Additional file 2: of Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

Figure S1. Phylogenetic tree of mtDNA macrohaplogroup L complete African sequences produced in this study. (XLSX 71 kb

Additional file 1: of Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

Table S1. Complete mtDNA macrohaplogroup L sequences. Table S2. Frequencies of mtDNA haplogroups L2 and L3 and Y-chromosome haplogroup E lineages across Africa. Table S3. Coalescence ages in thousand years (kya) with 95% coefficient intervals (CI), or standard deviations, for the main mitochondrial DNA African haplogroups. Table S4. Coalescence ages in thousand years (kya) with 95% coefficient intervals (CI), or standard deviations, for Y-chromosome most recent common ancestor (MRCA), the out-of-Africa event, and the splits of haplogroup DE and E. Table S5. Population clustering into five classes. Table S6. k-means cluster results using African populations characterized by mtDNA L3 and Y-chromosome E haplogroup frequencies. Table S7. k-means cluster results using African populations characterized by mtDNA L2 and L3 and Y-chromosome E haplogroup frequencies. (XLSX 403 kb

Additional file 2: Table S1. of Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

Haplogroup M in Saudi Arabia. In bold haplotypes from this study. Table S2. Super-haplogroup Ages and Geographic links. Table S3. Haplogroup M geographic ranges and ages in kiloyears (kya). Table S4. Populations used in the AMOVA and k-means clustering analyses. Table S5. Mitochondrial DNA M haplogroup ages and coordinates for their respective geographic centers used in the correlation analysis. Table S6. Modern human oldest fossil dating in different regions of Asia and oldest archaeological dating at the eastern side of the Wallace Line. (XLSX 91 kb

Additional file 1: Figure S1. of Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

Phylogenetic tree of M complete sequences from this study. (XLSX 66 kb

Additional file 1: Table S1. of Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area

Worldwide mtDNA haplogroup U3 sequences. Table S2. MtDNA haplogroup U3 haplotypic frequencies (%) in Eurasian and northern Africa main regions. Table S3. MtDNA complete U and P sequences obtained in this study. Table S4. Mitochondrial DNA haplogroup P frequencies (%) in the West Pacific Islands. Table S5. Mitochondrial DNA haplogroup frequencies (%) in Australia. Table S6. Frequency (%) of major mtDNA macrohaplogroup R branches in different regions of Eurasia and Australasia. Table S7. MtDNA macrohaplogroup M, N and R frequencies (%) in Eurasia and Australasia. Table S8. Mantel tests based on correlations between geographic distances (a), genetic distances (b), and genetic identities (c). Table S9. Coalescence ages for the main branches of mtDNA haplogroup R in different geographic areas. (XLSX 266 kb

Additional file 2: of Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area

Figure S1. MtDNA haplogroup U phylogeny with emphasis on the U3 branch. Figure S2. MtDNA haplogroup P phylogeny. (XLSX 175 kb

Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asian Route

<div><p>Background</p><p>The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route.</p><p>Methods</p><p>MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, and more than 70,000 partial mtDNA sequences were screened to establish their respective geographic ranges.</p><p>Results</p><p>The Saudi mtDNA profile confirms the absence of autochthonous mtDNA lineages in Arabia with coalescence ages deep enough to support population continuity in the region since the out-of-Africa episode. In contrast to Australia, where N(xR) haplogroups are found in high frequency and with deep coalescence ages, there are not autochthonous N(xR) lineages in India nor N(xR) branches with coalescence ages as deep as those found in Australia. These patterns are at odds with the supposition that Australian colonizers harboring N(xR) lineages used a route involving India as a stage. The most ancient N(xR) lineages in Eurasia are found in China, and inconsistently with the coastal route, N(xR) haplogroups with the southernmost geographical range have all more recent radiations than the Australians.</p><p>Conclusions</p><p>Apart from a single migration event via a southern route, phylogeny and phylogeography of N(xR) lineages support that people carrying mtDNA N lineages could have reach Australia following a northern route through Asia. Data from other disciplines also support this scenario.</p></div

Age estimates, in thousands of years, for L3, M, and the main branches of haplogroup N.

<p>1.- Age estimates from complete sequences using rho and the calculator provided by Soares et al. 2009.</p><p>2.- a = Derenko et al. 2013; b = Fernandes et al. 2012; c = Fu et al. 2013; d = Gonder et al. 2007; e = Kong et al. 2011; f = Kushniarevich et al. 2013; g = Pierron et al. 2011; h = Soares et al. 2009.</p><p>Age estimates, in thousands of years, for L3, M, and the main branches of haplogroup N.</p

Geographic dispersal routes of (A) AMH out of Africa migration, and (B) secondary worldwide human expansions, deduced from the age and geographic localization of L3 and N(xR) mtDNA haplogroups including Lineages O and S from Australia.

<p>Climatic marine isotope stages (MIS) and most probable places of genetic admixture with Neanderthals and Denisovans are depicted. Dotted lines in B mean probable gene flow between populations from different dispersals.</p

Coordinates for haplogroups assigned to the northern route with observed and expected age values.

<p>Coordinates for haplogroups assigned to the northern route with observed and expected age values.</p