Dating the age of admixture via wavelet transform analysis of genome-wide data

Pugach, Irina; Matveyev, Rostislav; Wollstein, Andreas; Kayser, Manfred; Stoneking, Mark

doi:10.1186/gb-2011-12-2-r19

Cited by 82 publications

(145 citation statements)

References 37 publications

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“…This suggestion, biologically plausible considering the short duration of the Lapita period in Remote Oceania (200-300 y, 12-15 human generations), is consistent with the results of genetic studies. There is a larger Near Oceanian contribution to the gene pool in populations living today in the western part of Remote Oceania (10,12) with the possibility of an admixture time at about 2,700 y ago (48). This interpretation is also supported by cultural evidence.…”

Section: Resultssupporting

confidence: 69%

Early Lapita skeletons from Vanuatu show Polynesian craniofacial shape: Implications for Remote Oceanic settlement and Lapita origins

Valentin

Détroit

Spriggs

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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With a cultural and linguistic origin in Island Southeast Asia the Lapita expansion is thought to have led ultimately to the Polynesian settlement of the east Polynesian region after a time of mixing/integration in north Melanesia and a nearly 2,000-y pause in West Polynesia. One of the major achievements of recent Lapita research in Vanuatu has been the discovery of the oldest cemetery found so far in the Pacific at Teouma on the south coast of Efate Island, opening up new prospects for the biological definition of the early settlers of the archipelago and of Remote Oceania in general. Using craniometric evidence from the skeletons in conjunction with archaeological data, we discuss here four debated issues: the Lapita–Asian connection, the degree of admixture, the Lapita–Polynesian connection, and the question of secondary population movement into Remote Oceania.

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Section: Resultssupporting

confidence: 69%

Early Lapita skeletons from Vanuatu show Polynesian craniofacial shape: Implications for Remote Oceanic settlement and Lapita origins

Valentin

Détroit

Spriggs

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…Moreover, this component is observed in similar proportions in all of the Australians, suggesting that it is uniform throughout the genome. By contrast, the "European" ancestry component is present in only a few Australians and in varying amounts, as expected, for very recent admixture such as observed in African Americans (20,37). These AUA individuals showing evidence of recent European ancestry were excluded from further analyses.…”

Section: Resultsmentioning

confidence: 99%

“…First, to place aboriginal Australians into a global context, we carried out principal component analysis (PCA) (20). The first two principal axes are driven by genetic differentiation between Africans, Australians/ Papua New Guineans, and Europeans/Indians/Asians (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…We next analyzed the genome-wide admixture pattern to estimate the time of admixture. We first used StepPCO (20) to obtain the block-like admixture signal across each chromosome for each Australian (excluding two individuals with evidence of European admixture). The NGH and India (represented, again, by Chenchu and Kurumba and the nontribal Dravidian speakers from South India) were used as proxies for the parental populations (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Genome-wide data substantiate Holocene gene flow from India to Australia

Pugach

Delfin

Gunnarsdóttir

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

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“…Furthermore, the distribution of ancestral chromosomal segments can be reshaped and rearranged by recombination in each generation, which essentially provides valuable information about population history. 1,[4][5][6] In general, the ancestral chromosomal segments from different parental populations are spliced into shorter pieces as the number of generation increases, while the ancestral chromosomal segments in a recent admixed population are usually much long due to a limited number of recombination events occurred. With the availability of high-density single-nucleotide polymorphisms data in recent years, it is now feasible to infer population history based on the length of ancestral chromosomal segments (LACS).…”

Section: Introductionmentioning

confidence: 99%

Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping

Jin

Zhou

et al. 2013

Eur J Hum Genet

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The ancestral chromosomal segments in admixed genomes are of significant importance for both population history inference and admixture mapping, because they essentially provide the basic information for tracking genetic events. However, the distributions of the lengths of ancestral chromosomal segments (LACS) under some admixture models remain poorly understood. Here we introduced a theoretical framework on the distribution of LACS in two representative admixture models, that is, hybrid isolation (HI) model and gradual admixture (GA) model. Although the distribution of LACS in the GA model differs from that in the HI model, we demonstrated that the mean LACS in the HI model is approximately half of that in the GA model if both admixture proportion and admixture time in the two models are identical. We showed that the theoretical framework greatly facilitated the inference and understanding of population admixture history by analyzing African-American and Mexican empirical data. In addition, we found the peak of association signatures in the HI model was much narrower and sharper than that in the GA model, indicating that the identification of putative causal allele in the HI model is more efficient than that in the GA model. Thus admixture mapping with case-only data would be a reasonable and economical choice in the HI model due to the weak background noise. However, according to our previous studies, many populations are likely to be gradually admixed and have pretty high background linkage disequilibrium. Therefore, we suggest using a case-control approach rather than a case-only approach to conduct admixture mapping to retain the statistics power in recently admixed populations.

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Dating the age of admixture via wavelet transform analysis of genome-wide data

Cited by 82 publications

References 37 publications

Early Lapita skeletons from Vanuatu show Polynesian craniofacial shape: Implications for Remote Oceanic settlement and Lapita origins

Early Lapita skeletons from Vanuatu show Polynesian craniofacial shape: Implications for Remote Oceanic settlement and Lapita origins

Genome-wide data substantiate Holocene gene flow from India to Australia

Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping

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