Carlos Alberto Rodrigues Fernandes (F413-49F5-CA96)

Curriculum Vitae

Carlos Alberto Rodrigues Fernandes

Following my PhD in phylogeography and molecular systematics in Professor Mike Bruford’s lab at Cardiff University, I started postdoctoral work funded by FCT in the research group of Professor Margarida Santos-Reis at the Centre for Environmental Biology (CBA) of the University of Lisbon (2005-2008). The aim of the postdoc was to develop species-specific mitochondrial markers for species identification of non-invasive and forensic biological samples from mammalian carnivores (Conserv Genet 2008 9:681) and microsatellites for population genetic studies (Conserv Genet 2009 10:1931; Mol Ecol Resour 2009 9:1205), and in the process effectively setting up a carnivore genetics lab in the Centre. In 2008, I earned an Assistant Researcher fellowship (2008-2013, ‘Ciência 2007’ Program of FCT) to initiate and conduct research in landscape genetics at CBA, and I successfully applied for a FCT research project grant in landscape genetics as principal investigator (2010-2013). Outputs of this work include the first assessment of genetic connectivity in small mammals between Natura 2000 sites using landscape genetics (Landscape Ecol 2015 30: 609), an experiment to disentangle the causes of the road barrier effect in small mammals (PLoS ONE 2016 11:e0151500), and the first study of fine-scale genetic structure in wild carnivores distributed throughout Portugal (PLoS ONE 2016 11:e0145165). During this second postdoc I also continued to oversee the development of microsatellite markers for carnivores (e.g., Conserv Genet Resour 2010 2:317; Eur J Wildl Res 2012 58:507) and started to work on evolutionary and conservation genetic studies of mammalian species in different parts of the world (e.g., Mol Ecol 2011 20:706; Mol Ecol 2013 22:5130). From 2013 to 2020 I was an invited assistant professor at the Department of Animal Biology (DBA) of FCUL, and I am currently a research group leader in wildlife genetics at CE3C (https://www.ce3c.pt/research/research-groups/evolutionary-perspectives-in-a-changing-world/wildlife-genetics/carlos-rodriguez-fernandes) and an invited assistant professor at FPUL. During this time I have taught a variety of courses at the undergraduate and master's level on Biology and Genetics, Animal Genetics, Conservation Genetics, Ex-situ Animal Conservation, Human and Forensic Genetics, and Evolutionary Biology. In terms of research, I have been expanding the range of issues and interests, taxonomic scope, and geographic coverage in my research activities on conservation genetics (Genes 2019 10:779; Mol Ecol 2022 31:4208; Conserv Genet 2023 24:125; Trends Ecol Evol 2022 37:197; Trends Genet 2023 39:545), phylogeography (Biol Invasions 2017 19:399; Mol Ecol 2017 26:4045; Gene 2020 739:144510; Mol Ecol 2022 31:993; Mamm Biol 2023 103:83), molecular systematics (Genetica 2016 144:191; Gene 2017 620:54), and evolution and phylogenetics (Mol Biol Evol 2018 35:287; Curr Biol 2018 28:3441; Mol Phylogenet Evol 2019 133:263). So far my research has yielded 55 peer-reviewed scientific publications (52 in international journals and three book chapters), of which I was first or last author on 24 (five of them with shared first authorship) and my H-index is 18 (in both Scopus and Web of Science); six other manuscripts are under review in international journals. I participated in nine research projects with competitive funding (one as coordinator, in the other eight as a team member), and I have supervised or co-supervised eight PhD theses (three of them ongoing), 14 MSc dissertations (three of them ongoing) and six research technicians. I participated in thesis defence committees of 10 PhD theses and 11 MSc theses.

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Identification

Personal identification

Full name: Carlos Alberto Rodrigues Fernandes

Citation names

Fernandes, Carlos
Rodríguez Fernandes, Carlos

Author identifiers

Ciência ID: F413-49F5-CA96
ORCID iD: 0000-0002-1386-8103
Google Scholar ID: UgM5v2kAAAAJ&hl=pt-PT
Researcher Id: J-3045-2013
Scopus Author Id: 8966321900

Email addresses

cafernandes@fc.ul.pt (Professional)
cafernandes@campus.ul.pt (Professional)
carlosfernandes@psicologia.ulisboa.pt (Professional)

Telephones

Telephone

217500000 Ext.: 22580 (Professional)

Addresses

CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Lisboa, Portugal (Professional)
Faculty of Psychology of the University of Lisbon (FPUL), Alameda da Universidade, 1649-013, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

Natural sciences - Biological Sciences - Genetics and Heredity
Natural sciences - Biological Sciences - Evolutionary Biology
Natural sciences - Biological Sciences - Biodiversity Conservation
Natural sciences - Biological Sciences - Zoology
Natural sciences - Biological Sciences - Ecology
Natural sciences - Biological Sciences - Behavioural Sciences Biology
Natural sciences - Biological Sciences - Molecular Biology
Natural sciences - Biological Sciences - Biology

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)
Spanish; Castilian	Intermediate (B1)	Advanced (C1)	Elementary (A2)	Upper intermediate (B2)	Upper intermediate (B2)
French	Elementary (A2)	Intermediate (B1)	Beginner (A1)	Elementary (A2)	Elementary (A2)

Education

	Degree	Classification
2005 Concluded	PhD (Doctor of Philosophy) Cardiff University, United Kingdom "Phylogeography and molecular systematics of species complexes in the Genus Genetta (Carnivora, Viverridae)" (THESIS/DISSERTATION)	Approved by Unanimity
1998 Concluded	Biologia (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal "-" (THESIS/DISSERTATION)	16 (out of 20)

Affiliation

Science

	Category Host institution	Employer
2020/10/01 - Current	Auxiliary Researcher (Research)	Centro de Ecologia Evolução e Alterações Ambientais, Portugal
	Centro de Ecologia Evolução e Alterações Ambientais, Portugal
2008/06/01 - 2013/05/31	Auxiliary Researcher (Research)	Universidade de Lisboa Faculdade de Ciências, Portugal
	Universidade de Lisboa Departamento de Biologia Animal, Portugal
2005/06/01 - 2008/05/31	Postdoc (Research)	Universidade de Lisboa Faculdade de Ciências, Portugal
	Universidade de Lisboa Departamento de Biologia Animal, Portugal

Teaching in Higher Education

	Category Host institution	Employer
2020/03/01 - Current	Invited Assistant Professor (University Teacher)	Universidade de Lisboa Faculdade de Psicologia, Portugal
	Universidade de Lisboa Faculdade de Psicologia, Portugal
2013/09/01 - 2020/02/29	Invited Assistant Professor (University Teacher)	Universidade de Lisboa Faculdade de Ciências, Portugal
	Universidade de Lisboa Departamento de Biologia Animal, Portugal

Projects

Contract

	Designation	Funders
2025/01/01 - 2026/06/30	The role of genetic variation and soil microbiome in the diversity of terpene specialized metabolism in Thymus caespititius 2023.15081.PEX Researcher Universidade de Lisboa Centro de Ecologia Evolução e Alterações Ambientais, Portugal	Fundação para a Ciência e a Tecnologia
2023/02/01 - 2026/01/31	OCELOT – One Health empirico-mechanistic modelling of antimicrobial resistance 2022.01539.PTDC Researcher Universidade de Lisboa Centro de Ecologia Evolução e Alterações Ambientais, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2023/01/01 - 2024/12/31	INVASIVES - Biological invasions across terrestrial and marine habitats: histories, common traits, and ecological impacts #11 Researcher Universidade de Lisboa Faculdade de Ciências, Portugal	Universidade de Lisboa Faculdade de Ciências Ongoing
2019/01/01 - 2019/12/31	Centro de Ecologia, Evolução e Alterações Ambientais UID/BIA/00329/2019 Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal Fundação Gaspar Frutuoso, Portugal FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal Universidade de Lisboa Centro de Ecologia Evolução e Alterações Ambientais, Portugal Universidade de Lisboa Faculdade de Ciências, Portugal Universidade de Lisboa, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2011/01/01 - 2013/12/31	Projecto Estratégico - UI 329 - 2011-2012 PEst-OE/BIA/UI0329/2011 Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal Universidade de Lisboa Faculdade de Ciências, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/01/01 - 2013/06/30	Effects of habitat fragmentation on the population structure and connectivity of forest-dwelling species: a comparative landscape genetics approach info:eu-repo/grantAgreement/FCT/3599-PPCDT/101511/PT Principal investigator Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/01/01 - 2013/06/30	DILEMA - Alien species and conservation dilemmas: the effects of native competitors and alien prey species on the spread of the American mink in Portugal info:eu-repo/grantAgreement/FCT/3599-PPCDT/102433/PT Researcher Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/01/01 - 2013/06/30	Guinea-Bissau Endangered Chimpanzee Conservation Genetics: Biological Anthropology contribution to biodiversity conservation info:eu-repo/grantAgreement/FCT/3599-PPCDT/99184/PT Researcher Universidade de Lisboa Instituto Superior de Ciências Sociais e Políticas, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2007/01/01 - 2010/12/31	Identifying highly diagnostic molecular markers from domestication genes to efficiently detect hybrids between wolf/dog and wild/domestic cat PTDC/CVT/71683/2006 Researcher Universidade de Lisboa Centro de Ecologia Evolução e Alterações Ambientais, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2005/01/01 - 2008/12/31	Comparative phylogeography and evolution of sympatric carnivores in the Mediterranean region POCTI/BIA-BDE/61491/2004 Post-doc Universidade de Lisboa Centro de Ecologia Evolução e Alterações Ambientais, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2003/01/01 - 2005/12/31	Non-invasive monitoring of Iberian carnivores: using molecular scatology towards conservation (NIMIC) POCTI/BSE/40788/2001 Integration into Research Grant Fellow Universidade de Lisboa Centro de Ecologia Evolução e Alterações Ambientais, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Outputs

Publications

Book chapter	Rosalino, L.M.; Bassetti, L.A.B; Silva-Brandão, K.L.; Fernandes, Carlos. "A ecologia molecular como ferramenta na gestão e conservação de espécies silvestres". In Abordagens Moleculares em Veterinária, edited by Cunha, M.V.; Inácio, J., 205-216. Lisboa, Portugal: LIDEL, 2014. Published Costa, Mafalda Bento; Fernandes, Carlos; Maria Margarida Mello Santos Reis. "Ecology and conservation of the polecat Mustela putorius in Portugal: a review". In Conservation and Management of Semi-Aquatic Mammals of Southwestern Europe, edited by Ruiz-González, A.; Luzuriaga, L.; Rubines, J., 77-85. San Sebastian, Spain: Aranzadi Society of Sciences, 2014. Published Fernandes, Carlos A.. "Bayesian coalescent inference from mitochondrial DNA variation of the colonization time of Arabia by the hamadryas baboon (Papio hamadryas hamadryas)". In The evolution of human populations in Arabia: Paleoenvironments, Prehistory and Genetics, edited by Petraglia, M.D.; Rose, J.I., 89-100. Dordrecht, Netherlands: Springer Netherlands, 2009. Published • 10.1007/978-90-481-2719-1_7 Sousa, C; Casanova, C.; Fernandes, Carlos. "Contributions of molecular data to the study of non-human primates". In Recent Advances in Molecular Biology and Evolution: Applications to Biological Anthropology, edited by Santos, C; Lima, M., 115-166. Kerala, India: Research Signpost, 2007. Published
Conference abstract	do Mar Oom, Maria; Silva, Raquel Matoso; Kjöllerström, Helena J.; Rampin, M.; Fernandes, Carlos; Pas, A.; Vercammen, Paul; et al. "Chromosome differentiation in the two non-African isolates of Genetta genetta". Paper presented in 19th International Colloquium on animal cytogenetics and gene mapping, Krakow, 2010. Published • 10.1007/s10577-010-9145-8 Sá, R.; Sousa, C; Casanova, C.; Fernandes, Carlos. "Genetic Characterization of a Chimpanzee (Pan troglodytes verus) Community in Cantanhez Region, Guinea-Bissau". Paper presented in Iberian Primatology: Present and Future Challenges, Peniche, 2008. Published • 10.1159/000134266
Journal article	Simona Secomandi; Guido Roberto Gallo; Riccardo Rossi; Carlos Rodríguez Fernandes; Erich D. Jarvis; Andrea Bonisoli-Alquati; Luca Gianfranceschi; Giulio Formenti. "Pangenome graphs and their applications in biodiversity genomics". Nature Genetics (2025): https://doi.org/10.1038/s41588-024-02029-6. 10.1038/s41588-024-02029-6 Ana Luísa Barros; Diogo Raposo; João David Almeida; Hugo Jesus; Maria Alexandra Oliveira; Carlos Rodríguez Fernandes; Darryl I. MacKenzie; Margarida Santos-Reis. "An integrated assessment of niche partitioning reveals mechanisms of coexistence between mesocarnivores". Global Ecology and Conservation (2024): http://dx.doi.org/10.1016/j.gecco.2024.e03116. 10.1016/j.gecco.2024.e03116 João P. Marques; Paulo C. Alves; Isabel R. Amorim; Ricardo J. Lopes; Monica Moura; Eugene Myers; Manuela Sim-sim; et al. "Building a Portuguese coalition for biodiversity genomics". npj Biodiversity (2024): http://dx.doi.org/10.1038/s44185-024-00061-7. 10.1038/s44185-024-00061-7 Ann M. Mc Cartney; Giulio Formenti; Alice Mouton; Diego De Panis; Luísa S. Marins; Henrique G. Leitão; Genevieve Diedericks; et al. "The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics". npj Biodiversity (2024): http://dx.doi.org/10.1038/s44185-024-00054-6. 10.1038/s44185-024-00054-6 Aoife Leonard; Javier Abalos; Titus Adhola; Windsor Aguirre; Ostaizka Aizpurua; Shahzad Ali; Franco Andreone; et al. "A global initiative for ecological and evolutionary hologenomics". Trends in Ecology & Evolution (2024): http://dx.doi.org/10.1016/j.tree.2024.03.005. 10.1016/j.tree.2024.03.005 Luís M. Rosalino; Gonçalo Matias; João Carvalho; Francisco Álvares; Alexandre Azevedo; Victor Bandeira; Carlos Fernandes; et al. "Three decades of research on Iberian wild Carnivora: trends, highlights, and future directions". Mammal Review (2023): https://doi.org/10.1111/mam.12322. 10.1111/mam.12322 Ali E Basuony; Mostafa Saleh; Moustafa Sarhan; Mahmoud Younes; Fouad Abdel-Hamid; Carlos Rodriguez Fernandes; Paul Vercammen; et al. "Paraphyly of the widespread generalist red fox (Vulpes vulpes): introgression rather than recent divergence of the arid-adapted Rüppell’s fox (Vulpes rueppellii)?". Biological Journal of the Linnean Society (2023): http://dx.doi.org/10.1093/biolinnean/blad001. 10.1093/biolinnean/blad001 Yasaman Hassan-Beigi; Mónica Rodrigues; Mohammad Ali Adibi; Seyed Massoud Madjdzadeh; Paul Vercammen; Mohammad S. Farhadinia; Carlos Rodríguez Fernandes. "Mitochondrial DNA variation of the caracal (Caracal caracal) in Iran and range-wide phylogeographic comparisons". Mammalian Biology (2023): https://doi.org/10.1007/s42991-022-00328-1. 10.1007/s42991-022-00328-1 Kathrin Theissinger; Carlos Fernandes; Giulio Formenti; Iliana Bista; Paul R. Berg; Christoph Bleidorn; Aureliano Bombarely; et al. "How genomics can help biodiversity conservation". Trends in Genetics (2023): http://dx.doi.org/10.1016/j.tig.2023.01.005. 10.1016/j.tig.2023.01.005 René Meißner; Sven Winter; Uta Westerhüs; Alexander Sliwa; Carola Greve; Lena Godsall Bottriell; Paul Bottriell; et al. "The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management". Conservation Genetics (2023): https://doi.org/10.1007/s10592-022-01483-1. 10.1007/s10592-022-01483-1 Tânia Minhós; Filipa Borges; Bárbara Parreira; Rúben Oliveira; Isa Aleixo-Pais; Fabien H. Leendertz; Roman Wittig; et al. "The importance of well protected forests for the conservation genetics of West African colobine monkeys". American Journal of Primatology (2023): https://doi.org/10.1002/ajp.23453. 10.1002/ajp.23453 "Genomic Analyses Show Extremely Perilous Conservation Status of African and Asiatic cheetahs (Acinonyx jubatus).". Molecular Ecology (2022): http://dx.doi.org/10.1111/mec.16577. 10.1111/mec.16577 Grilo, Clara; Afonso, Beatriz C.; Afonso, Filipe; Alexandre, Marta; Aliácar, Sara; Almeida, Ana; Alonso, Ivan Prego; et al. "MAMMALS IN PORTUGAL: A data set of terrestrial, volant, and marine mammal occurrences in Portugal". Ecology 103 6 (2022): http://dx.doi.org/10.1002/ecy.3654. 10.1002/ecy.3654 Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano; Bleidorn, Christoph; Ciofi, Claudio; et al. "The era of reference genomes in conservation genomics". Trends in Ecology & Evolution 37 3 (2022): 197-202. http://dx.doi.org/10.1016/j.tree.2021.11.008. Open access • 10.1016/j.tree.2021.11.008 McDevitt, Allan D.; Coscia, Ilaria; Browett, Samuel S.; Ruiz-González, Aritz; Statham, Mark J.; Ruczynska, Iwona; Roberts, Liam; et al. "Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe". Molecular Ecology 31 3 (2021): 993-1006. http://dx.doi.org/10.1111/mec.16276. 10.1111/mec.16276 Ashrafzadeh, Mohammad Reza; Khosravi, Rasoul; Fernandes, Carlos; Aguayo, Cecilia; Bagi, Zoltán; Lavadinovic, Vukan M.; Szendrei, László; et al. "Assessing the origin, genetic structure and demographic history of the common pheasant (Phasianus colchicus) in the introduced European range". Scientific Reports 11 1 (2021): http://dx.doi.org/10.1038/s41598-021-00567-1. Open access • 10.1038/s41598-021-00567-1 Margarida Alexandra Duarte; Carlos Rodríguez Fernandes; Gerald Heckel; Maria da Luz Mathias; Cristiane Bastos-Silveira. "Variation and Selection in the Putative Sperm-Binding Region of ZP3 in Muroid Rodents: A Comparison between Cricetids and Murines". Genes 12 9 (2021): 1450-1450. https://doi.org/10.3390/genes12091450. Open access • Published • 10.3390/genes12091450 Pablo Ruiz-Capillas; Cristina Mata; Beatriz Fernández; Carlos Fernandes; Juan E. Malo. "Do Roads Alter the Trophic Behavior of the Mesocarnivore Community Living Close to Them?". Diversity 13 4 (2021): 173-173. https://doi.org/10.3390/d13040173. Open access • Published • 10.3390/d13040173 Silva, André P.; Mukherjee, Shomita; Ramakrishnan, Uma; Fernandes, Carlos; Björklund, Mats. "Closely related species show species-specific environmental responses and different spatial conservation needs: Prionailurus cats in the Indian subcontinent". Scientific Reports 10 18705 (2020): http://dx.doi.org/10.1038/s41598-020-74684-8. Open access • Published • 10.1038/s41598-020-74684-8 Derouiche, Louiza; Irzagh, Ahmed; Rahmouni, Rafiq; Tahri, Redouane; Hadjeloum, Mohamed; Bouhadad, Rachid; Fernandes, Carlos. "Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini)". Gene 739 (2020): 144510. http://dx.doi.org/10.1016/j.gene.2020.144510. Published • 10.1016/j.gene.2020.144510 Santos, T.; Fernandes, C.; Henley, M.; Dawson, D.; Mumby, H.. "Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa". Genes 10 10 (2019): 779. http://dx.doi.org/10.3390/genes10100779. Open access • Published • 10.3390/genes10100779 Sousa-Santos, C.; Jesus, T.F.; Fernandes, C.; Robalo, J.I.; Coelho, M.M.. "Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data". Molecular Phylogenetics and Evolution 133 (2019): 263-285. http://dx.doi.org/10.1016/j.ympev.2018.12.020. Published • 10.1016/j.ympev.2018.12.020 Gopalakrishnan, Shyam; Sinding, Mikkel-Holger S.; Ramos-Madrigal, Jazmín; Niemann, Jonas; Samaniego Castruita, Jose A.; Vieira, Filipe G.; Carøe, Christian; et al. "Interspecific Gene Flow Shaped the Evolution of the Genus Canis". Current Biology 28 21 (2018): 3441-3449.e5. http://dx.doi.org/10.1016/j.cub.2018.08.041. Published • 10.1016/j.cub.2018.08.041 Detry, Cleia; Cardoso, João Luís; Heras Mora, Javier; Bustamante-Álvarez, Macarena; Silva, Ana Maria; Pimenta, João; Fernandes, Isabel; Fernandes, Carlos. "Did the Romans introduce the Egyptian mongoose (Herpestes ichneumon) into the Iberian Peninsula?". The Science of Nature 105 (2018): 63. http://dx.doi.org/10.1007/s00114-018-1586-5. Published • 10.1007/s00114-018-1586-5 Adega, Filomena; Matoso Silva, Raquel; Kjöllerström, Helena J.; Vercammen, Paul; Raudsepp, Terje; Collares-Pereira, Maria J.; Fernandes, Carlos; do Mar Oom, Maria; Chaves, Raquel. "Comparative Chromosome Painting in Genets (Carnivora, Viverridae, Genetta), the Only Known Feliforms with a Highly Rearranged Karyotype". Cytogenetic and Genome Research 156 (2018): 35-44. http://dx.doi.org/10.1159/000491868. Published • 10.1159/000491868 Liu, Yan-Hu; Wang, Lu; Xu, Tao; Guo, Xiaomin; Li, Yang; Yin, Ting-Ting; Yang, He-Chuan; et al. "Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites". Molecular Biology and Evolution 35 2 (2017): 287-298. http://dx.doi.org/10.1093/molbev/msx258. Published • 10.1093/molbev/msx258 Derouiche, Louiza; Vercammen, Paul; Bouhadad, Rachid; Fernandes, Carlos. "Genetic evidence supporting the taxonomic separation of the Arabian and Northwest African subspecies of the desert hedgehog (Paraechinus aethiopicus)". Gene 620 (2017): 54-65. http://dx.doi.org/10.1016/j.gene.2017.04.009. Published • 10.1016/j.gene.2017.04.009 Afonso Silva, Ana C.; Bragg, Jason G.; Potter, Sally; Fernandes, Carlos; Coelho, Maria Manuela; Moritz, Craig. "Tropical specialist vs. climate generalist: Diversification and demographic history of sister species of Carlia skinks from northwestern Australia". Molecular Ecology 26 15 (2017): 4045-4058. http://dx.doi.org/10.1111/mec.14185. Published • 10.1111/mec.14185 Rodrigues, Monica; Bos, Arthur R.; Schembri, Patrick J.; de Lima, Ricardo F.; Lymberakis, Petros; Parpal, Lluis; Cento, Michele; et al. "Origin and introduction history of the least weasel (Mustela nivalis) on Mediterranean and Atlantic islands inferred from genetic data (vol 19, pg 399, 2017)". Biological Invasions (2017): https://publons.com/wos-op/publon/1305303/. 10.1007/S10530-016-1347-3 Rodrigues, Mónica; Bos, Arthur R.; Schembri, Patrick J.; de Lima, Ricardo F.; Lymberakis, Petros; Parpal, Lluís; Cento, Michele; et al. "Origin and introduction history of the least weasel (Mustela nivalis) on Mediterranean and Atlantic islands inferred from genetic data". Biological Invasions 19 1 (2016): 399-421. http://dx.doi.org/10.1007/s10530-016-1287-y. Published • 10.1007/s10530-016-1287-y Ascensão, Fernando; Mata, Cristina; Malo, Juan E.; Ruiz-Capillas, Pablo; Silva, Catarina; Silva, André P.; Santos-Reis, Margarida; Fernandes, Carlos. "Disentangle the Causes of the Road Barrier Effect in Small Mammals through Genetic Patterns". PLOS ONE 11 3 (2016): e0151500. http://dx.doi.org/10.1371/journal.pone.0151500. Open access • Published • 10.1371/journal.pone.0151500 Rodrigues, Mónica; Bos, Arthur R.; Hoath, Richard; Schembri, Patrick J.; Lymberakis, Petros; Cento, Michele; Ghawar, Wissem; et al. "Taxonomic status and origin of the Egyptian weasel (Mustela subpalmata) inferred from mitochondrial DNA". Genetica 144 2 (2016): 191-202. http://dx.doi.org/10.1007/s10709-016-9889-y. Published • 10.1007/s10709-016-9889-y Derouiche, Louiza; Bouhadad, Rachid; Fernandes, Carlos. "Mitochondrial DNA and morphological analysis of hedgehogs (Eulipotyphla: Erinaceidae) in Algeria". Biochemical Systematics and Ecology 64 (2016): 57-64. http://dx.doi.org/10.1016/j.bse.2015.11.014. Published • 10.1016/j.bse.2015.11.014 Basto, Mafalda P.; Santos-Reis, Margarida; Simões, Luciana; Grilo, Clara; Cardoso, Luís; Cortes, Helder; Bruford, Michael W.; Fernandes, Carlos. "Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox". PLOS ONE 11 1 (2016): e0145165. http://dx.doi.org/10.1371/journal.pone.0145165. Open access • Published • 10.1371/journal.pone.0145165 Matoso Silva, Raquel; Adega, Filomena; Kjöllerström, Helena J.; Labuschagne, Kim; Kotze, Antoinette; Fernandes, Carlos; Chaves, Raquel; do Mar Oom, Maria. "Classical and Molecular Cytogenetics of the Panther Genet Genetta maculata (Mammalia, Carnivora, Viverridae)". Cytogenetic and Genome Research 149 4 (2016): 274-281. http://dx.doi.org/10.1159/000450627. Published • 10.1159/000450627 Vergara, María; Basto, Mafalda P.; Madeira, María José; Gómez-Moliner, Benjamín J.; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz. "Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study". PLOS ONE 10 7 (2015): e0134257. http://dx.doi.org/10.1371/journal.pone.0134257. Open access • Published • 10.1371/journal.pone.0134257 Mullins, Jacinta; Ascensão, Fernando; Simões, Luciana; Andrade, Leonardo; Santos-Reis, Margarida; Fernandes, Carlos. "Evaluating connectivity between Natura 2000 sites within the montado agroforestry system: a case study using landscape genetics of the wood mouse (Apodemus sylvaticus)". Landscape Ecology 30 4 (2014): 609-623. http://dx.doi.org/10.1007/s10980-014-0130-z. Published • 10.1007/s10980-014-0130-z Rodrigues, Diana C.; Simões, Luciana; Mullins, Jacinta; Lampa, Simone; Mendes, Raquel C.; Fernandes, Carlos; Rebelo, Rui; Santos-Reis, Margarida. "Tracking the expansion of the American mink (Neovison vison) range in NW Portugal". Biological Invasions 17 1 (2014): 13-22. http://dx.doi.org/10.1007/s10530-014-0706-1. Published • 10.1007/s10530-014-0706-1 Costa, M.; Fernandes, C.; Birks, J. D. S.; Kitchener, A. C.; Santos-Reis, M.; Bruford, M. W.. "The genetic legacy of the 19th-century decline of the British polecat: evidence for extensive introgression from feral ferrets". Molecular Ecology 22 20 (2013): 5130-5147. http://dx.doi.org/10.1111/mec.12456. Published • 10.1111/mec.12456 Costa, Mafalda; Fernandes, Carlos; Rodrigues, Mónica; Santos-Reis, Margarida; Bruford, Michael W.. "A panel of microsatellite markers for genetic studies of European polecats (Mustela putorius) and ferrets (Mustela furo)". European Journal of Wildlife Research 58 3 (2012): 629-633. http://dx.doi.org/10.1007/s10344-012-0627-1. Published • 10.1007/s10344-012-0627-1 Detry, Cleia; Bicho, Nuno; Fernandes, Hermenegildo; Fernandes, Carlos. "The Emirate of Córdoba (756–929 AD) and the introduction of the Egyptian mongoose (Herpestes ichneumon) in Iberia: the remains from Muge, Portugal". Journal of Archaeological Science 38 12 (2011): 3518-3523. http://dx.doi.org/10.1016/j.jas.2011.08.014. Published • 10.1016/j.jas.2011.08.014 Rodrigues, Mónica; Santos-Reis, Margarida; Elmeros, Morten; Fernandes, Carlos A.. "Microsatellite markers for genetic studies in the weasel (Mustela nivalis)". European Journal of Wildlife Research 58 2 (2011): 507-510. http://dx.doi.org/10.1007/s10344-011-0583-1. Published • 10.1007/s10344-011-0583-1 ROSALINO, L. M.; SANTOS, M. J.; FERNANDES, C.; SANTOS-REIS, M.. "Biogeographical region and host trophic level determine carnivore endoparasite richness in the Iberian Peninsula". Parasitology 138 6 (2011): 758-765. http://dx.doi.org/10.1017/s0031182011000345. 10.1017/s0031182011000345 CHARRUAU, P.; FERNANDES, C.; OROZCO-terWENGEL, P.; PETERS, J.; HUNTER, L.; ZIAIE, H.; JOURABCHIAN, A.; et al. "Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates". Molecular Ecology 20 4 (2011): 706-724. http://dx.doi.org/10.1111/j.1365-294x.2010.04986.x. Published • 10.1111/j.1365-294x.2010.04986.x Fernandes, Carlos A.. "Colonization time of Arabia by the White-tailed Mongoose Ichneumia albicauda as inferred from mitochondrial DNA sequences". Zoology in the Middle East 54 sup3 (2011): 111-124. http://dx.doi.org/10.1080/09397140.2011.10648903. Published • 10.1080/09397140.2011.10648903 Basto, Mafalda P.; Rodrigues, Mónica; Santos-Reis, Margarida; Bruford, Michael W.; Fernandes, Carlos A.. "Isolation and characterization of 13 tetranucleotide microsatellite loci in the Stone marten (Martes foina)". Conservation Genetics Resources 2 S1 (2010): 317-319. http://dx.doi.org/10.1007/s12686-010-9217-2. Published • 10.1007/s12686-010-9217-2 RODRIGUES, MÓNICA; FERNANDES, CARLOS A.; PALOMARES, FRANCISCO; AMORIM, ISABEL R.; BRUFORD, MICHAEL W.; SANTOS-REIS, MARGARIDA. "Isolation and characterization of 11 tetranucleotide microsatellite loci in the Egyptian mongoose (Herpestes ichneumon)". Molecular Ecology Resources 9 4 (2009): 1205-1208. http://dx.doi.org/10.1111/j.1755-0998.2009.02624.x. Published • 10.1111/j.1755-0998.2009.02624.x Fernandes, Carlos A.; Rodrigues, Mónica; Hajji, Ghaiet M.; Vercammen, Paul; Bruford, Michael W.; Santos-Reis, Margarida. "Isolation and characterisation of 11 tetranucleotide microsatellite loci in the common genet (Genetta genetta)". Conservation Genetics 10 6 (2009): 1931-1934. http://dx.doi.org/10.1007/s10592-009-9858-4. Published • 10.1007/s10592-009-9858-4 Fernandes, Carlos A.; Ginja, Catarina; Pereira, Iris; Tenreiro, Rogério; Bruford, Michael W.; Santos-Reis, Margarida. "Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula". Conservation Genetics 9 3 (2007): 681-690. http://dx.doi.org/10.1007/s10592-007-9364-5. Published • 10.1007/s10592-007-9364-5 Fernandes, Carlos A.; Rohling, Eelco J.; Siddall, Mark. "Absence of post-Miocene Red Sea land bridges: biogeographic implications". Journal of Biogeography 33 6 (2006): 961-966. http://dx.doi.org/10.1111/j.1365-2699.2006.01478.x. Published • 10.1111/j.1365-2699.2006.01478.x Martinoli, Adriano; Preatoni, Damiano; Galanti, Valeria; Codipietro, Paola; Kilewo, Morris; Fernandes, Carlos A. R.; Wauters, Luc A.; Tosi, Guido. "Species Richness and Habitat Use of Small Carnivores in the Arusha National Park (Tanzania)". Biodiversity and Conservation 15 5 (2006): 1729-1744. http://dx.doi.org/10.1007/s10531-004-5020-2. Published • 10.1007/s10531-004-5020-2 GAUBERT, PHILIPPE; TAYLOR, PETER J.; FERNANDES, CARLOS A.; BRUFORD, MICHAEL W.; VERON, GERALDINE. "Patterns of cryptic hybridization revealed using an integrative approach: a case study on genets (Carnivora, Viverridae, Genetta spp.) from the southern African subregion". Biological Journal of the Linnean Society 86 1 (2005): 11-33. http://dx.doi.org/10.1111/j.1095-8312.2005.00518.x. Published • 10.1111/j.1095-8312.2005.00518.x GAUBERT, PHILIPPE; FERNANDES, CARLOS A.; BRUFORD, MICHAEL W.; VERON, GERALDINE. "Genets (Carnivora, Viverridae) in Africa: an evolutionary synthesis based on cytochrome b sequences and morphological characters". Biological Journal of the Linnean Society 81 4 (2004): 589-610. http://dx.doi.org/10.1111/j.1095-8312.2004.00309.x. Published • 10.1111/j.1095-8312.2004.00309.x
Preprint	Jéssica Teodoro-Paulo; Carlos Fernandes; Lin Dong; Sara Magalhães; Alison B. Duncan; Juan M. Alba; Merijn R. Kant. "Tomato Defence Suppression is a Common Trait in Tetranychus urticae Collected from Field-Grown Tomatoes". 2023. https://doi.org/10.20944/preprints202302.0505.v1. 10.20944/preprints202302.0505.v1 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
Thesis / Dissertation	Fernandes, Carlos. "Phylogeography and Molecular Systematics of Species Complexes in the Genus Genetta (Carnivora, Viverridae)". PhD, Cardiff University Cardiff School of Biosciences, 2005. http://orca.cf.ac.uk/54538/1/U584656.pdf.

Other

Dataset

Rene Meissner; Sven Winter; Uta Westerhüs; Alexander Sliwa; Carola Greve; Lena Godsall Bottriell; Paul Bottriell; et al. The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management. 2022.
10.5061/dryad.b8gtht7h1

Activities

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2024 - Current	Genomic variation and adaptive phenotypic plasticity of terpene specialized metabolism in Thymus caespititius (Lamiaceae: Menthinae) Co-supervisor of Júlio Joel Laia	Biodiversidade, Genética e Evolução (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2025	"Impacts of anthropogenic pressure on genetic and phenotypic diversity of the anthropogenic pressure (Loxodonta africana) in southern Africa" Co-supervisor of Teresa Leonor Nunes Dos Santos Nobre Dos Santos	Biodiversidade, Genética e Evolução (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2024	Assessing mesocarnivores trophic niche using genetic identification of faecal samples Co-supervisor of Hugo Alexandre Pedro de Jesus	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2024	Non-invasive genetic monitoring and population size estimation of Iberian wolf Canis lupus signatus in northwest Portugal Co-supervisor of Margarida Quilhó de Almeida	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2024	Gene flow between Iberian wolves (Canis lupus signatus) from the Peneda/Gerês and the Alvão/Padrela nuclei Co-supervisor of Maria Natividade	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2024	Population Genomic Survey of Two Non-Human Primate Species in Sub-Saharan West Africa Co-supervisor of Francisco Silva	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2024	Reconstructing the evolutionary history of African golden wolves and Eurasian golden jackals using population genomics Co-supervisor of Nuno Filipe Gomes Martins	Københavns Universitet, Denmark
2018 - 2023	Genetic variation and trait plasticity in plant defence suppression Co-supervisor of Jéssica Teodoro-Paulo	Centro de Ecologia Evolução e Alterações Ambientais, Portugal
2020 - 2022	Non-invasive sampling and genetic variability, structure, and dynamics of the Barroso region wolf nucleus Co-supervisor of Maria Viegas Rodrigues	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2021	An integrative approach for evaluating and designing networks of protected areas under climate change: a test using small felids in India Co-supervisor	Uppsala Universitet Avdelningen för Zooekologi, Sweden
2019 - 2019	Spatial patterns of genetic diversity in Hyla molleri Co-supervisor	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2018	Identification of SNPs in genes potentially affected by domestication to efficiently detect hybridization between wild and domestic cats Supervisor	Biologia Evolutiva e do Desenvolvimento (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2018	Evolutionary history of sympatric rainbow skinks from the Australian monsoonal tropics Co-supervisor	Biologia (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017	Genetic structure and demographic history of two west african colobine monkeys: the effects of habitat fragmentation and hunting Co-supervisor	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017	Genetic characterisation of an African elephant (Loxodonta africana) population: the role of genetic relatedness in male social groups Supervisor	Biologia Evolutiva e do Desenvolvimento (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016	The relative importance of clade age, ecology and life-history traits in mammalian species richness Supervisor	Biologia Evolutiva e do Desenvolvimento (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015	Conservation biology of the caracal (Caracal caracal) in Iran: action plan and conservation genetics Supervisor	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2007 - 2014	Phylogeography and hybridisation in the European polecat (Mustela putorius) Co-supervisor	Biologia (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2013	Phylogenetic diversity of bird assemblages along different land-use gradients: regional and continental analysis Supervisor	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2010 - 2011	A landscape genetics approach to a contact zone of two Salamandra salamandra subspecies in southwest Portugal Co-supervisor	Biologia Evolutiva e do Desenvolvimento (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2010 - 2011	Avaliação da conectividade entre sítios Natura2000 para invertebrados terrestres usando modelos de distribuição de Carabídeos Supervisor	Biologia da Conservação (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2008	"Population and landscape genetics of the stone marten and red fox in Portugal: implications for conservation management of common carnivores" Co-supervisor	Biologia (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2024	Comparative demography of endangered species using genomic data (Thesis) Main arguer	Miguel Cisneiros e Faria Lourenço (Master)
2023	Genetic portrayal of two colobine monkeys inhabiting a continuous forest in Gola Rainforest National Park (Thesis) Main arguer	Darya Sevastópolska (Master)
2022	On the history of mixing: Knowledge trends on relevance, patterns and drivers of adaptive introgression Thesis Member	Pedro Horta (PhD)
2022	Lasts of their kind? Biogeography, ecology and action plan for the conservation of the critically endangered Asiatic cheetah Thesis Member	Leili Khalatbari (PhD)
2022	Population genomics of the endangered Bermuda petrel (Thesis) Main arguer	Rita Oliveira Afonso (Master)
2021	Life in deserts: a genomic history of adaptation and introgression in North African foxes Thesis Member	Joana Maria Laranjeira Rocha (PhD)
2021	Linking phylogeography and recent dispersal in high mountains: Insights from two Iberian amphibians Thesis Member	Federica Lucati (PhD)
2020	The sea turtles of São Tomé and Príncipe: ecology, genetics and current status of distinct species nesting on an oceanic archipelago Thesis Member	Joana Madeira Hancock (PhD)
2018	The population genomics of western Iberian Squalius freshwater fish species: a genotyping by sequencing approach (Thesis) Main arguer	Sofia Lopes Mendes (Master)
2018	Genomics of speciation in humpback dolphins (genus Sousa) (Thesis) Main arguer	Cátia Sofia Formas Chanfana (Master)
2017	High unexpected genetic diversity of a narrow endemic terrestrial mollusc (Thesis) Main arguer	Pedro Miguel Oliveira Madeira (Master)
2016	Population genomics and landscape genetics of the Iberian honey bee (Apis mellifera iberiensis) Thesis Member	Julio César Chávez Galarza (PhD)
2016	Evolutionary history and genetic diversity of native cyprinids from the Portuguese West region: implications for conservation management (Thesis) Main arguer	Ana Rita Pereira de Almeida (Master)
2014	Study on the diversification of flat periwinkles (Littorina fabalis and L. obtusata): insights from genetics and geometric morphometrics (Thesis) Main arguer	João Gonçalo Monteiro Carvalho (Master)
2013	Phylogeography, conservation genetics and parasitology of chimpanzees (Pan troglodytes verus) in Guinea-Bissau, West Africa Thesis Member	Rui Miguel Moutinho Sá (PhD)
2013	Ecologically scaled responses of forest-dwelling vertebrates to habitat fragmentation Thesis Member	Fernando Jorge Portela Martins Ascensão (PhD)
2012	Phylogeography and historical demography of Oceanodroma castro and Oceanodroma monteiroi: contrasting anonymous nuclear and mitochondrial loci (Thesis) Main arguer	Mauro Feliz da Silva (Master)
2011	Phylogeography and Population Genetics of the Bengal Tiger (Panthera tigris tigris) in the Indian Subcontinent Thesis Member	Samrat Mondol (PhD)
2011	Insights into the evolutionary relationships within the Delphininae, with focus on the genus Delphinus: a multi-locus, multi-disciplinary approach Thesis Member	Ana Rita Gabirro da Silva Teixeira do Amaral (PhD)
2011	Genetic diversity in a little known lemur species from the north of Madagascar (Microcebus tavaratra) (Thesis) Main arguer	Isa Gameiro Aleixo Pais (Master)
2008	Aplicação de técnicas de biologia molecular no estudo da diversidade genética (Thesis) Main arguer	Carla Cristina Santos Borges Fragoso (Master)

Association member

	Society Organization name	Role
2024 - Current	‘Earth Hologenome Initiative’ (https://www.earthhologenome.org/) (https://doi.org/10.1016/j.tree.2024.03.005)
2023 - Current	‘Biogenome Portugal’ network (https://www.nature.com/articles/s44185-024-00061-7)
2022 - Current	‘European Reference Genome Atlas’ (ERGA) network (https://www.erga-biodiversity.eu/) (https://www.nature.com/articles/s44185-024-00054-6)

Journal scientific committee

	Journal title (ISSN)	Publisher
2023 - Current	Frontiers in Mammal Science	Frontiers Media SA
2019 - Current	Genes	MDPI

Distinctions

Other distinction

1993	4th best first year student of the Faculty of Sciences of the University of Lisbon Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal