A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution

Human accelerated regions (HARs) are DNA sequences that changed very little throughout mammalian evolution, but then experienced a burst of changes in humans since divergence from chimpanzees. This unexpected evolutionary signature is suggestive of deeply conserved function that was lost or changed on the human lineage. Since their discovery, the actual roles of HARs in human evolution have remained somewhat elusive, due to their being almost exclusively non-coding sequences with no annotation. Ongoing research is beginning to crack this problem by leveraging new genome sequences, functional genomics data, computational approaches, and genetic assays to reveal that many HARs are developmental gene regulatory elements and RNA genes, most of which evolved their uniquely human mutations through positive selection before divergence of archaic hominins and diversification of modern humans.

Ascertaining regions affected by GC-biased gene conversion through weak-to-strong mutational hotspots

A major objective for evolutionary biology is to identify regions affected by positive selection. High dN/dS values for proteins and accelerated lineage-specific substitution rates for non-coding regions are considered classic signatures of positive selection. However, these could also be the result of non-adaptive phenomena, such as GC-biased gene conversion (gBGC), which favors the fixation of strong (C/G) over weak (A/T) nucleotides. Recent estimates indicate that gBGC affected up to 20% of regions with signatures of positive selection. Here we evaluate the impact of gBGC through its molecular signature of weak-to-strong mutational hotspots. We implemented specific modifications to the test proposed by Tang and Lewontin (1999) for identifying regions of differential variability and applied it to regions previously investigated for the influence of gBGC. While we found significant agreement with previous reports, our results suggest a smaller influence of gBGC than previously estimated, warranting further development of methods for its detection.

Meiotic recombination strongly influences GC-content evolution in short regions in the mouse genome

Meiotic recombination is known to influence GC-content evolution in large regions of mammalian genomes by favoring the fixation of G and C alleles and increasing the rate of A/T to G/C substitutions. This process is known as GC-biased gene conversion (gBGC). Until recently, genome-wide measures of fine-scale recombination activity were unavailable in mice. Additionally, comparative studies focusing on mouse were limited as the closest organism with its genome fully sequenced was rat. Here, we make use of the recent mapping of double strand breaks (DSBs), the first step of meiotic recombination, in the mouse genome and of the sequencing of mouse closely related subspecies to analyze the fine-scale evolutionary signature of meiotic recombination on GC-content evolution in recombination hotspots, short regions that undergo extreme rates of recombination. We measure substitution rates around DSB hotspots and observe that gBGC is affecting a very short region (≈ 1 kbp) in length around these hotspots. Furthermore, we can infer that the locations of hotspots evolved rapidly during mouse evolution.