DOI: 10.5061/dryad.2fqz612kn
title: Signals interpreted as archaic introgression are driven primarily by accelerated evolution in Africa

description: Non-African humans appear to carry a few percent archaic DNA due to
 ancient inter-breeding.  This modest legacy and its likely recent
 timing imply that most introgressed fragments will be rare and hence will
 occur mainly in the heterozygous state.  I tested this prediction
 by calculating D statistics, a measure of legacy size, for pairs of humans
 where one of the pair was conditioned always to be either homozygous or
 heterozygous.  Using coalescent simulations, I confirmed that
 conditioning the non-African to be heterozygous increased D while
 conditioning the non-African to be homozygous reduced D to zero. 
 Repeating with real data reveals the exact opposite pattern.  In
 African – non-African comparisons, D is near-zero if the African
 individual is held homozygous.  Conditioning one of two Africans
 to be either homozygous or heterozygous invariably generates large values
 of D, even when both individuals are drawn from the same
 population.  Invariably, the African with more heterozygous sites
 (conditioned heterozygous &gt; unconditioned &gt; conditioned
 homozygous) appears less related to the archaic.  In contrast,
 the same analysis applied to pairs of non-Africans always yields near-zero
 D, showing that conditioning does not create large D without an underlying
 signal to expose.  Large D values in humans are therefore driven
 almost entirely by heterozygous sites in Africans acting to increase
 divergence from related taxa such as Neanderthals.  In comparison
 with heterozygous Africans, individuals that lack African heterozygous
 sites, whether non-African or conditioned homozygous African, always
 appear more similar to archaic outgroups, a signal previously interpreted
 as evidence for introgression. I hope these analyses will encourage others
 to consider increased divergence as well as increased similarity to
 archaics as mechanisms capable of driving asymmetrical base-sharing.
description: These data are parsed versions of data derived from publicly
 available data.  For the Altai Neanderthal, I used simple C++ scripts
 applied to data available
 at http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/VCF/ to extract
 the minimal information required for my analyses: base location, human
 reference base and the four base counts, A, C, G , T in that order.  For
 the chimpanzee-human alignment, I downloaded raw alignments from http://www.ensembl.org/info/data/ftp/ and then extracted bases and aligned these to the human reference sequence hs37d5 used by the 1000 genomes project.  I excluded sites within 30 of either end of a contig.  Since most contigs are many tens of Kb long, the loss of information is minimal but at the same time, possible issues with alignment edge effects should be avoided.  
description: An annotated example of my
 C++ code is included as a supplementary file to the paper.  This
 can be pasted directly into, for example, Visual Studio.  The user will
 also need to download the equivalent chromosome vcf files from the 1000
 genomes project site, decompressing them and renaming them
 'ALL.chr[chromosome number].vcf', and edit my code so that the
 paths are appropriate for the computer on which the code is run.