Percorrer por autor "Carneiro, Miguel"
A mostrar 1 - 3 de 3
Resultados por página
Opções de ordenação
- A Ranking system for reference libraries of DNA Barcodes: application to marine fish species from PortugalPublication . Costa, Filipe O.; Landi, Monica; Martins, Rogelia; Costa, Maria H.; Lima Costa, Maria Emília; Carneiro, Miguel; Alves, Maria J.; Steinke, Dirk; Carvalho, Gary R.Background: The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal. Methodology/Principal Findings: Specimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A-E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E). Conclusion/Significance: We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the continuous revision and annotation required in taxonomic work.
- Building a Portuguese coalition for biodiversity genomicsPublication . Marques, João P.; Alves, Paulo C.; Amorim, Isabel R.; Lopes, Ricardo J.; Moura, Monica; Myers, Eugene; Sim-sim, Manuela; Sousa-Santos, Carla; Alves, M. Judite; Borges, Paulo A. V.; Brown, Thomas; Carneiro, Miguel; Carrapato, Carlos; Ceríaco, Luís M. P.; Ciofi, Claúdio; Silva, Luís P. da; Diedericks, Genevieve; Diroma, Maria Angela; Farelo, Liliana; Formenti, Giulio; Gil, Fátima; Grilo, Miguel; Iannucci, Alessio; Leitão, Henrique G.; Máguas,Cristina; Mc Cartney, Ann M.; Mendes, Sofia L.; Moreno, João M.; Morselli, Marco; Mouton, Alice; Natali, Chiara; Pereira, Fernando; Rego, Rúben M. C.; Resendes, Roberto; Roxo, Guilherme; Svardal, Hannes; Trindade, Helena; Vicente, Sara; Winkler, Sylke; Alvarenga, Marcela; Amaral, Andreia J.; Antunes, Agostinho; Campos, Paula F.; Canario, Adelino; Castilho, Rita; Castro, L. Filipe C.; Crottini, Angelica; Cunha, Mónica V.; Themudo, Gonçalo Espregueira; Esteves, Pedro J.; Faria, Rui; Rodríguez Fernandes, Carlos; Ledoux, Jean-Baptiste; Louro, Bruno; Magalhaes, Sara; Paulo, Octávio S.; Pearson, Gareth Anthony; Pimenta, João; Pina-Martins, Francisco; Santos, Teresa L.; Serrao, Ester A.; Melo-Ferreira, José; Sousa, Vítor C.The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation, or pathogen (re) emergence. The inventory, characterisation, and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures, and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative and its pilot effort to generate reference genomes for European biodiversity has reinforced the establishment of Biogenome Portugal.
- Inversions dominate evolution in the european sardine (sardina pilchardus) amid strong gene flowPublication . Sabatino, Stephen J.; Cabezas, M. Pilar; Pereira, Paulo; Garrido, Susana; Santos, António M.; Carneiro, Miguel; Santos, Paulo T.; Louro, Bruno; Cox, Cymon; Canario, Adelino; Veríssimo, AnaInversions can play key roles in the genetic architecture of adaptation, but the scale of their effects across different species remains poorly understood. Here, we use whole-genome sequencing and demographic modelling to investigate the influence of inversions on the population genomics of the r-selected European sardine (Sardina pilchardus). Allele frequency differences from millions of SNPs across 34 populations spanning the species' range were analysed. Genomic scans identified several extreme outlier regions overlapping large inversions (29–52Mbp), collectively representing over half the genome. Our findings suggest these inversions correlate with locally adapted life-history strategies. First, SNPs within outlier regions containing inversions exhibited striking allele frequency differences between Atlantic and Mediterranean sardines, which differ in key adaptive life-history traits. In the Atlantic, inversion allele frequencies varied latitudinally, while in the Mediterranean, they shifted longitudinally, aligning with temperature and oceanographic features that influence sardine life-history strategies. Moreover, adjacent populations in contrasting environments exhibited pronounced differences in inversion allele frequencies, accompanied by a marked reduction in migration between them. In contrast, spatial patterns at neutral loci showed widespread gene flow, isolation by distance within basins, and population structure between Atlantic and Mediterranean basins (except for the Canary Islands). These results suggest that the inversions studied are under selection and demonstrate the capacity of large inversions to shape genomewide patterns of genetic diversity and population structure in species characterized by widespread gene flow. Our work also offers crucial insights for stock delimitation and management of this commercially valuable species in the face of climate change.