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

Tucci, Serena; Vohr, Samuel H.; McCoy, Rajiv C.; Vernot, Benjamin; Robinson, Matthew R.; Barbieri, Chiara; Nelson, Brad J.; Fu, Wenqing; Purnomo, Gludhug A.; Sudoyo, Herawati; Eichler, Evan E.; Barbujani, Guido; Visscher, Peter M.; Akey, Joshua M.; Green, Edward

doi:10.1126/science.aar8486

Cited by 61 publications

(41 citation statements)

References 126 publications

(38 reference statements)

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“…While no genetic signals consistent with H. floresiensis (or H. erectus) were detected in the genomes of the modern population around Liang Bua, the study detected an enigmatic 'unknown' genomic signature compatible with introgression from a hominid source as divergent from modern humans as Neandertals and Denisovans 18 . Importantly, this signal was only detected on Flores and not elsewhere in ISEA/Melanesia, demonstrating that it is not the widespread initial EH1 genomic signal (Fig 1), or the Denisovan genomic component observed in the Australo-Papuan and Philippines populations 18 . This appears to point to an introgression event with a further extinct hominid (EH2), which given the location on Flores, implies that it had probably crossed Wallace's Line.…”

contrasting

confidence: 56%

“…The idea that multiple hominid populations may have been present east of Wallace's Line is further supported by recent genetic analyses of the modern, very short-statured population living near Liang Bua cave on Flores, where fossils of the diminutive hominid H. floresiensis were discovered 18 . While no genetic signals consistent with H. floresiensis (or H. erectus) were detected in the genomes of the modern population around Liang Bua, the study detected an enigmatic 'unknown' genomic signature compatible with introgression from a hominid source as divergent from modern humans as Neandertals and Denisovans 18 . Importantly, this signal was only detected on Flores and not elsewhere in ISEA/Melanesia, demonstrating that it is not the widespread initial EH1 genomic signal (Fig 1), or the Denisovan genomic component observed in the Australo-Papuan and Philippines populations 18 .…”

mentioning

confidence: 93%

“…The ancestor of Australo-Papuans, Philippines and other ISEA groups is then inferred to have experienced admixture with Denisovans (red 2), with a second subsequent phase (red 3) also detected in Philippines hunter-gatherer populations. Lastly, the genomes of modern short-statured AMH populations on Flores record input from yet another extinct hominid (EH2), seemingly different from EH1 18 . The phylogenetic relationships amongst the extinct hominids remains unclear, but appear to be of roughly similar genetic divergence, occurring around 600 ka.…”

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confidence: 99%

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A ‘Denisovan’ genetic history of recent human evolution

Teixeira

Cooper

2019

Preprint

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As anatomically modern humans (AMH) migrated out of Africa and around the rest of the world, they met and interbred with multiple extinct hominid species. The traces of genetic input from these past interbreeding events, recorded in the genomes of modern populations, have created a powerful record of recent human migrations. The first of these events occurred between Neandertals, and a small group of AMH shortly after they left Africa, somewhere in western Eurasia around 55-50 ka, and left a genomic signal of about 2% Neandertal DNA that was subsequently spread across the rest of the world. In contrast to the Neandertals, the interbreeding events with other extinct hominid groups – such as the Denisovans, the east Eurasian sister group of Neandertals – remain poorly understood, but are potentially far more complex.

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confidence: 56%

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confidence: 93%

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confidence: 99%

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A ‘Denisovan’ genetic history of recent human evolution

Teixeira

Cooper

2019

Preprint

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“…This convergent adaptation on the level of the phenotype comes from a mixture of selection on old standing variation, both derived and ancestral variants, and recent mutations (Norton et al, 2007;Edwards et al, 2010;Crawford et al, 2017). In the case of repeated evolution likely involving highly polygenic traits (such as human height and the convergent evolution of small body size; Perry and Dominy, 2009;Tucci et al, 2018), populations may be convergently adapting via very similar shared sets of alleles. This may reduce the independent information we can hope to glean about the genetics of height, but establishing that the phenotypic change occurred convergently is still important.…”

Section: Discussionmentioning

confidence: 99%

Population genomics perspectives on convergent adaptation

Lee

Coop

2018

Preprint

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Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely-related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information due to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research.

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“…Tucci et al. () presented genetic evidence from contemporary pygmies living on Flores Islands to suggest that dwarfism evolved independently on the island at least twice. Genomes from the living population showed admixture with Denisovans and Neanderthals but no other archaic lineages—which could have suggested an ancestral relationship with H. floresiensis , their famously diminutive predecessors on the island.…”

Section: Fluidity In Hominin Evolutionmentioning

confidence: 99%

Biological Anthropology in 2018: Grounded in Theory, Questioning Contexts, Embracing Innovation

Martin

2019

American Anthropologist

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Biological anthropology in 2018 encapsulated what past scholars envisioned for its future: a multidisciplinary approach to understanding human and nonhuman primate evolution and diversity using the most innovative techniques and rigorous standards available. This year also built on a tradition of introspection about what biological anthropology encompasses and by whom and how it is conducted. This review highlights research and movements in the field that reflect both of these pursuits. Studies drew on evolutionary theory to generate novel insights into human and nonhuman primate biology, behavior, and organization. Studies on hominin evolution and human biology have upended previous understandings by revealing more dynamic and context-dependent processes in our ancestry and phenotypic expressions. Across subdisciplines, biological anthropologists have advanced the use of new technologies and analytical techniques and begun to promote open, transparent, and reproducible science among a more diverse community of researchers. [year in review, evolutionary anthropology, context and variation, emerging technologies, transparent methods, researcher diversity] RESUMEN La biología antropológica en 2018 encapsuló lo que investigadores anteriores imaginaron para su futuro:una aproximación multidisciplinaria para entender la evolución de primates humanos y no humanos y diversidad utilizando las técnicas más innovadoras y los estándares rigurosos disponibles. Este año también desarrolló sobre una tradición de introspección acerca de lo que la antropología biológica abarca y por quién y cómo es llevada a cabo. Esta revisión resalta la investigación y los movimientos en el campo que reflejan estas búsquedas. Los estudios se basaron en la teoría evolucionaria para generar nuevos conocimientos en la biología de primates humanos y no humanos, comportamiento y organización. Los estudios sobre la evolución de los homíninos y la biología humana han cambiado drásticamente entendimientos previos al revelar procesos más dinámicos y dependientes del contexto en nuestra ascendencia y expresiones fenotípicas. A través de las subdisciplinas, los antropólogos biológicos han avanzado el uso de nuevas tecnologías y técnicas analíticas y empezado a promover una ciencia abierta, transparente y reproducible entre una comunidad más diversa de investigadores. [año en revisión, antropología evolucionaria, contexto y variación, tecnologías emergentes, métodos transparentes, diversidad de investigadores] T he history of biological anthropology has been underscored by attempts to properly situate the field in relation to other natural sciences and the discipline of anthropology as a whole (e.g., Calcagno

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

Cited by 61 publications

References 126 publications

A ‘Denisovan’ genetic history of recent human evolution

A ‘Denisovan’ genetic history of recent human evolution

Population genomics perspectives on convergent adaptation

Biological Anthropology in 2018: Grounded in Theory, Questioning Contexts, Embracing Innovation

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