C to T nucleotide misincorporations for the first and last 25 bases of endogenous mtDNA fragments.

<p>Red T; green C; blue A; purple G. The top panel shows that merged reads have an increased frequency of T at the 5’ end and A at the 3’ end (G to A misincorporation on the opposite strand of C to T misincorporation), a typical pattern of ancient DNA damage [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155046#pone.0155046.ref035" target="_blank">35</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155046#pone.0155046.ref036" target="_blank">36</a>]. The bottom panel shows that unmerged paired-end reads have an elevated frequency of T at the 5’ end, but in contrast with the above panel no increase in A at the 3’ end. This has occurred because mapDamage utilizes only the first read of a pair to calculate these frequencies. As the end of the first-read does not contain the sequence of the entire molecule, we would not expect to see an elevated A frequency at the end of the read. Therefore, these results are consistent with the unmerged reads originating from larger DNA fragments being ancient.</p

Final read depth and coverage for the mitochondrial genome of the ancient Phoenician from Carthage.

<p>The red line shows the mean read-depth of 33.15x.</p

Key variable sites from rCRS found in the young man from Byrsa, with the marker path of mutations defining Haplogroup U to U5b2c1.

<p>Note, the mutation 16192T was not present in our sample.</p

A maximum likelihood (ML) tree for the ancient Phoenician (KT760574) and other publicly available U5b2c sequences.

<p>All samples other than our Phoenician and the La Braña sample are from modern populations. Each node is annotated with the GenBank accession number or sample identification (e.g. Z2478 from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155046#pone.0155046.ref033" target="_blank">33</a>]), source or author if published, and the origin of the sample if recorded [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155046#pone.0155046.ref033" target="_blank">33</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155046#pone.0155046.ref038" target="_blank">38</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155046#pone.0155046.ref042" target="_blank">42</a>].</p

Mitochondrial haplogroups identified via complete mitochondrial genome sequencing in 47 modern Lebanese previously identified (based on HVR-1) as belonging to Haplogroup U.

<p>Mitochondrial haplogroups identified via complete mitochondrial genome sequencing in 47 modern Lebanese previously identified (based on HVR-1) as belonging to Haplogroup U.</p

Base frequency 5’ and 3’ of strand breaks.

<p>The gray brackets indicate the start and end of molecules (strand breaks). Frequencies are displayed for A, G, C, and T for the 10 bases 5’ and 3’ of the breaking site. The top panel shows that merged reads have an elevated frequency of purines (A and G) before strand breaks; this is consistent with the DNA molecules being ancient [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155046#pone.0155046.ref036" target="_blank">36</a>]. The bottom panel shows that unmerged reads have an elevated frequency of purines (A and G) before 5’ strand breaks but not 3’ strand breaks, this has occurred because mapDamage utilizes only the first read of a pair to calculate these frequencies. As the end of the first-read does not represent the end of the molecule, we would not expect to see an elevated purine frequency at the 3’ breaking site. Therefore, these results are consistent with the longer unmerged reads being ancient.</p

Divergence time estimates among European, Maghrebi, and Near Eastern ancestral populations.

<p>We use population-based F_st to estimate divergence time between each of the North African populations and the Qatari (green dots) and Tuscans (purple dots), respectively. We assume point estimates of effective population sizes based on autosomal haplotype heterozygosity estimates from Li et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397#pgen.1002397-Li1" target="_blank">[17]</a> (<i>Material and Methods</i>). We further estimate ancestral population clusters assigned at <i>k</i> = 5–8 with ADMIXTURE. Assuming that the ancestral clustering procedure has removed, or at least mitigated, the effect of recent migrations into Mediterranean populations, we then use F_st to estimate divergence times between these ancestral clusters. The range of <i>k</i>-based estimates for Maghrebi versus Near Eastern ancestry is indicated with light green polygon. The range of <i>k</i>-based estimates for Magrebi versus European ancestry is indicated with light purple polygon.</p

Multidimensional scaling components discriminating genetic clusters in Africa.

<p>We used multidimensional scaling (MDS) to discriminate clusters of genetic variation within Africa and neighboring regions. MDS was applied to the pairwise, individual identity-by-state (IBS) matrix of 279,500 SNPs using PLINK 1.07 software <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397#pgen.1002397-Purcell1" target="_blank">[45]</a>. The top three MDS components were plotted together using R 2.11.1. A) In axis one is plotted dimension 1 and in axis two is plotted dimension 2. B) In axis one is plotted dimension 1 and in axis two is plotted dimension 3. Population colors match <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397#pgen-1002397-g001" target="_blank">Figure 1B</a> (<i>k</i> = 8), with the exception that the Fulani group was highlighted as a distinct population, indicated in light green. North African populations are all indicated in turquoise except for Tunisians that are shown in dark blue.</p

Genome admixture deconvolution karyogram of an Egyptian.

<p>A single Egyptian individual is presented for ancestry assuming <i>k</i> = 4 source populations: Saharawi [SAH], Nilotic-speaking Maasai [MKK], Spanish Basque [BAS] and Arabic Qatari [QAT]. Maasai segments (which were inferred from <i>k</i> = 3 and were highly diverged from the SAH, QAT, BAS segments) are layered on top of the inferred Maghrebi/Qatari/Basque ancestral karyogram, for <i>k</i> = 4 putative source populations.</p

Correlation between ancestry proportions inferred from ADMIXTURE and PCADMIX.

<p>We compare the proportions of ancestry inferred from assuming 3 ancestral populations in individuals from South Morocco A) using a clustering algorithm set to <i>k</i> = 8 (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397#pgen-1002397-g001" target="_blank">Figure 1</a>) summing the sub-Saharan ancestry, both Qatar and European ancestry, and Maghrebi ancestry. We compared these estimates (left bar) to our PCA-based local ancestry assignment estimates (right bar). The three ancestral populations were Saharawi [SAH], Bantu-speaking Luhya [LWK], and Spanish Basque [BAS]. B) Genome admixture deconvolution on chromosome 1 of sixteen South Moroccans. Using a principal component-based method of admixture deconvolution, we assign local ancestry to South Moroccan individuals. We implement our PCA-based method for k = 3, and choose the ancestral populations based on the three ancestral populations were Saharawi [SAH], Bantu-speaking Luhya [LWK], and Spanish Basque [BAS]. Chromosome 1 for all sixteen South Moroccans is presented for both the maternal and paternal haplotypes.</p