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Publications (32)
Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. He...
Previous research indicates that human genetic diversity in Wallacea—islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves—has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter–gatherer communities. Yet, inferences based on present-day g...
Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new ins...
Significance
We know more about the settlement of Polynesia than we do about the settlement of the Mariana Islands in the western Pacific. There is debate over where people came from to get to the Marianas, with various lines of evidence pointing to the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago, and over how the ancestors of t...
Humans reached the Mariana Islands in the western Pacific by ~3500 years ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2000 years later. Yet, the settlement of Polynesia has rec...
Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether it remained habitable during the extreme cold of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extens...
Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new...
Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether this area remained habitable during the extremely cold period of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with a recent shared ancestry. Previous studies of the genetic history of Siberian populations were hamp...
In our paper (1), we demonstrate gene flow from India to Australia, which Price and Bird (2) do not question. Based on genetic evidence, we date this gene flow to around 4,200 y ago. This date is interesting and significant because it reappears in different contexts in debates about Australian prehistory concerning the mid-Holocene transition, whic...
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...
Although the Austronesian expansion had a major impact on the languages of Island Southeast Asia, controversy still exists over the genetic impact of this expansion. The coexistence of both Asian and Papuan genetic ancestry in Eastern Indonesia provides a unique opportunity to address this issue. Here, we estimate recombination breakpoints in admix...
It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations fro...
Supplementary figures. Additional file includes eight supplemental figures.
We describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixed human populations. The wavelet transform method offers bette...
Regional analysis of the Europe, North Africa, Middle East, and Central/South Asia groups. (A) Plot of PC1 vs. PC2. (B) frappe results for K = 5.
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Effect of sample size on the power of the lnRsb analysis to detect a positively-selected allele. For each sample size (n = number of chromosomes), the fraction of simulations (y-axis) in which a selected allele of a given selection coefficient (x-axis) was detected as a candidate region of selection, according to the criteria described in the Metho...
Effect of different parameter values on genotype calls obtained with the CHIAMO algorithm. Shown are the mean values (in percent) for heterozygous and homozygous mismatches between the Affymetrix and Illumina platforms, no calls for either or both platforms, and the sum of all mismatches and no calls. These values are given for the BRLMM algorithm...
Analysis of additional PCs for the worldwide populations. (A) Amount of variation explained and associated statistical significance for the first 45 PCs. (B) Heat plot of the values of the first 45 PCs. The PC values have been normalized to range from 0 to 1.
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Regional analysis of the East Asian groups. (A) Plot of PC1 vs. PC2. (B) frappe results for K = 2.
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List of the 255 HGDP-CEPH individuals genotyped in this study, including ID, population, location, region, population code, gender, heterozygosity for the Affymetrix SNPs, and heterozygosity for the Illumina SNPs.
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List of the candidate regions for recent positive selection identified in the population-level analyses, including the chromosome, start and end positions, HGNC gene ID, and populations (and signal rank) for which a positive signal was obtained.
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Comparison of PCA for the same 250 individuals genotyped on the Affymetrix vs. Illumina platforms. (A) Plots of PC1 vs. PC2. (B) The percent variation explained and the p-value of the TW statistic for the first 40 PCs. (C) Values of the first 40 PCs.
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Regional analysis of the sub-Saharan African groups. (A) Plot of PC1 vs. PC2. (B) frappe results for K = 4.
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Regional analysis of the groups from the Americas. (A) Plot of PC1 vs. PC2. (B) frappe results for K = 5.
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List of the candidate regions for recent positive selection identified in the regional-level analyses, including the chromosome, start and end positions, HGNC gene ID, and regions (and signal rank) for which a positive signal was obtained.
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Effect of the number of preceding SNPs (Nreg) used to predict SNP genotypes in the regression analysis on the percent variation explained by the first 10 PCs. Also shown is the effect of pruning SNPs that are in high LD.
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Regional analysis of the Europe, Middle East, Central/South Asia, and East Asia groups. (A) Plot of PC1 vs. PC2. (B) frappe results for K = 4.
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Genome-wide scans of hundreds of thousands of single-nucleotide polymorphisms (SNPs) have resulted in the identification of new susceptibility variants to common diseases and are providing new insights into the genetic structure and relationships of human populations. Moreover, genome-wide data can be used to search for signals of recent positive s...
Genome-wide scans for positive selection in humans provide a promising approach to establish links between genetic variants and adaptive phenotypes. From this approach, lists of hundreds of candidate genomic regions for positive selection have been assembled. These candidate regions are expected to contain variants that contribute to adaptive pheno...
Nitric oxide (NO) has a profound role in the generation, differentiation, survival, and physiology of neurons. We have created a novel transgenic model to study the action of NO in the adult brain, in which the neuronal isoform of NO synthase (nNOS) is expressed under control of the promoter of the calcium-calmodulin multifunctional kinase IIalpha...
Gonadectomy in adult male rats induces a series of changes in cortical catecholamine innervation that begins with a large, but transient decrease in the density of tyrosine hydroxylase- but not dopamine-beta-hydroxylase-immunoreactive axons in sensory, motor, and association cortices. More recent studies have shown that estradiol maintains these pr...