1
|
Woravatin W, Stoneking M, Srikummool M, Kampuansai J, Arias L, Kutanan W. South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture. PLoS One 2023; 18:e0291547. [PMID: 37708147 PMCID: PMC10501589 DOI: 10.1371/journal.pone.0291547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Previous genome-wide studies have reported South Asian (SA) ancestry in several Mainland Southeast Asian (MSEA) populations; however, additional details concerning population history, in particular the role of sex-specific aspects of the SA admixture in MSEA populations can be addressed with uniparental markers. Here, we generated ∼2.3 mB sequences of the male-specific portions of the Y chromosome (MSY) of a Tai-Kadai (TK)-speaking Southern Thai group (SouthernThai_TK), and complete mitochondrial (mtDNA) genomes of the SouthernThai_TK and an Austronesian (AN)-speaking Southern Thai (SouthernThai_AN) group. We identified new mtDNA haplogroups, e.g. Q3, E1a1a1, B4a1a and M7c1c3 that have not previously reported in Thai populations, but are frequent in Island Southeast Asia and Oceania, suggesting interactions between MSEA and these regions. SA prevalent mtDNA haplogroups were observed at frequencies of ~35-45% in the Southern Thai groups; both of them showed more genetic relatedness to Austroasiatic (AA) speaking Mon than to any other group. For MSY, SouthernThai_TK had ~35% SA prevalent haplogroups and exhibited closer genetic affinity to Central Thais. We also analyzed published data from other MSEA populations and observed SA ancestry in some additional MSEA populations that also reflects sex-biased admixture; in general, most AA- and AN-speaking groups in MSEA were closer to SA than to TK groups based on mtDNA, but the opposite pattern was observed for the MSY. Overall, our results of new genetic lineages and sex-biased admixture from SA to MSEA groups attest to the additional value that uniparental markers can add to studies of genome-wide variation.
Collapse
Affiliation(s)
- Wipada Woravatin
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Biométrie et Biologie Évolutive, UMR 5558, CNRS & Université de Lyon, Lyon, France
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Centre for Linguistics, Faculty of Humanities, Leiden University, Leiden, The Netherlands
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| |
Collapse
|
2
|
Henderson H, da Silva AM, da Silva M, Soares Xavier HA, Mendonca SA, de Araújo RM, Vaughan C, Bohren MA. Participatory Qualitative Research in a Multilingual Context: The Use of Panel Translation to Better Understand and Improve Sexual and Reproductive Health in Timor-Leste. QUALITATIVE HEALTH RESEARCH 2022; 32:1498-1513. [PMID: 35758872 PMCID: PMC9411783 DOI: 10.1177/10497323221110800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding and respecting different linguistic and socio-cultural needs of health service users is critical to design, adapt and provide appropriate health services. We explored access to male family planning methods in The Democratic Republic of Timor-Leste, a linguistically and culturally diverse nation, by conducting 14 participatory group discussions (PGDs) with 175 participants across seven municipalities. Participants (84 men and 91 women, aged 18 to 72) spoke 13 different languages. PGDs were audio-recorded and translated to English using a multilingual panel translation approach that enabled rigorous and reflexive discussion and learning between researchers about context and meaning. Planning for language diversity helped us to centre participant voices and to hear perspectives that may have otherwise been excluded or misrepresented. Our study affirms the need for research teams to include diverse members who help ensure meaning and voice is not lost across cultural and linguistic differences. Linguistic respect, inclusion and transparency are required to realise improved health and development outcomes.
Collapse
Affiliation(s)
- Helen Henderson
- Marie Stopes Timor-Leste, Dili, Timor-Leste
- Gender and Women’s Health Unit, Centre for Health Equity, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- MSI Asia Pacific, Melbourne, Victoria, Australia
| | | | | | | | | | | | - Cathy Vaughan
- Gender and Women’s Health Unit, Centre for Health Equity, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Meghan A. Bohren
- Gender and Women’s Health Unit, Centre for Health Equity, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| |
Collapse
|
3
|
Karmin M, Flores RJ, Saag L, Hudjashov G, Brucato N, Crenna-Darusallam C, Larena M, Endicott PL, Jakobsson M, Lansing JS, Sudoyo H, Leavesley M, Metspalu M, Ricaut FX, Cox MP. Episodes of diversification and isolation in Island Southeast Asian and Near Oceanian male lineages. Mol Biol Evol 2022; 39:6539761. [PMID: 35294555 PMCID: PMC8926390 DOI: 10.1093/molbev/msac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Island Southeast Asia (ISEA) and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40–25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world’s least understood regions.
Collapse
Affiliation(s)
- Monika Karmin
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Rodrigo J Flores
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
- Institute of Computer Science,University of Tartu, Tartu, 51009, Estonia
| | - Lauri Saag
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Georgi Hudjashov
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Nicolas Brucato
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées,CNRS, IRD, UPS, Toulouse
| | - Chelzie Crenna-Darusallam
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
| | - Maximilian Larena
- Department of Organismal Biology, University of Uppsala, Uppsala, 75236, Sweden
| | - Phillip L Endicott
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
- Department Hommes Natures Societies, Musée de l’Homme, Paris, Ile de France, 75016, France
| | - Mattias Jakobsson
- Department of Organismal Biology, University of Uppsala, Uppsala, 75236, Sweden
| | | | - Herawati Sudoyo
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
- School of Humanities and Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- CABAH and College of Arts, Society and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Matthew Leavesley
- School of Humanities and Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- CABAH and College of Arts, Society and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Mait Metspalu
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - François-Xavier Ricaut
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées,CNRS, IRD, UPS, Toulouse
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
| |
Collapse
|
4
|
Branco C, Kanellou M, González-Martín A, Arenas M. Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians. Genes (Basel) 2022; 13:genes13020384. [PMID: 35205429 PMCID: PMC8871837 DOI: 10.3390/genes13020384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
The last glacial period (LGP) promoted a loss of genetic diversity in Paleolithic populations of modern humans from diverse regions of the world by range contractions and habitat fragmentation. However, this period also provided some currently submersed lands, such as the Sunda shelf in Southeast Asia (SEA), that could have favored the expansion of our species. Concerning the latter, still little is known about the influence of the lowering sea level on the genetic diversity of current SEA populations. Here, we applied approximate Bayesian computation, based on extensive spatially explicit computer simulations, to evaluate the fitting of mtDNA data from diverse SEA populations with alternative evolutionary scenarios that consider and ignore the LGP and migration through long-distance dispersal (LDD). We found that both the LGP and migration through LDD should be taken into consideration to explain the currently observed genetic diversity in these populations and supported a rapid expansion of first populations throughout SEA. We also found that temporarily available lands caused by the low sea level of the LGP provided additional resources and migration corridors that favored genetic diversity. We conclude that migration through LDD and temporarily available lands during the LGP should be considered to properly understand and model the first expansions of modern humans.
Collapse
Affiliation(s)
- Catarina Branco
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Marina Kanellou
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonio González-Martín
- Department of Biodiversity, Ecology and Evolution, University Complutense of Madrid, 28040 Madrid, Spain;
| | - Miguel Arenas
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Correspondence: ; Tel.: +34-986-130-047
| |
Collapse
|
5
|
Mitogenomics of modern Mongolic-speaking populations. Mol Genet Genomics 2021; 297:47-62. [PMID: 34757478 DOI: 10.1007/s00438-021-01830-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022]
Abstract
Here, we present a comprehensive data set of 489 complete mitogenomes (211 of which are new) from four Mongolic-speaking populations (Mongols, Barghuts, Khamnigans, and Buryats) to investigate their matrilineal genetic structure, ancestry and relationship with other ethnic groups. We show that along with very high levels of genetic diversity and lack of genetic differentiation, Mongolic-speaking populations exhibit strong genetic resemblance to East Asian populations of Chinese, Japanese, and Uyghurs. Phylogeographic analysis of complete mitogenomes reveals the presence of different components in the gene pools of modern Mongolic-speaking populations-the main East Eurasian component is represented by mtDNA lineages of East Asian, Siberian and autochthonous (the Baikal region/Mongolian) ancestry, whereas the less pronounced West Eurasian component can be ascribed to Europe and West Asia/Caucasus. We also observed that up to one third of the mtDNA subhaplogroups identified in Mongolic-speaking populations can be considered as Mongolic-specific with the coalescence age of most of them not exceeding 1.7 kya. This coincides well with the population size growth which started around 1.1 kya and is detectable only in the Bayesian Skyline Plot constructed based on Mongolic-specific mitogenomes. Our data suggest that the genetic structure established during the Mongol empire is still retained in present-day Mongolic-speaking populations.
Collapse
|
6
|
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
|
7
|
Sahiratmadja E, Rini IA, Penggoam S, Charles A, Maskoen AM, Parwati I. Acetylator Status Among Newly Diagnosed and Recurrent Tuberculosis Patients from Kupang, Eastern Part of Indonesia. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:737-744. [PMID: 34188520 PMCID: PMC8235940 DOI: 10.2147/pgpm.s311952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/31/2021] [Indexed: 11/23/2022]
Abstract
Purpose N-acetyltransferase-2 enzyme in the liver, encoded by NAT2 gene, plays a central role in metabolizing tuberculosis (TB) drug isoniazid (INH). Low compliance of patients toward six-month TB therapy and internal host factors, ie comorbid diseases, immune status, and genetic profiles, are factors leading to treatment failure and recurrence of pulmonary TB infection. This study aimed to explore the NAT2 acetylator status among newly diagnosed and recurrent pulmonary TB patients in eastern part of Indonesia. Patients and Methods Archived DNA of TB patients (n=124) and healthy controls (n=124) were sequenced, and NAT2 acetylator status was determined, then categorized as fast, intermediate, or slow acetylators. Pulmonary TB patients who had no previous TB treatment history were designated as newly diagnosed pulmonary TB, whereas patients with a history of TB treatment were designated as recurrent pulmonary TB. The demographic, clinical, and microbiological data between pulmonary TB groups were compared, and acetylator status was described among groups. Results Male was more significantly prevalent in the recurrent pulmonary TB group (p=0.025), and anemia was more prevalent in new pulmonary TB (p=0.003). The acetylator status in pulmonary TB patients compared to healthy controls were rapid (33.9% vs 48.1%), intermediate (57.8% vs 33.0%), and slow acetylators (8.3% vs 18.9%), respectively. Interestingly, the rapid and intermediate acetylator were significantly more prevalent in pulmonary TB patients than in healthy controls (p=0.023, OR=2.58 (1.12–5.97). Furthermore, no differences were found in acetylator status between new and recurrent pulmonary (p=0.776). Conclusion Rapid and intermediate acetylators status predominated the pulmonary TB patients in Kupang, eastern part of Indonesia, postulating different genetic makeup in this area. As the pulmonary TB patients in Kupang exhibit more rapid acetylator phenotype, the acetylator status might be relevant to be checked before TB therapy for adjusting treatment dose to prevent drug resistances.
Collapse
Affiliation(s)
- Edhyana Sahiratmadja
- Division of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ika Agus Rini
- Health Research Unit, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Simeon Penggoam
- Laboratorium Mikrobiologi, RSUD Prof. Dr. WZ Johannes, Kupang, Indonesia
| | - Afandi Charles
- Health Research Unit, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ani Melani Maskoen
- Division of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.,Health Research Unit, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ida Parwati
- Department of Clinical Pathology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| |
Collapse
|
8
|
Charles A, Penggoam S, Maskoen AM, Sahiratmadja E. Influence of TLR-8 Gene Polymorphisms (rs3764880 and rs3788935) Associated to Pulmonary Tuberculosis in Kupang, Indonesia. INDONESIAN JOURNAL OF TROPICAL AND INFECTIOUS DISEASE 2021. [DOI: 10.20473/ijtid.v9i1.22056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Toll-like receptor 8 (TLR-8) is known as part of intracellular signaling transduction for bacterial phagocytosis. Mycobacterium tuberculosis (Mtb) is intracellular pathogenic bacteria that is recognized by this receptor, and genetic variation of TLR-8 might alter susceptibility of the host towards pulmonary tuberculosis (PTB). This study aimed to determine whether TLR-8 gene polymorphisms were associated to PTB in Kupang, Indonesia. This case-control study compared demographic and clinical data between 115 PTB patients and 115 controls, then two TLR-8 single nucleotide polymorphisms (rs3764880 and rs3788935) were explored using the GoldenGate® Genotyping for VeraCode® / BeadXpress Illumina®. There is no significant difference between sex distribution of patient vs control groups. The polymorphisms (rs3764880 and rs3788935) are in Hardy-Weinberg Equilibrium in this population (p > 0.05). The distribution of major vs minor genotypes and alleles of TLR-8 polymorphisms in PTB patients were as followed: rs3764880 (GG vs GA vs AA, 50.0% vs 21.4% vs 28.6% ; G vs A, 60.9% vs 39.1% ) and rs3788935 (GG vs GA vs AA, 53.0% vs 21.7% vs 25.3%; G vs A, 62.9% vs 37.1%). Neither genotypes nor alleles were associated with PTB in this population (P > 0.05). Besides, when the analyses were stratified by gender, none of the alleles of polymorphism in both genders were associated with PTB cases. None of the TLR-8 polymorphisms have associated the risk of developing PTB in Kupang, East Nusa Tenggara population (as opposed to other studies in different ethnic groups). These might reflect the diversity of genetic polymorphisms in eastern Indonesia populations, suggesting different genetic backgrounds with western part of Indonesia.
Collapse
|
9
|
Yue WQ, Sun ML, Han F, Li JJ, Rigzin T, Dhondup T, Liu HB, Li DY, Li X, Xu YM, Li XN. Investigation of control region sequences of mtDNA in Naqu Tibetan population from Northwestern China. Ann Hum Biol 2021; 48:70-77. [PMID: 33461338 DOI: 10.1080/03014460.2021.1877351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND The sequence polymorphisms of mitochondrial DNA (mtDNA) are valuable in forensic medicine and anthropological genetics. AIM We analysed the sequences of the mtDNA control region in 207 unrelated Tibetan individuals from the Naqu region, Tibet Autonomous Region in the People's Republic of China, and investigated the population structure of the region by population comparison with other groups. SUBJECTS AND METHODS Genomic DNA was extracted and hypervariable regions (HVS-I and HVS-II) were amplified and sequenced. Subsequently, sequences were aligned and compared with the revised Cambridge sequence. Moreover, population comparison was performed between the Naqu Tibetan group and the other groups. CONCLUSION Our study provided available data for exploring the mtDNA haplotype of the Tibetan population in the Naqu region, and population comparisons found that the Naqu Tibetan population has its own unique structure.
Collapse
Affiliation(s)
- Wen-Qing Yue
- School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Mao-Ling Sun
- School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Feng Han
- Medical Department, Shengjing Hospital affiliated to China Medical University, Shenyang, China
| | - Jiu-Jun Li
- Department of Pediatrics, Shengjing Hospital affiliated to China Medical University, Shenyang, China
| | - Tsewang Rigzin
- Department of Internal Medicine, Naqu People's Hospital in Tibet, Naqu, China
| | - Tashi Dhondup
- Department of Pediatrics, Shengjing Hospital affiliated to China Medical University, Shenyang, China.,Saijo Township Health Center, Naqu, China
| | - Hai-Bo Liu
- School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Dong-Yue Li
- School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Xuan Li
- School of Innovation, China Medical University, Shenyang, China
| | - Yan-Ming Xu
- School of Innovation, China Medical University, Shenyang, China
| | - Xiao-Na Li
- School of Fundamental Sciences, China Medical University, Shenyang, China
| |
Collapse
|
10
|
Bodner M, Parson W. The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets. Genes (Basel) 2020; 11:E901. [PMID: 32784546 PMCID: PMC7463946 DOI: 10.3390/genes11080901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 01/20/2023] Open
Abstract
STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates comprise additional STR loci and populations in the frequency database and many further STR-related aspects. One significant innovation is the autosomal STR data QC provided prior to publication of datasets. Such scrutiny was lacking previously, leaving QC to authors, reviewers and editors, which led to an unacceptably high error rate in scientific papers. The results from scrutinizing 184 STR datasets containing >177,000 individual genotypes submitted in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate. Almost no error-free submissions were received, which clearly shows that centralized QC and data curation are essential to maintain the high-quality standard required in forensic genetics. While many errors had minor impact on the resulting allele frequencies, multiple error categories were commonly found within single datasets. Several datasets contained serious flaws. We discuss the factors that caused the errors to draw the attention to redundant pitfalls and thus contribute to better quality of autosomal STR datasets and allele frequency reports.
Collapse
Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA;
| |
Collapse
|
11
|
Othman SN, Chen YH, Chuang MF, Andersen D, Jang Y, Borzée A. Impact of the Mid-Pleistocene Revolution and Anthropogenic Factors on the Dispersion of Asian Black-Spined Toads ( Duttaphrynus melanostictus). Animals (Basel) 2020; 10:E1157. [PMID: 32650538 PMCID: PMC7401666 DOI: 10.3390/ani10071157] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 11/28/2022] Open
Abstract
Divergence-time estimation critically improves the understanding of biogeography processes underlying the distribution of species, especially when fossil data is not available. We hypothesise that the Asian black-spined toad, Duttaphrynus melanostictus, expanded into the Eastern Indomalaya following the Quaternary glaciations with the subsequent colonisation of new landscapes during the Last Glacial Maximum. Divergence dating inferred from 364 sequences of mitochondrial tRNAGly ND3 supported the emergence of a common ancestor to the three D. melanostictus clades around 1.85 (±0.77) Ma, matching with the Lower to Mid-Pleistocene transition. Duttaphrynus melanostictus then dispersed into Southeast Asia from the central Indo-Pacific and became isolated in the Southern Sundaic and Wallacea regions 1.43 (±0.10) Ma through vicariance as a result of sea level oscillations. The clade on the Southeast Asian mainland then colonised the peninsula from Myanmar to Vietnam and expanded towards Southeastern China at the end of the Mid-Pleistocene Revolution 0.84 (±0.32) Ma. Population dynamics further highlight an expansion of the Southeast Asian mainland population towards Taiwan, the Northeastern edge of the species' range after the last interglacial, and during the emergence of the Holocene human settlements around 7000 BP. Thus, the current divergence of D. melanostictus into three segregated clades was mostly shaped by Quaternary glaciations, followed by natural dispersion events over land bridges and accelerated by anthropogenic activities.
Collapse
Affiliation(s)
- Siti N. Othman
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Yi-Huey Chen
- Department of Life Science, Chinese Culture University, Taipei 11114, Taiwan;
| | - Ming-Feng Chuang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Desiree Andersen
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
12
|
Samper Carro SC, Gilbert F, Bulbeck D, O'Connor S, Louys J, Spooner N, Questiaux D, Arnold L, Price GJ, Wood R, Mahirta. Somewhere beyond the sea: Human cranial remains from the Lesser Sunda Islands (Alor Island, Indonesia) provide insights on Late Pleistocene peopling of Island Southeast Asia. J Hum Evol 2019; 134:102638. [PMID: 31446971 DOI: 10.1016/j.jhevol.2019.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 01/29/2023]
Abstract
The migration of anatomically modern humans (AMH) from Africa to every inhabitable continent included their dispersal through Island Southeast Asia (ISEA) to Australia. Significantly, this involved overwater dispersal through the Lesser Sunda Islands between Sunda (continental Southeast Asia) and Sahul (Australia and New Guinea). However, the timing and direction of this movement is still debated. Here, we report on human skeletal material recovered from excavations at two rockshelters, known locally as Tron Bon Lei, on Alor Island, Indonesia. The remains, dated to the Late Pleistocene, are the first anatomically modern human remains recovered in Wallacea dated to this period and are associated with cultural material demonstrating intentional burial. The human remains from Tron Bon Lei represent a population osteometrically distinct from Late Pleistocene Sunda and Sahul AMH. Instead, morphometrically, they appear more similar to Holocene populations in the Lesser Sundas. Thus, they may represent the remains of a population originally from Sunda whose Lesser Sunda Island descendants survived into the Holocene.
Collapse
Affiliation(s)
- Sofía C Samper Carro
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia; School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, 2601, Australia; Centre d'Estudis del Patrimoni Arqueològic de la Prehistòria, Facultat de Lletres-Edifici B, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Felicity Gilbert
- School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, 2601, Australia
| | - David Bulbeck
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia
| | - Sue O'Connor
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia; ARC Centre of Excellence for Australian Biodiversity and Heritage, Australian National University, Canberra, 2601, Australia
| | - Julien Louys
- Australian Research Centre of Human Evolution (ARCHE), Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia
| | - Nigel Spooner
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia; Defence Science and Technology Group, PO Box 1500, Edinburgh, SA, 5111, UK
| | - Danielle Questiaux
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia
| | - Lee Arnold
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia
| | - Gilbert J Price
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Rachel Wood
- Earth Chemistry, Research School of Earth Sciences, Australian National University, Canberra, 2601, Australia
| | - Mahirta
- Jurusan Arkeologi, Fakultas Ilmu Budaya, Universitas Gadja Madja, Bulaksumur, Yogjakarta, 55281, Indonesia
| |
Collapse
|
13
|
Insights into matrilineal genetic structure, differentiation and ancestry of Armenians based on complete mitogenome data. Mol Genet Genomics 2019; 294:1547-1559. [DOI: 10.1007/s00438-019-01596-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023]
|
14
|
Macaulay V, Soares P, Richards MB. Rectifying long-standing misconceptions about the ρ statistic for molecular dating. PLoS One 2019; 14:e0212311. [PMID: 30779770 PMCID: PMC6380571 DOI: 10.1371/journal.pone.0212311] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 01/19/2019] [Indexed: 01/01/2023] Open
Abstract
When divided by a given mutation rate, the ρ (rho) statistic provides a simple estimator of the age of a clade within a phylogenetic tree by averaging the number of mutations from each sample in the clade to its root. However, a long-standing critique of the use of ρ in genetic dating has been quite often cited. Here we show that the critique is unfounded. We demonstrate by a formal mathematical argument and illustrate with a simulation study that ρ estimates are unbiased and also that ρ and maximum likelihood estimates do not differ in any systematic fashion. We also demonstrate that the claim that the associated confidence intervals commonly estimate the uncertainty inappropriately is flawed since it relies on a means of calculating standard errors that is not used by any other researchers, whereas an established expression for the standard error is largely unproblematic. We conclude that ρ dating, alongside approaches such as maximum likelihood (ML) and Bayesian inference, remains a useful tool for genetic dating.
Collapse
Affiliation(s)
- Vincent Macaulay
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- * E-mail:
| | - Martin B. Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
| |
Collapse
|
15
|
Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| |
Collapse
|
16
|
Hudjashov G, Karafet TM, Lawson DJ, Downey S, Savina O, Sudoyo H, Lansing JS, Hammer MF, Cox MP. Complex Patterns of Admixture across the Indonesian Archipelago. Mol Biol Evol 2017; 34:2439-2452. [PMID: 28957506 PMCID: PMC5850824 DOI: 10.1093/molbev/msx196] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.
Collapse
Affiliation(s)
- Georgi Hudjashov
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Estonian Biocentre, 51010 Tartu, Estonia
| | | | - Daniel J Lawson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Sean Downey
- Department of Anthropology, University of Maryland, College Park, MD
| | - Olga Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | | | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| |
Collapse
|
17
|
Derenko M, Denisova G, Malyarchuk B, Dambueva I, Bazarov B. Mitogenomic diversity and differentiation of the Buryats. J Hum Genet 2017; 63:71-81. [PMID: 29215085 DOI: 10.1038/s10038-017-0370-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022]
Abstract
In this paper we present a results of first comprehensive study of the complete mitogenomes in the Buryats with regard to their belonging to the main regional (eastern and western Buryats); tribal (Khori, Ekhirid, Bulagad, and Khongodor), and ethno-territorial (Aginsk, Alar, Balagansk, Barguzin, Ida, Khorinsk, Kuda, Selenga, Verkholensk, Olkhon, Tunka, and Shenehen Buryats) groups. The analysis of molecular variation performed using regional, tribal, and ethno-territorial divisions of the Buryats showed lack of genetic differentiation at all levels. Nonetheless, the complete mitogenome analysis revealed a very high level of genetic diversity in the Buryats which is the highest among Siberian populations and comparable to that in populations of eastern and western Asia. The AMOVA and MDS analyses results imply to a strong genetic similarity between the Buryats and eastern Asian populations of Chinese and Japanese, suggesting their origin on the basis of common maternal ancestry components. Several new Buryat-specific branches of haplogroup G (G2a2a, G2a1i, G2a5a) display signals of dispersals dating to 2.6-6.6 kya with a possible origin in eastern Asia, thus testifying Bronze Age and Neolithic arrival of ancestral eastern Asian component to the South Siberia region.
Collapse
Affiliation(s)
- Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
| | - Galina Denisova
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Irina Dambueva
- Institute of Mongolian, Buddhist and Tibetan Studies, Russian Academy of Sciences, Ulan-Ude, Russia
| | - Boris Bazarov
- Institute of Mongolian, Buddhist and Tibetan Studies, Russian Academy of Sciences, Ulan-Ude, Russia
| |
Collapse
|
18
|
Spencer PR, Sanders KA, Judge DS. Growth curves and the international standard: How children's growth reflects challenging conditions in rural Timor-Leste. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:286-298. [PMID: 29076525 DOI: 10.1002/ajpa.23350] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 11/08/2022]
Abstract
OBJECTIVES Population-specific growth references are important in understanding local growth variation, especially in developing countries where child growth is poor and the need for effective health interventions is high. In this article, we use mixed longitudinal data to calculate the first growth curves for rural East Timorese children to identify where, during development, deviation from the international standards occurs. MATERIALS AND METHODS Over an eight-year period, 1,245 children from two ecologically distinct rural areas of Timor-Leste were measured a total of 4,904 times. We compared growth to the World Health Organization (WHO) standards using z-scores, and modeled height and weight velocity using the SuperImposition by Translation And Rotation (SITAR) method. Using the Generalized Additive Model for Location, Scale and Shape (GAMLSS) method, we created the first growth curves for rural Timorese children for height, weight and body mass index (BMI). RESULTS Relative to the WHO standards, children show early-life growth faltering, and stunting throughout childhood and adolescence. The median height and weight for this population tracks below the WHO fifth centile. Males have poorer growth than females in both z-BMI (p = .001) and z-height-for-age (p = .018) and, unlike females, continue to grow into adulthood. DISCUSSION This is the most comprehensive investigation to date of rural Timorese children's growth, and the growth curves created may potentially be used to identify future secular trends in growth as the country develops. We show significant deviation from the international standard that becomes most pronounced at adolescence, similar to the growth of other Asian populations. Males and females show different growth responses to challenging conditions in this population.
Collapse
Affiliation(s)
- Phoebe R Spencer
- School of Human Sciences, The University of Western Australia, Crawley 6009, Western Australia
| | - Katherine A Sanders
- School of Human Sciences, The University of Western Australia, Crawley 6009, Western Australia
| | - Debra S Judge
- School of Human Sciences, The University of Western Australia, Crawley 6009, Western Australia
| |
Collapse
|
19
|
Yao L, Li H, Martin RD, Moreau CS, Malhi RS. Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens. Mol Phylogenet Evol 2017; 116:227-238. [PMID: 28863929 DOI: 10.1016/j.ympev.2017.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/23/2017] [Accepted: 08/13/2017] [Indexed: 12/01/2022]
Abstract
The biogeographical history of Southeast Asia is complicated due to the continuous emergences and disappearances of land bridges throughout the Pleistocene. Here, we use long-tailed macaques (Macaca fascicularis), which are widely distributed throughout the mainland and islands of Southeast Asia, asa model for better understanding the biogeographical patterns of diversification in this geographically complex region. A reliable intraspecific phylogeny including individuals from localities on oceanic islands, continental islands, and the mainland is needed to trace relatedness along with the pattern and timing of colonization in this region. We used high-throughput sequencing techniques to sequence mitochondrial genomes (mitogenomes) from 95 Southeast Asian M. fascicularis specimens housed at natural history museums around the world. To achieve a comprehensive picture, we more than tripled the mitogenome sample size for M. fascicularis from previous studies, and for the first time included documented samples from the Philippines and several small Indonesian islands. Confirming the result from a previous, recent intraspecific phylogeny for M. fascicularis, the newly reconstructed phylogeny of 135 specimens divides the samples into two major clades: Clade A includes haplotypes from the mainland and some from northern Sumatra, while Clade B includes all insular haplotypes along with lineages from southern Sumatra. This study resolves a previous disparity by revealing a disjunction in the origin of Sumatran macaques, with separate lineages originating within the two major clades, suggesting that at least two major migrations to Sumatra occurred. However, our dated phylogeny reveals that the two major clades split ∼1.88Ma, which is earlier than in previously published phylogenies. Our new data reveal that most Philippine macaque lineages diverged from the Borneo stock within the last ∼0.06-0.43Ma. Finally, our study provides insight into successful sequencing of DNA across museums and shotgun sequencing of DNA specimens asa method to sequence the mitogenome.
Collapse
Affiliation(s)
- Lu Yao
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA.
| | - Hongjie Li
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
| | - Robert D Martin
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA; Institute of Evolutionary Medicine, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Corrie S Moreau
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
| |
Collapse
|
20
|
Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
Collapse
Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| |
Collapse
|
21
|
Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, Ballantyne KN, Wilcox L, Papac L, Cooke K, van Oorschot RAH, McAllister P, Williams L, Kayser M, Mitchell RJ. Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity. Sci Rep 2017; 7:43041. [PMID: 28287095 PMCID: PMC5347126 DOI: 10.1038/srep43041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/17/2017] [Indexed: 01/06/2023] Open
Abstract
Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia’s first settlers.
Collapse
Affiliation(s)
- Nano Nagle
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands
| | - Stephen Wilcox
- Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - Sheila van Holst Pellekaan
- Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia.,School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Kaye N Ballantyne
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands.,Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, Victoria, Australia
| | - Leah Wilcox
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Luka Papac
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Karen Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, Victoria, Australia
| | | | - Lesley Williams
- Community Elder and Cultural Advisor, Brisbane, Queensland, Australia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands
| | - R John Mitchell
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | | |
Collapse
|
22
|
Gomes SM, van Oven M, Souto L, Morreira H, Brauer S, Bodner M, Zimmermann B, Huber G, Strobl C, Röck AW, Côrte-Real F, Parson W, Kayser M. Lack of gene-language correlation due to reciprocal female but directional male admixture in Austronesians and non-Austronesians of East Timor. Eur J Hum Genet 2017; 25:246-252. [PMID: 27485412 PMCID: PMC5255940 DOI: 10.1038/ejhg.2016.101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 06/13/2016] [Accepted: 06/21/2016] [Indexed: 11/08/2022] Open
Abstract
Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene-language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene-language correlation in this region. Aiming to investigate gene-language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN- and NAN-speaking groups. Y-SNP (single-nucleotide polymorphism) data were newly generated for 273 samples and combined with previously established Y-STR (short tandem repeat) data of the same samples, and with previously established mtDNA data of 290 different samples with, however, very similar representation of geographic and linguistic coverage of the country. We found NRY and mtDNA haplogroups of previously described putative East/Southeast Asian (E/SEA) and Near Oceanian (NO) origins in both AN and NAN speakers of East Timor, albeit in different proportions, suggesting reciprocal genetic admixture between both linguistic groups for females, but directional admixture for males. Our data underline the dual genetic origin of East Timorese in E/SEA and NO, and highlight that substantial genetic admixture between the two major linguistic groups had occurred, more so via women than men. Our study therefore provides another example where languages and genes do not conform due to sex-biased genetic admixture across major linguistic groups.
Collapse
Affiliation(s)
- Sibylle M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Luis Souto
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Helena Morreira
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Silke Brauer
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander W Röck
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| |
Collapse
|
23
|
Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania. J Hum Genet 2016; 62:343-353. [PMID: 27904152 DOI: 10.1038/jhg.2016.147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/30/2022]
Abstract
Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.
Collapse
|