Abstract
BackgroundAlu elements are the most abundant mobile elements in the human genome, with over 1 million copies and constituting more than 10% of the genome. The majority of these Alu elements were inserted into the primate genome 35 to 60 million years ago, but certain subfamilies of Alu elements are relatively very new and suspected to be still evolving. We attempted to trace the source/master copies of all human-specific members of the Alu Yb lineage using a computational approach by clustering similar Yb elements and constructing an evolutionary relation among the members of a cluster.ResultsWe discovered that one copy of Yb8 at 10p14 is the source of several active Yb8 copies, which retrotransposed to generate 712 copies or 54% of all human-specific Yb8 elements. We detected eight other Yb8 elements that had generated ten or more copies, potentially acting as 'stealth drivers’. One Yb8 element at 14q32.31 seemed to act as the source copy for all Yb9 elements tested, having producing 13 active Yb9 elements, and subsequently generated a total of 131 full-length copies. We identified and characterized three new subclasses of Yb elements: Yb8a1, Yb10 and Yb11. Their copy numbers in the reference genome are 75, 8 and 16. We analysed personal genome data from the 1000 Genome Project and detected an additional 6 Yb8a1, 3 Yb10 and 15 Yb11 copies outside the reference genome. Our analysis indicates that the Yb8a1 subfamily has a similar age to Yb9 (1.93 million years and 2.15 million years, respectively), while Yb10 and Yb11 evolved only 1.4 and 0.71 million years ago, suggesting a linear evolutionary path from Yb8a1 to Yb10 and then to Yb11. Our preliminary data indicate that members in Yb10 and Yb11 are mostly polymorphic, indicating their young age.ConclusionsOur findings suggest that the Yb lineage is still evolving with new subfamilies being formed. Due to their very young age and the high rate of being polymorphic, insertions from these young subfamilies are very useful genetic markers for studying human population genetics and migration patterns, and the trend for mobile element insertions in the human genome.
Highlights
Alu elements are the most abundant mobile elements in the human genome, with over 1 million copies and constituting more than 10% of the genome
Our study focuses on human-specific Alu elements from the Yb lineage, mainly because they are the second largest young family by the number of copies in the human genome, comprising 40% of all humanspecific Alu elements with more than 30% of these copies being polymorphic between individuals and/or populations [15,16,21]
Evolution of recent Alu Yb elements Of all Yb copies found in the human genome, 80% (2,545 of 3,179) are identified as human-specific, that is, they became integrated into the human genome after the human–chimp divergence, and they only include members of the Yb8 and Yb9 subfamilies (Tang et al, manuscript in preparation)
Summary
Alu elements are the most abundant mobile elements in the human genome, with over 1 million copies and constituting more than 10% of the genome. Since almost all of these young Alu elements were inserted into the human genome after the human– chimp divergence, they are only found in humans Some of these young active Alu elements have accumulated new mutations and have acted as source or master copies by generating subsets of elements that are identifiable as new subfamilies. Some of these subfamilies are so recent that they have members that are polymorphic for their presence or absence between individuals and/or populations [12,13,14]. The homoplasy-free nature of Alu elements makes their polymorphic insertions very useful in phylogenetic studies, human population studies, forensics and DNA fingerprinting [9,17,18,19,20]
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