Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia

Serena Tucci^{1

2

3}, Samuel H Vohr⁴, Rajiv C McCoy^{1

2}, Benjamin Vernot⁵, Matthew R Robinson^{6

7}, Chiara Barbieri^{8

9}, Brad J Nelson¹⁰, Wenqing Fu¹⁰, Gludhug A Purnomo¹¹, Herawati Sudoyo^{11

12}, Evan E Eichler^{10

13}, Guido Barbujani³, Peter M Visscher^{14

15}, Joshua M Akey^{16

2}, Richard E Green¹⁷

Affiliations

¹ Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
² Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA.
³ Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy.
⁴ Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA.
⁵ Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
⁶ Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland.
⁷ Swiss Institute of Bioinformatics, Génopode, Quatier Sorge, Lausanne, Switzerland.
⁸ Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany.
⁹ Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland.
¹⁰ Department of Genome Sciences, University of Washington, Seattle, WA, USA.
¹¹ Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
¹² Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.
¹³ Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
¹⁴ Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
¹⁵ Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
¹⁶ Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA. ed@soe.ucsc.edu jakey@princeton.edu.
¹⁷ Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA. ed@soe.ucsc.edu jakey@princeton.edu.

PMID: 30072539
PMCID: PMC6709593
DOI: 10.1126/science.aar8486

Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia

Serena Tucci et al. Science. 2018.

. 2018 Aug 3;361(6401):511-516.

doi: 10.1126/science.aar8486.

Authors

Affiliations

¹ Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
² Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA.
³ Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy.
⁴ Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA.
⁵ Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
⁶ Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland.
⁷ Swiss Institute of Bioinformatics, Génopode, Quatier Sorge, Lausanne, Switzerland.
⁸ Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany.
⁹ Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland.
¹⁰ Department of Genome Sciences, University of Washington, Seattle, WA, USA.
¹¹ Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
¹² Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.
¹³ Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
¹⁴ Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
¹⁵ Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
¹⁶ Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA. ed@soe.ucsc.edu jakey@princeton.edu.
¹⁷ Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA. ed@soe.ucsc.edu jakey@princeton.edu.

PMID: 30072539
PMCID: PMC6709593
DOI: 10.1126/science.aar8486

Abstract

Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.

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