Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia
Open accessAbstract
The genetics of human short stature: Flores Island in Indonesia has a long history of hominin occupation, including by the extinct Homo floresiensis and a more recent settlement by modern humans. Furthermore, Flores has an extant population of pygmy humans, and H. floresiensis exhibited a diminutive adult size relative to other hominins. Tucci et al. examined genetic variation among 32 individuals, including 10 sequenced genomes, from a population of pygmies living close to the cave where H. floresiensis remains were discovered. These individuals exhibit signatures of polygenic selection explaining the short stature and have genomic content from both Neanderthals and Denisovans, but no additional archaic lineages. Thus, restricted height is under selection at this location and has evolved independently at least twice in hominins. Science , this issue p. 511
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The patterning of Denisovan ancestry across Island Southeast Asia is consistent with separate Denisovan introgression events in the Philippines and, potentially, in Flores.
“Indeed, the patterning of Denisovan ancestry across ISEA is consistent with separate Denisovan introgression events in the Philippines 19 and, potentially, in Flores 23,43 , the island homes of H. luzonensis and H. floresiensis , respectively.”
From Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture (2021) · cites this paper as [43]
The passage on archaic ancestry (page unavailable) reports Denisovan ancestry in Flores and its distribution relative to other populations. It does not identify a separate introgression event in Flores; instead, it suggests that the ancestry originated east of Wallace’s Line and was subsequently diluted in Flores. This paper does not address a separate event in the Philippines. (LLM, conf=0.85)
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Homo floresiensis-like fossils from the early Middle Pleistocene of Flores
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Phasing of Many Thousands of Genotyped Samples
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Adaptive Evolution of the FADS Gene Cluster within Africa
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Self-citationHeight-reducing variants and selection for short stature in Sardinia
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Did the Denisovans Cross Wallace's Line?
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Dietary adaptation of FADS genes in Europe varied across time and geography
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Origins of modern human ancestry
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Multiple Deeply Divergent Denisovan Ancestries in Papuans
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Philippine Ayta possess the highest level of Denisovan ancestry in the world
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Self-citationMore than a decade of genetic research on the Denisovans
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“There is, however, no evidence of an excess of Denisovan or archaic ancestry among Indigenous populations from Flores 61,94 .”
Evolutionary perspectives on polygenic selection, missing heritability, and GWAS
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Population genomics perspectives on convergent adaptation
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Reconstruction of the Austronesian Diaspora in the Era of Genomics
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Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World
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Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island
Chen, H., Lin, R., Lü, Y., Zhang, R., Gao, Y., He, Y., & Xu, S. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac210 · Cited by 31 · see citing works
“In addition, a reported variant under selection in Indonesia Flores pygmy (Tucci et al. 2018), rs174547-C tagging ancestral haplotype, was also fixed in HNL with 0%”
BackgroundInfluentialOur Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture
Ahlquist, K. D., Bañuelos, M. M., Funk, A., Lai, J., Rong, S., Villanea, F. A., & Witt, K. E. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab115 · Cited by 33 · see citing works
Human adaptation over the past 40,000 years
Mathieson, I. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.06.003 · Cited by 31 · see citing works
“Some authors have argued that using GWAS effect sizes estimated in an outgroup population avoids bias associated with population stratification (54, 55).”
BackgroundIannucci, A., Benazzo, A., Natali, C., Arida, E. A., Zein, M. S. A., Jessop, T. S., Bertorelle, G., & Ciofi, C. (2021) · Molecular Ecology · doi:10.1111/mec.16121 · Cited by 30 · see citing works
“The colonization of Flores by anatomically modern humans around 50 ka and their subsequent population expansion (Aubert et al., 2014; Tucci et al., 2018) coincides with the beginning of a steep descent of Komodo dragon Ne curve.”
BackgroundGenome diversity and signatures of natural selection in mainland Southeast Asia
He, Y., Zhang, X., Peng, M., Li, Y.-C., Liu, K., Zhang, Y., Mao, L., Guo, Y., Ma, Y., Zhou, B., et al. (2025) · Nature · doi:10.1038/s41586-025-08998-w · Cited by 24 · see citing works
Zhang, T., Yeung, S. L. A., & Schooling, C. M. (2021) · Nutrients · doi:10.3390/nu13051489 · Cited by 19 · see citing works
“We specifically used genetic variants independent of the highly pleiotropic Flores and Inuit haplotype rs174547 [21] and excluded variants associated with known pleiotropic traits.”
MethodReconstruction of the Austronesian Diaspora in the Era of Genomics
Chambers, G. K., & Edinur, H. A. (2020) · Human Biology · doi:10.13110/humanbiology.92.4.04 · Cited by 19 · see citing works
Sun, Q., Wang, M., Lu, T., Duan, S., Liu, Y., Chen, J., Wang, Z., Sun, Y., Li, X., Wang, S., et al. (2024) · BMC Biology · doi:10.1186/s12915-024-01854-9 · Cited by 18 · see citing works
“High frequencies of the ancestral allele are present in other Southeast Asian groups as well, indicating strong selection in their common ancestor followed by drift and further selection occurring in island Southeast Asian populations [63].”
BackgroundZhang, X., Liu, Q., Zhang, H., Zhao, S., Huang, J., Sovannary, T., Bunnath, L., Aun, H. S., Samnom, H., Su, B., et al. (2021) · National Science Review · doi:10.1093/nsr/nwab072 · Cited by 18 · see citing works
“In addition, a study on the aboriginal population living on the Flores island of Indonesia found that multiple height-related loci are significantly enrichedbypopulationdifferentiation [6].”
BackgroundCarro, S. S., Gilbert, F., Bulbeck, D., O’Connor, S., Louys, J., Spooner, N. A., Questiaux, D. G., Arnold, L. J., Price, G. J., Wood, R. E., et al. (2019) · Journal of Human Evolution · doi:10.1016/j.jhevol.2019.07.002 · Cited by 17 · see citing works
Skeletal remains of a Pleistocene modern human (Homo sapiens) from Sulawesi
Brumm, A., Bulbeck, D., Hakim, B., Burhan, B., Oktaviana, A. A., Sumantri, I., Zhao, J., Aubert, M., Sardi, R., McGahan, D. P., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0257273 · Cited by 16 · see citing works
Sergeant, S., Keith, B., Seeds, M. C., Legins, J. A., Young, C. B., Vitolins, M. Z., & Chilton, F. H. (2023) · Frontiers in Nutrition · doi:10.3389/fnut.2023.1111624 · Cited by 14 · see citing works
“Indeed, the FADS locus appears to be an important site under selective and evolutionary pressures for adaptations to the presence of diet-derived nutrients that are critical for normal development and immune system integrity (11, 12, 17, 41, 42).”
BackgroundBiological Anthropology in 2018: Grounded in Theory, Questioning Contexts, Embracing Innovation
Martin, M. A. (2019) · American Anthropologist · doi:10.1111/aman.13233 · Cited by 11 · see citing works
“Tucci et al. (2018) presented genetic evidence from contemporary pygmies living on Flores Islands to suggest that dwarfism evolved independently on the island at least twice.”
BackgroundGenetic variants influencing obesity-related traits in Japanese population
Nakayama, K., & Inaba, Y. (2019) · Annals of Human Biology · doi:10.1080/03014460.2019.1644373 · Cited by 10 · see citing works
“For instance, sets of loci influencing height showed a signature of recent natural selections in European, Japanese, and Indonesian populations (Turchin et al. 2012; Robinson et al. 2015; Field et al. 2016; Okada et al. 2018; Tucci et al. 2018).”
BackgroundMethods for detecting introgressed archaic sequences
Sankararaman, S. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.026 · Cited by 10 · see citing works
Schooling, C. M., Kwok, M. K., & Zhao, J. V. (2023) · International Journal of Epidemiology · doi:10.1093/ije/dyad108 · Cited by 10 · see citing works
Beyond ‘heightism’ and ‘height premium’: An anthropology and sociology of human stature
Lasco, G. (2023) · Sociology Compass · doi:10.1111/soc4.13178 · Cited by 9 · see citing works
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Allele frequency differentiation at height-associated SNPs among continental human populations
Chen, M., & Chiang, C. W. K. (2021) · European Journal of Human Genetics · doi:10.1038/s41431-021-00938-2 · Cited by 5 · see citing works
“Although lower statistical power is not necessarily the only explanation for a negative result, our simulations do suggest that genetic redundancy could be a plausible explanation for our observations here for human height, as the trait architecture is likely largely shared among all humans [30–33] but recent adaptati…”
BackgroundResultLiu, H., Zhu, B., Wang, T., Dong, Y., Ju, Y., Li, Y., Su, W., Zhang, R., Dong, S., Wang, H., et al. (2025) · BMC Genomics · doi:10.1186/s12864-025-11541-w · Cited by 6 · see citing works
Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania
Reilly, P. F., Rong, S., Tejada-Martínez, D., Miller, S. L., Tjahjadi, A., Liu, C., Akers, J. F., Pomer, A., Prentice, M. E., Merriwether, D. A., et al. (2026) · Science · doi:10.1126/science.adr6749 · Cited by 3 · see citing works
Self-citationEvidence of polygenic adaptation at height-associated loci in mainland Europeans and SardiniansPreprint
Chen, M., Sidore, C., Akiyama, M., Ishigaki, K., Kamatani, Y., Schlessinger, D., Cucca, F., Okada, Y., & Chiang, C. W. K. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/776377 · Cited by 3 · see citing works
“Finally, pygmies from the Indonesian island Flores exhibited lower genetic height than expected, based on height loci ascertained in the distantly related UKB population (Tucci et al., 2018).”
BackgroundWhat Does DNA Tell Us about Past Connections and the Settlement of Sahul?
Matisoo-Smith, E. A., & Gosling, A. L. (2021) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780190095611.013.11 · Cited by 2 · see citing works
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Pulungan, A. B., Andarie, A. A., Soesanti, F., Yassien, M. R., de Bruin, C., Wijaya, A., Firmansyah, A., & Wit, J. M. (2021) · Journal of Pediatric Endocrinology and Metabolism · doi:10.1515/jpem-2020-0526 · Cited by 2 · see citing works
Population Genomics of High-Altitude Adaptation
Deng, L., & Xu, S. (2021) · Evolutionary studies · doi:10.1007/978-4-431-56904-6_3 · Cited by 1 · see citing works
Howard, G. C. (2021) · doi:10.1093/oso/9780190687724.001.0001 · Cited by 1 · see citing works
Kolesnikov, N. A., Харьков, В. Н., Вагайцева, К. В., Зарубин, А. А., & Степанов, В. А. (2023) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vjgb-23-08 · Cited by 1 · see citing works
“…that affect the level of LC-PUFAs, as well as the metabolic efficiency by which LC-PUFAs are formed in populations of the Pygmies on Flores Island (Tucci et al., 2018), Greenland Inuit (Fumagalli et al., 2015) and Native Americans (Amorim et al., 2017; Harris et al., 2019), is also thought to be…”
BackgroundAndrocentrism in Biological Typing
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Romero‐Hidalgo, S., Sagaceta‐Mejía, J., Villalobos‐Comparán, M., Tejero, M. E., Domínguez‐Pérez, M., Jacobo‐Albavera, L., Posadas‐Sánchez, R., Vargas‐Alarcón, G., Posadas‐Romero, C., Kauffer, L. R. M., et al. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e35477 · Cited by 1 · see citing works
Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.003.0004 · Cited by 1 · see citing works
Human, almost human: how many human species are there?
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A ‘Denisovan’ genetic history of recent human evolutionPreprint
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Threats to terrestrial biodiversity
Corlett, R. T. (2019) · Oxford University Press eBooks · doi:10.1093/oso/9780198817017.003.0007
Conservation in the Anthropocene
Corlett, R. T. (2019) · Oxford University Press eBooks · doi:10.1093/oso/9780198817017.003.0008
Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast AsiaPreprint
Teixeira, J. C., Jacobs, G. S., Stringer, C. B., Tuke, J., Hudjashov, G., Purnomo, G. A., Sudoyo, H., Cox, M. P., Tobler, R., TURNEY, C. S. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.24.219048
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The Archaeology and Philosophy of Health: Navigating the New Normal Problem
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Thoughts on the Future of Evolutionary Biology and Society
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Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.003.0001
Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.003.0007
Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.003.0016
Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.003.0014
Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.003.0005
Burns, K. C. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108379953.002
Burns, K. C. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108379953.008
Burns, K. C. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108379953.001
Burns, K. C. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108379953.005
Burns, K. C. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108379953.006
The ecology of plants: from seed to seed
Corlett, R. T. (2019) · Oxford University Press eBooks · doi:10.1093/oso/9780198817017.003.0004
Burns, K. C. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108379953.009
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Corlett, R. T. (2019) · Oxford University Press eBooks · doi:10.1093/oso/9780198817017.003.0006
Burns, K. C. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108379953.004
Verhoeven’s Living Negritos and the Story of Zakharias Ze
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Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.003.0002
Ashes to Ashes and Dust to Dust
Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.003.0006
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Death in Bacteria, Fungi, and Protista
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Programmed Cell Death in Humans
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Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.002.0003
Howard, G. C. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190687724.002.0007
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Paleogenomic insights into the evolution of human complex traits
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“…in modern human genomic data and GWAS-related causal or associated variants over the past two decades has facilitated the identification of genetic loci associated with forensic DNA phenotyping to predict traits such as skin pigmentation [72, 73], stature [74, 75], and facial morphology [74, 76].”
- Authors
- Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., Eichler, E. E., Barbujani, G., Visscher, P. M., Akey, J. M., & Green, R. E.
- Affiliations
- Princeton University (US)
- University of California, Santa Cruz (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- SIB Swiss Institute of Bioinformatics (CH)
- University of Zurich (CH)
- University of Washington (US)
- Eijkman Institute for Molecular Biology (ID)
- Howard Hughes Medical Institute (US)
- University of Ferrara (IT)
- The University of Queensland (AU)
- Corresponding author
- Akey, Joshua M.
- Green, Richard E.
- ORCID
- Venue
- Science
- Published
- 2018-08-03
- Volume
- 361
- Issue
- 6401
- Pages
- 511-516
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC6709593
- OpenAlex
- W2887541646
- Semantic Scholar
- 87d9bdeafa6ee7c7d5f2ec79dcc36620f2025c15
- Cited by
- 97
- References
- 127
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 5 · 2023: 5 · 2022: 6 · 2021: 39 · 2020: 5 · 2019: 31
- FWCI
- 79.48
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- UNICA IRIS Institutional Research Information System (University of Cagliari) (submittedVersion)
- IRIS (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion)
- Institutional Research Information System University of Ferrara (University of Ferrara) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- NIH (R01GM110068)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- short stature, Homo floresiensis, polygenic selection, human adaptation, Neanderthal admixture, Denisovan admixture, hominin evolution, human genetic variation
- MeSH terms
- Adaptation, Biological, Animals, Body Height, Dwarfism, Biological Evolution, Humans, Indonesia, Population, Selection, Genetic, Genome, Human, Gene Flow, Neanderthals, Islands
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