1. The Divergence of Neandertal and Modern Human Y Chromosomes
Fernando L. Mendez, G. David Poznik, Sergi Castellano, Carlos D. Bustamante 
The American Journal of Human Genetics 
Volume 98, Issue 4, Pages (April 2016)
DOI: /j.ajhg
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2. Figure 1
Tree Inference
(A) A priori, three trees could feasibly have related the Y chromosomes of the chimpanzee (Chimp), the Neandertal (Neander), haplogroup A00, and the human reference (Ref). Mutations on branch a support topology i, with the Neandertal lineage as the outgroup to those of modern humans, whereas mutations on branches b and c support topologies ii and iii, respectively. Branches d, e, and f correspond to mutations private to individual lineages.
(B) Counts of SNVs consistent with each branch. Columns refer to sets of coordinates considered (see Materials and Methods). Incompatible sites are those that cannot be explained by a single mutation on any of the three trees.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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3. Figure 2 Estimating the TMRCA of Neandertal and Modern Y Chromosomes
The quantity of primary interest is TNR = TNM + TAR. Branches are labeled as in Figure 1, and “M” denotes the most recent common ancestor of modern human lineages.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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4. Figure 3
Relationship of Neandertal Y Chromosome to Those of Modern Humans
The genealogy (red tree) can be parsimoniously explained as mirroring the population divergence (gray tree). We find no evidence for (a) a highly divergent super-archaic origin of the Neandertal Y chromosome, (b) ancient gene flow post-dating the population split, or (c) relatively recent introgression of a modern human Y chromosome into the Neandertal population.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
Copyright © 2016 The Authors Terms and Conditions