Costa Filipe

Filipe Costa

People Detail

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 ( – 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.

Ongoing Projects

2021- River2Ocean– Socio-ecological and biotechnological solutions for the conservation and valorization of aquatic biodiversity in the Minho Region. NORTE-01-0145-FEDER-000068. Research Line 1 Coordinator.

2020- A-Fish-DNA-Scan: Cutting-edge DNA-based approaches for improved monitoring and management of fisheries resources along Magellan-Elcano´s Atlantic route. Funded by FCT: CIRCNA/BRB/0156/2019. Principal Investigator

2020- ATLANTIDA - Platform for the monitoring of the North Atlantic ocean and tools for the sustainable exploitation of the marine resources. Funded by Portugal 2020 / ref. 03/SAICT/2019. Task leader.

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

Concluded Projects

2016- DNAqua-Net: Developing new genetic tools for bio- assessment of aquatic ecosystems in Europe. COST Action CA 15219. Management Committee Member

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

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


Post-doc fellows

Bruno Bellisario (2018-2019)- Pos-Doctoral fellowship in the scope of the grant “The Next-Sea” (NORTE-01-0145-FEDER-0000032)

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.


Cláudia Machado (ongoing). Exploring the use of environmental DNA to monitor the ichthyofauna and provide data to assist fish stock assessment in the Atlantic. Universidade do Minho, UMINHO/BID/2021/36

João Tadeu Fontes (ongoing). Meta-species screening for genetic divergence and phylogeographic reconstruction in Atlantic marine fish species, Universidade do Minho, UI/BD/150910/2021.

André Ferreira (ongoing). DNA-based monitoring of ichthyoplankton for application to fish biodiversity conservation and fisheries management. Universidade do Minho, DFA/BD/6653/2020

Ana Sofia Lavrador (ongoing). Optimization of DNA metabarcoding for the early detection and improved monitoring of non-indigenous species (NIS) in Portuguese coastal ecosystems. Universidade do Minho, UI/BD/150871/2021

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 (2021) 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 (2021) 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

Mônica Silva Coelho (2019). Avaliação de marcadores moleculares para identificação de peixes neotropicais através de amostragem por eDNA. / Universidade Federal do Pará, Brazil.

Dora Henriques (2018). Genomic phylogeography and demographic history of the Iberian honeybee (Apis mellifera iberiensis). Pursuing PhD Degree, Universidade do Minho. SFRH/BD/84195/2012

Pedro Vieira (2017) 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

Bellisario B, Fais, M, Duarte S, Vieira PE, Canchaya C, Costa FO (2021). The network structure of intertidal meiofaunal communities from environmental DNA metabarcoding surveys in Northwest Iberia. Aquatic Sciences 83: 71.

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,

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,

Leite BR, Vieira PE, Teixeira MAL, Lobo-Arteaga 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 (doi:10.1016/j.rsma.2020.101307).

Fais M, Duarte S, Vieira PE, Sousa R, Hajibabaei M, Canchaya M, 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).

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, 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.

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.

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, 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.