This will be a very short post. I came across a paper published in Nature in 2020, by V. M. Cabrera (Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock. BMC Evol. Biol. 20, 1–9 , 2020) which, as you can see by its title is about the uneven rate at which mutations accumulate in mitochondrial genomes, it can run faster or slower and the research cited by Cabrera attributes it to "changes in the effective population size of the human populations." Another factor mentioned by Cabrera are " "transient polymorphisms... play a slowdown role in the evolutionary rate deduced from haplogroup intraspecific trees".
Transient polymorphisms
These are short-lived variants that through selection take over and displace another. Later, they are themselves replaced, hence their name (transient). An example is the classical moths of England, they came in two varieties, light colored and dark. Before the industrial revolution, the light ones prevailed, as the dark ones were very visible (easy preys) on the pale tree trunks. Then, when the industrial soot of coal furnaces darkened the bark, the situation changed, and the dark ones were less visible. Soon they displaced the ligher colored moths (dark allele replaced pale one). However, in the 1970s, with pollution abating measures in place, the bark of trees became pale once again, and the light colored moths now prevail over the dark ones.
Regarding variability as time passes, Cabrera mentions an interesting fact: "For example, an ancient mtDNA study has corroborated empirically the persistence of an ancestral M lineage unaltered along a period of more than 8000 years" and adds that "Consequently, a lineage could remain immutable for several generations while identical lineages in the same population suffer one or several mutational changes in the same time interval."
This situation is shown in the paper's Figure 2, shown below, which very clearly shows how mutations can be overlooked when building a tree, and its effect on the mutation rate that is inferred from it. Cabrera describes the figure as follows: "We represent such a scenario in Fig. 2A as a maternal genealogy. Notice that the ancestral lineage can give rise to offspring in different generations throughout its existence in the population. In this way, when the population is sampled after n generations, we can find, in addition to the ancestral lineage (e), lineages derived from it that have accumulated significant mutational differences in their branches (f, h). However, this fact is not reflected in the tree built from the same sample (Fig. 2B) because, irrespective of the generation in which they appeared, all derived lineages sprout at the same time from the ancestral node (e). This difference between genealogies and trees has notable consequences. On the one hand, it could explain the lack of mutation rate homogeneity between lineages found in intraspecific haplogroup.""
Cabrera then calculates the ages of the different mtDNA haplogroups, and finds a relatively old age for the entry of humans into America:
"Finally, although we proposed a unique migration for the colonization of the Americas around 40,000 years ago (20) which is directly or indirectly supported by archaeological dates, it seems possible that this first migration, signaled by the ages of haplogroups A2 and B2 was followed afterwards by a second wave, also before the Last Glacial Maximum, marked by haplogroups C1, D1, D4h3a and X2a around 27,500 years ago (Table 3).
Note 1. The figures from Table 3 are these: C1: 30 ky, D1: 32 ky, D4h3a: 26 ky, and X2a: 22 ky.
Note 2. Cabrera in (20) is citing himself! (Cabrera, V. M., 2020, Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock. BMC Evol. Biol. 20, 1–9.)
This second paper by Cabreera, cited above as (20), states that "Finally, the time of human expansion to the American Continent deduced from the haplogroup B2 phylogeny was approximately 37,000 ya (Table 1, and Table S11). This age supports a pre-Clovis occupation of the New World, well before the last glacial maximum."
I am happy to see someone who is pushing the boundaries towards an older date, 40-37 ky ago. This is positive. It will open the door for others to use this information to validate their findings of an even earlier date for the arrival of modern humans to America.
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