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I am currently a Principal Investigator and the group leader of the EVOLGEN group (Evolutionary Genetics and Genomics) at CIBIO/InBIO, University of Porto. EVOLGEN brings together researchers that are interested in evolutionary change and in the genetic determinants underlying the immense biological diversity in nature. More broadly, my ultimate goal is to map phenotypic variation to the gene level, and equipped with this information, I aim to shed light on the mutational mechanisms explaining both simple and complex trait variation and contribute to help answering questions of general interest in biology associated with multiple evolutionary processes, such as speciation, sexual selection, host-parasite coevolution, adaptation, and domestication. My research integrates population genetics and genomics to study patterns of genetic variation in both natural and domesticated populations, together with genetic crosses and a diverse array of molecular biology tools for experimental validation of the main findings and compellingly map phenotype onto genotype. Since I initiated my PhD in 2006, I authored 70 papers in international SCI journals. Papers in which I had a leading role are published in prestigious international peer-reviewed multi-disciplinary journals (Science, Nature, PNAS, Science Advances, Nature Ecology and Evolution, and Current Biology) and in major international peer-reviewed journals in the fields of evolution, genetics, and genomics, such as PLoS Genetics, Molecular Biology and Evolution, Evolution, Genetics, Proceedings of the Royal Society B, Molecular Ecology, among others. A complete list of publications is available at https://scholar.google.pt/citations?user=onCfzJ4AAAAJ&hl=pt-PT. I devote a substantial part of my scientific activity to the supervision of junior researchers at undergraduate, graduate and postgraduate levels. I am currently mentoring 5 PhD students, as well as 4 postdoctoral researchers. I have secured competitive funding as a Principal Investigator on multiple occasions, including an ERC Consolidator Grant (2 million euros).
Read full resume ↓
Identification

Personal identification

Full name
Miguel Carneiro

Citation names

  • Carneiro, Miguel

Author identifiers

Ciência ID
6C1C-97ED-86AB
ORCID iD
0000-0001-9882-7775

Telephones

Mobile phone
  • 969190100 (Personal)

Knowledge fields

  • Natural sciences - Biological Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Spanish; Castilian Advanced (C1) Advanced (C1) Beginner (A1) Advanced (C1)
Affiliation

Science

Category
Host institution 		Employer
2019/11/01 - Current Principal Investigator (Research) Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
2015/02/01 - 2019/10/31 Auxiliary Researcher (Research) Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
2003/04/01 - 2006/03/31 Research Assistant (Research) Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal

Others

Category
Host institution 		Employer
2015/02/01 - Current FCT (Portuguese Science foundation) Investigator Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
2011/04/01 - 2015/01/31 Post-Doctoral fellow Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
2006/04/01 - 2010/12/02 PhD student The University of Arizona, United States
2003/10/01 - 2005/07/16 Master student Universidade do Porto Faculdade de Ciências, Portugal
Projects

Grant

Designation Funders
2021/01/06 - Current ERC Consolidator. EYESPOT - The Genetic, Cellular, and Photonic Mechanisms of Avian Structural Colouration
EYESPOT
Principal investigator
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
Ongoing
2023/09 - 2024/08 Carotenoides e Saúde - A genómica à descoberta do elo perdido
2022.06261.PTDC
Associação BIOPOLIS - Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing

Contract

Designation Funders
2013/05/30 - Current HybridAdapt - Hybridization, adaptation and historical demography: a population genomics study
info:eu-repo/grantAgreement/FCT/3599-PPCDT/127522/PT
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
2012/05/01 - Current COMBINING POPULATION GENOMICS AND QUANTITATIVE GENETICS TO DECIPHER THE MOLECULAR BASIS OF PHENOTYPIC CHANGE DURING THE EARLY STAGES OF ANIMAL DOMESTICATION
info:eu-repo/grantAgreement/FCT/COMPETE/122943/PT
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
2011/04/01 - Current CRYPSIS - Genetic determination and evolution of seasonal phenotype variation of coat-colour in boreal species
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/115069/PT
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2010/06/01 - Current Host-pathogen interaction: the Rabbit Haemorrhagic Disease (RHD) and the European Brown Hare Syndrome (EBHS)
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/108490/PT
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
2010 - Current A multidisciplinary experimental evaluation of the mechanisms contributing to the emergence of reproductive isolation between two subspecies, Oryctolagus cuniculus algirus and O. c. cuniculus, of the European rabbit
PTDC/BIA-EVF/111368/2009
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2006 - Current Evaluating the importance of the X-chromosome "large effect" in the initial stages of reproductive isolation between two pairs of divergent lagomorph taxa
PTDC/BIA-BDE/72277/2006
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
2021/01/01 - 2025/12/31 Research Network in Biodiversity and Evolutionary Biology (InBIO)
LA/P/0048/2020
10.54499/LA/P/0048/2020
Researcher
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2022/01/15 - 2025/01/14 The role of chromosomal inversions in adaptation and reproductive isolation across the speciation continuum
PTDC/BIA-EVL/1614/2021
10.54499/PTDC/BIA-EVL/1614/2021
Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

Universidade de Vigo Facultade de Bioloxía, Spain
Fundação para a Ciência e a Tecnologia
Ongoing
2021/03/01 - 2024/11/30 GrapeVision, genómica de DNA moderno e antigo para potenciar os recursos genéticos da vinha em Portugal
PTDC/BIA-FBT/2389/2020
10.54499/PTDC/BIA-FBT/2389/2020
Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Universidade de Lisboa Centro de Investigação em Agronomia Alimentos Ambiente e Paisagem, Portugal

Instituto Nacional de Investigação Agrária e Veterinária, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Coimbra, Portugal

Universidade de Coimbra Centro de Estudos Interdisciplinares do Século XX, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2020/01/01 - 2023/12/31 Research Network in Biodiversity and Evolutionary Biology
UIDB/50027/2020
10.54499/UIDB/50027/2020
Researcher
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2020/01/01 - 2023/12/31 Research Network in Biodiversity and Evolutionary Biology
UIDP/50027/2020
10.54499/UIDP/50027/2020
Researcher
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2018/09/15 - 2021/09/14 SALOMICS: Genetic and ecological drivers of reproductive mode shifts in salamanders: a comparative approach
PTDC/BIA-EVL/28475/2017
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/26 - 2021/07/25 Colours hidden in the forest: evolutionary genomics of colour patterns in Neotropical frogs
PTDC/BIA-EVL/28621/2017
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/26 - 2021/07/25 Mapping genetic incompatibilities implicated in the early stages of species formation using the European rabbit hybrid zone
PTDC/BIA-EVL/30628/2017
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/06/01 - 2021/05/31 BIRDS ON THE MOVE: adaptive migratory behaviour in response to global environmental change
PTDC/BIA-ECO/28176/2017
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/05/01 - 2021/04/30 Genomics and quantitative genetics of vocal learning in birds
PTDC/BIA-EVL/31569/2017
Principal investigator
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/05/01 - 2021/04/30 ORIGIN AND MAINTENANCE OF COLOR POLYMORPHISMS: AN INTEGRATIVE APPROACH COMBINING GENOMICS, BEHAVIOR AND A POPULATION STUDY
PTDC/BIA-EVL/30288/2017
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
Ongoing
2016/07/01 - 2020/03/31 CHANGE – Seasonal Coat Colour and the impact of Climate Change on the genetic composition of boreal species
PTDC/BIA-EVF/1624/2014
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2015/02/01 - 2020/01/31 Genotype-phenotype associations through a multidisciplinary approach: the genetics basis of tameness and vocalization in domestic rabbits and canaries
FCT 2015 - IF/00283/2014/CP1256/CT0012
Principal investigator
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Lopes, Ricardo Jorge; Carneiro, Miguel. Corresponding author: Lopes, Ricardo Jorge. "Canary domestication as a model for genomics research and avian evolution". In The Canary. Natural History, Science and Cultural Significance, 255-282. London, United Kingdom: Academic Press, 2024.
    Published
Journal article
  1. Giulia Magnabosco; Barbosa, Soraia; Andrade, Pedro; Carneiro, Miguel; Nicholas Vogel. "The “recipe” for the perfect color". Frontiers for Young Minds (2024):
    Accepted • 10.3389/frym.2024.1432589
  2. Roberto Arbore; Soraia Barbosa; Jindrich Brejcha; Yohey Ogawa; Yu Liu; Michaël P.J. Nicolaï; Paulo Pereira; et al. "A molecular mechanism for bright color variation in parrots". Science (2024): http://dx.doi.org/10.1126/science.adp7710.
    10.1126/science.adp7710
  3. Prem Aguilar; Guillem Pérez i de Lanuza; Miguel Carneiro; Pedro Andrade; Catarina Pinho. "The role of historical biogeography in shaping colour morph diversity in the common wall lizard". Molecular Ecology (2024): https://doi.org/10.1111/mec.17338.
    10.1111/mec.17338
  4. Henrique Batalha-Filho; Silvia Britto Barreto; Mario Henrique Barros Silveira; Cristina Yumi Miyaki; Sandra Afonso; Nuno Ferrand; Miguel Carneiro; Fernando Sequeira. "Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil". Heredity (2024): https://doi.org/10.1038/s41437-023-00662-1.
    10.1038/s41437-023-00662-1
  5. Shatadru Ghosh Roy; Anna Bakhrat; Moty Abdu; Sandra Afonso; Paulo Pereira; Miguel Carneiro; Uri Abdu; D Bannasch. "Mutations in SLC45A2 lead to loss of melanin in parrot feathers". G3: Genes, Genomes, Genetics (2023): https://doi.org/10.1093/g3journal/jkad254.
    10.1093/g3journal/jkad254
  6. Verwilligen, Robin A.F.; Mulder, Lindsay; Araújo, Pedro M.; Carneiro, Miguel; Bussmann, Jeroen; Hoekstra, Menno; Van Eck, Miranda. "Zebrafish as outgroup model to study evolution of scavenger receptor class B type I functions". Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 1868 6 (2023): 159308. http://dx.doi.org/10.1016/j.bbalip.2023.159308.
    10.1016/j.bbalip.2023.159308
  7. Pedro Andrade; Mariana L Lyra; Juliana Zina; Deivson F O Bastos; Andrés E Brunetti; Délio Baêta; Sandra Afonso; et al. "Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana". G3 Genes|Genomes|Genetics (2022): https://doi.org/10.1093/g3journal/jkac270.
    10.1093/g3journal/jkac270
  8. Joel M. Alves; Miguel Carneiro; Jonathan P. Day; John J. Welch; Janine A. Duckworth; Tarnya E. Cox; Mike Letnic; et al. "A single introduction of wild rabbits triggered the biological invasion of Australia". Proceedings of the National Academy of Sciences (2022): https://doi.org/10.1073/pnas.2122734119.
    10.1073/pnas.2122734119
  9. Stephen J. Sabatino; Paulo Pereira; Miguel Carneiro; Jolita Dilyte; John Patrick Archer; Antonio Munoz; Francesco Nonnis-Marzano; Antonio Murias. "The genetics of adaptation in freshwater Eurasian shad ( Alosa )". Ecology and Evolution (2022): https://doi.org/10.1002/ece3.8908.
    10.1002/ece3.8908
  10. Toomey, M.B.; Marques, C.I.; Araújo, P.M.; Huang, D.; Zhong, S.; Liu, Y.; Schreiner, G.D.; et al. "A mechanism for red coloration in vertebrates". Current Biology 32 19 (2022): 4201-4214.e12. http://www.scopus.com/inward/record.url?eid=2-s2.0-85139301992&partnerID=MN8TOARS.
    10.1016/j.cub.2022.08.013
  11. Alonso-Alvarez, C.; Andrade, P.; Cantarero, A.; Morales, J.; Carneiro, M.. "Relocation to avoid costs: A hypothesis on red carotenoid-based signals based on recent CYP2J19 gene expression data". BioEssays 44 12 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85139514736&partnerID=MN8TOARS.
    10.1002/bies.202200037
  12. Pedro Andrade; Miguel Carneiro. "Pterin-based pigmentation in animals". Biology Letters (2021): https://doi.org/10.1098/rsbl.2021.0221.
    10.1098/rsbl.2021.0221
  13. D. Azevedo-Silva; J.A. Rasmussen; M. Carneiro; M.T.P. Gilbert; H. Azevedo. "Feasibility of applying shotgun metagenomic analyses to grapevine leaf, rhizosphere and soil microbiome characterisation". Australian Journal of Grape and Wine Research (2021): https://doi.org/10.1111/ajgw.12508.
    10.1111/ajgw.12508
  14. Miguel Carneiro; Gregory P. Copenhaver; Jennifer Vieillard; Pedro Andrade; Samuel Boucher; Sandra Afonso; José A. Blanco-Aguiar; et al. "A loss-of-function mutation in RORB disrupts saltatorial locomotion in rabbits". PLOS Genetics (2021): https://doi.org/10.1371/journal.pgen.1009429.
    10.1371/journal.pgen.1009429
  15. Pedro Andrade; Kelly A. Dyer; Malgorzata A. Gazda; Pedro M. Araújo; Sandra Afonso; Jacob. A. Rasmussen; Cristiana I. Marques; et al. "Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates". PLOS Genetics (2021): https://doi.org/10.1371/journal.pgen.1009404.
    10.1371/journal.pgen.1009404
  16. Pedro Andrade; Daniele Cataldo; Rémi Fontaine; Tiago M. Rodrigues; João Queirós; Verónica Neves; Amélia Fonseca; Miguel Carneiro; David Gonçalves. "Selection underlies phenotypic divergence in the insular Azores woodpigeon". Zoologica Scripta 50 1 (2021): 1-15. https://doi.org/10.1111/zsc.12456.
    10.1111/zsc.12456
  17. Sato, D.X.; Rafati, N.; Ring, H.; Younis, S.; Feng, C.; Blanco-Aguiar, J.A.; Rubin, C.-J.; et al. "Brain transcriptomics of wild and domestic rabbits suggests that changes in dopamine signaling and ciliary function contributed to evolution of tameness". Genome Biology and Evolution 12 10 (2021): 1918-1928. http://www.scopus.com/inward/record.url?eid=2-s2.0-85094932995&partnerID=MN8TOARS.
    10.1093/GBE/EVAA158
  18. Freitas, S.; Gazda, M.A.; Rebelo, M.A.; Munoz-Pajares, A.J.; Vila-Vicosa, C.; Munoz-Merida, A.; Goncalves, L.M.; et al. "Pervasive hybridization with local wild relatives in Western European grapevine varieties". Science Advances 7 47 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85119958243&partnerID=MN8TOARS.
    10.1126/sciadv.abi8584
  19. Alejandro Cantarero; Pedro Andrade; Miguel Carneiro; Adrián Moreno-Borrallo; Carlos Alonso-Alvarez. "Testing the carotenoid-based sexual signalling mechanism by altering CYP2J19 gene expression and colour in a bird species". Proceedings of the Royal Society B: Biological Sciences 287 1938 (2020): 20201067-20201067. https://doi.org/10.1098/rspb.2020.1067.
    10.1098/rspb.2020.1067
  20. Malgorzata A. Gazda; Pedro Miguel Araújo; Ricardo J. Lopes; Matthew B. Toomey; Pedro Andrade; Sandra Afonso; Cristiana I. Marques; et al. "A genetic mechanism for sexual dichromatism in birds". Science (2020):
    Accepted • 10.1525/auk.2008.07113
  21. Gazda, Malgorzata Anna; Toomey, Matthew B; Araújo, Pedro M; Lopes, Ricardo J; Afonso, Sandra; Myers, Connie A; Serres, Kyla; et al. "GENETIC BASIS OF DE NOVO APPEARANCE OF CAROTENOID ORNAMENTATION IN BARE-PARTS OF CANARIES". Molecular Biology and Evolution (2020): http://dx.doi.org/10.1093/molbev/msaa006.
    10.1093/molbev/msaa006
  22. Letko, A.; Ammann, B.; Jagannathan, V.; Henkel, J.; Leuthard, F.; Schelling, C.; Carneiro, M.; Drögemüller, C.; Leeb, T.. "A deletion spanning the promoter and first exon of the hair cycle-specific ASIP transcript isoform in black and tan rabbits". Animal Genetics 51 1 (2020): 137-140. http://www.scopus.com/inward/record.url?eid=2-s2.0-85075123120&partnerID=MN8TOARS.
    10.1111/age.12881
  23. Gazda, M.A.; Araújo, P.M.; Lopes, R.J.; Toomey, M.B.; Andrade, P.; Afonso, S.; Marques, C.; et al. "A genetic mechanism for sexual dichromatism in birds". Science 368 6496 (2020): 1270-1274. http://www.scopus.com/inward/record.url?eid=2-s2.0-85086424030&partnerID=MN8TOARS.
    10.1126/science.aba0803
  24. Joel M. Alves; Miguel Carneiro; Jade Y. Cheng; Ana Lemos de Matos; Masmudur M. Rahman; Liisa Loog; Paula F. Campos; et al. "Parallel adaptation of rabbit populations to myxoma virus". Science 363 6433 (2019): 1319-1326. https://doi.org/10.1126/science.aau7285.
    10.1126/science.aau7285
  25. Koepfli, K.-P.; Tamazian, G.; Wildt, D.; Dobrynin, P.; Kim, C.; Frandsen, P.B.; Godinho, R.; et al. "Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations". G3: Genes, Genomes, Genetics 9 6 (2019): 1785-1793. http://www.scopus.com/inward/record.url?eid=2-s2.0-85067127074&partnerID=MN8TOARS.
    10.1534/g3.119.400084
  26. Andrade, P.; Pinho, C.; de Lanuza, G.P.I.; Afonso, S.; Brejcha, J.; Rubin, C.-J.; Wallerman, O.; et al. "Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard". Proceedings of the National Academy of Sciences of the United States of America 116 12 (2019): 5633-5642. http://www.scopus.com/inward/record.url?eid=2-s2.0-85063253299&partnerID=MN8TOARS.
    10.1073/pnas.1820320116
  27. Pina-Cabral, L.B.; Carneiro, M.; Criado, B.; Esteves, P.J.. "Maximum likelihood approach suggests positive selection in platelet integrin aIIbß3 in mammalian species". Platelets 30 4 (2019): 460-466. http://www.scopus.com/inward/record.url?eid=2-s2.0-85044938826&partnerID=MN8TOARS.
    10.1080/09537104.2018.1457783
  28. Cardoso-Moreira, M.; Halbert, J.; Valloton, D.; Velten, B.; Chen, C.; Shao, Y.; Liechti, A.; et al. "Gene expression across mammalian organ development". Nature 571 7766 (2019): 505-509. http://www.scopus.com/inward/record.url?eid=2-s2.0-85065531911&partnerID=MN8TOARS.
    10.1038/s41586-019-1338-5
  29. Marchandeau, S.; Queney, G.; Alves, J.M.; Carneiro, M.; Ferrand, N.. "Myxomatosis: rabbits have separately developed the same mechanisms of genetic resistance in France, Australia and the United Kingdom,Myxomatose - Les lapins ont développé indépendamment les mêmes mécanismes de résistance génétique en France, en Australie et au Royaume-Uni". Medecine sciences : M/S 35 8-9 (2019): 611-613. http://www.scopus.com/inward/record.url?eid=2-s2.0-85072293322&partnerID=MN8TOARS.
    10.1051/medsci/2019118
  30. Matthew B. Toomey; Cristiana I. Marques; Pedro Andrade; Pedro M. Araújo; Stephen Sabatino; Malgorzata A. Gazda; Sandra Afonso; et al. "A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch". Proceedings of the Royal Society B: Biological Sciences (2018): https://doi.org/10.1098/rspb.2018.1788.
    10.1098/rspb.2018.1788
  31. Nima Rafati; José A. Blanco-Aguiar; Carl J. Rubin; Shumaila Sayyab; Stephen J. Sabatino; Sandra Afonso; Chungang Feng; et al. "A genomic map of clinal variation across the European rabbit hybrid zone". Molecular Ecology (2018): https://doi.org/10.1111%2Fmec.14494.
    10.1111/mec.14494
  32. Takashi Makino; Carl-Johan Rubin; Miguel Carneiro; Erik Axelsson; Leif Andersson; Matthew T Webster. "Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants". Genome Biology and Evolution 10 1 (2018): 276-290. https://doi.org/10.1093%2Fgbe%2Fevy004.
    10.1093/gbe/evy004
  33. Mark F Richardson; Fernando Sequeira; Daniel Selechnik; Miguel Carneiro; Marcelo Vallinoto; Jack G Reid; Andrea J West; et al. "Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader". GigaScience 7 1 (2018): 1-7. https://doi.org/10.1093/gigascience/gix114.
    10.1093/gigascience/gix114
  34. Edwards, R.J.; Tuipulotu, D.E.; Amos, T.G.; O'Meally, D.; Richardson, M.F.; Russell, T.L.; Vallinoto, M.; et al. "Draft genome assembly of the invasive cane toad, Rhinella marina". GigaScience 7 9 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85055910505&partnerID=MN8TOARS.
    10.1093/gigascience/giy095
  35. Gazda, M.A.; Andrade, P.; Afonso, S.; Dilyte, J.; Archer, J.P.; Lopes, R.J.; Faria, R.; Carneiro, M.. "Signatures of selection on standing genetic variation underlie athletic and navigational performance in racing pigeons". Molecular Biology and Evolution 35 5 (2018): 1176-1189. http://www.scopus.com/inward/record.url?eid=2-s2.0-85053934374&partnerID=MN8TOARS.
    10.1093/molbev/msy030
  36. Brusini, I.; Carneiro, M.; Wang, C.; Rubin, C.-J.; Ring, H.; Afonso, S.; Blanco-Aguiar, J.A.; et al. "Changes in brain architecture are consistent with altered fear processing in domestic rabbits". Proceedings of the National Academy of Sciences of the United States of America 115 28 (2018): 7380-7385. http://www.scopus.com/inward/record.url?eid=2-s2.0-85049643502&partnerID=MN8TOARS.
    10.1073/pnas.1801024115
  37. Ricardo Jorge Lopes; Antonio Muñoz Mérida; Miguel Carneiro. "Unleashing the Potential of Public Genomic Resources to Find Parasite Genetic Data". Trends in Parasitology 33 10 (2017): 750-753. https://doi.org/10.1016%2Fj.pt.2017.06.006.
    10.1016/j.pt.2017.06.006
  38. Nourisson, C.; Muñoz-Merida, A.; Carneiro, M.; Sequeira, F.. "De novo transcriptome assembly and polymorphism detection in two highly divergent evolutionary units of Bosca's newt (Lissotriton boscai) endemic to the Iberian Peninsula". Molecular Ecology Resources 17 3 (2017): 546-549. http://www.scopus.com/inward/record.url?eid=2-s2.0-84994477231&partnerID=MN8TOARS.
    10.1111/1755-0998.12563
  39. Toomey, M.B.; Lopes, R.J.; Araújo, P.M.; Johnson, J.D.; Gazda, M.A.; Afonso, S.; Mota, P.G.; et al. "High-density lipoprotein receptor SCARB1 is required for carotenoid coloration in birds". Proceedings of the National Academy of Sciences of the United States of America 114 20 (2017): 5219-5224. http://www.scopus.com/inward/record.url?eid=2-s2.0-85019581853&partnerID=MN8TOARS.
    10.1073/pnas.1700751114/-/DCSupplemental
  40. Ricardo J. Pereira; Felipe S. Barreto; N. Tessa Pierce; Miguel Carneiro; Ronald S. Burton. "Transcriptome-wide patterns of divergence during allopatric evolution". Mol Ecol 25 7 (2016): 1478-1493. http://dx.doi.org/10.1111/mec.13579.
    10.1111/mec.13579
  41. Luca Fontanesi; Federica Di Palma; Paul Flicek; Andrew T. Smith; Carl-Gustaf Thulin; Paulo C. Alves; the Lagomorph Genomics Consortium*. "LaGomiCs—Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order". JHERED 107 4 (2016): 295-308. http://dx.doi.org/10.1093/jhered/esw010.
    10.1093/jhered/esw010
  42. Kevin P. Mulder; André Lourenço; Miguel Carneiro; Guillermo Velo-Antón. "The complete mitochondrial genome of Salamandra salamandra (Amphibia: Urodela: Salamandridae)". Mitochondrial DNA Part B 1 1 (2016): 880-882. https://doi.org/10.1080%2F23802359.2016.1253042.
    10.1080/23802359.2016.1253042
  43. Miguel Carneiro; Dou Hu; John Archer; Chungang Feng; Sandra Afonso; Congying Chen; José A. Blanco-Aguiar; et al. "Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus". Genetics 205 2 (2016): 955-965. https://doi.org/10.1534%2Fgenetics.116.196667.
    10.1534/genetics.116.196667
  44. Lopes, R.J.; Johnson, J.D.; Toomey, M.B.; Ferreira, M.S.; Araujo, P.M.; Melo-Ferreira, J.; Andersson, L.; et al. "Genetic Basis for Red Coloration in Birds". Current Biology 26 11 (2016): 1427-1434. http://www.scopus.com/inward/record.url?eid=2-s2.0-84975462338&partnerID=MN8TOARS.
    10.1016/j.cub.2016.03.076
  45. Carneiro, M.; Piorno, V.; Rubin, C.-J.; Alves, J.M.; Ferrand, N.; Alves, P.C.; Andersson, L.. "Candidate genes underlying heritable differences in reproductive seasonality between wild and domestic rabbits". Animal Genetics 46 4 (2015): 418-425. http://www.scopus.com/inward/record.url?eid=2-s2.0-84937974756&partnerID=MN8TOARS.
    10.1111/age.12299
  46. Melo-Ferreira, J.; Lemos de Matos, A.; Areal, H.; Lissovsky, A.A.; Carneiro, M.; Esteves, P.J.. "The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach". Molecular Phylogenetics and Evolution 84 (2015): 240-244. http://www.scopus.com/inward/record.url?eid=2-s2.0-84922593747&partnerID=MN8TOARS.
    10.1016/j.ympev.2015.01.004
  47. Piorno, V.; Villafuerte, R.; Branco, M.; Carneiro, M.; Ferrand, N.; Alves, P.C.. "Low persistence in nature of captive reared rabbits after restocking operations". European Journal of Wildlife Research 61 4 (2015): 591-599. http://www.scopus.com/inward/record.url?eid=2-s2.0-84938973651&partnerID=MN8TOARS.
    10.1007/s10344-015-0934-4
  48. Alves, J.M.; Carneiro, M.; Afonso, S.; Lopes, S.; Garreau, H.; Boucher, S.; Allain, D.; et al. "Levels and patterns of genetic diversity and population structure in domestic rabbits". PLoS ONE 10 12 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84957111852&partnerID=MN8TOARS.
    10.1371/journal.pone.0144687
  49. Chávez-Galarza, J.; Henriques, D.; Johnston, J.S.; Carneiro, M.; Rufino, J.; Patton, J.C.; Pinto, M.A.. "Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: Maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia". Molecular Ecology 24 12 (2015): 2973-2992. http://www.scopus.com/inward/record.url?eid=2-s2.0-84932093796&partnerID=MN8TOARS.
    10.1111/mec.13223
  50. M. Carneiro; C.-J. Rubin; F. Di Palma; F. W. Albert; J. Alfoldi; A. M. Barrio; G. Pielberg; et al. "Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication". Science 345 6200 (2014): 1074-1079. http://dx.doi.org/10.1126/science.1253714.
    10.1126/science.1253714
  51. Miguel Carneiro; Frank W. Albert; Sandra Afonso; Ricardo J. Pereira; Hernan Burbano; Rita Campos; José Melo-Ferreira; et al. "The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit". PLoS Genet 10 8 (2014): e1003519-e1003519. http://dx.doi.org/10.1371/journal.pgen.1003519.
    10.1371/journal.pgen.1003519
  52. Seixas, F.A.; Juste, J.; Campos, P.F.; Carneiro, M.; Ferrand, N.; Alves, P.C.; Melo-Ferreira, J.. "Colonization history of Mallorca Island by the European rabbit, Oryctolagus cuniculus, and the Iberian hare, Lepus granatensis (Lagomorpha: Leporidae)". Biological Journal of the Linnean Society 111 4 (2014): 748-760. http://www.scopus.com/inward/record.url?eid=2-s2.0-84897461424&partnerID=MN8TOARS.
    10.1111/bij.12248
  53. Sousa, Vitor C.; Carneiro, Miguel; Ferrand, Nuno; Hey, Jody. "Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models". Genetics 194 1 (2013): 211-+.
    10.1534/genetics.113.149211
  54. Carneiro, Miguel; Baird, Stuart J. E.; Afonso, Sandra; Ramirez, Esther; Tarroso, Pedro; Teotonio, Henrique; Villafuerte, Rafael; Nachman, Michael W.; Ferrand, Nuno. "Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit". Molecular Ecology 22 9 (2013): 2511-2525.
    10.1111/mec.12272
  55. Nowick, K.; Carneiro, M.; Faria, R.. "A prominent role of KRAB-ZNF transcription factors in mammalian speciation?". Trends in Genetics 29 3 (2013): 130-139. http://www.scopus.com/inward/record.url?eid=2-s2.0-84875254039&partnerID=MN8TOARS.
    10.1016/j.tig.2012.11.007
  56. Gayral, P.; Melo-Ferreira, J.; Glémin, S.; Bierne, N.; Carneiro, M.; Nabholz, B.; Lourenco, J.M.; et al. "Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate-Invertebrate Gap". PLoS Genetics 9 4 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84876855375&partnerID=MN8TOARS.
    10.1371/journal.pgen.1003457
  57. Melo-Ferreira, J.; Boursot, P.; Carneiro, M.; Esteves, P. J.; Farelo, L.; Alves, P. C.. "Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) Revealed by Species-Tree Inference and Coalescent Simulations". Systematic Biology 61 3 (2012): 367-381.
    10.1093/sysbio/syr114
  58. Carneiro, Miguel; Albert, Frank W.; Melo-Ferreira, Jose; Galtier, Nicolas; Gayral, Philippe; Blanco-Aguiar, Jose A.; Villafuerte, Rafael; Nachman, Michael W.; Ferrand, Nuno. "Evidence for Widespread Positive and Purifying Selection Across the European Rabbit (Oryctolagus cuniculus) Genome". Molecular Biology and Evolution 29 7 (2012): 1837-1849.
    10.1093/molbev/mss025
  59. Albert, F.W.; Somel, M.; Carneiro, M.; Aximu-Petri, A.; Halbwax, M.; Thalmann, O.; Blanco-Aguiar, J.A.; et al. "A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals". PLoS Genetics 8 9 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84866914794&partnerID=MN8TOARS.
    10.1371/journal.pgen.1002962
  60. Carneiro, Miguel; Afonso, Sandra; Geraldes, Armando; Garreau, Herve; Bolet, Gerard; Boucher, Samuel; Tircazes, Aurelie; et al. "The Genetic Structure of Domestic Rabbits". Molecular Biology and Evolution 28 6 (2011): 1801-1816.
    10.1093/molbev/msr003
  61. Carneiro, Miguel; Blanco-Aguiar, Jose A.; Villafuerte, Rafael; Ferrand, Nuno; Nachman, Michael W.. "SPECIATION IN THE EUROPEAN RABBIT (ORYCTOLAGUS CUNICULUS): ISLANDS OF DIFFERENTIATION ON THE X CHROMOSOME AND AUTOSOMES". Evolution 64 12 (2010): 3443-3460.
    10.1111/j.1558-5646.2010.01092.x
  62. Carneiro, Miguel; Ferrand, Nuno; Nachman, Michael W.. "Recombination and Speciation: Loci Near Centromeres Are More Differentiated Than Loci Near Telomeres Between Subspecies of the European Rabbit (Oryctolagus cuniculus)". Genetics 181 2 (2009): 593-606.
    10.1534/genetics.108.096826
  63. Esteves, P. J.; Abrantes, J.; Carneiro, M.; Muller, A.; Thompson, G.; van der Loo, W.. "Detection of positive selection in the major capsid protein VP60 of the rabbit haemorrhagic disease virus (RHDV)". Virus Research 137 2 (2008): 253-256.
    10.1016/j.virusres.2008.07.025
  64. Surridge, Alison K.; van der Loo, Wessel; Abrantes, Joana; Carneiro, Miguel; Hewitt, Godfrey M.; Esteves, Pedro J.. "Diversity and evolutionary history of the MHC DQA gene in leporids". Immunogenetics 60 9 (2008): 515-525.
    10.1007/s00251-008-0309-z
  65. Geraldes, A.; Carneiro, M.; Delibes-Mateos, M.; Villafuerte, R.; Nachman, M.W.; Ferrand, N.. "Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula". Molecular Ecology 17 20 (2008): 4489-4499. http://www.scopus.com/inward/record.url?eid=2-s2.0-53749100999&partnerID=MN8TOARS.
    10.1111/j.1365-294X.2008.03943.x
  66. Carneiro, Miguel; Ferrand, Nuno. "Extensive intragenic recombination and patterns of linkage disequilibrium at the CSN3 locus in European rabbit". Genetics Selection Evolution 39 3 (2007): 341-352.
    10.1051/gse:2007007
Preprint
  1. Pedro Andrade; Aldina M. A. Franco; Marta Acácio; Sandra Afonso; Cristiana I. Marques; Francisco Moreira; Miguel Carneiro; Inês Catry. "Mechanisms underlying the loss of migratory behaviour in a long-lived bird". 2024. https://doi.org/10.1101/2024.03.06.583673.
    10.1101/2024.03.06.583673
  2. Uri Abdu; Shatadru Ghosh Roy; Jindrich Brejcha; Petr Maršík; Anna Bakhrat; Moty Abdu; Roberto Arbore; et al. "Multiple mutations in polyketide synthase led to disruption of Psittacofulvin production across diverse parrot species". 2024. https://doi.org/10.21203/rs.3.rs-4575697/v1.
    10.21203/rs.3.rs-4575697/v1
  3. Shatadru Ghosh Roy; Anna Bakhrat; Moty Abdu; Sandra Afonso; Paulo Pereira; Miguel Carneiro; Uri Abdu. "Mutation in SLC45A2 leads to loss of melanin in parrot feathers". 2023. https://doi.org/10.1101/2023.08.29.555428.
    10.1101/2023.08.29.555428

Intellectual property

Patent
  1. Barbosa, Soraia; Carneiro, Miguel; Arbore, Roberto; Araújo Pedro Miguel. 2024. "In vitro or ex vivo method for determining the color phenotype of parrot species based on genetic markers". Portugal.
    Pending

Other

Other output
  1. A mitochondria-targeted antioxidant and a thyroid hormone affect carotenoid ketolase gene expression and bill redness in zebra finches. 2020. Alejandro Cantarero; Pedro Andrade; Miguel Carneiro; Adrián Moreno-Borrallo; Carlos Alonso-Alvarez. https://doi.org/10.1101/2020.01.14.905745.
    10.1101/2020.01.14.905745
  2. Retinoid-Related Orphan Nuclear Receptor RORB is Required for Saltatorial Locomotion in Rabbits. 2019. Carneiro, M.; Vieillard, J.; Andrade, P.; Boucher, S.; Afonso, S.; Blanco-Aguiar, J.A.; Santos, N.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85109343927&partnerID=MN8TOARS.
    10.2139/ssrn.3479444
  3. Genetic basis of de novo appearance of carotenoid ornamentation in bare-parts of canaries. 2019. Gazda, M.A.; Toomey, M.B.; Araújo, P.M.; Lopes, R.J.; Afonso, S.; Myers, C.A.; Serres, K.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095655893&partnerID=MN8TOARS.
    10.1101/762112
  4. Regulatory Changes in Pterin and Carotenoid Genes Underlie Balanced Color Polymorphisms in the Wall Lizard. 2018. Andrade, P.; Pinho, C.; de Lanuza, G.P.I.; Afonso, S.; Brejcha, J.; Rubin, C.-J.; Wallerman, O.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095619123&partnerID=MN8TOARS.
    10.1101/481895
  5. A computational method for detection of structural variants using Deviant Reads and read pair Orientation: DevRO. 2016. Shumaila Sayyab; Nima Rafati; Miguel Carneiro; Herve Garreau; Goran Andersson; Leif Andersson; Carl Johan Rubin. https://doi.org/10.1101%2F094474.
    10.1101/094474
Activities

Other jury / evaluation

Activity description Institution / Organization
2017 - Current I routinely act as a reviewer to a wide range of journals (incomplete list from the last three years), including Nature Reviews Genetics, PNAS, Nature Ecology and Evolution, Genome Research, PLoS Genetics, Trends in Ecology and Evolution, Nature Communications, Molecular Biology and Evolution, Molecular Ecology, and many others. Guest editor for PLoS Genetics.
2017 - Current Reviewer for research agencies; during the last two years I reviewed for the Swiss National Science Foundation, Dutch Research Council, National Science Center in Poland, and the Research Grants Council of Hong Kong
2017 - Current I routinely participate in PhD committees and thesis defences (MsC and PhD).