A Signal of Neandertal Admixture in Modern Human mtDNA?

Russian Journal of Genetics, September 2013, Vol. 49, No. 9, 975-978
Mitochondrial DNA Polymorphisms Shared Between Modern Humans and Neanderthals: Adaptive Convergence or Evidence for Interspecific Hybridization
Malyarchuk, Boris A.
An analysis of the variability of the nucleotide sequences in the mitochondrial genome of modern humans, neanderthals, Denisovans, and other primates has shown that there are shared polymorphisms at positions 2758 and 7146 between modern Homo sapiens (in phylogenetic cluster L2′3′4′5′6) and Homo neanderthalensis (in the group of European neanderthals younger than 48 000 years). It is suggested that the convergence may be due to adaptive changes in the mitochondrial genomes of modern humans and neanderthals or interspecific hybridization associated with mtDNA recombination.
It’s an intriguing publication by a Magadan-based Russian geneticist Boris Malyarchuk (Борис Малярчук) known for his team leadership on several English-language publications devoted to mtDNA variation in Siberia and the New World. Using a novel statistical program, Malyarchuk identified two nucleotide positions identical between European Neandertals and modern humans belonging to the African L2’3’4’5’6 cluster and extra-African M, N and R lineages (under current mtDNA phylogenies M and N are part of L3 and R is part of N) (see below).
Gisele Horvat has kindly provided me with the actual sequence data around the two sites identified by Malyarchuk as uniquely shared between humans and Neandertals (reproduced below, with permission).
I will continue to update the post as I investigate more around its significance. At face value, if we give preference to the admixture hypothesis over the convergence hypothesis, the data seems to furnish a missing link between a) autosomal data suggesting that “Neandertal admixture” is present in all non-Africans (to a various degree) plus East Africans (see more here); b) and the Y-DNA phylogeny indicating that the main African Y-DNA clade E is a subset of the Eurasian clade CT (xC-F, xD-E). It’s especially notable that the clade showing an introgression from Neandertals encompasses all of African mtDNAs but haplogroups L0 and L1. Hgs L0 and L1 correspond closely to Y-DNA hgs A and B (both sets are highly frequent in Khoisans and Pygmies, are phylogenetically basal and not found outside of Africa).