The time when Y-chromosomal Adam lived is determined by applying a molecular clock to human Y-chromosomes. In contrast to mitochondrial DNA, which has a short sequence of 16,000 base pairs, and mutates frequently, the Y chromosome is significantly longer at 60 million base pairs, and has a lower mutation rate. These features of the Y chromosome have slowed down the identification of its polymorphisms and as a consequence, reduced the accuracy of Y-chromosome mutation rate estimates. Initial studies, such as Thomson et al. 2000, proposed that Y-chromosomal Adam lived about 59,000 years ago. This date suggested that Y-chromosomal Adam lived tens of thousands of years after his female counterpart Mitochondrial Eve, who lived 150,000–200,000 years ago. This date also meant that Y-chromosomal Adam lived at a time very close to, and possibly after, the migration from Africa which is believed to have taken place 50,000–80,000 years ago.
One explanation given for this discrepancy in the dates of Adam and Eve was that females have a better chance of reproducing than males due to the practice of polygyny. When a male individual has several wives, he has effectively prevented other males in the community from reproducing and passing on their Y chromosomes to subsequent generations. On the other hand, polygyny doesn't prevent most females in a community from passing on their mitochondrial DNA to subsequent generations. This differential reproductive success of males and females can lead to fewer male lineages relative to female lineages persisting into the future. These fewer male lineages are more sensitive to drift and would most likely coalesce on a more recent common ancestor. This would potentially explain the more recent dates associated with Y-chromosomal Adam.
The 2011 study by Cruciani et al. found that Y-chromosomal Adam lived about 142,000 years ago, significantly earlier than previous estimates, such as the 59,000 years ago estimate proposed by Thomson et al. 2000. The older TMRCA was due to the discovery of additional mutations and the rearrangement of the backbone of the y-chromosome phylogeny following the resequencing of Haplogroup A lineages. According to the study, determining the precise date when Y-chromosomal Adam lived depends on the accuracy of the mutation rate used. But the repositioning of the MRCA from the root of Haplogroups A and BT to the root of Haplogroups A1b and A1a still entails that Y-chromosomal Adam is older than previously thought. According to Cruciani et al., the much older date is easier to reconcile with models of human origins.
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