Friday, October 7, 2016

Pagani et al., Paragraphs 6-11:

Pagani et al
Published online

Paragraphs 6-11:

"Using fineSTRUCTURE, we find in the genomes of Papuans and Philippine Negritos more short haplotypes assigned as African than seen in genomes for individuals from other non-African populations (Extended Data Fig. 7). This pattern remains after correcting for potential confounders such as phasing errors and sampling bias (Supplementary Information 2.2.1). These shorter shared haplotypes would be consistent with an older population split [25].  Indeed, the Papuan–Yoruban median genetic split time (using multiple sequential Markovian coalescent (MSMC)) of 90 kya predates the split of all mainland Eurasian populations from Yorubans at ~75 kya (Supplementary Table 1:2.2.3-I, Extended Data Fig. 4, Fig. 2a).  This result is robust to phasing artefacts (Extended Data Fig. 8, see Methods). Furthermore, the Papuan–Eurasian MSMC split time of ~40 kya is only slightly older than splits between west Eurasian and East Asian populations dated at ~30 kya (Extended Data Fig. 4).  The Papuan split times from Yoruba and Eurasia are therefore incompatible with a simple bifurcating population tree model.

"At least two main models could explain our estimates of older divergence dates for Sahul populations from Africa than mainland Eurasians in our sample:  1) admixture in Sahul with a potentially un-sampled archaic human population that split from modern humans either before or at the same time as did Denisova and Neanderthal; or 2) admixture in Sahul with a modern human population (extinct OoA line; xOoA) that left Africa after the split between modern humans Africa after the split between modern humans.

"We consider support for these two non-mutually exclusive scenarios.  Because the introgressing lineage has not been observed with aDNA, standard methods are limited in their ability to distinguish between these hypotheses. Furthermore, we show (Supplementary Information 2.2.7) that single-site statistics, such as Pattersons D [9],[18] and sharing of non-African Alleles (nAAs), are inherently affected by confounding effects owing to archaic introgression in non-African populations [23]Our approach therefore relies on multiple lines of evidence using haplotype-based MSMC and fineSTRUCTURE comparisons (which we show should have power at this timescale [26]; Supplementary Information 2.2.13).

"We located and masked putatively introgressed [27] Denisova haplotypes from the genomes of Papuans, and evaluated phasing errors by symmetrically phasing Papuans and Eurasians genomes (Methods). Neither modification (Fig. 2a, Supplementary Information 2.2.9, Supplementary Table 1:2.2.9-I) changed the estimated split time (based on MSMC) between Africans and Papuans (Methods, Supplementary Information 2.2.8, Extended Data Fig. 8, Supplementary Table 1.2.8-I). MSMC dates behave approximately linearly under admixture (Extended Data Fig. 8), implying that the hypothesized lineage may have split from most Africans around 120 kya (Supplementary Information 2.2.4 and 2.2.8).


"We compared the effect on the MSMC split times of an xOoA or a Denisova lineage in Papuans by extensive coalescent simulations Supplementary Information 2.2.8). We could not simulate the large Papuan–African and Papuan–Eurasian split times inferred from the data, unless assuming an implausibly large contribution from a Denisova-like population. Furthermore, while the observed shift in the African–Papuan MSMC split curve can be qualitatively reproduced when including a 4% genomic component that diverged 120 kya from the main human lineage within Papuans, a similar quantity of Denisova admixture does not produce any significant effect (Extended Data Fig. 8). This favours a small presence of xOoA lineages rather than Denisova admixture alone as the likely cause of the observed deep African–Papuan split. We also show (Methods) that such a scenario is compatible with the observed mitochondrial DNA and Y chromosome lineages in Oceania, as also previously argued [13,28].

"We further tested our hypothesized xOoA model by analysing haplotypes in the genomes of Papuans that show African ancestry not found in other Eurasian populations. We re-ran fineSTRUCTURE adding the Denisova, Altai Neanderthal and the Human Ancestral Genome sequences [29] to a subset of the diversity set.  FineSTRUCTURE infers haplotypes that have a most recent common ancestor (MRCA) with another individual. Papuan haplotypes assigned as African had, regardless, an elevated level of non-African derived alleles (that is, nAAs fixed ancestral in Africans) compared to such haplotypes in Eurasians. They therefore have an older mean coalescence time with our African samples."


"Figure 2a.  Evidence of an xOoA signature in the genomes of modern Papuans. a, MSMC split times plot. The Yoruba–Eurasia split curve shows the mean of all Eurasian genomes against one Yoruba genome. The grey area represents top and bottom 5% of runs. We chose a Koinanbe (sic) genome
as representative of the Sahul populations."

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