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However, a very similar mutation rate estimate of 0.76 × 10 per bp per yr was determined independently from a different ancient DNA specimen of much older age by a recent study (Fu et al. We uncovered new phylogenetic structure and reappraised haplogroup definitions and their branch lengths in the global phylogeny (Fig. 2013) to root the phylogeny and to determine the ancestral versus derived states of the variable sites (Supplemental Table S8).

We estimated the age of the split between A00 and the rest at 254 thousand yr ago (kya) (95% CI 192–307 kya; Supplemental Table S7).

Y chromosome (Chr Y) data from X-degenerate nonrecombining regions was extracted using cgatools and analyzed in combination with publicly available data (Drmanac et al. This information was based on STR profiles and SNP genotyping (Mendez et al. Sequencing was performed on the Illumina Hi Seq 2000 machines at the Genomic Research Center, Gene by Gene, Houston, Texas, at 30× aimed coverage. was supported by ERC Starting Investigator grant FP7-261213.

We used BWA 0.5.9 (Li and Durbin 2009) to map the paired-end reads to the GRCh37 human reference sequence, removing PCR duplicates with SAMtools 0.1.19 rmdup command (Li et al. was additionally supported by Russian Federation President Grant for young scientists MK-2845.2014.4.

We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males. Only main haplogroup labels are shown (details are provided in Supplemental Information 6).

Despite the higher per-base-mutation rate of mt DNA, the much greater length of the Y chromosome (Chr Y) offers the highest genealogical resolution of all non-recombining loci in the human genome. As a result, the precise order and timing of the phylogenetic splits has only recently started to emerge from whole Y chromosome sequences (Francalacci et al. Colors indicate geographic origin of samples (Supplemental Table S1), and fill proportions of the collapsed clades represent the proportion of samples from a given region.

A historical example might be the Mongol expansions (Zerjal et al. Innovations in transportation technology (e.g., the invention of the wheel, horse and camel domestication, and open water sailing) might have contributed to this pattern. was supported by The Russian Foundation for Basic Research 5-a, The Russian Humanitarian Scientific Foundation 4, and the Program of the Basic Research of the RAS Presidium “Biological diversity.” B. was supported by Presidium of Russian Academy of Sciences grant number 12-I-P30-12.

Data quality assessment by evaluating SNP differences between father-son pairs resulted in an average of approximately one mutation per pair, indicating a low false-positive rate, and only 588 recurrent sites (1.6%) observed in the filtered data.

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we combine 299 new whole Y chromosome high-coverage sequences from 110 populations with similar publicly available data (Fig. We use these 456 sequences to estimate the coalescent times and order of haplogroup splits (Supplemental Information 3,4), and we use simulations (Supplemental Information 5) to test the scenarios that can explain the observed patterns in the mt DNA and Y chromosome data for a subset of 320 individuals.

Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. The phylogenetic tree of 456 whole Y chromosome sequences and a map of sampling locations.

Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. The phylogenetic tree is reconstructed using BEAST.

In contrast to demographic reconstructions based on mt DNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. Clades coalescing within 10% of the overall depth of the tree have been collapsed.

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Further insights into the causes of such sex-specific patterns will benefit from population-scale Y chromosome data from ancient DNA studies and their interpretation in an interdisciplinary framework including also archaeological and paleoclimatic evidence and integrative spatially explicit simulations. For quality checks, we used additional data from 10 Estonian first-degree relatives, 24 Dutch father-son pairs, and four duplicate samples. was supported by the Centre of Translational Genomics of the University of Tartu SP1GVARENG.