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Human Males Underwent Bursts of Population Growth, According to Y Chromosome Sequence Analysis

NEW YORK (GenomeWeb) – Human males underwent bursts of population growth, according to a new analysis of Y chromosome sequences.

As they reported today in Nature Genetics, researchers from the Wellcome Trust Sanger Institute and elsewhere analyzed the Y chromosomes of more than 1,200 men from 26 populations using data collected by the 1000 Genome Project. After examining about 65,000 variants contained within this dataset, the researchers constructed a phylogenetic tree — a tree, they noted, that more closely resembled a bush in some spots.

"This pattern tells us that there was an explosive increase in the number of men carrying a certain type of Y chromosome, within just a few generations," co-lead author Yali Xue from the Sanger Institute said in a statement. "We only observed this phenomenon in males, and only in a few groups of men."

Xue and her colleagues drew upon a set of 1,244 Y chromosomes from men belonging to 26 world populations that had been sequenced to a median haploid coverage of 4.3X. After mapping the reads generated against the human reference assembly, the researchers called more than 65,000 variants — including single-nucleotide variants, indels, multiple-nucleotide variants, copy-number variants, and short tandem repeats. Most of those variants — some 60,500 — were SNVs.

Once they'd identified each man's Y-chromosome haplogroup, the researchers used the 60,555 SNVs they uncovered to construct a maximum-likelihood phylogenetic tree. This tree, they noted, encompasses all except two of the major world haplogroups. In their estimation — based on a mutation rate of 0.76 x 10-9 mutations per base pair per year — the time to most recent common ancestor of all males is some 190,000 years.

While they said that the phylogenetic tree they generated reflects the expected tree structure, the researchers also reported some refinements.

Xue and her colleagues noted that the branching patterns they observed among several lineages indicated extreme expansion some 50,000 years to 55,000 years ago as well as within the last few thousand years. The expansion 50,000 years to 55,000 years ago was also linked to an increase in lineages outside of Africa and could, they suggested, reflect the expansion of Eurasian populations.

It also supports the previously proposed notion that haplogroup E, which is the most predominant one in Africa, actually arose outside the continent and arrived there through gene flow from Asia some 50,000 years to 80,000 years ago.

The phylogenetic tree also hints that lineages that have spread throughout Eurasia may have first diversified within South and Southeast Asia. A Vietnamese man within this dataset belongs to a rare F lineage that is an outgroup for the rest of the megahaplogroup. This man's sequence also includes the derived allele for 147 SNPs that are specific to the F-haplogroup Y chromosomes in the sample, though his lineage split off from the rest about 55,000 years ago. Based on this, Xue and her colleagues determined that there is a new megagroup, dubbed GHIK-M3638, that includes most non-African men.

Xue and her colleagues also modeled the growth of these haplogroups. They found that 20 nodes of the phylogenetic tree fit a pattern marked by a rapid phase of growth followed by moderate growth phase — a pattern not observed in mitochondrial DNA.

They suggested that these bursts of male population growth might correspond to historical events. For instance, they noted an expansion of the Q1a-M3 lineage in the Americas some 15,000 years ago, which roughly corresponds with initial peopling there. In addition, they found that both the Eb1-M180 lineages in sub-Saharan Africa underwent an expansion about 5,000 years ago at about the time of the Bantu expansion. Finally, within Western Europe, they said the expansion of the R1b-L11 lineages some 4,800 years to 5,900 years ago could be associated with the rise of the Bronze Age Yamnaya culture.

The researchers were less certain about the reasons behind some of the other late expansions they observed.

"The best explanation is that they may have resulted from advances in technology that could be controlled by small groups of men," the Sanger Institute's Chris Tyler­-Smith added. "Wheeled transport, metal working, and organized warfare are all candidate explanations that can now be investigated further."