Dr. Vera G. Fonseca

Former Head of Metabarcoding Section

Mail: v.fonseca [at] leibniz-zfmk.de

Tabs

Profile

Field of work

Metagenetics and Metabarcoding; Ecology of eukaryotes (distribution patterns, functional ecology, communities assemblages); Transcriptomic responses to environmental perturbations; Biodiversity in a taxonomic and evolutionary perspective; Development of molecular markers to assess genetic diversity but also as a diagnostic tool for specific pathologies

Research interests

I have been using Meta-Genetics/Barcoding approaches to know and understand levels of biodiversity, richness and community structure in eukaryotes. To further taxonomically classify and compare metazoan communities within these large-scale environmental datasets I have been using molecular clustering approaches (OTUs), with the help of available pipelines and open software packages.

My main interests of research focus on the molecular causes underlying the diversity of life, the ecology and evolution of organisms and ecosystems. What shapes community structure/patterns and diversity? How does this diversity and richness drives community structure and ultimately the ecosystem? Who is driving whom: dispersal vs niche driven factors vs community composition/structure?

Projects

2017

Alexander von Humboldt Foundation

“Assessing insect biodiversity along spatial and temporal dimensions in natural and agricultural areas in Brazil with NGS” (co-PI) (12,00 EUR)

2016

German Barcode of Life German Federal Ministry of Education and Research (BMBF)

“Biomonitoring diversity at the Eifel National Park using metabarcoding” GBOL2 (PI) (250,000 EUR)

DGS, Deutsche Gesellschaft für Säugetierkunde e.V.

“Establishing the distribution and molecular genetics of the Endangered Nimba Otter shrew (Micropotamogale lamottei) in the Putu Region of Liberia” (co-I) (8655 EUR)

2015

Research Council of Norway at NTNU University Museum, Norway (RCN)

“Environmental Barcoding of Aquatic Invertebrates (EBAI, MILJØ2015)”, Research Council of Norway at NTNU University Museum, Norway (Co-PI 104,850.00 EUR).

2011

GBOL- German Barcode of Life

"German Barcode of Life" ( GBOL ) is a project sponsored by the BMBF and includes the creation of inventories for the gentic characterization of the animals, fungi and plants of germany, using DNA-Barcodes.

Project lead:

Prof. Dr. J. Wolfgang Wägele

Funding:

Federal Ministry of Education and Research

Publications

2017

Vause BJ, Morley SA, Fonseca VG, Jażdżewska A, Ashton GV, Barnes DKA, Clark MS, Giebner H and Peck LS (2017). Latitudinal patterns in shallow soft sediment community: Global influences on Antarctic biodiversity and abundance. (submitted J Biogeography)

Potter C, Tang CQ, Fonseca VG, Lallias D, Gaspar JM, Thomas K, Creer S. (2017) De novo species delimitation in metabarcoding datasets using ecology and phylogeny. PeerJ Preprints 5:e3121v1 doi.org/10.7287/peerj.preprints.3121v1

Fonseca VG, Frederic S, Vause BJ, Gaspar J, Creer S, Power DM, Peck LS, Clark MS (2017). Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach. Nat Sci Reports 7. doi:10.1038/s41598-017-06687-x.

Batista FM, Fonseca VG, Ruano F, Boudry P (2017). Asynchrony in settlement time between the closely related oysters Crassostrea angulata and C. gigas in Ria Formosa lagoon (Portugal). Marine Biology 164:10. DOI 10.1007/s00227-017-3145-6.

2016

Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Bj.rnsd.ttir S, Boets P, Boggero A, Bones A, Borja ., Bruce K, Bursić V, Carlsson J, Čiampor F, Čiamporov.-Zatovičov. Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls ., Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot J, Fonseca V, Fontaneto D, et al. (2016) DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. Research Ideas and Outcomes 2: e11321. doi: 10.3897/rio.2.e11321

Fonseca VG & Lallias D (2016). Metabarcoding marine sediments: preparation of amplicon libraries. Methods Mol Biol. 2016;1452:183-96. doi: 10.1007/978-1-4939-3774-5_12.

Batista FM, Lopez-Sanmartin M, Boudry P, Navas JI, Ruano F, Renault T, Fonseca VG, Leitao (2016). Insights on the association between somatic aneuploidy and ostreid herpesvirus 1 detection in the oysters Crassostrea gigas, C. angulata and their F1 hybrids. Aquaculture Research 47 (5), 1530-1536. doi: 10.1111/are.12613

2015

Majaneva M, Bongard T, Diserud OH, Ekrem T, Fonseca VG, Hajibabaei M, Hob.k A, Misof B, Stur E (2015) “Environmental barcoding of aquatic invertebrates in Norway”. Genome, 2015, 58(5) doi: 163-303,10.1139/gen-2015-0087

Astrin J, Fonseca VG, Geiger M, Grobe P, Rulik B and Wagele W (2015). “Lessons from the first phase of the German Barcode of Life initiative (2012–2015)”. Genome 58(5) doi: 163-303. 10.1139/gen-2015-0087.

Felix RC, Trindade M, Pires IR, Fonseca VG, Martins RS, Silveira H, Power DM, Cardoso JC. (2015). Unravelling the Evolution of the Allatostatin-Type A, KISS and Galanin Peptide-Receptor Gene Families in Bilaterians: Insights from Anopheles Mosquitoes. PLoS One. 2015 Jul 2;10(7): e0130347. doi: 10.1371/journal.pone.0130347

Cardoso JCR, Félix RC, Martins RST, Trindade M, Fonseca VG, Fuentes J and Power DM
(2015). PACAP system evolution and its role in melanophore function in teleost fish skin.
Molecular and Cellular Endocrinology. 411:130-45. DOI: 10.1016/j.mce.2015.04.020

D Lallias, J Hiddink, VG Fonseca, J Gaspar, W Sung, SP Neill, N Barnes, T Ferrero, N Hall, PJD Lambshead, M Packer, KW Thomas and S Creer (2015). Environmental metabarcoding reveal heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. The ISME Journal doi:10.1038/ismej.2014.213.

2014

Fonseca VG, Carvalho GR, Nichols B, Quince C, Johnson HF, Neill SP, Lambshead PJD, Thomas WK, Power DM, and Creer S. (2014). Metagenetic analysis provides new insights into the macroecology of marine meiobenthic eukaryotes. Global Ecology and Biogeography 23: 1293–1302. doi: 10.1111/geb.12223.

2012

CR Cardoso, RC Félix, VG Fonseca and DM Power. (2012). Conservation of G-Protein Coupled Receptor (GPCR) signaling in feeding. Frontiers in Endocrinology 3: 157. doi:10.3389/fendo.2012.00157

VG Fonseca, B Nichols, D Lallias, GR Carvalho, DM Power, C Quince, & S Creer (2012). Sample richness and diversity as a driver of chimera formation in nSSU metagenetic data. Nucleic Acids Research. 40 (9): 1-9. doi:10.1093/nar/gks002

2011

VG Fonseca, M Packer, GR Carvalho, DM Power, PJD Lambshead & S Creer (2011). Isolation of marine meiofauna from sandy sediments: from decanting to DNA extraction. Nature Protocol Exchange doi :10.1038/nprot.2010.157.

VG Fonseca, J Rosa, V Laizé, PJ Gavaia & ML Cancela (2011). Identification of a new cartilage-specific S100-like protein up-regulated during endo/perichondral mineralization in gilthead seabream. Gene Expression Patterns 11(7): 448-55. doi: 10.1016/j.gep.2011.07.003

2010

VG Fonseca, GR Carvalho, W Sung, HF Johnson, DM Power, SP Neill, M Packer, ML Blaxter, PJD Lambshead, WK Thomas & S Creer (2010). Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications 1(7): 98. doi:10.1038/ncomms1095

S Creer*, VG Fonseca*, DL Porazinska, RM Giblin-Davis, W Sung, DM Power, GR Carvalho, ML Blaxter, PJD Lambshead & WK Thomas (2010). Ultrasequencing of the meiofaunal biosphere: practice, promises and pitfalls. Molecular Ecology 19(1): 4-20. (*joint first authors) doi: 10.1111/j.1365-294X.2009.04473.x

FM Batista, R Ben-Hamadou, VG Fonseca, N Taris, F Ruano, MA Henriques & P.Boudry (2008). Comparative study of shell shape and muscle scar pigmentation in the closely related cupped oyster taxa Crassostrea angulata, C. gigas and their reciprocal hybrids. Aquatic Living Resources 21: 31–38.

2007

VG Fonseca*, V Laizé*, MS Valente & ML Cancela (2007). Identification of an osteopontin-like protein in fish associated with mineral formation. FEBS Journal 274: 4428-4439. (*joint first authors) DOI: 10.1111/j.1742-4658.2007.05972.x

FM Batista, A Leitão, VG Fonseca, R Ben-Hamadou, F Ruano, MA Henriques, H Guedes-Pinto, P Boudry (2007). Individual relationship between aneuploidy of gill cells and growth rate in the cupped oysters Crassostrea angulata, C. gigas and their reciprocal hybrids. Journal of Experimental Marine Biology and Ecology 352: 226–233.

2005

VG Fonseca, A Lago-Lestón, V Laizé & ML Cancela (2005). Rapid identification of differentially expressed genes by in situ screening of bacteria. Molecular Biotechnology 30(2): 163-166.

VG Fonseca, N Grade & L Cancela da Fonseca (2005). Waterbird breeding on salinas in Ria Formosa, southern Portugal. Wader Study Group Bulletin 106: 58-59. (Peer Reviewed)

2004

VG Fonseca, N Grade. & L Cancela da Fonseca (2004). Patterns of association and habitat use by migrating shorebirds on intertidal mudflats and salt works on the Tavira Estuary, Ria Formosa, southern Portugal. Wader Study Group Bulletin 105: 50–55. (Peer Reviewed)

Conference proceedings

Majaneva M, Bongard T, Diserud OH, Ekrem T, Fonseca VG, Hajibabaei M, Hobæk A, Misof B, Stur E (2015) “Environmental barcoding of aquatic invertebrates in Norway”. In: Scientific abstracts from the 6th International Barcode of Life Conference, Guelph. Genome, 2015, 58(5): 163-303, 10.1139/gen-2015-0087

Astrin J, Fonseca VG, Geiger M, Grobe P, Rulik B and Wagele W (2015). “Lessons from the first phase of the German Barcode of Life initiative (2012–2015)” In: Scientific abstracts from the 6th International Barcode of Life Conference / Résumés scientifiques du 6e congrès international Barcode of Life. Genome 58(5): 163-303. 10.1139/gen-2015-0087.

FM Batista, VG Fonseca, R Ben Hamadou, N Taris, MA Henriques & P Boudry (2007). Hybridization and morphological differences between the close related oyster taxa Crassostrea angulata and C. gigas. Aquaculture 272: S244.

Published in

2024

Hein, N., Astrin, J. J., Beckers, N., Giebner, H., Langen, K., Löffler, J., Misof, B. & Fonseca, V. G. (2024). Arthropod diversity in the alpine tundra using metabarcoding: Spatial and temporal differences in alpha‐and beta‐diversity. Ecology and Evolution, 14(2), e10969.

[more]

Links:

https://doi.org/10.1002/ece3.10969

2019

Vause, B. J., Morley, S. A., Fonseca, V. G., Jażdżewska, A. , Ashton, G. V., Barnes, D. K. A., Giebner, H., et. al. (2019). Spatial and temporal dynamics of Antarctic shallow soft‑bottom benthic communities: ecological drivers under climate change. BMC Ecology 19: 27. https://doi.org/10.1186/s12898-019-0244-x

[more]

2018

Fonseca, V. G. (2018): Pitfalls in relative abundance estimation using eDNA Metabarcoding. - Molecular Ecology Resources 18 (5): 923-926. https://doi.org/10.1111/1755-0998.12902

[more]

2017

Batista, F. M., Fonseca, V. G., Ruano, F., Boudry, P. (2017): Asynchrony in settlement time between the closely related oysters Crassostrea angulata and C. gigas in Ria Formosa lagoon (Portugal). - Marine Biology 164:110. https://doi.org/10.1007/s00227-017-3145-6

[more]

Fonseca, V. G., Frederic, S., Vause, B. J., Gaspar, J., Creer, S., Power, D. M., Peck, L. S., et. al. (2017): Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach. Scientific Reports 7: 6094. https://doi.org/10.1038/s41598-017-06687-x

[more]

Potter, C., Tang, C. Q., Fonseca, V. G., Lallias, D., Gaspar, J. M., Thomas, K., Creer, S. (2017): De novo species delimitation in metabarcoding datasets using ecology and phylogeny. - PeerJ Preprints 5:e3121v1. https://doi.org/10.7287/peerj.preprints.3121v1

[more]

2016

Fonseca, V. G. & Lallias, D. (2016): Metabarcoding marine sediments: preparation of amplicon libraries. In: Bourlat, S. J. (ed.): Marine Genomics - Methods and protocols. - Springer (New York). pp. 183-196. https://doi.org/10.1007/978-1-4939-3774-5_12

[more]

Leese, F., Altermatt, F., Bouchez, A., Torbjørn, E., Hering, D., Meissner, K., …, Fonseca, V. G., et al. (2016): DNAqua-Net: developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. - Research Ideas and Outcomes 2: e11321. https://doi.org/10.3897/rio.2.e11321

[more]

2015

Astrin, J.J., Fonseca, V., Geiger, M.F., Grobe, P., Rulik, B., Wägele, W. Lessons from the first phase of the German Barcode of Life initiative (2012–2015) In: Scientific abstracts from the 6th International Barcode of Life Conference / Résumés scientifiques du 6e congrès international Barcode of Life. Genome 58(5): 190.

[more]

Presentations

Talks

2015

- “WG2: Technical issues of metabarcoding & ideas for practical barcode applications”. “European National Barcode Campaigns”, ECBOL, 27 -28th January, ZFMK- Bonn.

- “Assessing Biodiversity using metabarcoding”. Evolutionary Biology Colloquium, May, ZFMK - Bonn.

2011

- “Assessing Meiobenthic Diversity”. The European Network of Marine Institutes and Stations. MARS Directors meeting and WAMS Steering Committee meeting. Towards a global perspective for marine science. 5-7 December 2011 Real Marina Hotel, Olhão, Portugal.

Poster

Hein N, Astrin J, Fonseca VG, Misof B, Löffler J (2016). Coupling next generation sequencing and biogeographic approaches to understand spatial and temporal variations of arthropods in arctic-alpine ecosystems. AK Biogeographie 15th -17th March, Universität Trier, Germany (Poster).

Hein N, Astrin J, Fonseca VG, Misof B, Löffler J (2015). The ecology and biogeography of spiders (Araneae) in alpine-tundra ecosystems. National Symposium on Biodiversity and DNA barcoding, 11th-12th November , Trondheim (Poster).

Fonseca VG, B Nichols, C Quince, GR Carvalho, Clark M, DM Power and S Creer (2014). Marine Metagenetics. Micro B3 Marine Metagenomics Bioinformatics Course, 23-29 March Hinxton, Cambridge UK (Poster).

Fonseca VG, B. Nichols, D. Lallias, C. Quince, G.R. Carvalho, D.M. Power and S. Creer (2012). Marine eukaryotic metagenetics: methodological insights. ASSEMBLE scientific Conference, October 23-25 in Olhão, Portugal (Poster).

Media (TV, Radio...)

2014

"Macroecology of microorganisms”. Radio Interview at RTP International, 25 October "Cientificamente. http://www.rtp.pt/play/p401/e170161/cientifica-mente.

2012

“Vera Fonseca, pioneer on the biodiversity of marine eukaryotes”.University of Algarve Magazine, September, UALGzine.

2010

"Eukaryotic biodiversity". TV interview at "Biosfera" RTP2 program, December.

Education

2011 Ph.D. in Biological Sciences, Bangor University, Wales, United Kingdom.

2005 M.Sc. in Biotechnology, Faculty of Engineering and Natural Resources, FERN, University of Algarve, Portugal.

2000 B.Sc. in Marine Biology, Faculty of Marine Sciences and Environment, FCMA, University of Algarve, Portugal.

Scientific Career

2014- current Head of the metabarcoding department, Zoological Research Museum Alexander Koenig (ZFMK), Centre for Molecular Biodiversity Research, Bonn, Germany

2011-2014 Post-Doc at the Comparative Molecular Endocrinology Laboratory. University of Algarve, Portugal.

2007-2011 Ph.D. at Bangor University, Molecular Ecology Fisheries and Evolution Genetics Group, United Kingdom.

2005-2006 Research Assistant at the Comparative Molecular Endocrinology Laboratory. University of Algarve, Portugal.

2005 Research Assistant at IFREMER- Genetics and Pathology Laboratory. La Tremblade, France.

2000-2005 Research Assistant at the Molecular Biology of Marine Organisms Laboratory, University of Algarve, Portugal.

Grants and Awards

2013 Post-Doc Research Grant, (SFRH/BPD/80447/2011), from the Portuguese Foundation for Science and Technology (CCMAR, PT), “Marine biodiversity: a metagenetic approach" (57.718€ stipend)

2011 Post-Doc Research Grant, (SFRH/BPD/80447/2011), from the Portuguese Foundation for Science and Technology (CCMAR, PT), “Hunger for blood: are GPCRs the drivers of appetite signaling in mosquito Anopheles gambiae?"

2011 Research Grant, GPCRs (PTDC/BIA-BCM/114395/2009), ”Characterization of orphan receptors from the 2GPCR gene family”

2007-2011 PhD Research Grant (SFRH/BD/27413/2006) from the Portuguese Foundation for Science and Technology (Bangor University, Wales, UK),“ Metagenetics on the Biodiversity of Marine Eukaryotes” (86.400 € stipend and 50.000 € fees)

2006 Research Grant, “FINEFISH” (CCMAR/BTI/0035/2005),“Improving sustainability of European aquaculture by control of malformations”

2005 Postgraduate Training Grant “AQUAFIRST” (FP6-POLICIES_513692), “Combined genetic and functional genomic approaches for stress and disease resistance marker assisted selection in fish and shellfish”

2003-2005 Research Grant “SaMGP” (POCTI/BCI/48748/2002), “Effect of extracellular calcium on MGP gene expression”

2002-2003 Research Grant “M&Ms” (EVK3-CT-2000-00044),“Monitoring and Managing of European Seagrass Ecosystems”

2001-2002 Research Grant “BIOPORT” (PDCTM/P/MAR/15292/99), “The Portuguese coast as biogeographic limit: reproductive success, local adaptation and population structure”

2000-2001 Research Grant “ALGSTRESS” (PRAXIS/P/BIO/12203/98), ”Molecular responses to hidric stress in algae with high tolerance to salinity and dissection”.

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Dr. Vera G. Fonseca

Tabs

Field of work

Research interests

2017

2016

2015

2011

GBOL- German Barcode of Life

2017

2016

2015

2014

2012

2011

2010

2007

2005

2004

Conference proceedings

2024

2019

2018

2017

2016

2015

Talks

2015

2011

Poster

Media (TV, Radio...)

2014

2012

2010

Education

Scientific Career

Grants and Awards

Staff search