Researcher ID : https://publons.com/researcher/B-5890-2009/
Researchgate : https://www.researchgate.net/profile/Filipe_Costa5
Research Area : Biodiversity
Position : Integrated members
Current and past assignments: 2019-present: Universidade do Minho, Braga – Associate Professor, Department of Biology; 2008-2019: Universidade do Minho, Braga – Assistant Professor, Department of Biology; 2008-present: Centre of Molecular and Environmental Biology (CBMA) - Integrated member/ group leader; 2009-present: International Barcode of Life (www.ibol.org) – Portugal delegate and member of the Scientific Steering Committee;
ME-Barcode: Molecular Ecology and Biodiversity and DNA barcoding In the ME-Barcode research group we are broadly interested in the description and interpretation of the biological and ecological basis for the genetic diversity of natural populations and species over time and space. There are currently three main research topics addressed in our team: 1) molecular biodiversity, i.e. DNA barcoding and derived research, 2) comparative phylogeography of marine species at regional and global scales, and 3) population genetics of natural populations. Molecular biodiversity projects seek to develop a reference library of DNA barcodes for marine life of Portugal, in order to improve the taxonomic knowledge of the target taxa, and to develop a suite of applications where routine identifications of species are required. My main research target organisms and communities have been mostly crustaceans, fish and the marine benthos. Currently the focus is in the development and application high-thoughput sequencing DNA metabarcoding and eDNA metabarcoding for environmental monitoring of marine organisms and communities.
2018- NIS-DNA: Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools. Funded by FCT: PTDC/BIA-BMA/29754/2017. Co-Principal Investigator
2016- NEXT-SEA: Next generation monitoring of coastal ecosystems in a scenario of global change. Structured– Project R&D&I Norte-45-2015-02. Team Member
2016- DNAqua-Net: Developing new genetic tools for bio- assessment of aquatic ecosystems in Europe. COST Action CA 15219. Management Committee Member
2012- DiverseShores - Testing associations between genetic and community diversity in European rocky shore environments. Funded by FCT: PTDC/BIA-BIC/114526/2009. Team Member
2011- Benthic Estuarine Barcode (BEstBarcode): Development and application of massively paralelized sequencing for monitoring of estuarine macrobenthic communities. Funded by FCT, starting April 2011: Principal Investigator.
2010 - METAFISHCODE: Fish genetic diversity and meta-species phylogeography at global and regional scales: implications for fisheries management. Funded by FCT, starting April 2010: Principal Investigator.
2010- Patterns and processes of (neutral and adaptive) variation in the honey bee (Apis mellifera iberiensis) hybrid zone of the Iberian Peninsula: a population genetics approach integrating population genomics and landscape genetics. Funded by FCT. Project Partner.
2008- LusoMarBoL - Integrating molecular approaches into marine biodiversity research in Portugal: implementing DNA barcoding and investigating phylogeographic patterns. Funded by FCT: Principal Investigator.
2008- LusoAquaBarcode - Implementing DNA barcoding into aquatic biodiversity research in Portugal and priming new macrobenthos monitoring tools). European Reintegration Grant, Funded by EC, starting September 2008: Principal Investigator
Pedro Vieira (2018-ongoing)- Pos-Doctoral fellowship n the scope of the grant “The Next-Sea” (NORTE-01-0145-FEDER-0000032)
Bruno Sampieri (2018). DNA barcode e o género Laeonereis (Phyllodocida: Nereididae). Fellowship frpm FAPESP, Brazil.
Sofia Duarte (2016-ongoing). Metabarcoding of meio and macrobenthic estuarine communities: performance assessment and implementation in monitoring programmes.
Claudia Hollatz (2014-2016). Development of a biomonitoring tool for estuarine macrobenthic communities based on DNA barcoding coupled with second generation sequencing.
Monica Landi (2009-2014). Molecular biodiversity and meta-species phylogeography of fish from the NE Atlantic and the Mediterranean.
Manuela Parente (2007). Biodiversity and evolution of brown seaweeds from Portuguese waters and adjacent oceanographic regions. Institute of Marine Research, Portugal.
Cátia Bartilotti (2010-2012) – Phylogeny, phylogeography and ontogeny of the worldwide distributed shrimp genus Plesionika: contrasting molecular and morphology-based approaches.
Luisa Borges (2009-2011). Molecular biodiversity and advanced monitoring tools for use in macrobenthic communities in Portuguese costal ecosystems.
Mônica Silva Coelho (2019). Avaliação de marcadores moleculares para identificação de peixes neotropicais através de amostragem por eDNA. / Universidade Federal do Pará, Brazil.
Marcos Teixeira (ongoing). Phyllodocida (Annelida, Polychaeta) of the North East Atlantic as model for the investigation of cryptic species Universidade do Minho, SFRH/BD/131527/2017
Barbara Leite (ongoing) Monitoring coastal benthic colonization of artificial substrates with the support of DNA metabarcoding approaches, Pursuing PhD Degree, Universidade do Minho. PD/BD/127994/2016
Maria Fais (ongoing) Development of metabarcoding approaches for investigating the coupled dynamics of estuarine meio and macrobenthic communities. Pursuing PhD Degree, Universidade do Minho. PD/BD/113547/2015
Dora Henriques (ongoing). Genomic phylogeography and demographic history of the Iberian honeybee (Apis mellifera iberiensis). Pursuing PhD Degree, Universidade do Minho. SFRH/BD/84195/2012
Pedro Vieira (ongoing) Associations between genetic and community diversity in Northeast Atlantic rocky shore environments: the case of the peracarids. Pursuing PhD Degree, Universidade de Aveiro. SFRH/BD/86536/2012
Jorge Lobo Arteaga (2016): Molecular biodiversity and advanced monitoring tools for macrobenthic communities of Portuguese coastal ecosystems. PhD Thesis, Universidade do Minho. SFRH/BD/69750/2010
Julio César Chávez Galarza (2016): Population genomics and landscape genetics of the Iberian honey bee (Apis mellifera iberiensis). PhD Thesis, Universidade do Minho. SFRH/BD/68682/2010
Joana Matzen (2012): Biodiversity and molecular evolution of crustaceans from bathyal ecosystems of the Portuguese margin. Ph.D. Thesis, Universidade de Aveiro, Portugal. SFRH/BD/25568/2005
Ilisa Antunes (2016). Biblioteca de referência de DNA barcodes de anfípodes (Crustacea: Amphipoda) da costa Portuguesa
Ana Paula Vilela (2015). Biblioteca de referência de DNA barcodes de bivalves (Mollusca: Bivalvia) e de gastrópodes (Mollusca: Gastropoda) da costa Portuguesa. Tese de Mestrado, Universidade do Minho.
Barbara Leite (2015). Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities. Tese de Mestrado, Universidade do Minho.
Luis Manuel Oliveira (2015). Compilação de uma biblioteca de referência de DNA barcodes para peixes marinhos Europeus. Tese de Mestrado, Universidade do Minho.
Nuno Gomes (2015). Construção de uma biblioteca de referência de DNA barcodes para isópodes marinhos (Crustacea Isopoda) de Portugal e da Macaronésia. Tese de Mestrado, Universidade do Minho.
Marcos Teixeira (2014). Lançamento de uma biblioteca de referência de DNA barcodes para poliquetas de estuários de Portugal e do mar profundo da Península Ibérica. Tese de Mestrado, Universidade do Minho.
Claudia Soraia Castro (2014). Compilação de uma biblioteca de referência de DNA barcodes para peixes marinhos de Portugal e estudo filogeográfico da espécie Zeus faber. Tese de Mestrado, Universidade do Minho.
Artur Oliveira (2012). Compilação de uma biblioteca de referência de DNA barcodes de macroalgas vermelhas e castanhas reportadas para Portugal e análise dos seus perfis fitoquímicos. Tese de Mestrado, Universidade do Minho.
Ben Gilbert (2007): DNA barcodes of European fish species: assisting taxonomic revisions and gaining insight into meta-species phylogeographic patterns. M.Sc. in Ecology, University of Wales, Bangor (Co-supervised with Prof. Gary Carvalho)
Selection of 15 publications
Weigand H, Beermann AJ, Ciampor F, Costa FO et al. (2019) DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Science of the Total Environment 678: 499-524 (doi: 10.1016/j.scitotenv.2019.04.247)
Vieira P, Desiderato A, Holdich DM, Soares P, Creer S, Carvalho GR, 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).
Hupalo K, Teixeira MAL, Rewicz T, Sezgin M, Iannilli V, Karaman GS, Grabowski M & Costa FO (2019). Persistence of phylogeographic footprints helps to understand cryptic diversity detected in two marine amphipods widespread in the Mediterranean basin. Molecular Phylogenetics and Evolution 132: 53-66 (doi: 10.1016/j.ympev.2018.11.013)
Lobo J, Ferreira MS, Antunes IC, Teixeira MAL, Borges LMS, Sousa R, Gomes PA, Costa MH, Cunha MR, Costa FO (2017) Contrasting morphological and DNA barcode suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast. Genome 60: 147-157.
Lobo J, Teixeira MAL, Borges LMS, Ferreira MSG, Hollatz C, Gomes PA, Sousa R, Ravara A, Costa MH, Costa FO (2016). Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast. Molecular Ecology Resources 16: 298-313.
Carneiro M, Martins R, Landi M, Costa FO (2014). Updated checklist of marine fishes (Chordata: Craniata) from Portugal and the proposed extension of the Portuguese continental shelf. European Journal of Taxonomy 73: 1-73.
Knebelsberger T, Landi M, Neumann H, Kloppmann M, Sell A, Campbell PD, Laakmann S, Raupach MJ, Carvalho GR, Costa FO (2014). A reliable DNA barcode reference library for the identification of the North European shelf fish fauna. Molecular Ecology Resources 14: 1060-1071. doi: 10.1111/1755-0998.12238
Lobo J, Costa PM, Teixeira MAL, Ferreira MS, Costa MH, Costa FO (2013). Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans. BMC Ecology 13: 34.
Costa FO, Landi M, Martins R, Costa MH, Costa ME, Carneiro M, Alves MJ, Steinke D, Carvalho GR (2012). A ranking system for reference libraries of DNA barcodes: Application to marine fish species from Portugal. PLoS One 7: e35858.
Matzen da Silva J, Creer S, dos Santos A, Costa AC, Cunha MR, Costa FO, Carvalho GR (2011). Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One 6: e19449.
Costa FO, Henzler CM, Lunt DH, Whiteley N, Rock J (2009). Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes. Systematics & Biodiversity 7: 365-379.
Costa FO, Carvalho GR (2007). The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics, Society and Policy 3: 29-40.
Costa FO, deWaard JR, Boutillier J, Ratnasingham S, Dooh R, Hajibabaei M, Hebert, PDN (2007). Biological identifications through DNA barcodes: the case of the Crustacea. Can. J. Fish. Aquat. Sci. 64: 272-295.
Costa FO, Neuparth T, Theodorakis CW, Costa MH, Shugart LR (2004). RAPD analysis of southern populations of Gammarus locusta: comparison with allozyme data and ecological inferences. Mar. Ecol. Progr. Ser. 277: 197-207.
Costa FO, Costa MH (1999). Life history of the amphipod Gammarus locusta in the Sado Estuary (Portugal). Acta Oecologica 20: 305-314.