The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome

Abstract

Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338 000 years ago (95% CI ¼ 237 000-581 000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100 000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208 300 (95% CI ¼ 163 900-260 200) years ago.

Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences

“…/bp/year as there is currently much uncertainty regarding mutation rates [5,40,41,51,52]. The resulting phylogenies are in general consistent with the existing mtDNA and NRY phylogenies [31,53], although there are some discrepancies, for example, in the mtDNA tree ( Figure 3A) L1 sequences group with L0 sequences rather than on the other side of the root, while additional discrepancies can be found in the NRY trees.…”

The Role of Geomagnetic Field Intensity in Late Quaternary Evolution of Humans and Large Mammals

“…However, other researchers (e.g., Wang et al, ) have pointed out that this ancient TMRCA can be partially attributed to the low substitution rate used by the authors. By using either a higher mutation rate or more extensive sequencing data, the estimate of TMRCA becomes much younger at about 208 ka (Elhaik et al, ) or 257 ka (D'Atanasio et al, ).…”

“…However, other researchers (e.g., Wang et al, 2014) have pointed out that this ancient TMRCA can be partially attributed to the low substitution rate used by the authors. By using either a higher mutation rate or more extensive sequencing data, the estimate of TMRCA becomes much younger at about 208 ka (Elhaik et al, 2014) Phylogeny based on mtDNA sequence data has provided an estimate of TMRCA (190 ka) with branching episodes at~120,~70,~40, and~15 ka, which coincide with AMH dispersal patterns (Oppenheimer, 2012). Wei et al (2013) used five substitution models to assess phylogenetic nodes from the TMRCA of 29 Y chromosomes that yielded branching ages for one of the models (GENETREE-2) of 112 ±12 ka, 68 ±7 ka, 49 ±6 ka, and 13 ±2 ka.…”

Reply to Mendez et al: the ‘extremely ancient’ chromosome that still isn’t

“…In Elhaik et al (2014), we discussed many such choices and there is no need to refute every "refutation" in Mendez et al (2014) as their arguments depart from the central issues we had raised. In the following we will focus on two choices left unexplained by Mendez et al (2013).…”