1
|
Reyna-Blanco CS, Caduff M, Galimberti M, Leuenberger C, Wegmann D. Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies. Mol Biol Evol 2024; 41:msae137. [PMID: 38958167 PMCID: PMC11255385 DOI: 10.1093/molbev/msae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.
Collapse
Affiliation(s)
- Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Marco Galimberti
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| |
Collapse
|
2
|
King B, Greenhill SJ, Reid LA, Ross M, Walworth M, Gray RD. Bayesian phylogenetic analysis of Philippine languages supports a rapid migration of Malayo-Polynesian languages. Sci Rep 2024; 14:14967. [PMID: 38942799 PMCID: PMC11213883 DOI: 10.1038/s41598-024-65810-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 06/24/2024] [Indexed: 06/30/2024] Open
Abstract
The Philippines are central to understanding the expansion of the Austronesian language family from its homeland in Taiwan. It remains unknown to what extent the distribution of Malayo-Polynesian languages has been shaped by back migrations and language leveling events following the initial Out-of-Taiwan expansion. Other aspects of language history, including the effect of language switching from non-Austronesian languages, also remain poorly understood. Here we apply Bayesian phylogenetic methods to a core-vocabulary dataset of Philippine languages. Our analysis strongly supports a sister group relationship between the Sangiric and Minahasan groups of northern Sulawesi on one hand, and the rest of the Philippine languages on the other, which is incompatible with a simple North-to-South dispersal from Taiwan. We find a pervasive geographical signal in our results, suggesting a dominant role for cultural diffusion in the evolution of Philippine languages. However, we do find some support for a later migration of Gorontalo-Mongondow languages to northern Sulawesi from the Philippines. Subsequent diffusion processes between languages in Sulawesi appear to have led to conflicting data and a highly unstable phylogenetic position for Gorontalo-Mongondow. In the Philippines, language switching to Austronesian in 'Negrito' groups appears to have occurred at different time-points throughout the Philippines, and based on our analysis, there is no discernible effect of language switching on the basic vocabulary.
Collapse
Affiliation(s)
- Benedict King
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Simon J Greenhill
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Lawrence A Reid
- National Museum of the Philippines, 1000, Ermita, Manila, Metro Manila, Philippines
- Department of Linguistics, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Malcolm Ross
- School of Culture, History and Language, Australian National University, Canberra, 2601, Australia
| | - Mary Walworth
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Russell D Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
| |
Collapse
|
3
|
Yang C, Zhang X, Yan S, Yang S, Wu B, You F, Cui Y, Xie N, Wang Z, Jin L, Xu S, Zhang M. Large-scale lexical and genetic alignment supports a hybrid model of Han Chinese demic and cultural diffusions. Nat Hum Behav 2024; 8:1163-1176. [PMID: 38740988 DOI: 10.1038/s41562-024-01886-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
The Han Chinese history is shaped by substantial demographic activities and sociocultural transmissions. However, it remains challenging to assess the contributions of demic and cultural diffusion to Han culture and language, primarily due to the lack of rigorous examination of genetic-linguistic congruence. Here we digitized a large-scale linguistic inventory comprising 1,018 lexical traits across 926 dialect varieties. Using phylogenetic analysis and admixture inference, we revealed a north-south gradient of lexical differences that probably resulted from historical migrations. Furthermore, we quantified extensive horizontal language transfers and pinpointed central China as a dialectal melting pot. Integrating genetic data from 30,408 Han Chinese individuals, we compared the lexical and genetic landscapes across 26 provinces. Our results support a hybrid model where demic diffusion predominantly impacts central China, while cultural diffusion and language assimilation occur in southwestern and coastal regions, respectively. This interdisciplinary study sheds light on the complex social-genetic history of the Han Chinese.
Collapse
Affiliation(s)
- Chengkun Yang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China
| | - Xiaoxi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Sizhe Yang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China
| | - Baihui Wu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China
| | - Fengshuo You
- Department of Chinese Language and Literature, Fudan University, Shanghai, China
| | - Yue Cui
- Department of Cultural Heritage and Museology, Fudan University, Shanghai, China
| | - Ni Xie
- Department of Linguistics and Modern Languages, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhiyi Wang
- Department of Chinese Language and Literature, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China.
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai, China.
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China.
| |
Collapse
|
4
|
Kusuma P, Cox MP, Barker G, Sudoyo H, Lansing JS, Jacobs GS. Deep ancestry of Bornean hunter-gatherers supports long-term local ancestry dynamics. Cell Rep 2023; 42:113346. [PMID: 37917587 DOI: 10.1016/j.celrep.2023.113346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/30/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Borneo was a crossroad of ancient dispersals, with some of the earliest Southeast Asian human remains and rock art. The island is home to traditionally hunter-gatherer Punan communities, whose origins, whether of subsistence reversion or long-term foraging, are unclear. The connection between its past and present-day agriculturalist inhabitants, who currently speak Austronesian languages and have composite and complex genetic ancestry, is equally opaque. Here, we analyze the genetic ancestry of the northeastern Bornean Punan Batu (who still practice some mobile hunting and gathering), Tubu, and Aput. We find deep ancestry connections, with a shared Asian signal outgrouping modern and ancient Austronesian-ancestry proxies, suggesting a time depth of more than 7,500 years. They also largely lack the mainland Southeast Asian signals of agricultural Borneans, who are themselves genetically heterogeneous. Our results support long-term inhabitation of Borneo by some Punan ancestors and reveal unexpected complexity in the origins and dispersal of Austronesian-expansion-related ancestry.
Collapse
Affiliation(s)
- Pradiptajati Kusuma
- Division of Genome Diversity and Diseases, Mochtar Riady Institute for Nanotechnology, Banten, Indonesia.
| | - Murray P Cox
- Department of Statistics, University of Auckland, Auckland, New Zealand; School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Graeme Barker
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Herawati Sudoyo
- Division of Genome Diversity and Diseases, Mochtar Riady Institute for Nanotechnology, Banten, Indonesia
| | - J Stephen Lansing
- Santa Fe Institute, Santa Fe, NM, USA; Complexity Science Hub Vienna, Vienna, Austria
| | - Guy S Jacobs
- Department of Archaeology, University of Cambridge, Cambridge, UK.
| |
Collapse
|
5
|
Williams MP, Flegontov P, Maier R, Huber CD. Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566841. [PMID: 38014190 PMCID: PMC10680674 DOI: 10.1101/2023.11.13.566841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Paleogenomics has expanded our knowledge of human evolutionary history. Since the 2020s, the study of ancient DNA has increased its focus on reconstructing the recent past. However, the accuracy of paleogenomic methods in answering questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation within the historical period remains an open question. We used two simulation approaches to evaluate the limitations and behavior of commonly used methods, qpAdm and the f3-statistic, on admixture inference. The first is based on branch-length data simulated from four simple demographic models of varying complexities and configurations. The second, an analysis of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We show that under conditions resembling historical populations, qpAdm can identify a small candidate set of true sources and populations closely related to them. However, in typical ancient DNA conditions, qpAdm is unable to further distinguish between them, limiting its utility for resolving fine-scaled hypotheses. Notably, we find that complex gene-flow histories generally lead to improvements in the performance of qpAdm and observe no bias in the estimation of admixture weights. We offer a heuristic for admixture inference that incorporates admixture weight estimate and P-values of qpAdm models, and f3-statistics to enhance the power to distinguish between multiple plausible candidates. Finally, we highlight the future potential of qpAdm through whole-genome branch-length f2-statistics, demonstrating the improved demographic inference that could be achieved with advancements in f-statistic estimations.
Collapse
Affiliation(s)
- Matthew P. Williams
- Pennsylvania State University, Department of Biology, University Park, PA 16802, USA
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian D. Huber
- Pennsylvania State University, Department of Biology, University Park, PA 16802, USA
| |
Collapse
|
6
|
Liu D, Ko AMS, Stoneking M. The genomic diversity of Taiwanese Austronesian groups: Implications for the "Into- and Out-of-Taiwan" models. PNAS NEXUS 2023; 2:pgad122. [PMID: 37200801 PMCID: PMC10187666 DOI: 10.1093/pnasnexus/pgad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/20/2023]
Abstract
The origin and dispersal of the Austronesian language family, one of the largest and most widespread in the world, have long attracted the attention of linguists, archaeologists, and geneticists. Even though there is a growing consensus that Taiwan is the source of the spread of Austronesian languages, little is known about the migration patterns of the early Austronesians who settled in and left Taiwan, i.e. the "Into-Taiwan" and "out-of-Taiwan" events. In particular, the genetic diversity and structure within Taiwan and how this relates to the into-/out-of-Taiwan events are largely unexplored, primarily because most genomic studies have largely utilized data from just two of the 16 recognized Highland Austronesian groups in Taiwan. In this study, we generated the largest genome-wide data set of Taiwanese Austronesians to date, including six Highland groups and one Lowland group from across the island and two Taiwanese Han groups. We identified fine-scale genomic structure in Taiwan, inferred the ancestry profile of the ancestors of Austronesians, and found that the southern Taiwanese Austronesians show excess genetic affinities with the Austronesians outside of Taiwan. Our findings thus shed new light on the Into- and Out-of-Taiwan dispersals.
Collapse
Affiliation(s)
- Dang Liu
- To whom correspondence should be addressed: ;
| | | | | |
Collapse
|
7
|
Abstract
Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. Here, we provide an overview of Holocene dispersals in the light of genomic evidence and conclude that they have a complex history. Even when there is a demonstrated connection between a demographic expansion of people, the spread of agriculture, and the spread of a particular language family, the outcome in the results of contact between expanding and resident groups is highly variable. Further research is needed to identify the factors and social circumstances that have influenced this variation and complex history.
Collapse
|
8
|
Taufik L, Teixeira JC, Llamas B, Sudoyo H, Tobler R, Purnomo GA. Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects. Genes (Basel) 2022; 13:genes13122373. [PMID: 36553640 PMCID: PMC9778601 DOI: 10.3390/genes13122373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.
Collapse
Affiliation(s)
- Leonard Taufik
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
- Correspondence: (L.T.); (G.A.P.)
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
- Centre for Interdisciplinary Studies, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2601, Australia
- Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, SA 5001, Australia
| | - Herawati Sudoyo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
| | - Gludhug A. Purnomo
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (L.T.); (G.A.P.)
| |
Collapse
|
9
|
Alva O, Leroy A, Heiske M, Pereda-Loth V, Tisseyre L, Boland A, Deleuze JF, Rocha J, Schlebusch C, Fortes-Lima C, Stoneking M, Radimilahy C, Rakotoarisoa JA, Letellier T, Pierron D. The loss of biodiversity in Madagascar is contemporaneous with major demographic events. Curr Biol 2022; 32:4997-5007.e5. [PMID: 36334586 DOI: 10.1016/j.cub.2022.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large-bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.
Collapse
Affiliation(s)
- Omar Alva
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anaïs Leroy
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Margit Heiske
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Lenka Tisseyre
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jean-François Deleuze
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jorge Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Villeurbanne, France
| | - Chantal Radimilahy
- Musée d'Art et d'Archéologie, University of Antananarivo, Antananarivo, Madagascar
| | | | - Thierry Letellier
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Denis Pierron
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France.
| |
Collapse
|
10
|
Rodriguez JJRB, Cuales JMD, Herrera MJB, Zubiri LAM, Muallil RM, Ishmael AI, Jimenez EB, Stoneking M, De Ungria MCA. Ethical challenges in genetic research among Philippine Indigenous Peoples: Insights from fieldwork in Zamboanga and the Sulu Archipelago. Front Genet 2022; 13:901515. [DOI: 10.3389/fgene.2022.901515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
The Philippines, with the recent discovery of an archaic hominin in Luzon and an extensive ethnolinguistic diversity of more than 100 Indigenous peoples, is crucial to understanding human evolution and population history in Island Southeast Asia. Advances in DNA sequencing technologies enable the rapid generation of genomic data to robustly address questions about origins, relatedness, and population movements. With the increased genetic sampling in the country, especially by international scientists, it is vital to revisit ethical rules and guidelines relevant to conducting research among Indigenous peoples. Our team led fieldwork expeditions between 2019 and February 2020 in Zamboanga and the Sulu Archipelago, a chain of islands connecting the Mindanao and Borneo landmasses. The trips concluded with a collection of 2,149 DNA samples from 104 field sites. We present our fieldwork experience among the mostly sea-oriented Sama-Bajaw and Tausug-speaking communities and propose recommendations to address the ethical challenges of conducting such research. This work contributes toward building an enabling research environment in the Philippines that respects the rights and autonomy of Indigenous peoples, who are the rightful owners of their DNA and all genetic information contained therein.
Collapse
|
11
|
Gunn JC, Berkman LK, Koppelman J, Taylor AT, Brewer SK, Long JM, Eggert LS. Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex. Ecol Evol 2022; 12:e9370. [PMID: 36225830 PMCID: PMC9534746 DOI: 10.1002/ece3.9370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/05/2022] Open
Abstract
The Neosho Bass (Micropterus velox), a former subspecies of the keystone top-predator and globally popular Smallmouth Bass (M. dolomieu), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single-nucleotide polymorphisms (SNPs) obtained through ddRAD-seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.
Collapse
Affiliation(s)
- Joe C. Gunn
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| | | | | | - Andrew T. Taylor
- Department of BiologyUniversity of Central OklahomaEdmondOklahomaUSA
- Department of BiologyUniversity of North GeorgiaDahlonegaGeorgiaUSA
| | - Shannon K. Brewer
- U.S. Geological Survey, Alabama Cooperative Fish and Wildlife Research Unit, School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - James M. Long
- U.S. Geological Survey, Oklahoma Cooperative Fish and Wildlife Research Unit, Department of Natural Resource Ecology and ManagementOklahoma State UniversityStillwaterOklahomaUSA
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| |
Collapse
|
12
|
Chen H, Lin R, Lu Y, Zhang R, Gao Y, He Y, Xu S. Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island. Mol Biol Evol 2022; 39:6731089. [PMID: 36173765 PMCID: PMC9585476 DOI: 10.1093/molbev/msac210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30-50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, that is, Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000-3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B-cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.
Collapse
Affiliation(s)
| | | | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Gao
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | | | | |
Collapse
|
13
|
Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens. Sci Rep 2022; 12:14609. [PMID: 36028749 PMCID: PMC9418149 DOI: 10.1038/s41598-022-18904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985–4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467–2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.
Collapse
|
14
|
Aghakhanian F, Hoh BP, Yew CW, Kumar Subbiah V, Xue Y, Tyler-Smith C, Ayub Q, Phipps ME. Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers. Sci Rep 2022; 12:13743. [PMID: 35962005 PMCID: PMC9374673 DOI: 10.1038/s41598-022-17884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.
Collapse
Affiliation(s)
- Farhang Aghakhanian
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,TropMed and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia.,Department of Medicine, Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, 56000, Cheras, Kuala Lumpur, Malaysia.,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Chee-Wei Yew
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Qasim Ayub
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,TropMed and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Maude E Phipps
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia.
| |
Collapse
|
15
|
Brucato N, André M, Hudjashov G, Mondal M, Cox MP, Leavesley M, Ricaut FX. Chronology of natural selection in Oceanian genomes. iScience 2022; 25:104583. [PMID: 35880026 PMCID: PMC9308150 DOI: 10.1016/j.isci.2022.104583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul. 239 human genomes from both sides of the Wallacean ecogeographical barriers Signals of selection are dated between -54,000 to -52,000 in modern Oceanian genomes Genes related to immunity and diet were under strong selection Denisovan introgressions participated to the genetic adaptations present in Oceanians
Collapse
Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
| | - Mathilde André
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France.,Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Georgi Hudjashov
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, National Capital District 134, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, QLD 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
| |
Collapse
|
16
|
Huang X, Xia ZY, Bin X, He G, Guo J, Adnan A, Yin L, Huang Y, Zhao J, Yang Y, Ma F, Li Y, Hu R, Yang T, Wei LH, Wang CC. Genomic Insights Into the Demographic History of the Southern Chinese. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.853391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.
Collapse
|
17
|
Ancient genomes from the last three millennia support multiple human dispersals into Wallacea. Nat Ecol Evol 2022; 6:1024-1034. [PMID: 35681000 PMCID: PMC9262713 DOI: 10.1038/s41559-022-01775-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/13/2022] [Indexed: 12/27/2022]
Abstract
Previous research indicates that human genetic diversity in Wallacea-islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves-has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region's demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600-250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.
Collapse
|
18
|
The Tibetan-Yi region is both a corridor and a barrier for human gene flow. Cell Rep 2022; 39:110720. [PMID: 35476999 DOI: 10.1016/j.celrep.2022.110720] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 11/08/2021] [Accepted: 03/31/2022] [Indexed: 11/22/2022] Open
Abstract
The Tibetan-Yi Corridor (TYC) region between Tibet and the rest of east Asia has served as a crossroads for human migrations for thousands of years. The lack of whole-genome sequencing data specific to the TYC populations has hindered the understanding of the fundamental patterns of migration and divergence between humans in east Asia and southeast Asia. Here, we provide 248 individual whole genomes from the 16 TYC and 3 outgroup populations to elucidate historical relationships. We find that the Tibetan plateau forms an important barrier to gene flow, with a more Tibetan-like ancestry in northern populations and a southern east Asian-related ancestry in south populations. An isolated population, Achang, shows a prolonged isolation and genetic drift compared to other TYC populations. We also note that previous claims regarding the history and structure of TYC populations inferred by linguistics are incompatible with the genetic evidence.
Collapse
|
19
|
Rodríguez-Rodríguez JE, Ioannidis AG, Medina-Muñoz SG, Barberena-Jonas C, Blanco-Portillo J, Quinto-Cortés CD, Moreno-Estrada A. The genetic legacy of the Manila galleon trade in Mexico. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200419. [PMID: 35430879 PMCID: PMC9014187 DOI: 10.1098/rstb.2020.0419] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The population of Mexico has a considerable genetic substructure due to both its pre-Columbian diversity and due to genetic admixture from post-Columbian trans-oceanic migrations. The latter primarily originated in Europe and Africa, but also, to a lesser extent, in Asia. We analyze previously understudied genetic connections between Asia and Mexico to infer the timing and source of this genetic ancestry in Mexico. We identify the predominant origin within Southeast Asia—specifically western Indonesian and non-Negrito Filipino sources—and we date its arrival in Mexico to approximately 13 generations ago (1620 CE). This points to a genetic legacy from the seventeenth century Manila galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco. Indeed, within Mexico we observe the highest level of this trans-Pacific ancestry in Acapulco, located in the state of Guerrero. This colonial Spanish trade route from East Asia to Europe was centred on Mexico and appears in historical records, but its legacy has been largely ignored. Identities and stories were suppressed due to slavery, assimilation of the immigrants as ‘Indios’ and incomplete historical records. Here we characterize this understudied Mexican ancestry. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
Collapse
Affiliation(s)
- Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Santiago G. Medina-Muñoz
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| |
Collapse
|
20
|
Lansing JS, Jacobs GS, Downey SS, Norquest PK, Cox MP, Kuhn SL, Miller JH, Malik SG, Sudoyo H, Kusuma P. Deep ancestry of collapsing networks of nomadic hunter-gatherers in Borneo. EVOLUTIONARY HUMAN SCIENCES 2022; 4:e9. [PMID: 37588920 PMCID: PMC10426063 DOI: 10.1017/ehs.2022.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Theories of early cooperation in human society often draw from a small sample of ethnographic studies of surviving populations of hunter-gatherers, most of which are now sedentary. Borneo hunter-gatherers (Punan, Penan) have seldom figured in comparative research because of a decades-old controversy about whether they are the descendants of farmers who adopted a hunting and gathering way of life. In 2018 we began an ethnographic study of a group of still-nomadic hunter-gatherers who call themselves Punan Batu (Cave Punan). Our genetic analysis clearly indicates that they are very unlikely to be the descendants of neighbouring agriculturalists. They also preserve a song language that is unrelated to other languages of Borneo. Dispersed travelling groups of Punan Batu with fluid membership use message sticks to stay in contact, co-operate and share resources as they journey between rock shelters and forest camps. Message sticks were once widespread among nomadic Punan in Borneo, but have largely disappeared in sedentary Punan villages. Thus the small community of Punan Batu offers a rare glimpse of a hunting and gathering way of life that was once widespread in the forests of Borneo, where prosocial behaviour extended beyond the face-to-face community, facilitating successful collective adaptation to the diverse resources of Borneo's forests.
Collapse
Affiliation(s)
- J. Stephen Lansing
- Santa Fe Institute, Santa Fe, California, USA
- Complexity Science Hub Vienna, Vienna, Austria
| | - Guy S. Jacobs
- Department of Archaeology, University of Cambridge, Cambridge, UK
- Complexity Institute, Nanyang Technological University, Singapore
| | - Sean S. Downey
- Department of Anthropology, Ohio State University, Columbus, Ohio, USA
| | - Peter K. Norquest
- Department of Linguistics, University of Arizona, Tucson, Arizona, USA
| | - Murray P. Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Te Pūnaha Matatini, New Zealand Centre of Research Excellence for Complex Systems, Auckland, New Zealand
| | - Steven L. Kuhn
- School of Anthropology, University of Arizona, Tucson, Arizona, USA
| | - John H. Miller
- Santa Fe Institute, Santa Fe, California, USA
- Social and Decision Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Safarina G. Malik
- Laboratory of Genome Diversity and Diseases, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Herawati Sudoyo
- Laboratory of Genome Diversity and Diseases, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Pradiptajati Kusuma
- Complexity Institute, Nanyang Technological University, Singapore
- Laboratory of Genome Diversity and Diseases, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| |
Collapse
|
21
|
Hoh BP, Deng L, Xu S. The Peopling and Migration History of the Natives in Peninsular Malaysia and Borneo: A Glimpse on the Studies Over the Past 100 years. Front Genet 2022; 13:767018. [PMID: 35154269 PMCID: PMC8829068 DOI: 10.3389/fgene.2022.767018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/07/2022] [Indexed: 12/05/2022] Open
Abstract
Southeast Asia (SEA) has one of the longest records of modern human habitation out-of-Africa. Located at the crossroad of the mainland and islands of SEA, Peninsular Malaysia is an important piece of puzzle to the map of peopling and migration history in Asia, a question that is of interest to many anthropologists, archeologists, and population geneticists. This review aims to revisit our understanding to the population genetics of the natives from Peninsular Malaysia and Borneo over the past century based on the chronology of the technology advancement: 1) Anthropological and Physical Characterization; 2) Blood Group Markers; 3) Protein Markers; 4) Mitochondrial and Autosomal DNA Markers; and 5) Whole Genome Analysis. Subsequently some missing gaps of the study are identified. In the later part of this review, challenges of studying the population genetics of natives will be elaborated. Finally, we conclude our review by reiterating the importance of unveiling migration history and genetic diversity of the indigenous populations as a steppingstone towards comprehending disease evolution and etiology.
Collapse
Affiliation(s)
- Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, UCSI Hospital, Port Dickson, Malaysia
- *Correspondence: Boon-Peng Hoh,
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
22
|
Deng L, Pan Y, Wang Y, Chen H, Yuan K, Chen S, Lu D, Lu Y, Mokhtar SS, Rahman TA, Hoh BP, Xu S. Genetic connections and convergent evolution of tropical indigenous peoples in Asia. Mol Biol Evol 2021; 39:6481554. [PMID: 34940850 PMCID: PMC8826522 DOI: 10.1093/molbev/msab361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
Collapse
Affiliation(s)
- Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Yinan Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Sihan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Siti Shuhada Mokhtar
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia
| | - Thuhairah Abdul Rahman
- Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia
| | - Boon-Peng Hoh
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, UCSI Heights 56000 Cheras, Kuala Lumpur, Malaysia
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
23
|
Gautier M, Vitalis R, Flori L, Estoup A. ƒ-statistics estimation and admixture graph construction with Pool-Seq or allele count data using the R package poolfstat. Mol Ecol Resour 2021; 22:1394-1416. [PMID: 34837462 DOI: 10.1111/1755-0998.13557] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/16/2021] [Accepted: 11/08/2021] [Indexed: 11/27/2022]
Abstract
By capturing various patterns of the structuring of genetic variation across populations, f -statistics have proved highly effective for the inference of demographic history. Such statistics are defined as covariance of SNP allele frequency differences among sets of populations without requiring haplotype information and are hence particularly relevant for the analysis of pooled sequencing (Pool-Seq) data. We here propose a reinterpretation of the F (and D) parameters in terms of probability of gene identity and derive from this unified definition unbiased estimators for both Pool-Seq data and standard allele count data obtained from individual genotypes. We implemented these estimators in a new version of the R package poolfstat, which now includes a wide range of inference methods: (i) three-population test of admixture; (ii) four-population test of treeness; (iii) F4-ratio estimation of admixture rates; and (iv) fitting, visualization and (semi-automatic) construction of admixture graphs. A comprehensive evaluation of the methods implemented in poolfstat on both simulated Pool-Seq (with various sequencing coverages and error rates) and allele count data confirmed the accuracy of these approaches, even for the most cost-effective Pool-Seq design involving relatively low sequencing coverages. We further analyzed a real Pool-Seq data made of 14 populations of the invasive species Drosophila suzukii which allowed refining both the demographic history of native populations and the invasion routes followed by this emblematic pest. Our new package poolfstat provides the community with a user-friendly and efficient all-in-one tool to unravel complex population genetic histories from large-size Pool-Seq or allele count SNP data.
Collapse
Affiliation(s)
- Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Renaud Vitalis
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Laurence Flori
- SelMet, INRAE, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Arnaud Estoup
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| |
Collapse
|
24
|
Wang CZ, Li S, Hao X, Wang CC, Bai RF, Li H, Ma SH. Forensic characteristics and phylogenetic analysis of the Chinese Han population from Chongqing Municipality, Southwest China. Leg Med (Tokyo) 2021; 53:101954. [PMID: 34399366 DOI: 10.1016/j.legalmed.2021.101954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/20/2021] [Accepted: 08/04/2021] [Indexed: 02/05/2023]
Abstract
Chongqing Han is an important southern Han group, but investigations on its paternal genetic structure are still limited. Here, we analyzed the forensic and phylogenetic characteristics of the Chongqing Han population based on 27 Y-STR and predicted Y-SNP markers. Based on AMOVA, haplogroup distribution and network analysis, we explored the genetic relationship between Chongqing Han, other Chinese groups and some southern indigenous groups (speaking Kra-Dai, Austronesian, etc).
Collapse
Affiliation(s)
- Chi-Zao Wang
- Department of Radiology, the First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China; Shantou University Medical College, Shantou, Guangdong 515041, China; Guangdong Key Laboratory of Medical Molecular Imaging, Shantou 515041, China; MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuang Li
- Shapingba Branch of Chongqing Public Security Bureau, Chongqing 400030, China
| | - Xu Hao
- Shapingba Branch of Chongqing Public Security Bureau, Chongqing 400030, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Ru-Feng Bai
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Shu-Hua Ma
- Department of Radiology, the First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China; Shantou University Medical College, Shantou, Guangdong 515041, China; Guangdong Key Laboratory of Medical Molecular Imaging, Shantou 515041, China.
| |
Collapse
|
25
|
Jinam TA, Hosomichi K, Nakaoka H, Phipps ME, Saitou N, Inoue I. Allelic and haplotypic HLA diversity in indigenous Malaysian populations explored using Next Generation Sequencing. Hum Immunol 2021; 83:17-26. [PMID: 34615609 DOI: 10.1016/j.humimm.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/04/2022]
Abstract
The heterogenous population of Malaysia includes more than 50 indigenous groups, and characterizing their HLA diversity would not only provide insights to their ancestry, but also on the effects of natural selection on their genome. We utilized hybridization-based sequence capture and short-read sequencing on the HLA region of 172 individuals representing seven indigenous groups in Malaysia (Jehai, Kintaq, Temiar, Mah Meri, Seletar, Temuan, Bidayuh). Allele and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DQA1, -DQB1, -DPA1, and -DPB1 revealed several ancestry-informative markers. Using SNP-based heterozygosity and pairwise Fst, we observed signals of natural selection, particularly in HLA-A, -C and -DPB1 genes. Consequently, we showed the impact of natural selection on phylogenetic inference using HLA and non-HLA SNPs. We demonstrate the utility of Next Generation Sequencing for generating unambiguous, high-throughput, high-resolution HLA data that adds to our knowledge of HLA diversity and natural selection in indigenous minority groups.
Collapse
Affiliation(s)
- Timothy A Jinam
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, Tokyo, Japan
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| |
Collapse
|
26
|
Lo YH, Cheng HC, Hsiung CN, Yang SL, Wang HY, Peng CW, Chen CY, Lin KP, Kang ML, Chen CH, Chu HW, Lin CF, Lee MH, Liu Q, Satta Y, Lin CJ, Lin M, Chaw SM, Loo JH, Shen CY, Ko WY. Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People. Mol Biol Evol 2021; 38:4149-4165. [PMID: 33170928 PMCID: PMC8476137 DOI: 10.1093/molbev/msaa276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.
Collapse
Affiliation(s)
- Yun-Hua Lo
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Hsueh-Chien Cheng
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Show-Ling Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Han-Yu Wang
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Wei Peng
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Yu Chen
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Kung-Ping Lin
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Mei-Ling Kang
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | | | - Mei-Hsuan Lee
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Quintin Liu
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Cheng-Jui Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Wen-Ya Ko
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| |
Collapse
|
27
|
Brucato N, André M, Tsang R, Saag L, Kariwiga J, Sesuki K, Beni T, Pomat W, Muke J, Meyer V, Boland A, Deleuze JF, Sudoyo H, Mondal M, Pagani L, Romero IG, Metspalu M, Cox MP, Leavesley M, Ricaut FX. Papua New Guinean genomes reveal the complex settlement of north Sahul. Mol Biol Evol 2021; 38:5107-5121. [PMID: 34383935 PMCID: PMC8557464 DOI: 10.1093/molbev/msab238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our dataset, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.
Collapse
Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Mathilde André
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France.,Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Roxanne Tsang
- School of Humanities, Languages and Social Science and Place, Evolution and Rock Art Heritage Unit, Griffith University Centre for Social and Cultural Research, Griffith University, Australia.,Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Jason Kariwiga
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea.,School of Social Science, University of Queensland, Australia, St Lucia, QLD 4072, Australia
| | - Kylie Sesuki
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Teppsy Beni
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - John Muke
- Social Research Institute, Papua New Guinea
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Luca Pagani
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia.,Department of Biology, University of Padua, Italy
| | | | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Murray P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, Queensland, 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New south Wales, 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| |
Collapse
|
28
|
Godinez CJP, Dadios PJD, Espina DM, Matsunaga M, Nishibori M. Population Genetic Structure and Contribution of Philippine Chickens to the Pacific Chicken Diversity Inferred From Mitochondrial DNA. Front Genet 2021; 12:698401. [PMID: 34367257 PMCID: PMC8340678 DOI: 10.3389/fgene.2021.698401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
The Philippines is considered one of the biodiversity hotspots for animal genetic resources. In spite of this, population genetic structure, genetic diversity, and past population history of Philippine chickens are not well studied. In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity (Hd = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine-Pacific subclade was evident, suggesting a Philippine origin of Pacific chickens. Here, we observed Philippine red junglefowls (RJFs) at the basal position of the tree within haplogroup D indicating an earlier introduction into the Philippines potentially via mainland Southeast Asia (MSEA). Another observation was the significantly low genetic differentiation and high rate of gene flow of Philippine chickens into Pacific chicken population. The negative Tajima's D and Fu's Fs neutrality tests revealed that Philippine chickens exhibited an expansion signal. The analyses of mismatch distribution and neutrality tests were consistent with the presence of weak phylogeographic structuring and evident population growth of Philippine chickens (haplogroup D) in the islands of Southeast Asia (ISEA). Furthermore, the Bayesian skyline plot (BSP) analysis showed an increase in the effective population size of Philippine chickens, relating with human settlement, and expansion events. The high level of genetic variability of Philippine chickens demonstrates conservation significance, thus, must be explored in the future.
Collapse
Affiliation(s)
- Cyrill John P. Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| | - Peter June D. Dadios
- College of Aquatic and Applied Life Sciences, Southern Leyte State University, Southern Leyte, Philippines
| | - Dinah M. Espina
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| | - Megumi Matsunaga
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| |
Collapse
|
29
|
Molloy EK, Durvasula A, Sankararaman S. Advancing admixture graph estimation via maximum likelihood network orientation. Bioinformatics 2021; 37:i142-i150. [PMID: 34252951 PMCID: PMC8336447 DOI: 10.1093/bioinformatics/btab267] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 11/18/2022] Open
Abstract
Motivation Admixture, the interbreeding between previously distinct populations, is a pervasive force in evolution. The evolutionary history of populations in the presence of admixture can be modeled by augmenting phylogenetic trees with additional nodes that represent admixture events. While enabling a more faithful representation of evolutionary history, admixture graphs present formidable inferential challenges, and there is an increasing need for methods that are accurate, fully automated and computationally efficient. One key challenge arises from the size of the space of admixture graphs. Given that exhaustively evaluating all admixture graphs can be prohibitively expensive, heuristics have been developed to enable efficient search over this space. One heuristic, implemented in the popular method TreeMix, consists of adding edges to a starting tree while optimizing a suitable objective function. Results Here, we present a demographic model (with one admixed population incident to a leaf) where TreeMix and any other starting-tree-based maximum likelihood heuristic using its likelihood function is guaranteed to get stuck in a local optimum and return an incorrect network topology. To address this issue, we propose a new search strategy that we term maximum likelihood network orientation (MLNO). We augment TreeMix with an exhaustive search for an MLNO, referring to this approach as OrientAGraph. In evaluations including previously published admixture graphs, OrientAGraph outperformed TreeMix on 4/8 models (there are no differences in the other cases). Overall, OrientAGraph found graphs with higher likelihood scores and topological accuracy while remaining computationally efficient. Lastly, our study reveals several directions for improving maximum likelihood admixture graph estimation. Availability and implementation OrientAGraph is available on Github (https://github.com/sriramlab/OrientAGraph) under the GNU General Public License v3.0. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Erin K Molloy
- Department of Computer Science, University of California, Los Angeles, LA 90095, USA.,Institute for Advanced Computer Studies, University of Maryland, College Park, College Park, MD 20740, USA
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, LA 90095, USA
| | - Sriram Sankararaman
- Department of Computer Science, University of California, Los Angeles, LA 90095, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, LA 90095, USA.,Bioinformatics Interdepartmental Program, University of California, Los Angeles, LA 90095, USA.,Department of Computational Medicine, University of California, Los Angeles, LA 90095, USA
| |
Collapse
|
30
|
Alam O, Gutaker RM, Wu CC, Hicks KA, Bocinsky K, Castillo CC, Acabado S, Fuller D, d'Alpoim Guedes JA, Hsing YI, Purugganan MD. Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia. Mol Biol Evol 2021; 38:4832-4846. [PMID: 34240169 PMCID: PMC8557449 DOI: 10.1093/molbev/msab209] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The dispersal of rice (Oryza sativa) following domestication influenced massive social and cultural changes across South, East, and Southeast Asia. The history of dispersal across islands of Southeast Asia, and the role of Taiwan and the Austronesian expansion in this process remain largely unresolved. Here, we reconstructed the routes of dispersal of O. sativa ssp. japonica rice through Taiwan and the northern Philippines using whole-genome re-sequencing of indigenous rice landraces coupled with archaeological and paleoclimate data. Our results indicate that japonica rice found in the northern Philippines diverged from Indonesian landraces as early as 3500 BP. In contrast, rice cultivated by the indigenous peoples of the Taiwanese mountains has complex origins. It comprises two distinct populations, each best explained as a result of admixture between temperate japonica that presumably came from northeast Asia, and tropical japonica from the northern Philippines and mainland Southeast Asia respectively. We find that the temperate japonica component of these indigenous Taiwan populations diverged from northeast Asia subpopulations at about 2600 BP, while gene flow from the northern Philippines occurred before ∼1300 years BP. This coincides with a period of intensified trade established across the South China Sea. Finally, we find evidence for positive selection acting on distinct genomic regions in different rice subpopulations, indicating local adaptation associated with the spread of japonica rice.
Collapse
Affiliation(s)
- Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
| | - Rafal M Gutaker
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA.,Royal Botanic Garden, Kew, Richmond, London, TW9 3AE UK
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.,Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Karen A Hicks
- Department of Biology, Kenyon College, Gambier, Ohio 43022 USA
| | | | | | - Stephen Acabado
- Department of Anthropology, University of California, Los Angeles, CA USA
| | - Dorian Fuller
- Institute of Archaeology, University College London, London, United Kingdom.,School of Cultural Heritage, North-West University, Xi'an, China
| | - Jade A d'Alpoim Guedes
- Department of Anthropology and Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA.,Institute for the Study of the Ancient World, New York University, New York, NY 10028 USA
| |
Collapse
|
31
|
Evans CL, Greenhill SJ, Watts J, List JM, Botero CA, Gray RD, Kirby KR. The uses and abuses of tree thinking in cultural evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200056. [PMID: 33993767 PMCID: PMC8126464 DOI: 10.1098/rstb.2020.0056] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Modern phylogenetic methods are increasingly being used to address questions about macro-level patterns in cultural evolution. These methods can illuminate the unobservable histories of cultural traits and identify the evolutionary drivers of trait change over time, but their application is not without pitfalls. Here, we outline the current scope of research in cultural tree thinking, highlighting a toolkit of best practices to navigate and avoid the pitfalls and 'abuses' associated with their application. We emphasize two principles that support the appropriate application of phylogenetic methodologies in cross-cultural research: researchers should (1) draw on multiple lines of evidence when deciding if and which types of phylogenetic methods and models are suitable for their cross-cultural data, and (2) carefully consider how different cultural traits might have different evolutionary histories across space and time. When used appropriately phylogenetic methods can provide powerful insights into the processes of evolutionary change that have shaped the broad patterns of human history. This article is part of the theme issue 'Foundations of cultural evolution'.
Collapse
Affiliation(s)
- Cara L. Evans
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Simon J. Greenhill
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- ARC Centre of Excellence for the Dynamics of Language, ANU College of Asia and the Pacific, Australian National University, Canberra 2700, Australia
| | - Joseph Watts
- Religion Programme, University of Otago, Dunedin 9016, New Zealand
- Centre for Research on Evolution, Belief and Behaviour, University of Otago, Dunedin 9016, New Zealand
| | - Johann-Mattis List
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Carlos A. Botero
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
| | - Russell D. Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- School of Psychology, University of Auckland, Auckland 1010, New Zealand
| | - Kathryn R. Kirby
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| |
Collapse
|
32
|
Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact. Genes (Basel) 2021; 12:genes12070965. [PMID: 34202821 PMCID: PMC8306604 DOI: 10.3390/genes12070965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 11/17/2022] Open
Abstract
The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.
Collapse
|
33
|
Wu D, Li PY, Pan B, Tiang Z, Dou J, Williantarra I, Pribowo AY, Nurdiansyah R, Foo RSY, Wang C. Genetic admixture in the culturally unique Peranakan Chinese population in Southeast Asia. Mol Biol Evol 2021; 38:4463-4474. [PMID: 34152401 PMCID: PMC8476152 DOI: 10.1093/molbev/msab187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.75-6.46%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.69-1.53%), southern Chinese (0.86%, 0.57-1.31%), and northern Chinese (0.25%, 0.18-0.33%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345-1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159-213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.
Collapse
Affiliation(s)
- Degang Wu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peter Yiqing Li
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
| | - Bangfen Pan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zenia Tiang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jinzhuang Dou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ivanna Williantarra
- Department of Anatomy and Medical Imaging, School of Medical Science, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Department of Biotechnology, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Amadeus Yeremia Pribowo
- Department of Biotechnology, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Rizky Nurdiansyah
- Department of Bioinformatics, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | | | - Roger S Y Foo
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Corresponding authors: E-mails: ;
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Corresponding authors: E-mails: ;
| |
Collapse
|
34
|
The first quantitative assessment of radiocarbon chronologies for initial pottery in Island Southeast Asia supports multi-directional Neolithic dispersal. PLoS One 2021; 16:e0251407. [PMID: 34077445 PMCID: PMC8171956 DOI: 10.1371/journal.pone.0251407] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 04/27/2021] [Indexed: 11/29/2022] Open
Abstract
Neolithization, or the Holocene demographic expansion of farming populations, accounts for significant changes in human and animal biology, artifacts, languages, and cultures across the earth. For Island Southeast Asia, the orthodox Out of Taiwan hypothesis proposes that Neolithic expansion originated from Taiwan with populations moving south into Island Southeast Asia, while the Western Route Migration hypothesis suggests the earliest farming populations entered from Mainland Southeast Asia in the west. These hypotheses are also linked to competing explanations of the Austronesian expansion, one of the most significant population dispersals in the ancient world that influenced human and environmental diversity from Madagascar to Easter Island and Hawai‘i to New Zealand. The fundamental archaeological test of the Out of Taiwan and Western Route Migration hypotheses is the geographic and chronological distribution of initial pottery assemblages, but these data have never been quantitatively analyzed. Using radiocarbon determinations from 20 archaeological sites, we present a Bayesian chronological analysis of initial pottery deposition in Island Southeast Asia and western Near Oceania. Both site-scale and island-scale Bayesian models were produced in Oxcal using radiocarbon determinations that are most confidently associated with selected target events. Our results indicate multi-directional Neolithic dispersal in Island Southeast Asia, with the earliest pottery contemporaneously deposited in western Borneo and the northern Philippines. This work supports emerging research that identifies separate processes of biological, linguistic, and material culture change in Island Southeast Asia.
Collapse
|
35
|
Chang FLC, Coomarasamy C, Jarrett P. The epidemiology of mycosis fungoides in New Zealand. Australas J Dermatol 2021; 62:414-416. [PMID: 34009650 DOI: 10.1111/ajd.13616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/27/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Fen-Lan Cherry Chang
- Department of Dermatology, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Christin Coomarasamy
- Research and Evaluation Office, Ko Awatea, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Paul Jarrett
- Department of Dermatology, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand.,Department of Medicine, The University of Auckland, Auckland, New Zealand
| |
Collapse
|
36
|
New insights into human immunity from ancient genomics. Curr Opin Immunol 2021; 72:116-125. [PMID: 33992907 PMCID: PMC8452260 DOI: 10.1016/j.coi.2021.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022]
Abstract
Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity.
Collapse
|
37
|
Zhang X, Liu Q, Zhang H, Zhao S, Huang J, Sovannary T, Bunnath L, Aun HS, Samnom H, Su B, Chen H. The distinct morphological phenotypes of Southeast Asian aborigines are shaped by novel mechanisms for adaptation to tropical rainforests. Natl Sci Rev 2021; 9:nwab072. [PMID: 35371514 PMCID: PMC8970429 DOI: 10.1093/nsr/nwab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
Southeast Asian aborigines, the hunter-gatherer populations living in tropical rainforests, exhibit distinct morphological phenotypes, including short stature, dark skin, curly hair and a wide and snub nose. The underlying genetic architecture and evolutionary mechanism of these phenotypes remain a long-term mystery. We conducted whole genome deep sequencing of 81 Cambodian aborigines from eight ethnic groups. Through a genome-wide scan of selective sweeps, we discovered key genes harboring Cambodian-enriched mutations that may contribute to their phenotypes, including two hair morphogenesis genes (TCHH and TCHHL1), one nasal morphology gene (PAX3) and a set of genes (such as ENTPD1-AS1) associated with short stature. The identified new genes and novel mutations suggest an independent origin of the distinct phenotypes in Cambodian aborigines through parallel evolution, refuting the long-standing argument on the common ancestry of these phenotypes among the worldwide rainforest hunter-gatherers. Notably, our discovery reveals that various types of molecular mechanisms, including antisense transcription and epigenetic regulation, contribute to human morphogenesis, providing novel insights into the genetics of human environmental adaptation.
Collapse
Affiliation(s)
- Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Qi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tuot Sovannary
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Long Bunnath
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Hong Seang Aun
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Ham Samnom
- Capacity Development Facilitator for Handicap International Federation and Freelance Research, Battambang 02358, Cambodia
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| |
Collapse
|
38
|
Liu D, Duong NT, Ton ND, Van Phong N, Pakendorf B, Van Hai N, Stoneking M. Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity. Mol Biol Evol 2021; 37:2503-2519. [PMID: 32344428 PMCID: PMC7475039 DOI: 10.1093/molbev/msaa099] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Vietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia. Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here, we analyze newly generated genome-wide single-nucleotide polymorphism data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in Mainland Southeast Asia. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. In contrast to previous studies that suggested a largely indigenous origin for Vietnamese genetic diversity, we find that Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that likely reflect different sources for the ancestry associated with each language family. However, linguistic diversity does not completely match genetic diversity: There have been extensive interactions between the Hmong-Mien and Tai-Kadai groups; different Austro-Asiatic groups show different affinities with other ethnolinguistic groups; and we identified a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages during the past 2,500 years. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically diverse region, such as Vietnam.
Collapse
Affiliation(s)
- Dang Liu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nguyen Thuy Duong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Van Phong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Brigitte Pakendorf
- Laboratoire Dynamique du Langage, UMR5596, CNRS & Université de Lyon, Lyon, France
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| |
Collapse
|
39
|
Tao S, Kichula KM, Harrison GF, Farias TDJ, Palmer WH, Leaton LA, Hajar CGN, Zefarina Z, Edinur HA, Zhu F, Norman PJ. The combinatorial diversity of KIR and HLA class I allotypes in Peninsular Malaysia. Immunology 2021; 162:389-404. [PMID: 33283280 PMCID: PMC7968402 DOI: 10.1111/imm.13289] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/16/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIRs) interact with polymorphic human leucocyte antigen (HLA) class I molecules, modulating natural killer (NK) cell functions and affecting both the susceptibility and outcome of immune-mediated diseases. The KIR locus is highly diverse in gene content, copy number and allelic polymorphism within individuals and across geographical populations. To analyse currently under-represented Asian and Pacific populations, we investigated the combinatorial diversity of KIR and HLA class I in 92 unrelated Malay and 75 Malaysian Chinese individuals from the Malay Peninsula. We identified substantial allelic and structural diversity of the KIR locus in both populations and characterized novel variations at each analysis level. The Malay population is more diverse than Malay Chinese, likely representing a unique history including admixture with immigrating populations spanning several thousand years. Characterizing the Malay population are KIR haplotypes with large structural variants present in 10% individuals, and KIR and HLA alleles previously identified in Austronesian populations. Despite the differences in ancestries, the proportion of HLA allotypes that serve as KIR ligands is similar in each population. The exception is a significantly reduced frequency of interactions of KIR2DL1 with C2+ HLA-C in the Malaysian Chinese group, caused by the low frequency of C2+ HLA. One likely implication is a greater protection from preeclampsia, a pregnancy disorder associated with KIR2DL1, which shows higher incidence in the Malay than in the Malaysian Chinese. This first complete, high-resolution, characterization of combinatorial diversity of KIR and HLA in Malaysians will form a valuable reference for future clinical and population studies.
Collapse
Affiliation(s)
- Sudan Tao
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
- Blood Center of Zhejiang ProvinceKey Laboratory of Blood Safety Research of Zhejiang ProvinceHangzhouZhejiangChina
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Genelle F. Harrison
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Ticiana Della Justina Farias
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - William H. Palmer
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Laura Ann Leaton
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | | | - Zulkafli Zefarina
- School of Medical SciencesUniversiti Sains Malaysia, Health CampusKelantanMalaysia
| | - Hisham Atan Edinur
- School of Health SciencesUniversiti Sains Malaysia, Health CampusKelantanMalaysia
| | - Faming Zhu
- Blood Center of Zhejiang ProvinceKey Laboratory of Blood Safety Research of Zhejiang ProvinceHangzhouZhejiangChina
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| |
Collapse
|
40
|
Abstract
A key link to understand human history in Island Southeast Asia is the Philippine archipelago and its poorly investigated genetic diversity. We analyzed the most comprehensive set of population-genomic data for the Philippines: 1,028 individuals covering 115 indigenous communities. We demonstrate that the Philippines were populated by at least five waves of human migration. The Cordillerans migrated into the Philippines prior to the arrival of rice agriculture, where some remain as the least admixed East Asians carrying an ancestry shared by all Austronesian-speaking populations, thereby challenging an exclusive out-of-Taiwan model of joint farming–language–people dispersal. Altogether, our findings portray the Philippines as a crucial gateway, with a multilayered history, that ultimately changed the genetic landscape of the Asia-Pacific region. Island Southeast Asia has recently produced several surprises regarding human history, but the region’s complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive “out-of-Taiwan” model of farming–language–people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting ∼1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.
Collapse
|
41
|
Wang CC, Yeh HY, Popov AN, Zhang HQ, Matsumura H, Sirak K, Cheronet O, Kovalev A, Rohland N, Kim AM, Mallick S, Bernardos R, Tumen D, Zhao J, Liu YC, Liu JY, Mah M, Wang K, Zhang Z, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Carlson KSD, Culleton BJ, Eccles L, Freilich S, Keating D, Lawson AM, Mandl K, Michel M, Oppenheimer J, Özdoğan KT, Stewardson K, Wen S, Yan S, Zalzala F, Chuang R, Huang CJ, Looh H, Shiung CC, Nikitin YG, Tabarev AV, Tishkin AA, Lin S, Sun ZY, Wu XM, Yang TL, Hu X, Chen L, Du H, Bayarsaikhan J, Mijiddorj E, Erdenebaatar D, Iderkhangai TO, Myagmar E, Kanzawa-Kiriyama H, Nishino M, Shinoda KI, Shubina OA, Guo J, Cai W, Deng Q, Kang L, Li D, Li D, Lin R, Nini, Shrestha R, Wang LX, Wei L, Xie G, Yao H, Zhang M, He G, Yang X, Hu R, Robbeets M, Schiffels S, Kennett DJ, Jin L, Li H, Krause J, Pinhasi R, Reich D. Genomic insights into the formation of human populations in East Asia. Nature 2021; 591:413-419. [PMID: 33618348 PMCID: PMC7993749 DOI: 10.1038/s41586-021-03336-2] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023]
Abstract
The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.
Collapse
Affiliation(s)
- Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Nanyang, Singapore
| | - Alexander N Popov
- Scientific Museum, Far Eastern Federal University, Vladivostok, Russia
| | - Hu-Qin Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | | | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Alexey Kovalev
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alexander M Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Dashtseveg Tumen
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Jing Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yi-Chang Liu
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Jiun-Yu Liu
- Department of Anthropology, University of Washington, Seattle, WA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Laurie Eccles
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Richard Chuang
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Jung Huang
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Hana Looh
- Institute of History and Philology, Institute of History and Philology, Academia Sinica, Taipei, Taiwan
| | - Chung-Ching Shiung
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Yuri G Nikitin
- Museum of Archaeology and Ethnology, Institute of History, Archaeology and Ethnology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Andrei V Tabarev
- Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey A Tishkin
- Department of Archeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Song Lin
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zhou-Yong Sun
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiao-Ming Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xi Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Liang Chen
- School of Cultural Heritage, Northwest University, Xi'an, China
| | - Hua Du
- Xi'an AMS Center, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | | | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia
| | | | | | - Erdene Myagmar
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | | | | | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Olga A Shubina
- Department of Archeology, Sakhalin Regional Museum, Yuzhno-Sakhalinsk, Russia
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wangwei Cai
- Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Qiongying Deng
- Department of Human Anatomy and Center for Genomics and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Ministry of Education, School of Medicine, Xizang Minzu University (Tibet University for Nationalities), Xianyang, China
| | - Dawei Li
- Institute for History and Culture of Science & Technology, Guangxi University for Nationalities, Nanning, China
| | - Dongna Li
- Department of Biology, Hainan Medical University, Haikou, China
| | - Rong Lin
- Department of Biology, Hainan Medical University, Haikou, China
| | - Nini
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Ministry of Education, School of Medicine, Xizang Minzu University (Tibet University for Nationalities), Xianyang, China
| | - Rukesh Shrestha
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ling-Xiang Wang
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Lanhai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guangmao Xie
- College of History, Culture and Tourism, Guangxi Normal University, Guilin, China
- Guangxi Institute of Cultural Relics Protection and Archaeology, Nanning, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology, Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, China
| | - Manfei Zhang
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rong Hu
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Martine Robbeets
- Eurasia3angle Research group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Douglas J Kennett
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
42
|
Sun J, Li YX, Ma PC, Yan S, Cheng HZ, Fan ZQ, Deng XH, Ru K, Wang CC, Chen G, Wei LH. Shared paternal ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within China. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:686-700. [PMID: 33555039 DOI: 10.1002/ajpa.24240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The aim of this research was to explore the origin, diversification, and demographic history of O1a-M119 over the past 10,000 years, as well as its role during the formation of East Asian and Southeast Asian populations, particularly the Han, Tai-Kadai-speaking, and Austronesian-speaking populations. MATERIALS AND METHODS Y-chromosome sequences (n = 141) of the O1a-M119 lineage, including 17 newly generated in this study, were used to reconstruct a revised phylogenetic tree with age estimates, and identify sub-lineages. The geographic distribution of 12 O1a-M119 sub-lineages was summarized, based on 7325 O1a-M119 individuals identified among 60,009 Chinese males. RESULTS A revised phylogenetic tree, age estimation, and distribution maps indicated continuous expansion of haplogroup O1a-M119 over the past 10,000 years, and differences in demographic history across geographic regions. We propose several sub-lineages of O1a-M119 as founding paternal lineages of Han, Tai-Kadai-speaking, and Austronesian-speaking populations. The sharing of several young O1a-M119 sub-lineages with expansion times less than 6000 years between these three population groups supports a partial common ancestry for them in the Neolithic Age; however, the paternal genetic divergence pattern is much more complex than previous hypotheses based on ethnology, archeology, and linguistics. DISCUSSION Our analyses contribute to a better understanding of the demographic history of O1a-M119 sub-lineages over the past 10,000 years during the emergence of Han, Austronesians, Tai-Kadai-speaking populations. The data described in this study will assist in understanding of the history of Han, Tai-Kadai-speaking, and Austronesian-speaking populations from ethnology, archeology, and linguistic perspectives in the future.
Collapse
Affiliation(s)
- Jin Sun
- Xingyi Normal University for Nationalities, Xingyi, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Ying-Xiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Kai Ru
- Enlighten Co., Ltd., Shanghai, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| |
Collapse
|
43
|
Carlhoff S, Duli A, Nägele K, Nur M, Skov L, Sumantri I, Oktaviana AA, Hakim B, Burhan B, Syahdar FA, McGahan DP, Bulbeck D, Perston YL, Newman K, Saiful AM, Ririmasse M, Chia S, Hasanuddin, Pulubuhu DAT, Suryatman, Supriadi, Jeong C, Peter BM, Prüfer K, Powell A, Krause J, Posth C, Brumm A. Genome of a middle Holocene hunter-gatherer from Wallacea. Nature 2021; 596:543-547. [PMID: 34433944 PMCID: PMC8387238 DOI: 10.1038/s41586-021-03823-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.
Collapse
Affiliation(s)
- Selina Carlhoff
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Akin Duli
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Kathrin Nägele
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Muhammad Nur
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Laurits Skov
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Iwan Sumantri
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Adhi Agus Oktaviana
- grid.512005.30000 0001 2178 7840Pusat Penelitian Arkeologi Nasional (ARKENAS), Jakarta, Indonesia ,grid.1022.10000 0004 0437 5432Place, Evolution and Rock Art Heritage Unit, Griffith Centre for Social and Cultural Research, Griffith University, Gold Coast, Queensland Australia
| | - Budianto Hakim
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Basran Burhan
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | | | - David P. McGahan
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | - David Bulbeck
- grid.1001.00000 0001 2180 7477Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australian Capital Territory Australia
| | - Yinika L. Perston
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | - Kim Newman
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | | | - Marlon Ririmasse
- grid.512005.30000 0001 2178 7840Pusat Penelitian Arkeologi Nasional (ARKENAS), Jakarta, Indonesia
| | - Stephen Chia
- grid.11875.3a0000 0001 2294 3534Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Hasanuddin
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Dwia Aries Tina Pulubuhu
- grid.412001.60000 0000 8544 230XDepartemen Sosiologi, Fakultas Ilmu Sosial, Universitas Hasanuddin, Makassar, Indonesia
| | - Suryatman
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Supriadi
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Choongwon Jeong
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Benjamin M. Peter
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kay Prüfer
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam Powell
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.10392.390000 0001 2190 1447Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Adam Brumm
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| |
Collapse
|
44
|
SUZUKI HITOSHI. The time-dependent evolutionary rate of mitochondrial DNA in small mammals inferred from biogeographic calibration points with reference to the late Quaternary environmental changes in the Japanese archipelago. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.201201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- HITOSHI SUZUKI
- Graduate School of Environmental Science, Hokkaido University, Sapporo
| |
Collapse
|
45
|
OSADA NAOKI, KAWAI YOSUKE. Exploring models of human migration to the Japanese archipelago using genome-wide genetic data. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.201215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NAOKI OSADA
- Faculty of Information Science and Technology, Hokkaido University, Sapporo
| | - YOSUKE KAWAI
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo
| |
Collapse
|
46
|
Luo R. Heat conduction in two-dimensional momentum-conserving and -nonconserving gases. Phys Rev E 2020; 102:052104. [PMID: 33327068 DOI: 10.1103/physreve.102.052104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/18/2020] [Indexed: 06/12/2023]
Abstract
Compared to that for two-dimensional (2D) lattices, our understanding of heat conduction in 2D gases is still limited. Here we study heat conduction behavior of 2D gas systems with momentum-conserving and -nonconserving interparticle interactions by using the nonequilibrium and equilibrium molecular dynamics methods. For the momentum-conserving system, we find that when the dimensionality of the system is changed from 2D to quasi-one-dimensional (quasi-1D), the heat conductivity κ diverges with the system size L as κ∼lnL (the theoretical prediction for 2D systems) for a short L and shows, in the thermodynamic limit, a tendency to κ∼L^{1/3} like that predicted in 1D fluids. This suggests that the dimensional-crossover effect of heat conduction exists in 2D systems with conserved momentum. In contrast, for the momentum-nonconserving system, as L increases, finite heat conductivity independent of L is observed. These findings are in agreement with the predictions given by hydrodynamic theory and thus further confirm the validity of the theory in 2D gases.
Collapse
Affiliation(s)
- Rongxiang Luo
- Department of Physics, Fuzhou University, Fuzhou 350108, Fujian, China and Fujian Science and Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, Fujian, China
| |
Collapse
|
47
|
Sun J, Wei LH, Wang LX, Huang YZ, Yan S, Cheng HZ, Ong RTH, Saw WY, Fan ZQ, Deng XH, Lu Y, Zhang C, Xu SH, Jin L, Teo YY, Li H. Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians. Am J Hum Biol 2020; 33:e23486. [PMID: 32851723 DOI: 10.1002/ajhb.23486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/16/2020] [Accepted: 07/10/2020] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES The origin and differentiation of Austronesian populations and their languages have long fascinated linguists, archeologists, and geneticists. However, the founding process of Austronesians and when they separated from their close relatives, such as the Daic and Austro-Asiatic populations in the mainland of Asia, remain unclear. In this study, we explored the paternal origin of Malays in Southeast Asia and the early differentiation of Austronesians. MATERIALS AND METHODS We generated whole Y-chromosome sequences of 50 Malays and co-analyzed 200 sequences from other Austronesians and related populations. We generated a revised phylogenetic tree with time estimation. RESULTS We identified six founding paternal lineages among the studied Malays samples. These founding lineages showed a surprisingly coincident expansion age at 5000 to 6000 years ago. We also found numerous mostly close related samples of the founding lineages of Malays among populations from Mainland of Asia. CONCLUSION Our analyses provided a refined phylogenetic resolution for the dominant paternal lineages of Austronesians found by previous studies. We suggested that the co-expansion of numerous founding paternal lineages corresponds to the initial differentiation of the most recent common ancestor of modern Austronesians. The splitting time and divergence pattern in perspective of paternal Y-chromosome evidence are highly consistent with the previous theories of ethnologists, linguists, and archeologists.
Collapse
Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | | | - Yun-Zhi Huang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China
| | - Chao Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Shu-Hua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Hui Li
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| |
Collapse
|
48
|
Abstract
Despite the efforts made to reconstruct the history of modern humans, there are still poorly explored regions that are key for understanding the phylogeography of our species. One of them is the Philippines, which is crucial to unravel the colonization of Southeast Asia and Oceania but where little is known about when and how the first humans arrived. In order to shed light into this settlement, we collected samples from 157 individuals of the Philippines with the four grandparents belonging to the same region and mitochondrial variants older than 20,000 years. Next, we analyzed the hypervariable I mtDNA region by approximate Bayesian computation based on extensive spatially explicit computer simulations to select among several migration routes towards the Philippines and to estimate population genetic parameters of this colonization. We found that the colonization of the Philippines occurred more than 60,000 years ago, with long-distance dispersal and from both north and south migration routes. Our results also suggest an environmental scenario especially optimal for humans, with large carrying capacity and population growth, in comparison to other regions of Asia. In all, our study suggests a rapid expansion of modern humans towards the Philippines that could be associated with the establisment of maritime technologies and favorable environmental conditions.
Collapse
|
49
|
Jarrett P, Scragg R. Evolution, Prehistory and Vitamin D. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17020646. [PMID: 31963858 PMCID: PMC7027011 DOI: 10.3390/ijerph17020646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Aspects of human evolutionary biology and prehistory are discussed in relation to vitamin D. The evolution of hairlessness, combined with the need for efficient eccrine sweat production for cooling, provided evolutionary pressure to protect the skin from ultraviolet damage by developing cutaneous pigmentation. There was a subsequent loss of pigmentation as humans journeyed to northern latitudes. Their increasing mastery of technology outstripped evolution's finite pace as further dispersal occurred around the globe. A timeline for the development of clothing to provide warmth, and the consequent shielding from ultraviolet light, which diminished vitamin D synthesis, can be inferred by an examination of mutations in the human louse.
Collapse
Affiliation(s)
- Paul Jarrett
- Department of Dermatology, Middlemore Hospital, Auckland 2025, New Zealand
- Department of Medicine, The University of Auckland, Auckland 1023, New Zealand
| | - Robert Scragg
- Department of Population Health, The University of Auckland, Auckland 1072, New Zealand;
| |
Collapse
|
50
|
Go MC, Hefner JT. Morphoscopic ancestry estimates in Filipino crania using multivariate probit regression models. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:386-401. [DOI: 10.1002/ajpa.24008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/19/2019] [Accepted: 01/02/2020] [Indexed: 01/27/2023]
Affiliation(s)
- Matthew C. Go
- Department of AnthropologyUniversity of Illinois at Urbana‐Champaign 109 Davenport Hall, 607 South Mathews Avenue, Urbana Illinois
- SNA International, supporting the Department of Defense POW/MIA Accounting Agency 590 Moffet Street, Building 4077, Joint Base Pearl Harbor‐Hickam Hawaii
| | - Joseph T. Hefner
- Department of AnthropologyMichigan State University 655 Auditorium Drive, East Lansing Michigan
| |
Collapse
|