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Michael F Hammer - One of the best experts on this subject based on the ideXlab platform.
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a haplotype at stat2 introgressed from neanderthals and serves as a candidate of positive selection in papua new guinea
American Journal of Human Genetics, 2012Co-Authors: Fernando L Mendez, Joseph C Watkins, Michael F HammerAbstract:Signals of archaic admixture have been identified through comparisons of the draft Neanderthal and Denisova genomes with those of living humans. Studies of individual loci contributing to these genome-wide average signals are required for characterization of the introgression process and investigation of whether archaic variants conferred an adaptive advantage to the ancestors of contemporary human populations. However, no definitive case of adaptive introgression has yet been described. Here we provide a DNA sequence analysis of the innate immune gene STAT2 and show that a haplotype carried by many Eurasians (but not sub-Saharan Africans) has a sequence that closely matches that of the Neanderthal STAT2. This haplotype, referred to as N, was discovered through a resequencing survey of the entire coding region of STAT2 in a global sample of 90 individuals. Analyses of publicly available complete genome sequence data show that haplotype N shares a recent common ancestor with the Neanderthal sequence (∼80 thousand years ago) and is found throughout Eurasia at an average frequency of ∼5%. Interestingly, N is found in Melanesian populations at ∼10-fold higher frequency (∼54%) than in Eurasian populations. A neutrality test that controls for demography rejects the hypothesis that a variant of N rose to high frequency in Melanesia by genetic drift alone. Although we are not able to pinpoint the precise target of positive selection, we identify nonsynonymous mutations in ERBB3, ESYT1, and STAT2—all of which are part of the same 250 kb introgressive haplotype—as good candidates.
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global genetic variation at oas1 provides evidence of archaic admixture in Melanesian populations
Molecular Biology and Evolution, 2012Co-Authors: Fernando L Mendez, Joseph C Watkins, Michael F HammerAbstract:Recent analysis of DNA extracted from two Eurasian forms of archaic human shows that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. Although these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We resequenced a 7-kb region encompassing the OAS1 gene in 88 individuals from six Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5# region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of .3 myr, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of .1,500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ;90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.
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autosomal and x linked single nucleotide polymorphisms reveal a steep asian Melanesian ancestry cline in eastern indonesia and a sex bias in admixture rates
Proceedings of The Royal Society B: Biological Sciences, 2010Co-Authors: Murray P Cox, Tatiana M Karafet, Stephen J Lansing, Herawati Sudoyo, Michael F HammerAbstract:The geographical region between mainland Asia and New Guinea is characterized by numerous small islands with isolated human populations. Phenotypically, groups in the west are similar to their neighbours in mainland Southeast Asia, eastern groups near New Guinea are similar to Melanesians, and intervening populations are intermediate in appearance. A long-standing question is whether this pattern primarily reflects mixing between groups with distinct origins or whether natural selection has shaped this range of variation by acting differentially on populations across the region. To address this question, we genotyped a set of 37 single nucleotide polymorphisms that are evolutionarily independent, putatively neutral and highly informative for Asian–Melanesian ancestry in 1430 individuals from 60 populations spanning mainland Asia to Melanesia. Admixture analysis reveals a sharp transition from Asian to Melanesian genetic variants over a narrow geographical region in eastern Indonesia. Interestingly, this admixture cline roughly corresponds to the human phenotypic boundary noted by Alfred Russell Wallace in 1869. We conclude that this phenotypic gradient probably reflects mixing of two long-separated ancestral source populations—one descended from the initial Melanesian-like inhabitants of the region, and the other related to Asian groups that immigrated during the Paleolithic and/or with the spread of agriculture. A higher frequency of Asian X-linked markers relative to autosomal markers throughout the transition zone suggests that the admixture process was sex-biased, either favouring a westward expansion of patrilocal Melanesian groups or an eastward expansion of matrilocal Asian immigrants. The matrilocal marriage practices that dominated early Austronesian societies may be one factor contributing to this observed sex bias in admixture rates.
Guido Barbujani - One of the best experts on this subject based on the ideXlab platform.
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early modern human dispersal from africa genomic evidence for multiple waves of migration
Investigative Genetics, 2015Co-Authors: Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle T Vilaca, Lisa De Santi, Guido BarbujaniAbstract:Anthropological and genetic data agree in indicating the African continent as the main place of origin for anatomically modern humans. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Oceania, and later through a northern route crossing the Levant. Here, we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of either hybridization with archaic human forms in Australo-Melanesia or back migration from Europe into Africa. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa
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early modern human dispersal from africa genomic evidence for multiple waves of migration
bioRxiv, 2015Co-Authors: Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle T Vilaca, Lisa De Santi, Guido BarbujaniAbstract:Background. Anthropological and genetic data agree in indicating the African continent as the main place of origin for modern human. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab peninsula into Southern Asia and Oceania, and later through a Northern route crossing the Levant. Results. Here we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa, and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of hybridization with archaic human forms in Australo-Melanesia. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. Conclusions. We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity, and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa
Paul Zimmet - One of the best experts on this subject based on the ideXlab platform.
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mortality in micronesian nauruans and Melanesian and indian fijians is not associated with obesity
American Journal of Epidemiology, 1996Co-Authors: Allison M Hodge, Veronica R Collins, G K Dowse, Paul ZimmetAbstract:The association of obesity with mortality was investigated in population-based samples of Micronesian Nauruans (n = 1,400), Melanesian Fijians (n = 1,279), and Indian Fijians (n = 1,182), over 10 years from 1982 in Nauru, and 11 years from 1980 in Fiji. At the end of follow-up, vital status was known for all Nauruans and all but 3.5% of Fijians. Mortality rates were higher in Nauru than Fiji, and in Melanesians than Indians. The mean body mass index of decedents was similar to or less than (Nauruan men, p < 0.001) that of survivors in each sex-ethnic group. Crude mortality rates showed an inverse relation with body mass index in Nauruan men, with inconsistent relations in other sex-ethnic groups. After stratification by diabetes status, there was no relation between mortality and obesity in nondiabetic subjects, but an inverse relation was observed among diabetic subjects in each population. These findings persisted even after the exclusion of subjects who died within the first 2 years of follow-up. After controlling for age, smoking, and diabetes status in Cox proportional hazard models, body mass index (as a continuous variable) was not related to mortality in any sex/ethnic group and tended to be negatively associated with mortality risk. Interactions of body mass index with age, smoking, and diabetes status were not significant. Mortality risk was significantly increased in older subjects and in diabetic subjects, and cigarette smoking also increased risk in some groups. Stratification of analyses according to cigarette smoking did not alter the nature of the results. The association of mortality and body mass index categorized by quartiles was also investigated. After adjusting for age alone, or age, smoking, and diabetes status, the lower quartiles of body mass index were consistently associated with the highest relative risk for mortality. Quadratic terms for body mass index did not improve Cox models in subjects with normal glucose tolerance. Relations with cardiovascular disease mortality were also assessed and results were inconsistent, although positive trends were observed in Nauruan women (p = 0.02) and Melanesian men (p = 0.06). Overall, there was little evidence to suggest that obesity was a risk factor for total or cardiovascular mortality in these populations. However, obesity is clearly associated with a high risk of diabetes and other morbid conditions and at least on this basis it would seem desirable to prevent obesity in these and other Pacific populations.
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high mortality from cardiovascular disease and analysis of risk factors in indian and Melanesian fijians
International Journal of Epidemiology, 1996Co-Authors: Veronica R Collins, G K Dowse, Sereima Cabealawa, Parshu Ram, Paul ZimmetAbstract:Here we report 11-year all-cause and cause-specific mortality rates and risk factors for total CVD [cardiovascular disease] and coronary heart disease (CHD) for indigenous Melanesian and Asian Indian people of Fiji....Following a baseline risk factor survey in 1980 mortality surveillance continued until 1991 in a representative cohort of 1325 Melanesians and 1221 Indians from urban and rural areas of Fiji....Total mortality rates in Melanesians were 15.9 and 9.2/1000 person-years and in Indians were 13.5 and 6.8/1000 person-years in men and women respectively. Death due to CHD was more common in men than women and in Indian than Melanesian men although total CVD deaths were more common in Melanesian men. Deaths due to CHD were more common in the urban than the rural area. After adjusting for other risk factors Indian ethnicity was associated with a significantly reduced risk of total and CVD mortality in men and total mortality in women....Cardiovascular disease is now responsible for a large proportion of total mortality in both Indian and Melanesian Fijians. The major risk factors identified in Fijians are similar to those observed in developed populations. (EXCERPT)
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non insulin dependent diabetes and 11 year mortality in asian indian and Melanesian fijians
Diabetic Medicine, 1996Co-Authors: Veronica R Collins, G K Dowse, Sereima Cabealawa, Parshu Ram, Paul ZimmetAbstract:This study reports 11-year all-cause and cause-specific mortality rates according to baseline glucose tolerance for a population-based sample of adult Melanesian and Indian Fijians (n = 2638), first surveyed in 1980. Risk factors for all-cause and cardiovascular disease (CVD) mortality in subjects with non-insulin-dependent diabetes (NIDDM) are also described. The baseline survey included 75 g oral glucose tolerance tests, measurements of blood pressure, body mass index, and triceps skinfold, assays of plasma cholesterol and triglycerides, electrocardiograms, and details of smoking habits and physical activity. Mortality status was ascertained for 2546 subjects through surveillance of death certificates, medical records and interview of subjects (or relatives). Mortality rates were increased in diabetic men and women of both ethnic groups: relative risks compared to subjects without diabetes at baseline were 1.7 (CI:0.9-3.1) and 2.0 (1.1-3.7) in Melanesian and 4.2 (2.7-6.5), 3.2 (1.9-5.7) in Indian men and women, respectively. A large proportion of mortality among diabetic subjects was attributed to CVD (62%, 66% in Melanesian and 54%, 58% in Indian men and women, respectively). Mortality rates tended to be higher in Melanesians than Indians, except for diabetic men where Indians had higher total and cardiovascular disease rates. In contrast to non-diabetic Fijians, diabetic women of both ethnic groups lost their relative protection from coronary heart disease (CHD). Cox regressions for diabetic subjects showed age and fasting plasma glucose to be independent predictors of all-cause mortality in men, and age, body mass index (inversely) and systolic blood pressure in women, but lipid concentrations, and cigarette smoking were not related. After accounting for conventional CVD risk factors, diabetes conferred significantly increased risk of total, CVD, and CHD mortality. The mortality experience of Melanesian and Indian Fijians with NIDDM is similar to that documented in developed populations, with excess mortality due to cardiovascular causes.
Sibelle T Vilaca - One of the best experts on this subject based on the ideXlab platform.
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early modern human dispersal from africa genomic evidence for multiple waves of migration
Investigative Genetics, 2015Co-Authors: Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle T Vilaca, Lisa De Santi, Guido BarbujaniAbstract:Anthropological and genetic data agree in indicating the African continent as the main place of origin for anatomically modern humans. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Oceania, and later through a northern route crossing the Levant. Here, we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of either hybridization with archaic human forms in Australo-Melanesia or back migration from Europe into Africa. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa
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early modern human dispersal from africa genomic evidence for multiple waves of migration
bioRxiv, 2015Co-Authors: Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle T Vilaca, Lisa De Santi, Guido BarbujaniAbstract:Background. Anthropological and genetic data agree in indicating the African continent as the main place of origin for modern human. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab peninsula into Southern Asia and Oceania, and later through a Northern route crossing the Levant. Results. Here we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa, and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of hybridization with archaic human forms in Australo-Melanesia. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. Conclusions. We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity, and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa
Ryutaro Ohtsuka - One of the best experts on this subject based on the ideXlab platform.
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the serum leptin level and body mass index in Melanesian and micronesian solomon islanders focus on genetic factors and urbanization
American Journal of Human Biology, 2011Co-Authors: Takuro Furusawa, Izumi Naka, Minato Nakazawa, Taro Yamauchi, Kazumi Natsuhara, Ryosuke Kimura, Takafumi Ishida, Nao Nishida, Ricky Eddie, Ryutaro OhtsukaAbstract:Objectives: This study examined the association between the serum leptin level and body mass index (BMI) and the effects of urbanization and polymorphisms of leptin (LEP) or leptin receptor (LEPR) genes on the leptin level in three Solomon Islands populations. Methods: A Melanesian population living in a remote area (participants: 106 males and 106 females, ages: 18–74 years), a Melanesian population in an urban area (89 and 94, 18–79 years), and a Micronesian population who migrated to a peri-urban area in the 1960s (84 and 69, 18–71 years) were studied. Anthropometric and serum leptin measurements and genotyping for LEP G-2548A and LEPR K109R and Q223R were performed. Results: The prevalence of obesity (BMI ≥ 30 kg/m2) was the highest in the Micronesian population (30.1%), followed by the urban (18.6%) and the rural (2.4%) Melanesian population. The serum leptin concentration was the highest in the urban Melanesian, followed by the Micronesian and the rural Melanesian populations (P < 0.05). Interestingly, the parameter coefficients of the leptin concentrations on the BMIs were nearly identical in the urban and rural Melanesians after adjusting for age and gender. The LEPR 223Q/Q genotype was associated with an increased leptin level only in the Micronesian population after adjusting for BMI (P = 0.0008 and 0.0016 referenced to the Q/R and the R/R types, respectively). Conclusions: These observations suggest that the increase in obesity in the Micronesians had a genetic component while that in Melanesians might have been related with the urbanization. Am. J. Hum. Biol., 2011. © 2010 Wiley-Liss, Inc.
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gene flow and natural selection in oceanic human populations inferred from genome wide snp typing
Molecular Biology and Evolution, 2008Co-Authors: Ryosuke Kimura, Ryutaro Ohtsuka, Jun Ohashi, Tsukasa Inaoka, Minato Nakazawa, Yasuhiro Matsumura, Motoki Osawa, Katsushi TokunagaAbstract:It is suggested that the major prehistoric human colonizations of Oceania occurred twice, namely, about 50,000 and 4,000 years ago. The first settlers are considered as ancestors of indigenous people in New Guinea and Australia. The second settlers are Austronesian-speaking people who dispersed by voyaging in the Pacific Ocean. In this study, we performed genome-wide single-nucleotide polymorphism (SNP) typing on an indigenous Melanesian (Papuan) population, Gidra, and a Polynesian population, Tongans, by using the Affymetrix 500K assay. The SNP data were analyzed together with the data of the HapMap samples provided by Affymetrix. In agreement with previous studies, our phylogenetic analysis indicated that indigenous Melanesians are genetically closer to Asians than to Africans and European Americans. Population structure analyses revealed that the Tongan population is genetically originated from Asians at 70% and indigenous Melanesians at 30%, which thus supports the so-called Slow train model. We also applied the SNP data to genome-wide scans for positive selection by examining haplotypic variation and identified many candidates of locally selected genes. Providing a clue to understand human adaptation to environments, our approach based on evolutionary genetics must contribute to revealing unknown gene functions as well as functional differences between alleles. Conversely, this approach can also shed some light onto the invisible phenotypic differences between populations.
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brief communication mitochondrial dna variation suggests extensive gene flow from polynesian ancestors to indigenous Melanesians in the northwestern bismarck archipelago
American Journal of Physical Anthropology, 2006Co-Authors: Jun Ohashi, Izumi Naka, Katsushi Tokunaga, Tsukasa Inaoka, Yuji Ataka, Minato Nakazawa, Yasuhiro Matsumura, Ryutaro OhtsukaAbstract:Archaeological, linguistic, and genetic studies show that Austronesian (AN)-speaking Polynesian ancestors came from Asia/Taiwan to the Bismarck Archipelago in Near Oceania more than 3,600 years ago, and then expanded into Remote Oceania. However, it remains unclear whether they extensively mixed with indigenous Melanesians who had populated the Bismarck Archipelago before their arrival. To examine the extent of admixture between Polynesian ancestors and indigenous Melanesians, mitochondrial DNA (mtDNA) variations in the D-loop region and the cytochrome oxidase and lysine transfer RNA (COII/tRNA(Lys)) intergenic 9-bp deletion were analyzed in the following three Oceanian populations: 1) Balopa Islanders as AN-speaking Melanesians living in the northwestern end of the Bismarck Archipelago, 2) Tongans as AN-speaking Polynesians, and 3) Gidra as non-Austronesian-speaking Melanesians in the southwestern lowlands of Papua New Guinea. Phylogenetic analysis of mtDNA sequences revealed that more than 60% of mtDNA sequences in the Balopa Islanders were very similar to those in Tongans, suggesting an extensive gene flow from Polynesian ancestors to indigenous Melanesians. Furthermore, analysis of pairwise difference distributions for the D-loop sequences with the 9-bp deletion and the Polynesian motif (i.e., T16217C, A16247G, and C16261T) suggested that the expansion of Polynesian ancestors possessing these variations occurred approximately 7,000 years ago.
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molecular polymorphism of abo blood group gene in austronesian and non austronesian populations in oceania
Tissue Antigens, 2004Co-Authors: Ryutaro Ohtsuka, Jun Ohashi, Izumi Naka, Katsushi Tokunaga, Tsukasa Inaoka, Yuji Ataka, Minato Nakazawa, Yasuhiro MatsumuraAbstract:: A number of archeological, linguistic, and genetic studies have been carried out on the peopling of the Pacific, while the origin of Polynesians or the Lapita people is still open to debate. The Lapita people are believed to have populated the Bismarck Archipelago more than 3600 years ago. However, their Melanesian descendants still living in the Bismarck Archipelago have not been genetically clarified yet. To address this question, polymorphism of the ABO blood group gene was investigated in the following three populations who are considered to be almost free from recent admixtures: (i) Balopa islanders as Austronesian (AN)-speaking Melanesians living in the northwestern end of the Bismarck Archipelago; (ii) Gidra as non-Austronesian (NAN)-speaking Melanesians in southwestern lowlands of Papua New Guinea; and (iii) Tongan living in Ha'apai island as AN-speaking Polynesians. Interestingly, there were marked differences in allele frequencies of ABO*A101 and ABO*A102 among the three populations. The allele frequencies of ABO*A101 and ABO*A102 were 7.9 and 19.3% in Balopa, 23.2 and 0.0% in Gidra, and 2.9 and 25.0% in Tongan. Both phylogenetic and correspondence analyses suggested that Balopa was more close to Tongan than to Gidra and that Balopa was genetically placed between Tongan and Asian populations. Our results imply that Balopa may be Melanesian descendants of the Lapita people who populated the Bismarck Archipelago.