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Filipe de Portugal da Silveira Teixeira de Sousa. Concluiu o Doutoramento em Biologia em 2015 pela Göteborgs Universitet, tem Mestrado em Plant Diversity - Taxonomy and Evolution stream concluído em em 2007 pela University of Reading e Licenciatura em em Biologia concluída em 2005 pela Faculdade de Ciências da Universidade do Porto. É investigador a termo certo e professor auxiliar convidado na Faculdade de Ciências da Universidade de Lisboa.
Identification

Personal identification

Full name
Filipe de Portugal da Silveira Teixeira de Sousa

Citation names

  • Sousa, Filipe

Author identifiers

Ciência ID
4711-41AD-D52F
ORCID iD
0000-0003-4681-8951

Knowledge fields

  • Natural sciences - Biological Sciences - Evolutionary Biology

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
French Intermediate (B1) Advanced (C1) Intermediate (B1) Advanced (C1)
German Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Spanish; Castilian Advanced (C1) Advanced (C1) Upper intermediate (B2) Advanced (C1)
Swedish Elementary (A2) Elementary (A2) Beginner (A1) Intermediate (B1)
Portuguese (Mother tongue)
Education
Degree Classification
2015
Concluded
 Doctor of Philosophy (Doutoramento)
Göteborgs Universitet, Sweden
"Next-generation Molecular Systematics and Evolution - insights into Medicago" (THESIS/DISSERTATION)
 pass
2013
Concluded
 Biologia (Licence)
Major in Biologia
Göteborgs Universitet, Sweden
"Towards a better understanding of phylogenetic incongruence: new sampling and analysis strategies" (THESIS/DISSERTATION)
2007
Concluded
 MSc Plant Diversity - Taxonomy and Evolution stream (Mestrado)
University of Reading, United Kingdom
"A Revision of Apuleia Martius (Leguminosae: Cassieae)" (THESIS/DISSERTATION)
 distinction
2005
Concluded
 Licenciatura em Biologia (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
"Influência de factores ecológicos abióticos na distribuição hierárquica da Fitodiversidade: O exemplo do Parque Nacional da Peneda-Gerês" (THESIS/DISSERTATION)
 13 valores
Affiliation

Science

Category
Host institution 		Employer
2023/05/01 - Current Researcher (Research) FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
Centro de Ecologia Evolução e Alterações Ambientais, Portugal
2020/11/05 - 2022/09/30 Contracted Researcher (Research) Centro de Ecologia Evolução e Alterações Ambientais, Portugal
Centro de Ecologia Evolução e Alterações Ambientais, Portugal
2016/09/01 - 2019/12/31 Postdoc (Research) Centro de Ciências do Mar, Portugal
2016/02/01 - 2016/06/30 Postdoc (Research) Centro de Ciências do Mar, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2023/09/01 - 2024/02/29 Invited Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2022/11/01 - 2023/04/30 Invited Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Faculdade de Ciências, Portugal

Others

Category
Host institution 		Employer
2010/07/15 - 2015/05/30 Doutorando Göteborgs universitet Institutionen för Biologi och Miljövetenskap, Sweden
2008/10/01 - 2009/09/30 Bolsa de Investigação Científica Projecto IMBAMBA - Implementar o acesso à informação sobre biodiversidade e a gestão de colecções botânicas em Angola Instituto de Investigação Científica Tropical, Portugal
2007/10/15 - 2008/04/15 Bolsa de Estágio em Horticultura Jerusalem Botanical Gardens, Israel
2005/02/01 - 2005/07/31 Estágio de Investigação Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
Projects

Contract

Designation Funders
2019/01/01 - 2019/12/31 Centre of Marine Sciences
UID/Multi/04326/2019
Centro de Ciências do Mar, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2012/11/12 - 2015/06/30 Incongruence among gene phylogenies in an evolutionary context - a study case in Medicago
FO2012-1112
Principal investigator
Göteborgs universitet Institutionen för Biologi och Miljövetenskap, Sweden
 Stiftelsen Lars Hiertas Minne
Concluded
2011 - 2015/06/30 Development of a cheap and rapid gene enrichment method for systematics
NA
Principal investigator
Göteborgs universitet Institutionen för Biologi och Miljövetenskap, Sweden
 Göteborgs universitet Institutionen för Biologi och Miljövetenskap
Concluded
Outputs

Publications

Conference poster
  1. Galhofa, Davide; Sousa, Filipe; António Onofre Soares; Borges, Isabel; Oliveira, L.; Bielza, P.; Seabra, Sofia G.; Figueiredo, Elisabete; Paulo, Octavio. "DNA barcoding and phylogeny of Miridae specimens from the Azores, mainland Portugal and Spain, based on mithochodrial COI sequences". Paper presented in XIX ENBE Annual Meeting of the Portuguese Association for Evolutionary Biology, 2023.
  2. Galhofa, Davide; Viegas, Mariana; Sousa, Filipe; André Filipe Henriques; Sousa, Paulo; Pina-Martins, Francisco; Vanhove, Mathieu; et al. "Genotyping by Sequencing brings new insights into the population structure and local adaptation of Holm Oak". Paper presented in Frontiers in E3: 9th cE3c Annual Meeting, 2023.
  3. Sousa, F.; Neiva, João; Anderson, Laura; Raimondi, Peter T.; Martins, Neusa; Serrão, Ester A.; Pearson, Gareth A.. "Evolutionary rates and expression patterns in allopolyploid brown algae". Paper presented in Evolution meeting, 2017.
  4. Catarino, Luís; Figueira, Rui; ana isabel correia; joana A. Abreu; Sousa, Filipe; dulce ferreira; joão tavares; et al. "Valuing and giving access to the botanical collections of Angola: The IMBAMBA project". Paper presented in Iº Encontro Nacional sobre a Flora e Vegetação de Angola, 2011.
  5. Sousa, Filipe; Honrado,. "Abiotic ecological factors and the hierarchical distribution of phytodiversity: an example from northern Portugal". Paper presented in IAVS, 2005.
Journal article
  1. Sousa, Filipe de; Bertrand, Yann J.K.; Zizka, Alexander; Cangrén, Patrik; Oxelman, Bengt; Pfeil, Bernard E.. "Chloroplast genome and nuclear loci data for 71 Medicago species". Data in Brief 54 (2024): 110540. http://dx.doi.org/10.1016/j.dib.2024.110540.
    10.1016/j.dib.2024.110540
  2. Sousa, Filipe; Viegas, Mariana Bray; Costa, Joana; Marques, Isabel; Pina-Martins, Francisco; Simões, Fernanda; Matos, José; et al. "Haplotype diversity patterns in Quercus suber (Fagaceae) inferred from cpDNA sequence data". Plant Systematics and Evolution 309 6 (2023): http://dx.doi.org/10.1007/s00606-023-01879-7.
    10.1007/s00606-023-01879-7
  3. Almeida, Susana C.; Neiva, João; Sousa, Filipe; Martins, Neusa; Cox, Cymon J.; Melo-Ferreira, José; Guiry, Michael D.; Serrão, Ester A.; Pearson, Gareth A.. "A low-latitude species pump: Peripheral isolation, parapatric speciation and mating-system evolution converge in a marine radiation". Molecular Ecology (2022): http://dx.doi.org/10.1111/mec.16623.
    10.1111/mec.16623
  4. Sousa, Filipe; Costa, Joana; Ribeiro, Carla; Varandas, Marta; Pina-Martins, Francisco; Simoes, Fernanda; Matos, Jose; et al. "Population structure in Quercus suber L. revealed by nuclear microsatellite markers". PeerJ (2022): https://publons.com/wos-op/publon/54722417/.
    10.7717/PEERJ.13565
  5. Sousa, Filipe; Civán, Peter; Foster, Peter G.; Cox, Cymon J.. "The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models". Frontiers in Plant Science 11 (2020): http://dx.doi.org/10.3389/fpls.2020.01062.
    10.3389/fpls.2020.01062
  6. Sousa, Filipe; Civán, Peter; Brazão, João; Foster, Peter G.; Cox, Cymon J.. "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models". PeerJ 8 (2020): e8995. http://dx.doi.org/10.7717/peerj.8995.
    Open access • Published • 10.7717/peerj.8995
  7. Sousa, Filipe; Foster, Peter G.; Donoghue, Philip C. J.; Schneider, Harald; Cox, Cymon J.. "Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)". New Phytologist (2018): http://dx.doi.org/10.1111/nph.15587.
    Published • 10.1111/nph.15587
  8. Sousa, Filipe; Neiva, João; Martins, Neusa; Jacinto, Rita; Anderson, Laura; Raimondi, Peter T.; Serrão, Ester A.; Pearson, Gareth A.. "Increased evolutionary rates and conserved transcriptional response following allopolyploidization in brown algae". Evolution 73 1 (2018): 59-72. http://dx.doi.org/10.1111/evo.13645.
    Published • 10.1111/evo.13645
  9. Abreu, Narjara Lopes de; Alves, Ruy José Válka; Cardoso, Sérgio Ricardo Sodré; Bertrand, Yann J.K.; Sousa, Filipe; Hall, Climbiê Ferreira; Pfeil, Bernard E.; Antonelli, Alexandre. "The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss)". PeerJ 6 (2018): e4916. http://dx.doi.org/10.7717/peerj.4916.
    Published • 10.7717/peerj.4916
  10. Eriksson, Jonna S.; de Sousa, Filipe; Bertrand, Yann J. K.; Antonelli, Alexandre; Oxelman, Bengt; Pfeil, Bernard E.. "Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)". BMC Evolutionary Biology 18 1 (2018): http://dx.doi.org/10.1186/s12862-018-1127-z.
    Published • 10.1186/s12862-018-1127-z
  11. Sousa, F.; Bertrand, Y. J. K.; Doyle, J. J.; Oxelman, B.; Pfeil, B. E.. "Using Genomic Location and Coalescent Simulation to Investigate Gene Tree Discordance in Medicago L.". Systematic Biology 66 6 (2017): 934-949. http://dx.doi.org/10.1093/sysbio/syx035.
    Published • 10.1093/sysbio/syx035
  12. Eriksson, J.S.; Blanco-Pastor, J.L.; Sousa, F.; Bertrand, Y.J.K.; Pfeil, B.E.. "A cryptic species produced by autopolyploidy and subsequent introgression involving Medicago prostrata (Fabaceae)". Molecular Phylogenetics and Evolution 107 (2017): 367-381. http://dx.doi.org/10.1016/j.ympev.2016.11.020.
    Published • 10.1016/j.ympev.2016.11.020
  13. de Sousa, Filipe; Bertrand, Yann J. K.; Pfeil, Bernard E.. "Patterns of phylogenetic incongruence in Medicago found among six loci". Plant Systematics and Evolution 302 5 (2016): 493-513. http://dx.doi.org/10.1007/s00606-016-1278-6.
    Published • 10.1007/s00606-016-1278-6
  14. Bertrand, Yann J. K.; Scheen, Anne-Cathrine; Marcussen, Thomas; Pfeil, Bernard E.; de Sousa, Filipe; Oxelman, Bengt. "Assignment of Homoeologs to Parental Genomes in Allopolyploids for Species Tree Inference, with an Example from Fumaria (Papaveraceae)". Systematic Biology 64 3 (2015): 448-471. http://dx.doi.org/10.1093/sysbio/syv004.
    Published • 10.1093/sysbio/syv004
  15. Nilsson, R.H.; Tedersoo, L.; Ryberg, M.; Kristiansson, E.; Hartmann, M.; Unterseher, M.; Porter, T.M.; et al. "A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts". Microbes and Environments 30 2 (2015): 145-150. http://www.scopus.com/inward/record.url?eid=2-s2.0-84931464569&partnerID=MN8TOARS.
    10.1264/jsme2.ME14121
  16. de Sousa, Filipe; Bertrand, Yann J. K.; Nylinder, Stephan; Oxelman, Bengt; Eriksson, Jonna S.; Pfeil, Bernard E.. "Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing". PLoS ONE 9 10 (2014): e109704. http://dx.doi.org/10.1371/journal.pone.0109704.
    Published • 10.1371/journal.pone.0109704
  17. Nilsson, R. Henrik; Hyde, Kevin D.; Pawlowska, Julia; Ryberg, Martin; Tedersoo, Leho; Aas, Anders Bjørnsgard; Alias, Siti A.; et al. "Improving ITS sequence data for identification of plant pathogenic fungi". Fungal Diversity 67 1 (2014): 11-19. http://dx.doi.org/10.1007/s13225-014-0291-8.
    Published • 10.1007/s13225-014-0291-8
  18. Bengtsson-Palme, J.; Ryberg, M.; Hartmann, M.; Branco, S.; Wang, Z.; Godhe, A.; De Wit, P.; et al. "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data". Methods in Ecology and Evolution 4 10 (2013): 914-919. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885611996&partnerID=MN8TOARS.
    10.1111/2041-210X.12073
  19. De Sousa, F.; Figueiredo, E.; Smith, G. F.. "Vitaceae - A new and an overlooked record of Cyphostemma in Angola". Bothalia 41 2 (2011): http://dx.doi.org/10.4102/abc.v41i2.62.
    Published • 10.4102/abc.v41i2.62
  20. De Sousa, F.; Figueiredo, E.; Smith, G.F.. "The genus Cyphostemma (Planch.) Alston (Vitaceae) in Angola". Bradleya 29 (2011): 79-92. http://www.scopus.com/inward/record.url?eid=2-s2.0-85040191964&partnerID=MN8TOARS.
  21. Sousa, Filipe; Figueiredo, Estrela; Smith, Gideon F.. "Cyphostemma mendesii (Vitaceae), a new species from Angola". Phytotaxa 7 (2010): 35-39.
    Published
  22. de Sousa, Filipe de Portugal S. T.; Lewis, Gwilym P.; Hawkins, Julie A.. "A revision of the South American genus Apuleia (Leguminosae, Cassieae)". Kew Bulletin 65 2 (2010): 225-232. http://dx.doi.org/10.1007/s12225-010-9213-4.
    Published • 10.1007/s12225-010-9213-4
Report
  1. Sousa, Filipe; Sequeira, V.; Gordo, Leonel Serrano; Paulo, Octavio; Vieira, Ana Rita. 2022. TUNAPRINT 2.0: Molecular identification of tuna species used by the Portuguese canning industry. Progress Report. https://ulisboa-my.sharepoint.com/personal/arivieira_fc_ul_pt/_layouts/15/onedrive.aspx?id=%2Fpersonal%2Farivieira%5Ffc%5Ful%5Fpt%2FDocuments%2FAna%20Rita%20Documents%2FPROJECTOS%2FTUNAPRINT%5FOCEAN%C3%81RIO%2FTUNAPRINT%202%2E0%5FDez2021%2FRELAT%C3%93RIOS%2FTUNAPRINT%202%2E0%5FRelatorioPontoSituacao%5FDez2022%2Epdf&parent=%2Fpersonal%2Farivieira%5Ffc%5Ful%5Fpt%2FDocuments%2FAna%20Rita%20Documents%2FPROJECTOS%2FTUNAPRINT%5FOCEAN%C3%81RIO%2FTUNAPRINT%202%2E0%5FDez2021%2FRELAT%C3%93RIOS.

Other

Dataset
  1. Sousa, Filipe; Civán, Peter; Brazão, João; Foster, Peter G.; Cox, Cymon J.. Data from the article "The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models".
    10.5281/zenodo.3554148
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019/07/12 The monophyly of Bryophytes is supported by nuclear and plastidial protein phylogenies IAB-iMoss Meeting
Real Jardín Botanico, Madrid (Madrid, Spain)
2017/06 Are Bryophytes monophyletic? - Evidence from Organellar and Nuclear Protein-Coding Genes Evolution meeting
Society of Systematic Biologists (Portland, OR, United States)
2013/01 A coalescent-based test to distinguish between paralogy, hybridisation and lineage sorting International Legume Conference
Universidade de Joanesburgo (Joanesburgo, South Africa)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/10/01 - Current Detection of selection and codon evolution in phylogenomic datasets
Supervisor
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2022/12/01 - Current Estudo da interação entre moduladores da homeostasia do ferro na insuficiência cardíaca
Co-supervisor
 Mestrado em Biologia Humana e Ambiente (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022/12/01 - 2024/01/09 Estudo da contribuição de genes com funções no Sistema Nervoso na manifestação da insuficiência cardíaca
Co-supervisor
 Mestrado em Biologia Humana e Ambiente (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018/10 - 2019/06/30 Reconstructing the evolutionary history of the Palmophyllales, a group of multicellular deep sea green algae
Supervisor
Universidade do Algarve - Campus de Gambelas, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2014/08 - 2014/11 Organização do encontro "Systematikdagarna", 2014 (2014/11 - 2014/11)
Congress (Member of the Organising Committee)
 Göteborgs Universitet, Sweden

Association member

Society Organization name Role
2009 - Current CERCiência - Ciência em Rede membro fundador, tesoureiro

Committee member

Activity description
Role 		Institution / Organization
2012/01/01 - 2014/12/31 Representante dos doutorandos na comissão para a Igualdade do Departamento de Ciências Biológicas e do Ambiente, Universidade de Gotemburgo
Member

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2023/01/23 - 2023/02/03 Seminários em Biologia Evolutiva e do Desenvolvimento Seminários em Biologia Evolutiva e do Desenvolvimento (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2022/11/28 - 2022/12/16 Genética e Genómica das Alterações Ambientais Genética e Genómica das Alterações Ambientais (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2021/09/23 - 2022/10/21 Biologia Evolutiva Biologia Evolutiva Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2021/09/13 - 2022/10/14 Filogenética Filogenética (Mestrado) Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2013 - 2014 Florística Floristics (Bachelor) Göteborgs universitet Institutionen för Biologi och Miljövetenskap, Sweden
2013 - 2014 Biologia Base course in Biology (Bachelor) Göteborgs universitet Institutionen för Biologi och Miljövetenskap, Sweden
2011 - 2013 Farmacologia Botanical Pharmacology (Bachelor) Göteborgs universitet Institutionen för Biologi och Miljövetenskap, Sweden
2010 - 2013 Sistemática Advanced Systematics (Master) Göteborgs universitet Institutionen för Biologi och Miljövetenskap, Sweden
2011 - 2012 Botânica World Plant Diversity (Master) Göteborgs universitet Institutionen för Biologi och Miljövetenskap, Sweden

Journal scientific committee

Journal title (ISSN) Publisher
2022 - 2022 Journal of Biogeography
2022 - 2022 Mitochondrial DNA Part B: Resources
2020 - 2020 Journal of Systematics and Evolution
2020 - 2020 Frontiers in Ecology and Evolution
2019 - 2019 New Phytologist
2018 - 2018 PLoS ONE (1932-6203) Public Library of Science
2018 - 2018 Molecular Biology and Evolution (1537-1719) Oxford University Press
2017 - 2017 Webbia (2169-4060) Informa UK (Taylor & Francis)
2016 - 2016 Systematic Botany (1548-2324) American Society of Plant Taxonomists
2012 - 2012 Candollea (0373-2967) BioOne (Society of Conservatoire at Jardin Botaniques de la Ville de Geneve)