Research Area : Biodiversity
Position : Integrated members
Specialization in Bioinformatics PhD in Biology Msc in Molecular Biology Bsc in Biology
I have been working with DNA-based identification tools, phylogeography and DNA barcoding to understand biodiversity. Moreover, I have been using bioinformatic tools/programming languages and metabarcoding to improve the biomonitoring of marine communities. Research Involvement and Engagement: - DNA barcoding - (e)DNA metabarcoding analysis of meio and macrofauna. - Phylogeographic and phylogeny of target marine invertebrate taxa. - Island biogeography. - Develop and improve bioinformatic tools for next generation sequencing. - Programming languages. - Large data treatment, statistical and graphical analyses. - Data compilation and analysis of molecular data.
NIS-DNA: “Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools”
“Next-Sea: Next generation monitoring of coastal ecosystems in a scenario of global change” (operação NORTE-01-0145-FEDER-000032), supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF).
"DiverseShores - Testing associations between genetic and community diversity in European rocky shore environments" funded by FCT/MCTES (PIDDAC) and co-funded by Fundo Europeu de Desenvolvimento Regional (FEDER) trough COMPETE – Programa Operacional Fatores de Competitividade.
"Virulence factors associated with antimicrobial resistance determinants among Escherichia coli and Klebsiella spp. environmental strains: potential impact on public health" funded by ESCMID Research Grants 2010.
Master project (co-supervisor), 2019. University of Minho, Braga, Portugal.
- Cátia Gonçalves (Bioinformatics). Broad-scale DNA barcode-based meta-species analyses of patterns of molecular variation in marine Amphipoda (Crustacea).
- João Tadeu (Bioinformatics). Development of a semi-automated system for auditing and annotation of reference DNA barcode libraries. 2019.
- Rui Pires (Bioinformatics). Compilation, gap analyses and evaluation of species discrimination ability of reference libraries of DNA barcodes. 2019.
Final graduation project (main supervisor), 2019. University of Minho, Braga, Portugal.
- Duarte Oliveira (Applied Biology). Biodiversity of the marine invertebrates of the Moroccan coasts and the islands of Macaronesia. 2019.
- José Antunes (Applied Biology). Biodiversity of the marine invertebrates of the Moroccan coasts and the islands of Macaronesia. 2019.
Final graduation project (co-supervisor), 2019. University of Minho, Braga, Portugal.
- Miguel Dias (Biochemistry). Monitoring of native and non-indigenous species (NIS) in coastal ecosystems based on molecular tools. 2019.
Master thesis (scientific orientation), 2015. University of Bologna, Ravenna, Italy.
- Andrea Desiderato (Marine Biology). First insights into phylogenetic relationships among the Atlantic and Mediterranean species of the family Hyalidae.
- Fontes JT*, Vieira PE*, Ekrem T, Soares P, Costa FO (2020). BAGS: an automated Barcode, Audit & Grade System for DNA barcode reference libraries. Molecular Ecology Resources. doi: 10.1111/1755-0998.13262.
- Duarte S, Vieira PE, Lavrador AS, Costa FO (2021). Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding. Science of the Total Environment. 751: 141729. doi: 10.1016/j.scitotenv.2020.141729.
- Duarte S, Vieira PE, Costa FO (2020). Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. Metabarcoding and Metagenomics. 4: e55162. doi: 10.3897/mbmg.4.55162.
- Sampieri BR, Steiner TM, Baroni PC, Silva CF, Teixeira MAL, Vieira PE, Costa FO, Amaral ACZ (2020). How oogenesis analysis combined with DNA barcode can help to elucidate taxonomic ambiguities: a polychaete study-based approach. Biota Neotropica. 20(3): e20200959. doi: 10.1590/1676-0611-bn-2020-0959.
- Fais M, Bellisario B, Duarte S, Vieira PE, Sousa R, Canchaya CA, Costa FO (2020). Meiofauna metabarcoding in Lima estuary (Portugal) suggests high taxon replacement within a background of network stability. Regional Studies in Marine Science. 38: 101341. doi: 10.1016/j.rsma.2020.101341.
- Leite BR, Vieira PE, Teixeira MAL, Lobo J, Hollatz C, Borges LMS, Duarte S, Troncoso JS, Costa FO (2020). Gap-analysis and annotated reference library for supporting macroinvertebrate metabarcoding in Atlantic Iberia. Regional Studies in Marine Science. 36: 101307. doi:10.1016/j.rsma.2020.101307.
- Fais M, Duarte S, Vieira PE, Sousa R, Hajibabaei M, Canchaya CA, Costa FO (2020). Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding. Estuarine, Coastal and Shelf Science. 238: 106683. doi:10.1016/j.ecss.2020.106683.
- Teixeira MAL, Vieira PE, Pleijel F, Ravara A, Sampieri BR, Costa FO, Nygren A (2020). Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida, Polychaeta) species complex. Zoologica Scripta. 49(2):222-235. doi:10.1111/zsc.12397.
- Vieira PE, Desiderato D, Holdich DM, Soares P, Creer S, Carvalho G, Costa FO, Queiroga H (2019). Deep segregation in the open ocean: Macaronesia as an evolutionary hotspot for low dispersal marine invertebrates. Molecular Ecology. 28: 1784– 1800. doi: 10.1111/mec.15052
- Desiderato D, Costa FO, Serejo C, Abiatti M, Queiroga H, Vieira PE (2019). Macaronesian islands as promoters of diversification in amphipods: the remarkable case of the family Hyalidae (Crustacea, Amphipoda). Zoologica Scripta. 48(3): 359-375. doi:10.1111/zsc.12339.
- Vieira PE, Queiroga H, Costa FO, Holdich DM (2016) Distribution and species identification in the crustacean isopod genus Dynamene Leach, 1814 along the Northeast Atlantic-Black Sea axis. ZooKeys. 635: 1-29. doi:10.3897/zookeys.635.10240.
- Hoen R, Novoa EM, López A, Camacho N, Cubells L, Vieira P, Santos M, Marin-Garcia P, Bautista JM, Cortés A, Ribas de Pouplana L, Royo M (2013). Selective inhibition of an apicoplastic aminoacyl-tRNA synthetase from Plasmodium falciparum. Chemblochem. 14(4):499-509. doi: 10.1002/cbic.201200620.
- Mendonça N, Ramalho J, Vieira P, Da Silva GJ (2012). Association of plasmid-mediated quinolone resistance and virulence markers in Escherichia coli isolated from water. Journal of Water and Health. 10(2):288-94. doi: 10.2166/wh.2012.153.
*joint first authors.