowing activity suggested that most of the DNA released into the sediment occurs during burrowing. Overall, we demonstrate this new molecular-based tool is an efficient and effective complement to traditional monitoring activities targeting larval stages of sea lampreys
- Towards a unified eco-evolutionary framework for fisheries management: Coupling advances in next-generation sequencing with species distribution modellingPublication . Baltazar-Soares, Miguel; Lima, André R.A.; Silva, Gonçalo; Gaget, ElieThe establishment of high-throughput sequencing technologies and subsequent large-scale genomic datasets has flourished across fields of fundamental biological sciences. The introduction of genomic resources in fisheries management has been proposed from multiple angles, ranging from an accurate re-definition of geographical limitations of stocks and connectivity, identification of fine-scale stock structure linked to locally adapted subpopulations, or even the integration with individual-based biophysical models to explore life history strategies. While those clearly enhance our perception of patterns at the light of a spatial scale, temporal depth and consequently forecasting ability might be compromised as an analytical trade-off. Here, we present a framework to reinforce our understanding of stock dynamics by adding also a temporal point of view. We propose to integrate genomic information on temporal projections of species distributions computed by Species Distribution Models (SDMs). SDMs have the potential to project the current and future distribution ranges of a given species from relevant environmental predictors. These projections serve as tools to inform about range expansions and contractions of fish stocks and suggest either suitable locations or local extirpations that may arise in the future. However, SDMs assume that the whole population respond homogenously to the range of environmental conditions. Here, we conceptualize a framework that leverages a conventional Bayesian joint-SDM approach with the incorporation of genomic data. We propose that introducing genomic information at the basis of a joint-SDM will explore the range of suitable habitats where stocks could thrive in the future as a function of their current evolutionary potential.