High-throughput sequencing of complete human mtDNA genomes from the Philippines

Because of the time and cost associated with Sanger sequencing of complete human mtDNA genomes, practically all evolutionary studies have screened samples first to define haplogroups and then either selected a few samples from each haplogroup, or many samples from a particular haplogroup of interest, for complete mtDNA genome sequencing. Such biased sampling precludes many analyses of interest. Here, we used high-throughput sequencing platforms to generate, rapidly and inexpensively, 109 complete mtDNA genome sequences from random samples of individuals from three Filipino groups, including one Negrito group, the Mamanwa. We obtained on average ∼55-fold coverage per sequence, with <1% missing data per sequence. Various analyses attest to the accuracy of the sequences, including comparison to sequences of the first hypervariable segment of the control region generated by Sanger sequencing; patterns of nucleotide substitution and the distribution of polymorphic sites across the genome; and the observed haplogroups. Bayesian skyline plots of population size change through time indicate similar patterns for all three Filipino groups, but sharply contrast with such plots previously constructed from biased sampling of complete mtDNA genomes, as well as with an artificially constructed sample of sequences that mimics the biased sampling. Our results clearly demonstrate that the high-throughput sequencing platforms are the methodology of choice for generating complete mtDNA genome sequences

The Y-chromosome point mutation rate in humans.

Mutations are the fundamental source of biological variation, and their rate is a crucial parameter for evolutionary and medical studies. Here we used whole-genome sequence data from 753 Icelandic males, grouped into 274 patrilines, to estimate the point mutation rate for 21.3 Mb of male-specific Y chromosome (MSY) sequence, on the basis of 1,365 meioses (47,123 years). The combined mutation rate for 15.2 Mb of X-degenerate (XDG), X-transposed (XTR) and ampliconic excluding palindromes (rAMP) sequence was 8.71 × 10(-10) mutations per position per year (PPPY). We observed a lower rate (P = 0.04) of 7.37 × 10(-10) PPPY for 6.1 Mb of sequence from palindromes (PAL), which was not statistically different from the rate of 7.2 × 10(-10) PPPY for paternally transmitted autosomes. We postulate that the difference between PAL and the other MSY regions may provide an indication of the rate at which nascent autosomal and PAL de novo mutations are repaired as a result of gene conversion.Rannis, Icelandic Student Research Fund/1103340061 info:eu-repo/grantAgreement/EC/FP7/29034

Supplementary Figure 13. MDS plots with African reference populations (Affymetrix)

Plots showing the first two dimensions of an MDS analysis with HJ’s reconstructed maternal genome along with (a) African reference populations and (b) West African reference populations typed on the Affymetrix platforms

Supplementary Figure 8. Chromosome drop simulation

The results from simulations where the transmission of African fragments from a single ancestor’s genome was examined, conditional on the genealogical structure that connects HJ to his 182 genotyped descendants. The figure shows the null distributions for the expected proportion of genome covered by fragments transmitted to the 182 descendants under three different assumptions about the African ancestry of HJ: 25% (green), 50 % (yellow) and 100 % (blue). The observed proportion (0.38) of genome covered by African fragments found in the 182 HJ descendants is shown as a red line

Supplementary Figure 6. Filtering African fragments

A flowchart showing the filtering procedure applied to African fragments identified using HAPMIX. Red arrows indicate a negative outcome whereas green arrows indicate positive outcome. Both are labelled by the number of fragments affected. Parental origin is abbreviated as PO, Hans Jonatan is abbreviated as HJ and genotyped ancestor is abbreviated as GA

Supplementary Figure 4. African ancestry in all genotyped Icelanders

A comparison of African ancestry estimates from HAPMIX and ADMIXTURE for (a) 17,199 chip-typed Icelanders born between 1880-1930 (b) 63,099 chip-typed Icelanders born between 1931-1960 and (c) 70,716 chip-typed Icelanders born between 1961-2017. Descendants of HJ are shown as red squares and other Icelanders are shown as black circles. <a href="https://doi.org/10.6084/m9.figshare.5640985">See Supplementary Note for further details.</a><p></p

Supplementary Table 8. Estimation of imputation error rate

The imputed SNPs in the long-range phasing step was compared against the SNPs called from the sequencing data. We excluded SNPs where we found missing allele

Supplementary Note. African ancestry in Icelanders not descended from HJ

<div>This supplementary note describes analyses undertaken to determine whether African fragments identified in descendants of HJ could be derived from other ancestors from the Icelandic population with African ancestry.</div

Supplementary Table 3. Filtering HAPMIX inferred African fragments

African fragments inferred in HJ descendants by HAPMIX in haploid mode. Each putative African fragment is listed with information about the parent of origin, represented as “P” for paternal and “M” for maternal, and the breakpoints in physical positions and centi-Morgans (cM).When an ancestor on the path to HJ is also genotyped (GA), the following information is also provided for the most recent GA. First, whether the fragment is present in the GA (and if present, its parental origin in the GA) (ii). Second, whether the fragment is also identified as African in the GA. Third, the expected parent of origin in the GA. Two additional variables indicate whether a fragment is inherited from the correct parent of origin and is consistent with the genealogy (when GA is present). The number of genotyped Icelanders who are not descendants of HJ, but completely share the fragment, is also given (out of a total of 150,832)

Supplementary Figure 10. Decay of African ancestry

The probabilities of African ancestries as estimated by HAPMIX were averaged for the entire autosomal genome for every descendant. These ancestry estimates were plotted within each generation