CBMA

Molecular Ecology and Biodiversity Group

In the Molecular Ecology and Biodiversity 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 target organisms have been crustaceans and fish, and to a lesser extent seaweeds, trough co-supervision of a PDF. More recently I am also interested in development and application high-thoughput sequencing platforms in environmental monitoring  of marine communities.  

Current assignments

2009-present: International Barcode of Life (www.ibol.org) – Portugal delegate and member of the Scientific Steering Committee

2008-present: Centre of Molecular and Environmental Biology (CBMA) - Researcher

2008-present: Universidade do Minho, Braga – Assistant Professor, Department of Biology

2006-present Fish Barcode of Life (www.fishbol.org): Deputy-Chair and currently Chair of the European Regional Working Group

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, Antunes PM (2012). The contribution of the Barcode of Life initiative to the discovery and monitoring of Biodiversity. In: Natural Resources, Sustainability and Humanity - A Comprehensive View. Mendonça, A. et al. (Ed.). pp. 37-68, Springer, Dordrecht. 

Costa FO, Carvalho GR (2010). New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI). Theory in Biosciences 129: 149-157.

Costa FO, Henzler CM, Lunt DH, Whiteley N, Rock J (2009). Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes. Systematics & Biodiversity 7: 365-379.

Ward R.D., Costa F.O., Holmes B.H., Steinke D. (2008). DNA barcoding shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species. Aquatic Biology 3: 71-78.

Costa F.O., Carvalho G.R. (2007). The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics, Society and Policy 3: 29-40.

Costa F.O., deWaard, J. R., Boutillier, J., Ratnasingham S., Dooh R., Hajibabaei M., Hebert, P.D.N. (2007). Biological identifications through DNA barcodes: the case of the Crustacea. Can. J. Fish. Aquat. Sci. 64: 272-295.

Costa, F.O., Neuparth, T., Correia A.D., M. H. Costa (2005). Multi-level assessment of chronic toxicity of estuarine sediments with the amphipod Gammarus locusta: II. Organism and population-level endpoints. Mar. Environ. Res. 60: 93-110.

Costa F.O., Costa M.H. (1999). Life history of the amphipod Gammarus locusta in the Sado Estuary (Portugal). Acta Oecologica 20: 305-314.

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.

Selection of 15 papers

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(4): e35858.

Matzen da Silva J., Creer S., dos Santos A., Costa A.C., Cunha M.R., Costa F.O. and Carvalho, G.R. (2011). Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One 6: e19449.

Costa FO, Carvalho GR (2010). New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI). Theory in Biosciences 129: 149-157.

Costa FO, Henzler CM, Lunt DH, Whiteley N, Rock J (2009). Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes. Systematics & Biodiversity 7: 365-379.

Ward R.D., Costa F.O., Holmes B.H., Steinke D. (2008). DNA barcoding shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species. Aquatic Biology 3: 71-78.

Rock J., Costa F.O., Hutchinson, W, Walker, D. and Carvalho, G.R. (2008). DNA barcoding of fish of the Antarctic Scotia Sea indicate priority groups for taxonomic and systematics focus. Antarctic Science 20: 253-262.

Costa F.O., Carvalho G.R. (2007). The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics, Society and Policy 3: 29-40.

Costa F.O., deWaard, J. R., Boutillier, J., Ratnasingham S., Dooh R., Hajibabaei M., Hebert, P.D.N. (2007). Biological identifications through DNA barcodes: the case of the Crustacea. Can. J. Fish. Aquat. Sci. 64: 272-295.

Costa F.O., Neuparth T., Theodorakis C.W., Costa M.H., Shugart L.R. (2004). RAPD analysis of southern populations of Gammarus locusta: comparison with allozyme data and ecological inferences. Mar. Ecol. Progr. Ser. 277: 197-207.

Costa F.O., Neuparth T., Costa M. H., Theodorakis C.W., Shugart L.R. (2002). Detection of DNA strand-breakage in a marine amphipod (Crustacea) by agarose gel electrophoresis: exposure to X-rays and copper. Biomarkers 7: 451-463.

Neuparth T., Costa F.O., Costa M.H. (2002). Effects of temperature and salinity on the life history of Gammarus locusta (Amphipoda). Implications for ecotoxicological testing. Ecotoxicology 11: 61-73.

Correia A.D., Costa F.O., Neuparth T., Diniz M.E., Costa M.H. (2001). Sub-lethal effects of copper-spiked sediments on the amphipod Gammarus locusta. Evidence of hormesis? Ecotox. Environ. Rest. 4.2: 32-38.

Costa F.O., Costa M.H. (2000) Review of the ecology of Gammarus locusta (L.). Pol. Arch. Hydrobiol. 48: 541-559.

Costa F.O., Costa M.H. (1999). Life history of the amphipod Gammarus locusta in the Sado Estuary (Portugal). Acta Oecologica 20: 305-314.

Costa F.O., Correia A.D., Costa M.H. (1998). Acute marine sediment toxicity: A potential new test with the amphipod Gammarus locusta. Ecotox. Environ. Safety 40: 81-87.

Costa FO, Antunes PM (2012). The contribution of the Barcode of Life initiative to the discovery and monitoring of Biodiversity. In: Natural Resources, Sustainability and Humanity - A Comprehensive View. Mendonça, A. et al. (Ed.). pp. 37-68, Springer, Dordrecht.

Carvalho GR, Creer S, Allen MJ, Costa FO, Tsigenopoulos, CS, Le Goff-Vitry M, Magoulas AM, Medlin L, Metfies K (2010). Genomics in the discovery and monitoring of marine biodiversity. In: Introduction to Marine Genomics. M. Cock et al. (ed.), pp. 1-32. Springer, Netherlands.

Post-doctoral fellows

Cátia Bartilotti (started April 2010) – Phylogeny, phylogeography and ontogeny of the worldwide distributed shrimp genus Plesionika: contrasting molecular and morphology-based approaches.

Luisa Borges (started January 2009). Molecular biodiversity and advanced monitoring tools for use in macrobenthic communities in Portuguese costal ecosystems.

Monica Landi (started January 2009). Molecular biodiversity and meta-species phylogeography of fish from the NE Atlantic and the Mediterranean.

Manuela Parente (starting June 2007). Biodiversity and evolution of brown seaweeds from Portuguese waters and adjacent oceanographic regions. Institute of Marine Research, Portugal.

Ph.D. students

Joana Matzen (2006-2011): Biodiversity and molecular evolution of crustaceans from bathyal ecosystems of the Portuguese margin. Ph.D. Thesis in Biology, Universidade de Aveiro, Portugal. (Co-supervisor)

Jorge Lobo Arteaga (starting October 2011). Molecular biodiversity and advanced monitoring tools for macrobenthic communities of Portuguese coastal ecosystems.

Julio César Chávez Galarza (starting October 2011). Population genomics and landscape genetics of the Iberian honey bee (Apis mellifera iberiensis). Co-supervisor.

Sara Ferreira (2012-ongoing). Molecular biodiversity and phylogeography of Amphipoda from Portugal.
 

MSc.

Artur Oliveira (2012). Estudo do DNA barcode em algas (castanhas/vermelhas) e sua relação com a composição fitoquímica e bioactividades farmacológicas

Grantees

íris Sampaio (2011). Research Fellowship in the scope of LusoAquaBarcode

Current Undergraduate students

Ana Margarida Cunha (2011). Final BSc project.

Nuno Gomes (2011). Final BSc. project