Marcos Araújo Castro e Silva, Ph.D.
Unravelling the genetic history of Indigenous American and descendant Populations
I am a postdoctoral researcher at the Institut de Biologia Evolutiva (IBE), CSIC–Universitat Pompeu Fabra, in Barcelona. My research lies at the intersection of population genetics, anthropological genetics, archaeogenetics, and bioinformatics, with a focus on reconstructing the evolutionary history and genetic diversity of past and present Indigenous and descendant populations across the Americas.
I investigate how migration, admixture, population growth or collapse, and adaptation have shaped human genetic diversity over time. My work aims to uncover the deep and recent population histories of the Americas while contributing to a more inclusive understanding of global human diversity through the study of historically underrepresented populations.
I am particularly interested in how ancient demographic and evolutionary processes have shaped the genetic diversity of Indigenous populations in the Americas. I have also been investigating the genetic history of non-indigenous Latin American populations, which are characterized by complex admixture. More rencently, I have been exploring how these processes have influenced the phenotypic diversity of modern-day populations, including patterns of natural selection and medically relevant variation.
To address these questions, I integrate large-scale genomic datasets from both living and ancient individuals with population genetic theory, statistical and demographic modeling, and computational approaches, to reconstruct human population history and explore the evolutionary forces shaping human diversity.
Publications
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2026The evolutionary history and unique genetic diversity of Indigenous AmericansNature · 653, 134–145
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2025Demographic insights into paternal genetic diversity and regional substructure in the Spanish RomaBMC Genomics · 26, 1012
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2025Carrying APOL1 G1 allele is associated with cardiovascular complications during COVID−19 in an admixed populationHum. Genomics · 19, 105
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2025Admixture’s impact on Brazilian population evolution and healthScience · 388, 6748
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2025The genetic footprint of the European Roma diaspora: evidence from the Balkans to the Iberian PeninsulaHum. Genet. · 144, 463–479
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2023Indigenous people from Amazon show genetic signatures of pathogen-driven selectionScience Advances · 9, 10
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2023A multidisciplinary overview on the Tupi‐speaking people expansionAJBA · 186(1), e24876
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2022A genomic perspective on South American human historyGMB · 45 (3 Suppl 1)
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2022Population Histories and Genomic Diversity of South American NativesMBE · 39(1), msab339
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2021Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestryPNAS · 118(14), e2025739118
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2020Genomic insight into the origins and dispersal of the Brazilian coastal nativesPNAS · 117(5), 2372-2377
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2018The Zinc-Finger Thylakoid-Membrane Protein FIP Is Involved With Abiotic Stress Response in Arabidopsis thalianaFront. Plant Sci., · 9:504
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2015NIK1-mediated translation suppression functions as a plant antiviral immunity mechanismNature · 520, 679–682
Book chapters
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2025How did Evolutionary Processes Influence the Genetic Structure of Humans in the Neotropics?Population Genetics in the Neotropics · Springer Nature · Chapter 18, 377–417
Thesis and dissertations
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2021Genomic perspective on the origin, history, and diversity of indigenous peoples from South America: from the initial settlement to the European colonizationPhD thesis · 247 pages
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2015Convergent evolution of Arabidopsis thaliana FtsH5 protease and its putative negative regulator FIP (FtsH5 interacting protein)MSc dissertation · 92 pages
CV
Postdoctoral Researcher
Institut de Biologia Evolutiva, CSIC-UPF · Barcelona, Spain
Innovation Research Fellow
Fundação Faculdade de Medicina · São Paulo, Brazil
Technical Training Fellow
Universidade de São Paulo · São Paulo, Brazil
PhD student/Researcher
Instituto de Biociências, Universidade de São Paulo · São Paulo, Brazil
MSc student/Researcher
Universidade de São Paulo · Piracicaba, São Paulo (State), Brazil
Scientific initiation fellow
Universidade Federal de Viçosa · Viçosa, Minas Gerais (State), Brazil
PhD in Biology (Genetics)
Universidade de São Paulo · São Paulo, Brazil
Supervisor: Prof. Tábita Hunemeier
MSc in Genetics and Plant Breeding
Universidade de São Paulo · Piracicaba, São Paulo (State), Brazil
Supervisor: Prof. Marcio de Castro Silva-Filho
BSc in Biological Sciences
Universidade Federal de Viçosa · Viçosa, Minas Gerais (State), Brazil
Supervisor: Prof. Elizabeth Pacheco Batista Fontes
EMBO virtual Practical Course Population genomics: background and tools (60 hours)
European Molecular Biology Organization, EMBO/EMBL
PhD summer course in analyses of genotyping and sequencing data in medical and population genetics (140 hours)
University of Copenhagen · Copenhagen, Denmark
Cover feature in Nature (May 7, 2026 issue)
For the paper “The evolutionary history and unique genetic diversity of Indigenous Americans”
Seal of Excellence - MSCA Postdoctoral Fellowships 2025”
For my project proposal “Deep Population History of Admixed Americans submitted under the Horizon Europe Marie Skłodowska-Curie Actions call HORIZON-MSCA-2025-PF-01-01”
Young Investigator Attendance Award for the SMBE conference 2025
By the Society for Molecular Biology & Evolution
Wiley Top Viewed Article
For the paper “A multidisciplinary overview on the Tupi-speaking people expansion”, by the American Journal of Biological Anthropology”
MBE Honorable Mentions - Best Graduate Student Paper
For the paper “Population Histories and Genomic Diversity of South American Natives”, by the Society for Molecular Biology & Evolution
Young Geneticist Award “Francisco Mauro Salzano”
By the Sociedade Brasileira de Genética - SBG
USP Highlight Thesis Award 11th Edition
By the University of São Paulo - USP
CAPES Thesis Award
By the Brazilian national funding agency (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES)
American Society of Human Genetics' Trainee Paper Spotlight
For the paper “Genomic insight into the origins and dispersal of the Brazilian coastal natives”, by the American Society of Human Genetics - ASHG
Votes of praise for academic performance
Coordinating Committee of the Biological Sciences Course at the Universidade Federal de Viçosa - UFV
Postdoctoral Fellowship - Juan de la Cierva-Formación (JCI-F)
Project: Indigenous American Genome Project
Funding: Agencia Estatal de Investigación - AEI (Spain) (JDC2022-049175-I)
Institution: Universitat Pompeu Fabra, Spain
Total funding amount: EUR 67,400
Postdoctoral Fellowship - EUTOPIA-SIF Marie Sklodowska-Curie COFUND
Project: The impact of demography, admixture, and evolution on the health of Brazilian populations
Funding: European Union Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 945380
Institution: Universitat Pompeu Fabra, Spain
Total funding amount: EUR 95,160
Innovation Research Fellowship - FFM
Project: Establishment of a Reference Genome of the Brazilian Population
Funding: Fundação Faculdade de Medicina - FFM (Convênio 888379/2019 - Projeto Genoma Biociências)
Institution: Universidade de São Paulo, Brazil
Total funding amount: BRL 12,300
Technical Training Fellowship (TT5) - FAPESP
Project: Detection of Natural Selection Patterns in Native American Population by Machine Learning
Funding: Fundação de Amparo à Pesquisa do Estado de São Paulo - FAPESP (FAPESP/2021/12238-8)
Institution: Universidade de São Paulo, Brazil
Total funding amount: BRL 31,060.8
PhD scholarship - FAPESP
Project: Diversity and Evolution of Brazilian Populations
Funding: Fundação de Amparo à Pesquisa do Estado de São Paulo - FAPESP (FAPESP/2018/01371-6)
Institution: Universidade de São Paulo, Brazil
Total funding amount: BRL 96,499.2
PhD scholarship - CNPq
Project: Genetic Structure and Ancestry of Brazilian Admixed Populations
Funding: Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (140155/2017-1)
Institution: Universidade de São Paulo, Brazil
Total funding amount: BRL 50,600
MSc scholarship - CNPq
Project: Convergent evolution of Arabidopsis thaliana FtsH5 protease and its putative negative regulator FIP (FtsH5 interacting protein)
Funding: Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (130634/2013-1)
Institution: Escola Superior de Agricultura “Luiz de Queiroz” - Universidade de São Paulo, Brazil
Total funding amount: BRL 36,000
Scientific Initiation Scholarship - CNPq
Project: Transcriptional expression analysis of Arabidopsis thaliana immune system genes related to response against geminivirus
Funding: Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (160335/2012-4)
Institution: Universidade Federal de Viçosa, Brazil
Total funding amount: BRL 4,800
Giacomo Francesco Ena
Degree: PhD (defended with cum laude honors)
Project: Fine-scale genetic structure of Roma in Iberia
Institution: Universitat Pompeu Fabra, Spain
Research projects & lines of investigation
My research spans interconnected themes in human population genomics, anthropological genetics, and archaeogenetics:
Deep Ancestries in Admixed Latin American Genomes
This project integrates large-scale genomic resources of living and ancient populations to investigate the impact of deep demographic and evolutionary history on modern Latin American populations.
Indigenous American Genomic Diversity Project
A collaborative international effort designed to map the origins and genetic diversity of Indigenous populations through whole-genome sequencing.
"DNA do Brasil" Project
A research initiative using whole-genome sequencing data to characterize genetic diversity in Brazilian populations and its health implications.
Genomic Origins of European Roma
In collaboration with David Comas, I co-supervised a PhD student investigating the origins, genetic structure, and demography of Iberian and European Romani populations.
Researcher associated with the research project
Project: Latin American Genomes (Sequencing 1,000 contemporary Latin American genomes using long-read technology)
Funding: Broad Institute
Institution: Multiple institutions
Coordinators: Tábita Hünemeier and Andrés Moreno-Estrada
Total funding amount: USD 2,000,000
Researcher associated with the research project
Project: Predição de Fenótipos de Comportamento Adaptativos em Primatas Usando Aprendizado de Máquina
Funding: Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq
Institution: Universidade Federal do Rio Grande do Sul, Brazil
Coordinators: Maria Cátira Bortolini
Total funding amount: BRL 250,000
Researcher associated with the research project
Project: Descifrando la Historia Poblacional de los Romani Americanos a Traves del Analisis de Diversidad Genomica
Funding: Ministerio de Ciencia, Innovación y Universidades (Madrid, Madrid, ES) - PID2022-138755NB-I00
Institution: Universitat Pompeu Fabra, Spain
Coordinator: David Comas
Total funding amount: EUR 256,250
Permanent research member of the research project
Project: Establishment of a Reference Genome of the Brazilian Population (DNA do Brasil)
Funding: Health Ministry GRB/4 (Convênio 888379/2019 - Projeto Genoma Biociências)
Institution: Universidade de São Paulo, Brazil
Coordinator: Coordinators: Tábita Hünemeier, Lygia da Veiga Pereira e Alexandre C. Pereira.
Total funding amount: BRL 7,977,453
Researcher associated with the research project
Project: Native American genomic diversity
Funding: Fundação de Amparo à Pesquisa do Estado de São Paulo - FAPESP (FAPESP/2015/26875-9)
Institution: Universidade de São Paulo, Brazil
Coordinator: Tábita Hünemeier
Total funding amount: EUR 220,000
Teaching
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2025Population genomics of modern humansClass to master students · Teacher (2 hours)Universitat Pompeu Fabra, Barcelona, Spain
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2025Bioinformatics (20428)Undergraduate course · Teaching assistant (20 hours)Universitat Pompeu Fabra, Barcelona, Spain
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2025“Brief introduction to population structure and history inference from genetic data”Workshop · Tutor (2 hours)Universitat Pompeu Fabra, Barcelona, Spain
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2025Population genomics of modern humansClass · Teacher (2 hours)Master in Prehistoric Archeology/UAB, Barcelona, Spain
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2025“Avances en Genómica y Metagenómica: De la Microbiota Oral a las Poblaciones Nativas Americanas”Workshop · Tutor (2 hours)Universitat Pompeu Fabra, Barcelona, Spain
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2019“First Native American Studies” WorkshopWorkshop · Tutor (2 hours)Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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2017Evolutionary Biology (BIO0103)Undergraduate course · Teaching Improvement Program (120 hours)Universidade de São Paulo, São Paulo, Brazil
Blog posts
Occasional notes on current research and thoughts.
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September 2020Lendo a história do Brasil nos genomas brasileiros
O contato com os europeus e a colonização do assim chamado Novo Mundo levou ao extermínio em massa dos nativos americanos e ao ocultamento da maior parte da sua história, principalmente do período pré-contato. Estudos tem conseguido recuperar antigas migrações nativas brasileiras, bem como aspectos da história pós-contato dessas populações usando dados genômicos.
Contact
Office
Institut de Biologia Evolutiva (IBE)
CSIC – Universitat Pompeu Fabra
PRBB Building, 7th floor · Dr. Aiguader, 88
08003 · Barcelona, Spain