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I trained as a geneticist and biological anthropologist before getting a doctoral degree in ancient human population genomics. My main areas of research are the study of human populations from the past using ancient DNA, with a strong focus on social organisation, movement, admixture, evolution of societies, and development of bioinformatic tools for analytical automation. In parallel, I am also involved in the development of ancient DNA wet laboratory methodologies and protocols for bone sampling and DNA isolation that have become standard in the field. I also have substantial teaching experience in the R programming language and bioinformatics, and research experience on the use and development of bioinformatic tools and pipelines for the analysis of ancient population genomics, specifically targeting ancestry determination, phenotypic assessment, admixture simulations, and kinship.
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Identification

Personal identification

Full name
DANIEL FERNANDO MAGALHÃES FERNANDES

Citation names

  • Fernandes, Daniel M
  • Fernandes, Daniel
  • Daniel Magalhaes Fernandes

Author identifiers

Ciência ID
6115-488A-2A8B
ORCID iD
0000-0002-7434-6552

Knowledge fields

  • Natural sciences - Biological Sciences - Genetics and Heredity
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Social Sciences - Sociology - Anthropology

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) Advanced (C1) Elementary (A2)
German Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2013 - 2018
Concluded
 Paleogenomics (Doctor of Philosophy)
University College Dublin, Ireland
"Palaeogenetics of Neolithic Europe: Northern and Southern edges" (THESIS/DISSERTATION)
 PhD
2009 - 2011
Concluded
 Evolução e Biologia Humanas (Mestrado)
Universidade de Coimbra, Portugal
"Morphometric and microevolutive dental analysis using the occlusal cusp polygon method" (THESIS/DISSERTATION)
 MSc
2005 - 2009
Concluded
 Genética e Biotecnologia (Licenciatura)
Universidade de Trás-os-Montes e Alto Douro, Portugal
"Isolation of a new family of satellite DNA from the genome of Peromyscus eremicus (Cricetidae, Rodentia)" (THESIS/DISSERTATION)
 BSc
Affiliation

Science

Category
Host institution 		Employer
2024/09/01 - Current Researcher (Research) Universidade de Coimbra Centro de Investigação em Antropologia e Saúde, Portugal
2023/09/01 - 2024/05/01 Postdoc (Research) Max-Planck-Institut für evolutionäre Anthropologie, Germany
2015 - 2024 Visiting Researcher (Research) Universidade de Coimbra Centro de Investigação em Antropologia e Saúde, Portugal
2018/12 - 2023/04 Postdoc (Research) Universität Wien Department für Evolutionäre Anthropologie, Austria
2017 - 2018 Researcher (Research) Universität Wien Department für Evolutionäre Anthropologie, Austria
2013/02 - 2013/06 Visiting Researcher (Research) University of York, United Kingdom
Projects

Grant

Designation Funders
2024 - 2030 The tangled genomic history of Early Medieval Europe: The case of Thunau am Kamp, Austria
2023.08054.CEECIND
 Fundação para a Ciência e a Tecnologia
2013 - 2018 Population variation following the Neolithic revolution: assessing the palaeogenetics of southern Europeans throughout the Neolithic
GOIPG/2013/36
 Irish Research Council
2010/09 - 2011/01 Análise morfométrica e microevolutiva dentária através do método do polígono oclusal das cúspides
ERASMUS DRI/11/182
 European Commission

Contract

Designation Funders
2020 - 2024 CA19141 - Integrating Neandertal Legacy: From Past to Present
CA1914
Supervisor
European Cooperation in Science and Technology
Ongoing
Outputs

Publications

Book chapter
  1. Dias, Vanessa Sitima; Encarnação, Gisela; Quintino Arias, Yuliet; Fernandes, Daniel; Franco, Filipe; Pinhasi, Ron; Noé Conejo Delgado; Oliveira, César. ""Dar rosto à Villa" - Projecto de aproximação facial em torno de um esqueleto da Necrópole Romana do Moinho do Castelinho (Amadora, Portugal)". In Lisboa Romana - A morte no Ager olisiponensis. Lisboa, Portugal, 2022.
    Published
Journal article
  1. Iñigo Olalde; Pablo Carrión; Ilija Mikic; Nadin Rohland; Swapan Mallick; Iosif Lazaridis; Matthew Mah; et al. "A genetic history of the Balkans from Roman frontier to Slavic migrations". Cell (2023): http://dx.doi.org/10.1016/j.cell.2023.10.018.
    10.1016/j.cell.2023.10.018
  2. Moots, Hannah M.; Antonio, Margaret; Sawyer, Susanna; Spence, Jeffrey P.; Oberreiter, Victoria; Weiß, Clemens L.; Lucci, Michaela; et al. "A genetic history of continuity and mobility in the Iron Age central Mediterranean". Nature Ecology & Evolution 7 9 (2023): 1515-1524. http://dx.doi.org/10.1038/s41559-023-02143-4.
    10.1038/s41559-023-02143-4
  3. Daniel Magalhaes Fernandes; Kendra A Sirak; Olivia Cheronet; Mario Novak; Florian Brück; Evelyn Zelger; Alejandro Llanos-Lizcano; et al. "Density separation of petrous bone powders for optimized ancient DNA yields". Genome Research (2023): https://doi.org/10.1101/gr.277714.123.
    10.1101/gr.277714.123
  4. Gelabert, P.; Schmidt, R.W.; Fernandes, D.M.; Karsten, J.K.; Harper, T.K.; Madden, G.D.; Ledogar, S.H.; et al. "Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine". Scientific Reports 12 1 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85129348140&partnerID=MN8TOARS.
    10.21203/rs.3.rs-1044480
  5. Altinisik, N.E.; Kazanci, D.D.; Aydogan, A.; Gemici, H.C.; Erdal, Ö.D.; Sarialtun, S.; Vural, K.B.; et al. "A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition". Science Advances 8 44 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85141889925&partnerID=MN8TOARS.
    10.1126/sciadv.abo3609
  6. Lazaridis, I.; Alpaslan-Roodenberg, S.; Acar, A.; Açikkol, A.; Agelarakis, A.; Aghikyan, L.; Akyüz, U.; et al. "Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia". Science 377 6609 (2022): 982-987. http://www.scopus.com/inward/record.url?eid=2-s2.0-85138465915&partnerID=MN8TOARS.
    10.1126/science.abq0762
  7. Lazaridis, I.; Alpaslan-Roodenberg, S.; Acar, A.; Açikkol, A.; Agelarakis, A.; Aghikyan, L.; Akyüz, U.; et al. "The genetic history of the Southern Arc: A bridge between West Asia and Europe". Science 377 6609 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85138484640&partnerID=MN8TOARS.
    10.1126/science.abm4247
  8. Gelabert, P.; Blazyte, A.; Chang, Y.; Fernandes, D.M.; Jeon, S.; Hong, J.G.; Yoon, J.; et al. "Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea". Current Biology 32 15 (2022): 3232-3244.e6. http://www.scopus.com/inward/record.url?eid=2-s2.0-85135768117&partnerID=MN8TOARS.
    10.1016/j.cub.2022.06.004
  9. Bergström, A.; Stanton, D.W.G.; Taron, U.H.; Frantz, L.; Sinding, M.-H.S.; Ersmark, E.; Pfrengle, S.; et al. "Grey wolf genomic history reveals a dual ancestry of dogs". Nature 607 7918 (2022): 313-320. http://www.scopus.com/inward/record.url?eid=2-s2.0-85133199579&partnerID=MN8TOARS.
    10.1038/s41586-022-04824-9
  10. Reitsema, L.J.; Mittnik, A.; Kyle, B.; Catalano, G.; Fabbri, P.F.; Kazmi, AdamC.S.; Reinberger, K.L.; et al. "The diverse genetic origins of a Classical period Greek army". Proceedings of the National Academy of Sciences of the United States of America 119 41 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85139124112&partnerID=MN8TOARS.
    10.1073/pnas.2205272119
  11. Lazaridis, I.; Alpaslan-Roodenberg, S.; Acar, A.; Açikkol, A.; Agelarakis, A.; Aghikyan, L.; Akyüz, U.; et al. "A genetic probe into the ancient and medieval history of Southern Europe and West Asia". Science 377 6609 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85139162735&partnerID=MN8TOARS.
    10.1126/science.abq0755
  12. Patterson, Nick; Isakov, Michael; Booth, Thomas; Büster, Lindsey; Fischer, Claire-Elise; Olalde, Iñigo; Ringbauer, Harald; et al. "Large-scale migration into Britain during the Middle to Late Bronze Age". Nature 601 7894 (2021): 588-594. http://dx.doi.org/10.1038/s41586-021-04287-4.
    10.1038/s41586-021-04287-4
  13. Kendra A. Sirak; Daniel M. Fernandes; Mark Lipson; Swapan Mallick; Matthew Mah; Iñigo Olalde; Harald Ringbauer; et al. "Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia". Nature Communications (2021): https://doi.org/10.1038/s41467-021-27356-8.
    10.1038/s41467-021-27356-8
  14. Fernandes, Daniel M.; Cheronet, Olivia; Gelabert, Pere; Pinhasi, Ron. "TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data". Scientific Reports 11 1 (2021): http://dx.doi.org/10.1038/s41598-021-00581-3.
    10.1038/s41598-021-00581-3
  15. Daniel M. Fernandes; Kendra A. Sirak; Harald Ringbauer; Jakob Sedig; Nadin Rohland; Olivia Cheronet; Matthew Mah; et al. "A genetic history of the pre-contact Caribbean". Nature 590 7844 (2021): 103-110. https://doi.org/10.1038/s41586-020-03053-2.
    10.1038/s41586-020-03053-2
  16. Hernando, R.; Gamarra, B.; McCall, A.; Cheronet, O.; Fernandes, D.; Sirak, K.; Schmidt, R.; et al. "Integrating buccal and occlusal dental microwear with isotope analyses for a complete paleodietary reconstruction of Holocene populations from Hungary". Scientific Reports 11 1 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85103562884&partnerID=MN8TOARS.
    10.1038/s41598-021-86369-x
  17. Harney, E.; Cheronet, O.; Fernandes, D.M.; Sirak, K.; Mah, M.; Bernardos, R.; Adamski, N.; et al. "A minimally destructive protocol for DNA extraction from ancient teeth". Genome Research 31 3 (2021): 472-483. http://www.scopus.com/inward/record.url?eid=2-s2.0-85102537874&partnerID=MN8TOARS.
    10.1101/2020.08.19.256412
  18. Gelabert, P.; Sawyer, S.; Bergström, A.; Margaryan, A.; Collin, T.C.; Meshveliani, T.; Belfer-Cohen, A.; et al. "Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment". Current Biology 31 16 (2021): 3564-3574.e9. http://www.scopus.com/inward/record.url?eid=2-s2.0-85111696181&partnerID=MN8TOARS.
    10.1016/j.cub.2021.06.023
  19. Maria Teschler-Nicola; Daniel Fernandes; Marc Händel; Thomas Einwögerer; Ulrich Simon; Christine Neugebauer-Maresch; Stefan Tangl; et al. "Ancient DNA reveals monozygotic newborn twins from the Upper Palaeolithic". Communications Biology 3 1 (2020): https://doi.org/10.1038/s42003-020-01372-8.
    10.1038/s42003-020-01372-8
  20. Kendra Sirak; Daniel Fernandes; Olivia Cheronet; Eadaoin Harney; Matthew Mah; Swapan Mallick; Nadin Rohland; et al. "Human auditory ossicles as an alternative optimal source of ancient DNA". Genome Research 30 3 (2020): 427-436. https://doi.org/10.1101/gr.260141.119.
    10.1101/gr.260141.119
  21. Daniel M. Fernandes; Alissa Mittnik; Iñigo Olalde; Iosif Lazaridis; Olivia Cheronet; Nadin Rohland; Swapan Mallick; et al. "The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean". Nature Ecology & Evolution 4 3 (2020): 334-345. https://doi.org/10.1038/s41559-020-1102-0.
    10.1038/s41559-020-1102-0
  22. Daniel Fernandes; Peter F. Biehl; Kendra Sirak; Olivia Cheronet; Rachel Howcroft; Mislav Cavka; Dženi Los; et al. "Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia". PLOS ONE (2019): https://doi.org/10.1371/journal.pone.0216366.
    10.1371/journal.pone.0216366
  23. "Genome-Wide DNA from Degraded Petrous Bones and the Assessment of Sex and Probable Geographic Origins of Forensic Cases". Scientific Reports (2019): http://dx.doi.org/10.1038/s41598-019-44638-w.
    10.1038/s41598-019-44638-w
  24. "Isolating the human cochlea to generate bone powder for ancient DNA analysis". Nature Protocols (2019): http://dx.doi.org/10.1038/s41596-019-0137-7.
    10.1038/s41596-019-0137-7
  25. "The genomic history of the Iberian Peninsula over the past 8000 years". Science (2019): http://dx.doi.org/10.1126/science.aav4040.
    10.1126/science.aav4040
  26. "Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia". Scientific Reports (2019): http://dx.doi.org/10.1038/s41598-019-43147-0.
    10.1038/s41598-019-43147-0
  27. Antonio, M.L.; Gao, Z.; Moots, H.M.; Lucci, M.; Candilio, F.; Sawyer, S.; Oberreiter, V.; et al. "Ancient Rome: A genetic crossroads of Europe and the Mediterranean". Science 366 6466 (2019): 708-714. http://www.scopus.com/inward/record.url?eid=2-s2.0-85074693374&partnerID=MN8TOARS.
    10.1126/science.aay6826
  28. Narasimhan, V.M.; Patterson, N.; Moorjani, P.; Rohland, N.; Bernardos, R.; Mallick, S.; Lazaridis, I.; et al. "The formation of human populations in South and Central Asia". Science 365 6457 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85071752467&partnerID=MN8TOARS.
    10.1126/science.aat7487
  29. "A genomic Neolithic time transect of hunter-farmer admixture in central Poland". Scientific Reports (2018): http://dx.doi.org/10.1038/s41598-018-33067-w.
    10.1038/s41598-018-33067-w
  30. "Ancient genomes document multiple waves of migration in Southeast Asian prehistory". Science (2018): http://dx.doi.org/10.1126/science.aat3188.
    10.1126/science.aat3188
  31. "The genomic history of southeastern Europe". Nature (2018): http://dx.doi.org/10.1038/nature25778.
    10.1038/nature25778
  32. "The Beaker phenomenon and the genomic transformation of northwest Europe". Nature (2018): http://dx.doi.org/10.1038/nature25738.
    10.1038/nature25738
  33. "Sex estimation of sub-adult human remains and determination of geographic origin: New perspectives and methodologies". La Revue de Médecine Légale (2017): http://dx.doi.org/10.1016/j.medleg.2017.10.028.
    10.1016/j.medleg.2017.10.028
  34. "Genetic origins of the Minoans and Mycenaeans". Nature (2017): http://dx.doi.org/10.1038/nature23310.
    10.1038/nature23310
  35. "A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis". BioTechniques (2017): http://dx.doi.org/10.2144/000114558.
    10.2144/000114558
  36. "The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes". Scientific Reports (2017): http://dx.doi.org/10.1038/srep41529.
    10.1038/srep41529
  37. "Paleogenetic study of ancient DNA suggestive of X-linked acrogigantism". Endocrine-Related Cancer (2017): http://dx.doi.org/10.1530/erc-16-0558.
    10.1530/erc-16-0558
  38. "Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears". Molecular Ecology (2016): http://dx.doi.org/10.1111/mec.13800.
    10.1111/mec.13800
  39. "Genomic insights into the peopling of the Southwest Pacific". Nature (2016): http://dx.doi.org/10.1038/nature19844.
    10.1038/nature19844
  40. "Genomic insights into the origin of farming in the ancient Near East". Nature (2016): http://dx.doi.org/10.1038/nature19310.
    10.1038/nature19310
  41. "New approach to analysis of ancient DNA samples using next generation sequencing based on neolithic individuals". New Biotechnology (2016): http://dx.doi.org/10.1016/j.nbt.2016.06.1316.
    10.1016/j.nbt.2016.06.1316
  42. "The genetic history of Ice Age Europe". Nature (2016): http://dx.doi.org/10.1038/nature17993.
    10.1038/nature17993
  43. "Genome-wide patterns of selection in 230 ancient Eurasians". Nature (2015): http://dx.doi.org/10.1038/nature16152.
    10.1038/nature16152
  44. Pinhasi R; Fernandes D; Sirak K; Novak M; Connell S; Alpaslan-Roodenberg S; Gerritsen F; et al. "Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.". (2015): http://europepmc.org/abstract/med/26086078.
    10.1371/journal.pone.0129102
  45. "Dental microevolution in Portuguese Neolithic and modern samples using an alternative morphometric analysis". Anthropological Science (2013):
    10.1537/ase.120906
  46. "In vitro multiplication of Calendula arvensis for secondary metabolites extraction". Acta Horticulturae (2009): http://dx.doi.org/10.17660/actahortic.2009.812.33.
    10.17660/actahortic.2009.812.33

Other

Other output
  1. Reconstituição Dama Romana. Identificado nas campanhas arqueológicas do Moinho do Castelinho, o crânio de um indivíduo do sexo feminino foi minuciosamente estudado, medido e sequenciado.. 2021. Carvalho, Liliana Matias de; Encarnação, Gisela; Dias, Vanessa; Pinhasi, Ron; Fernandes, Daniel; Quintino Arias, Yuliet; Franco, Filipe. https://www.youtube.com/watch?v=T0f6AVFNXRk.
  2. The genomic formation of first american ancestors in east and northeast Asia. 2020. Ning, C.; Fernandes, D.; Changmai, P.; Flegontova, O.; Yüncü, E.; Maier, R.; Altinisik, N.E.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85098909529&partnerID=MN8TOARS.
    10.1101/2020.10.12.336628
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/03/10 Paleogenomica em Antropologia Aula Aberta no âmbito da disciplina de Antropologia Funerária do MEBH
Universidade de Coimbra (Coimbra, Portugal)
2021/09/22 The Western Mediterranean islands: Crossroads of different ancestries since the Chalcolithic TETRA - Territories in Transition
(Besancon, France)
2021/02/25 A genetic history of the pre-contact Caribbean A genetic history of the pre-contact Caribbean - A conversation with some of the authors
CIRCE Laboratory (Italy)
2019/12/04 O aparecimento das ancestralidades da estepe e do leste Mediterrânico no pos-Neolítico das Ilhas Baleares, Sardenha, e Sicília CIAS 25 years - General Session
Universidade de Coimbra (Coimbra, Portugal)
2019/11/01 The Western Mediterranean islands: Crossroads of different ancestries since the Chalcolithic MHAAM - From Homer to History with the Max Planck-Harvard Research Center: Recent Results from Bronze Age Investigations
Harvard University (Boston, United States)

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2022/07 - 2022/07 Organizador principal de curso intitulado "Introduction to Neanderthal palaeogenomic analyses for nongeneticists". (2022/07 - 2022/07)
Workshop (Co-organisor)
 Universität Wien, Austria

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2019/08/26 Bridging the Americas and Eurasia: Population History of American Arctic Peoples
(Thesis) Main arguer
 Ezgi Altinisik (PhD)

Committee member

Activity description
Role 		Institution / Organization
2021 - Current Membro do grupo de discussão "Current Issues in Ancient DNA Research Discussion Series", onde investigadores debatem o estado, problemas, e os desafios do campo de investigação do ADN antigo.
Member

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2021 - 2022 Human Evolution, human osteology and paleogenomics (Master) Universität Wien, Austria
2019 - 2022 Introduction to R for Anthropologists (Bachelor) Universität Wien, Austria
Distinctions

Award

2020 Faculty of Life Sciences Young Investigator Award 2020
Universität Wien Fakultät fur Lebenswissenschaften, Austria