ArticleGenome research2008
A novel DNA sequence database for analyzing human demographic history.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves.Molecular biology and evolution · 2018Article
- How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data.Genetics and molecular biology · 2018Article
- Response to HohenloheScience advances · 2017Article
- Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf.Science advances · 2016Article
- MC1R diversity in Northern Island Melanesia has not been constrained by strong purifying selection and cannot explain pigmentation phenotype variation in the region.BMC genetics · 2015Article
- Estimation of the ancestral effective population sizes of African great apes under different selection regimes.Genetica · 2014Article
- The impact of whole-genome sequencing on the reconstruction of human population history.Nature reviews. Genetics · 2014Review
- Imputation-based genomic coverage assessments of current human genotyping arrays.G3 (Bethesda, Md.) · 2013Article
- Patterns of nucleotide and haplotype diversity at ICAM-1 across global human populations with varying levels of malaria exposure.Human genetics · 2013Article
- Reconstructing past changes in locus-specific recombination rates.BMC genetics · 2013Article
- Deep whole-genome sequencing of 100 southeast Asian Malays.American journal of human genetics · 2013Article
- Great ape genomics.ILAR journal · 2013Review
- NRE: a tool for exploring neutral loci in the human genome.BMC bioinformatics · 2012Article
- A haplotype at STAT2 Introgressed from neanderthals and serves as a candidate of positive selection in Papua New Guinea.American journal of human genetics · 2012Article
- Comparative RNA sequencing reveals substantial genetic variation in endangered primates.Genome research · 2012Article
- High altitude adaptation in Daghestani populations from the Caucasus.Human genetics · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While there are now extensive databases of human genomic sequences from both private and public efforts to catalog human nucleotide variation, there are very few large-scale surveys designed for the purpose of analyzing human population history. Demographic inference from patterns of SNP variation in current large public databases is complicated by ascertainment biases associated with SNP discovery and the ways that populations and regions of the genome are sampled. Here, we present results from a resequencing survey of 40 independent intergenic regions on the autosomes and X chromosome comprising ~210 kb from each of 90 humans from six geographically diverse populations (i.e., a total of ~18.9 Mb). Unlike other public DNA sequence databases, we include multiple indigenous populations that serve as important reservoirs of human genetic diversity, such as the San of Namibia, the Biaka of the Central African Republic, and Melanesians from Papua New Guinea. In fact, only 20% of the SNPs that we find are contained in the HapMap database. We identify several key differences in patterns of variability in our database compared with other large public databases, including higher levels of nucleotide diversity within populations, greater levels of differentiation between populations, and significant differences in the frequency spectrum. Because variants at loci included in this database are less likely to be subject to ascertainment biases or linked to sites under selection, these data will be more useful for accurately reconstructing past changes in size and structure of human populations.
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