???global.info.a_carregar???
João Pedro Marques, post-doc researcher in evolutionary genomics at the EVOCHANGE group - Associação Biopolis. I have a Master Degree in Biochemistry but soon have changed my focus into bioinformatics applied to sequence analysis. I started working with transcriptomic data and gene expression applied to body metamorphosis and when, in 2014, I joined CIBIO-InBIO, the focus of my interests became the speciation and population genetics. As more complex questions started to arise, I started to produce and work with whole genome data (e.g.: genome assembly and annotation, cluster analysis, SNPcall) and got in touch with evolution and its unsolved questions. Because of this, the willing to apply for a PhD to study in detail some of these questions became stronger. I did my PhD in Biodiversity, Genetics and Evolution from the University of Porto (Portugal) in cotutele with University of Montpellier (France). My PhD was focused on an important conceptual problem – the role of natural selection on the formation and evolution of species. I tackled hares and mouse species in several contact zones with various degrees of divergence, gene flow and ecological differentiation and used massive amounts of genomic data resulting from modern sequencing tools, which allowed develop research in the forefront of evolutionary genomics. Genomics of non-model systems promises to shed novel light onto the fundamental processes that led to the formation and evolution of species and I am particularly interested in using genomics to study the role of selection in divergence, introgression and speciation.
Identification

Personal identification

Full name
João Pedro Nogueira Marques

Citation names

  • Marques, João P.
  • Marques, João Pedro

Author identifiers

Ciência ID
9917-41DB-73E5
ORCID iD
0000-0001-9834-1361
Google Scholar ID
https://scholar.google.pt/citations?user=g3aEndwAAAAJ&hl=pt-PT
Researcher Id
M-6187-2013
Scopus Author Id
56506389700

Email addresses

  • joao.marques@cibio.up.pt (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Evolutionary Biology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences - Genetics and Heredity

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Intermediate (B1) Advanced (C1) Intermediate (B1) Intermediate (B1)
Spanish; Castilian Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2017/10/01 - 2022/04/19
Concluded
Génétique et Génomique (Doctorat)
Université de Montpellier, France
"Utilisation des outils génomiques pour comprendre la différenciation et le mélange des espèces chez les lièvres et les souris" (THESIS/DISSERTATION)
2016/09 - 2022/04/19
Concluded
Doutoramento em Biodiversidade, Genética e Evolução (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal

Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal
"Using genomic tools to understand species differentiation and admixture in hares and mice." (THESIS/DISSERTATION)
2015
Concluded
Bioinformatics in Health Sciences (Pós-Graduação)
Universidade do Minho Escola de Medicina, Portugal
"n/a" (THESIS/DISSERTATION)
18 out of 20
2012
Concluded
Bioquímica, Ramo 1 - Especialização em Métodos Biomoleculares (Mestrado)
Universidade de Aveiro, Portugal
"Identification of determinants of resistance in P.falciparum - Proteomics approach 17 out of 20" (THESIS/DISSERTATION)
16 out of 20
2009
Concluded
Biochemistry (Licenciatura)
Universidade de Aveiro, Portugal
"Antioxidant effect of catalase- 16 out of 20" (THESIS/DISSERTATION)
13 out of 20
Affiliation

Science

Category
Host institution
Employer
2022/05 - Current Contracted Researcher (Research) Associação BIOPOLIS - Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal
2016/10 - 2022/04 Researcher (Research) Institut des sciences de l'évolution, France
2014/01 - 2022/04 Researcher (Research) Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal
2013/05/01 - 2014/01/31 Researcher (Research) Centro de Ciências do Mar, Portugal
2010/06/30 - 2010/09/01 Research Trainee (Research) Universität Bremen, Germany

Others

Category
Host institution
Employer
2012/01/21 - 2012/12/31 Science promoter in the environmental educational project "H20 Indaqua - Água limpa para beber dá saúde e faz crescer" INDAQUA, Portugal
Projects

Contract

Designation Funders
2021/01/01 - Current Research Network in Biodiversity and Evolutionary Biology (InBIO)
Researcher
Fundação para a Ciência e a Tecnologia
2020/01/01 - Current Research Network in Biodiversity and Evolutionary Biology
Researcher
Fundação para a Ciência e a Tecnologia
2020/01/01 - Current Research Network in Biodiversity and Evolutionary Biology
Researcher
Fundação para a Ciência e a Tecnologia
2023/03/01 - 2026/02/28 Biodiversity Genomics Europe
101059492
Post-doc
Associação BIOPOLIS - Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal
European Commission
Ongoing
2021/03/15 - 2022/02/28 HybridChange - The potential of hybridization to promote rapid adaptation during climate change
Post-doc
Associação BIOPOLIS - Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2019/12/31 Research Network in Biodiversity and Evolutionary Biology
UID/BIA/50027/2019
Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade do Minho Laboratório de Paisagens Património e Território, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2015/06 - 2017/02 HybridAdapt - Hybridization, adaptation and historical demography: a population genomics study
FCT-ANR/BIA-EVF/0250/2012
Master Student Fellow
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Institut des sciences de l'évolution, France
Fundação para a Ciência e a Tecnologia
2014/02 - 2015/05 Molecular and population genetic signatures of cytonuclear interactions: the Podarcis model
EXPL/BIA-EVF/1283/2012
Master Student Fellow
Fundação para a Ciência e a Tecnologia
2013/05 - 2014/01 Parathyroid hormone-related protein and Stanniocalcin: new metabolic hormones?
Master Student Fellow
Centro de Ciências do Mar, Portugal
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluded
Outputs

Publications

Conference paper
  1. Marques, João. "Genome-wide patterns of divergence among flat periwinkles: from ecotypes to species". 2015.
Conference poster
  1. Marques, João P.; Melo-Ferreira, J.; Pierre, Boursot. "A genomic view of differentiation and admixture history between subspecies of the house mouse (Mus musculus)". Paper presented in II Joint Congress on Evolutionary Biology – Montpellier, France, 2018.
  2. Marques, João P.; Melo-Ferreira, José. "The Role of Natural Selection in the Evolution of Lagomorphs". Paper presented in 5th World Lagomorph Conference 2016, 2016.
  3. Marques, João P.; Ferreira, Mafalda S.; Melo-Ferreira, José. "A guide to reconstruct “true” de novo transcriptomes". Paper presented in Congenomics 2016, 2016.
Journal article
  1. Schelle, Luca; Côrte-Real, João Vasco; Fayyaz, Sharmeen; del Pozo Ben, Augusto; Shnipova, Margarita; Petersen, Moritz; Lotke, Rishikesh; et al. "Evolutionary and functional characterization of lagomorph guanylate-binding proteins: a story of gain and loss and shedding light on expression, localization and innate immunity-related functions". Frontiers in Immunology 15 (2024): http://dx.doi.org/10.3389/fimmu.2024.1303089.
    10.3389/fimmu.2024.1303089
  2. Maltseva, A.L.; Lobov, A.A.; Pavlova, P.A.; Panova, M.; Gafarova, E.R.; Marques, João Pedro; Danilov, L.G.; Granovitch, A.I.. Corresponding author: Granovitch, A.I.. "Orphan gene in Littorina: An unexpected role of symbionts in the host evolution". Gene 824 (2022): 146389. http://dx.doi.org/10.1016/j.gene.2022.146389.
    10.1016/j.gene.2022.146389
  3. Neves, Fabiana; Marques, João Pedro; Areal, Helena; Pinto-Pinho, Patrícia; Colaço, Bruno; Melo-Ferreira, José; Fardilha, Margarida; Abrantes, Joana; Esteves, Pedro José. Corresponding author: Esteves, Pedro José. "TLR7 and TLR8 evolution in lagomorphs: different patterns in the different lineages". Immunogenetics 74 5 (2022): 475-485. http://dx.doi.org/10.1007/s00251-022-01262-9.
    10.1007/s00251-022-01262-9
  4. João P. Marques; Graciela Sotelo; Juan Galindo; Pragya Chaube; Diana Costa; Sandra Afonso; Marina Panova; et al. "Transcriptomic resources for evolutionary studies in flat periwinkles and related species". Scientific Data (2020): https://doi.org/10.1038/s41597-020-0408-8.
    10.1038/s41597-020-0408-8
  5. Louro, Bruno; Marques, João Pedro; Manchado, Manuel; Power, Deborah M.; Campinho, Marco António. "Sole head transcriptomics reveals a coordinated developmental program during metamorphosis". Genomics 112 1 (2020): 592-602. http://dx.doi.org/10.1016/j.ygeno.2019.04.011.
    10.1016/j.ygeno.2019.04.011
  6. Marques, João P; Seixas, Fernando A; Farelo, Liliana; Callahan, Colin M; Good, Jeffrey M; Montgomery, W Ian; Reid, Neil; et al. "An Annotated Draft Genome of the Mountain Hare (Lepus timidus)". Genome Biology and Evolution 12 1 (2019): 3656-3662. http://dx.doi.org/10.1093/gbe/evz273.
    10.1093/gbe/evz273
  7. Giska, Iwona; Farelo, Liliana; Pimenta, João; Seixas, Fernando A; Ferreira, Mafalda S.; Marques, João Pedro; Miranda, Inês; et al. "Introgression drives repeated evolution of winter coat color polymorphism in hares". Proceedings of the National Academy of Sciences 116 48 (2019): 24150-24156. http://dx.doi.org/10.1073/pnas.1910471116.
    10.1073/pnas.1910471116
  8. Marques, João P.; Ferreira, Mafalda S.; Farelo, Liliana; Callahan, Colin M.; Hackländer, Klaus; Jenny, Hannes; Montgomery, W. Ian; et al. "Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares". Scientific Data 4 1 (2017): http://dx.doi.org/10.1038/sdata.2017.178.
    10.1038/sdata.2017.178
  9. Ferreira, Mafalda S.; Alves, Paulo C.; Callahan, Colin M.; Marques, João P.; Mills, L. Scott; Good, Jeffrey M.; Melo-Ferreira, José. "The transcriptional landscape of seasonal coat colour moult in the snowshoe hare". Molecular Ecology 26 16 (2017): 4173-4185. http://dx.doi.org/10.1111/mec.14177.
    10.1111/mec.14177
  10. Marques, João P.; Sotelo, Graciela; Larsson, Tomas; Johannesson, Kerstin; Panova, Marina; Faria, Rui. "Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis , L. obtusata and L. saxatilis". Marine Genomics 32 (2017): 41-47. http://dx.doi.org/10.1016/j.margen.2016.10.006.
    10.1016/j.margen.2016.10.006
  11. Marques, João P.; Farelo, Liliana; Vilela, Joana; Vanderpool, Dan; Alves, Paulo C.; Good, Jeffrey M.; Boursot, Pierre; Melo-Ferreira, José. "Range expansion underlies historical introgressive hybridization in the Iberian hare". Scientific Reports 7 1 (2017): http://dx.doi.org/10.1038/srep40788.
    10.1038/srep40788
  12. Louro, Bruno; Marques, João Pedro; Power, Deborah M.; Canário, Adelino V.M.. "Having a BLAST: Searchable transcriptome resources for the gilthead sea bream and the European sea bass". Marine Genomics 30 (2016): 67-71. http://dx.doi.org/10.1016/j.margen.2016.10.004.
    10.1016/j.margen.2016.10.004
  13. Churcher, Allison M.; Hubbard, Peter C.; Marques, João Pedro; Canário, Adelino V. M.; Huertas, Mar. "Deep sequencing of the olfactory epithelium reveals specific chemosensory receptors are expressed at sexual maturity in the European eelAnguilla anguilla". Molecular Ecology 24 4 (2015): 822-834. http://dx.doi.org/10.1111/mec.13065.
    10.1111/mec.13065
Preprint
  1. Marques, João Pedro; Alves, Paulo Célio; Amorim, Isabel R.; Lopes, Ricardo J.; Moura, Mónica; Meyers, Gene; Sim-Sim, Manuela; et al. "Building a Portuguese Coalition for Biodiversity Genomics". 2023. http://dx.doi.org/10.32942/x20w3q.
    10.32942/x20w3q
  2. Mc Cartney, Ann M; Formenti, Giulio; Mouton, Alice; De Panis, Diego; Marins, Luísa S; Leitão, Henrique G; Diedericks, Genevieve; et al. "The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics". 2023. http://dx.doi.org/10.1101/2023.09.25.559365.
    10.1101/2023.09.25.559365
Thesis / Dissertation
  1. "Using genomic tools to understand species differentiation and admixture in hares and mice". PhD, Universidade do Porto, 2022. https://hdl.handle.net/10216/141124.
Activities

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2023/03/01 - Current The causes and consequences of ancient hybridization among hares (Lepus spp.)
Co-supervisor
Biodiversidade, Genética e Evolução (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2023/10 - 2027/12 The adaptive potential of sharks in a changing ocean: insights from comparative and population genomics
Co-supervisor
Biodiversidade, Genética e Evolução (PhD)
Universidade do Porto Faculdade de Ciências, Portugal

Université de Montpellier, France

Associação BIOPOLIS - Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Centre pour la Biodiversité Marine l'Exploitation et la Conservation, France
2024/01 - 2025/07 The dynamics of immune gene family evolution in Lagomorphs: a comparative genomics approach
Supervisor
Biodiversidade, Genética e Evolução (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2023/09/01 - 2024/07/26 Understanding the genetic determinants of behaviour differences between the sister species Mus spicilegus and Mus macedonicus using whole genome sequencing data
Supervisor
Biologia (Degree)
Universidade do Porto Faculdade de Ciências, Portugal
2023/09/01 - 2024/06/26 Studying the impact of climate change on genetic exchanges between hares across French Alps contact zone
Supervisor
Biologia (Degree)
Universidade do Porto Faculdade de Ciências, Portugal
2021/09 - 2022/11/17 Using genomics to dissect the history of divergence and hybridization in the sister broom and Corsican hares (Lepus spp.).
Co-supervisor
Mestrado em Biodiversidade, Genética e Evolução (Master)
Associação BIOPOLIS - Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2022/12 Using genomics to dissect the history of divergence and hybridization in the sister broom and Corsican hares (Lepus spp.)
Supervisor
João Manuel Meira do Souto (Master)
Universidade do Porto Faculdade de Ciências, Portugal