About

Maanasa Raghavan is an Assistant Professor in the Department of Human Genetics at the University of Chicago. Her doctoral research, earned from the University of Copenhagen in 2011, and her postdoctoral work at the Centre for GeoGenetics in Denmark and the University of Cambridge, focused on the early peopling of the Americas using ancient genomics. Her current research leverages modern and ancient DNA to investigate how and when patterns of worldwide genetic diversity were formed and explores the implications for present-day human health and disease.

Research topics

• Sociology
• Biology
• Ethnology
• Demography
• Evolutionary biology
• Ecology
• History
• Genealogy
• Archaeology
• Geography
• Political Science
• Computer Science
• Business
• Medicine
• Genetics
• Computational biology
• Environmental health

Selected publications

• Kinship Trouble: What, When, Where, Why, and How—and So What?

  Cambridge Archaeological Journal · 2026-04-14

  articleOpen access

  Abstract What is kinship trouble? When and where did it emerge? Why does it matter and how can we overcome it? These questions guide our discussion of kinship trouble, a term meant to capture the difficulties in reconstructing ancient kin relations, but also an attempt to resolve them through interdisciplinary collaboration and ethically adequate approaches. Motivated by the importance of crossing disciplinary boundaries and the urgency of working together to understand human diversity in the past and present, we reconsider kinship not only as a biological or genetic but also as a social phenomenon for the study of societies through archaeogenetic, archaeological, and socio-cultural anthropological approaches. As to the question of how kinship trouble could be overcome, we propose making more ‘oddkin’ ( sensu Haraway) to bring disciplines into the conversation and foster unexpected collaborations around three themes: ethical collaboration, the integration of biological and social approaches, and kinship studies as acts of care and (non)mutuality of being.

  PublisherOA PDFDOI

• Ancient human genomes from Ladakh reveal Tibetan, South Asian, and Central Asian admixture over the last three millennia

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-28

  articleOpen accessSenior authorCorresponding

  The trans-Himalayan region of Ladakh occupies a strategic position at the crossroads of South Asia, the Tibetan Plateau, and Central Asia, with archaeological evidence pointing to long-term cultural exchanges across these regions. However, the human genetic history of Ladakh remains largely unexplored. We generated paleogenomic data from seven individuals recovered from two sites in Western Ladakh - the Old Lady Spider Cave and Hanu - of which six are dated to 531-585 CE and one to the 19th century CE. The older individuals share substantial genetic ancestry with Tibetan groups but also harbor major contributions from two additional sources: one corresponding to the currently-oldest observation of the Ancestral North Indian genetic component that characterizes several present-day populations in North India and Pakistan, and another related to ancient Central Asian groups, with admixture events occurring between ~2,100-2,500 years ago. In contrast, the later individual falls within a previously described ancient northern Himalayan genetic cline based on ~1,100-1,300-year-old individuals from Himachal Pradesh, with ancestries related to ancient Tibetan and Steppe-related sources. Stable isotope analysis suggests that these individuals were local to Ladakh in late life and practiced an agro-pastoralist subsistence. Our study establishes that Ladakh's central role in Eurasian economic and socio-cultural networks was shaped by dynamic and sustained gene flow linking high-altitude Himalayan groups with both lowland South Asia and Inner Asia.

  PublisherDOI

• Distinct trajectories of urbanization shape the human gut microbiome across South Asia

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-23

  articleOpen accessSenior authorCorresponding

  Human gut microbiomes respond to lifestyle transitions, yet the extent to which these responses are conserved across spatio-cultural contexts remains undercharacterized. We present the South Asian MicroBiome ARray (SAMBAR), a population-scale 16S gut microbiome study of 575 adults from ten geographically and socio-culturally diverse South Asian communities. Each community was sampled in ancestral villages and urban centers, enabling controlled comparisons of geography and lifestyle. Relative to global cohorts, SAMBAR microbiomes occupy a distinct compositional space with stronger correlation to geography and community membership than lifestyle. Although urbanization is consistently associated with increased abundance of disease-linked taxa, microbiome responses to lifestyle transitions are largely community-driven, including the acquisition of wheat- and dairying-associated microbial modules in some communities that may facilitate non-genetic adaptation to lactase non-persistence. Microbiome responses to urbanization are heterogeneous even at regional scales, reflecting local culture and geography and underscoring the need for community-specific investigations of health impacts.

  PublisherDOI

• Dynamic human admixture histories over the past ~1300 years at the northern Himalayan frontier

  Science Advances · 2025-10-29 · 2 citations

  articleOpen accessCorresponding

  Archaeological and paleogenomic evidence from the Tibetan Plateau and high-altitude Central Himalayas suggest biocultural connections with each other and with lowland East, Central, and South Asia. However, genetic histories at the northern frontier of the Indian Himalayas, which is geographically more proximal to Central and lowland South Asia, remain underexplored. We analyzed genome-wide data from 7 ancient (~2300 to 100 years old) and 10 present-day individuals from the northern Indian Himalayas and one ~3370-year-old individual from the Central Himalayas in Nepal. Ancient and present-day individuals from the northern Himalayas predominantly have Tibetan-related genetic ancestry, likely the source of high-altitude adaptive variants in these individuals, with substantial Steppe-related genetic ancestry that is observed in all individuals dating between ~1300 years and present day. In addition, some present-day individuals have lowland South Asian admixture. Our analyses reveal a dynamic interplay between genetic admixture and continuity in the northern Himalayas.

  PublisherDOI

• Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes

  Current Biology · 2025-06-01 · 3 citations

  articleOpen accessSenior author

  Sri Lanka has played a key role in the peopling of South Asia, with archaeological evidence for human presence on the island dating back to ⁓40,000 years ago. Present-day Indigenous peoples of the island, the Adivasi, are proposed to have descended from early inhabitants of the region, while urban populations like the Sinhalese, the major ethnic group on the island, migrated from India in historical times. Using whole genomes from 19 Adivasi individuals belonging to two clans and from 35 Sinhalese, we find that the Adivasi and Sinhalese share high genetic similarities with each other and with other Sri Lankan and Indian populations, especially those with greater genetic affinity to Ancestral South Indians (ASI). Admixture modeling of the Sri Lankan groups reveals that despite shared ancestral components, the Adivasi retain higher genetic contributions from ancient hunter-gatherers compared with the Sinhalese. Additionally, in contrast to the Sinhalese, the Adivasi have maintained low effective population size and undergone strong founder events, which is consistent with their hunter-gatherer lifestyle, historic relocations, and habitat fragmentation. While the two Adivasi clans are genetically more similar to each other than to any other populations, we observe differing demographic histories, with the Interior Adivasi experiencing a stronger bottleneck than the Coastal Adivasi since their split. This whole-genome-based study addresses gaps in our understanding of the demographic and migratory history of two key Sri Lankan groups and, consequently, of broader South Asia by illuminating complex population structure that has been shaped by both demographic and socio-cultural factors.

  PublisherOA PDFDOI

• The genesis of paleogenetics

  Nature Reviews Genetics · 2025-03-27

  review1st authorCorresponding
  PublisherDOI

• Capturing Perspectives on Responsible Research Practice: A Delphi Study

  Peer Community In Registered Reports · 2024-06-02

  articleOpen accessSenior author

  A recommendation of: Sarahanne M. Field, Jackie Thompson, Tom van Drimmelen, Jennifer Ferrar, Bart Penders, Sarah de Rijcke, and Marcus R. Munafò Mapping Cross-Disciplinary Perspectives on Responsible Conduct of Research: A Delphi Study https://osf.io/6hqys

  PublisherOA PDFDOI

• Distinct positions of genetic and oral histories: Perspectives from India

  Human Genetics and Genomics Advances · 2024-05-07 · 3 citations

  articleOpen accessSenior author

  Over the past decade, genomic data have contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 156 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great's army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Ancient Ancestral South Indians. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.

  PublisherDOI

• The Genomic and Cultural Diversity of the Inka Qhapaq Hucha Ceremony in Chile and Argentina

  Genome Biology and Evolution · 2024-09-01 · 5 citations

  articleOpen access

  The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.

  PublisherDOI

• The genomic and cultural diversity of the Inka Qhapaq hucha ceremony in Chile and Argentina

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-02-21

  preprintOpen access

  Abstract The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly-generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies the Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.

  PublisherOA PDFDOI

Frequent coauthors

• Eske Willerslev

  University of Cambridge

  62 shared

• Ludovic Orlando

  Université Toulouse III - Paul Sabatier

  39 shared

• Paula F. Campos

  University of Copenhagen

  32 shared

• M. Thomas P. Gilbert

  Vitensenteret i Trondheim

  31 shared

• Morten Rasmussen

  27 shared

• Thorfinn Sand Korneliussen

  University of Copenhagen

  23 shared

• Andaine Seguin‐Orlando

  Université Toulouse III - Paul Sabatier

  22 shared

• Helena Malmström

  Uppsala University

  21 shared

Education

• PhD, Natural History Museum of Denmark

  Københavns Universitet

  2011

• MSc., Research Laboratory for Archaeology

  University of Oxford

  2007

• BSc. (Honours), Life Sciences (Molecular Genetics)

  University of Toronto

  2006