High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences - PubMed (original) (raw)

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences

Anna Schönberg et al. Eur J Hum Genet. 2011 Sep.

Abstract

To investigate the demographic history of human populations from the Caucasus and surrounding regions, we used high-throughput sequencing to generate 147 complete mtDNA genome sequences from random samples of individuals from three groups from the Caucasus (Armenians, Azeri and Georgians), and one group each from Iran and Turkey. Overall diversity is very high, with 144 different sequences that fall into 97 different haplogroups found among the 147 individuals. Bayesian skyline plots (BSPs) of population size change through time show a population expansion around 40-50 kya, followed by a constant population size, and then another expansion around 15-18 kya for the groups from the Caucasus and Iran. The BSP for Turkey differs the most from the others, with an increase from 35 to 50 kya followed by a prolonged period of constant population size, and no indication of a second period of growth. An approximate Bayesian computation approach was used to estimate divergence times between each pair of populations; the oldest divergence times were between Turkey and the other four groups from the South Caucasus and Iran (~400-600 generations), while the divergence time of the three Caucasus groups from each other was comparable to their divergence time from Iran (average of ~360 generations). These results illustrate the value of random sampling of complete mtDNA genome sequences that can be obtained with high-throughput sequencing platforms.

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Figures

Figure 1

Figure 1

Geographic location of sampling sites.

Figure 2

Figure 2

Plot of the number of differences in the HV1 sequences vs the number of differences in the coding region sequences for each pair of individuals. The best-fit regression line is indicated.

Figure 3

Figure 3

MDS plot for five groups from the South Caucasus, Iran and Turkey. (a) Based on complete mtDNA genome sequences. (b) Based on HV1 sequences only.

Figure 4

Figure 4

Bayesian skyline plots. The Y axis for each plot is the effective population size and the X axis is time in years. (a) Georgians; (b) Azeri; (c) Armenians; (d) Iranians and (e) Turks. The gray lines represent the 95% posterior density intervals.

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