Monday, September 14, 2009

Are Uyghurs a recent or ancient population?

They are basically seeing whether there are many private haplotypes in the Uyghur population compared to East Asian and European populations. They don't find this to be the case, thus suggesting that Uyghurs are the result of a recent admixture process.

Haplotype-Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors
Shuhua Xu, Wenfei Jin and Li Jin
Molecular Biology and Evolution 2009 26(10):2197-2206
Abstract: The Uyghur (UIG) are a group of people primarily residing in Xinjiang of China, which is geographically located in Central Asia, from where modern humans were presumably spread in all directions reaching Europe, east, and northeast Asia about 40 kya. A recent study suggested that the UIG are ancestry donors of the East Asian (EAS) gene pool. However, an alternative hypothesis, that is, the UIG is an admixture population with both EAS and EUR ancestries is also supported by our previous studies. To test the two competing hypotheses, here we conducted a haplotype-sharing analysis (HSA) based on empirical and simulated data of high-density single nucleotide polymorphisms. Our results showed that more than 95% of UIG haplotypes could be found in either EAS or EUR populations, which contradicts the expectation of the null models assuming that UIG are donors. Simulation studies further indicated that the proportion of UIG private haplotypes observed in empirical data is only expected in alternative models assuming that UIG is an admixture population. Interestingly, the estimated ancestry contribution of 44%:56% (EAS:EUR) based on HSA is consistent with our previous estimation with STRUCTURE analysis. Although the history of UIGs could be complex, our method is explicit and conservative in rejecting the null hypothesis. We concluded that the gene pool of modern UIGs is more likely a sole recipient with contribution from both EAS and EUR.

Tuesday, September 01, 2009

Human mutation rate estimate

via this story at Nature News, their estimate based on Y chromosome is 100-200 new mutations per genome per generation, or about one mutation in every 30 million bases, which is in agreement with previous indirect estimates. Apparently this is the first direct measurement of the human mutation rate.

Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree
Yali Xue, Qiuju Wang, Quan Long, Bee Ling Ng, Harold Swerdlow, John Burton, Carl Skuce, Ruth Taylor, Zahra Abdellah, Yali Zhao, Asan, Daniel G. MacArthur, Michael A. Quail, Nigel P. Carter, Huanming Yang and Chris Tyler-Smith
Current Biology, 27 August 2009
Abstract: Understanding the key process of human mutation is important for many aspects of medical genetics and human evolution. In the past, estimates of mutation rates have generally been inferred from phenotypic observations or comparisons of homologous sequences among closely related species [1,2,3]. Here, we apply new sequencing technology to measure directly one mutation rate, that of base substitutions on the human Y chromosome. The Y chromosomes of two individuals separated by 13 generations were flow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 11 or 20, respectively [4]. Candidate mutations were further examined by capillary sequencing in cell-line and blood DNA from the donors and additional family members. Twelve mutations were confirmed in 10.15 Mb; eight of these had occurred invitro and four invivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0x10-8 mutations/nucleotide/generation (95% CI: 8.9x10-9 7.0x10-8), consistent with estimates of 2.3x10-8 - 6.3x10-8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons [5] depending on the generation and split times assumed.
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