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Projeto de investigação
Teaming to Upgrade to Excellence in Environmental Biology, Ecosystem Research and AgroBiodiversity
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The mitochondrial genomes of Iberian freshwater and diadromous fishes
Publication . Veríssimo, Joana; Curto, Manuel; Alves, Maria Judite; de Almeida, Pedro Raposo; Aparicio, Enric; Clavero, Miguel; Chaves, Cátia; Fernandez-Delgado, Carlos; Hernández, Jesús; Jentoft, Sissel; Kalous, Lukáš; Magalhães, Maria Filomena; Martins, Filipa M.S.; Mateus, Catarina Sofia; Nogueira, Joana Garrido; Oliveira, Inês; Perdices, Anabel; Rocaspana, Rafel; Ribeiro, Filipe; Risueño, Pilar; Pou i Rovira, Quim; Queirós, João; Santos, Carlos David; Teixeira, Amílcar; Veríssimo, Ana; Volta, Pietro; Beja, Pedro; Gante, Hugo F.; Lopes-Lima, Manuel; MARE - Centro de Ciências do Mar e do Ambiente; Faculdade de Ciências e Tecnologia (FCT); Nature Research
The Iberian Peninsula, in southwestern Europe, is home to a distinctive freshwater fish fauna, predominantly composed of endemic species. This is a consequence of the prolonged isolation from western Europe caused by the Pyrenees, the diverse geological and climatic gradients, and the isolation of river basins. Freshwater and diadromous fishes have diversified in the Iberian Peninsula and include 72 currently recognized native species, 50 of which are endemic to the region. Habitat loss and degradation, the introduction of invasive species, and climate change have placed Iberian freshwater and diadromous fishes among the most threatened groups of vertebrates, with some species on the brink of extinction. Here, we present 60 new complete mitochondrial genome assemblies out of the 109 freshwater and diadromous fish species found in the Iberian Peninsula, including the mitogenomes of 37 endemics. These resources are crucial for characterising the mitochondrial evolution of species, reconstructing phylogeny and paleogeography, advancing species identification, delineation, and monitoring, and ultimately supporting conservation planning.
Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics
Publication . Curto, Manuel; Veríssimo, Ana; Riccioni, Giulia; Santos, Carlos D.; Ribeiro, Filipe; Jentoft, Sissel; Alves, Maria Judite; Gante, Hugo F.; MARE - Centro de Ciências do Mar e do Ambiente; DCEA - Departamento de Ciências e Engenharia do Ambiente; Faculdade de Ciências e Tecnologia (FCT); Blackwell Publishing Ltd
Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.
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European Commission
Programa de financiamento
H2020
Número da atribuição
857251