1. The role of gene conversion in preserving rearrangement hotspots in the human genome 
Jeffrey A. Fawcett, Hideki Innan 
Trends in Genetics 
Volume 29, Issue 10, Pages (October 2013)
DOI: /j.tig
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2. Figure 1
Diagram of non-allelic homologous recombination (NAHR) hotspots and two models of their evolution. (A) Illustration of NAHR between tandem segmental duplications (SDs; green arrows) that results in the duplication or deletion of the intervening region (the outcome would be an inversion if the SDs are in inverted orientation). Two models could explain the evolution of NAHR hotspots. (B) The turnover model assumes that the two SD copies diverge in proportion to time and, thus, quickly become unable to initiate NAHR. Therefore, new hotspots must constantly arise for a certain number of hotspots to remain in the genome. (C) The gene conversion model considers the effect of paralogous gene conversion, which maintains the similarity between the two copies. Therefore, the SD is able to initiate NAHR for a much longer period of time.
Trends in Genetics  , DOI: ( /j.tig )
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3. Figure 2
The probability for observing the longest identical stretch present in the segmental duplications (SDs) flanking the copy number variants (CNVs). (A) The observed longest identical stretch (bp) within each SD pair flanking a CNV region is plotted against the divergence level. The significance of the observed length for each SD was evaluated by creating random patterns of divergence where the diverged nucleotide positions are distributed randomly across the entire SD, and are shown as filled squares, triangles, and circles when significant (P <0.05, <0.01, and <0.0001, respectively), and by open circles when not significant. (B) Typical distribution of the longest identical stretch in the randomized data used for evaluating the significance in (A). Only some of the data are shown to demonstrate the point. The vertical gray lines show the time corresponding to the average genome-wide nucleotide divergence between human and chimpanzee, orangutan, and macaque [62].
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4. Figure I
The probability that a given segmental duplication (SD) pair of 1kb, 10kb, and 100kb (red, green, and blue lines, respectively) will retain an identical stretch of ≥200bp based on simulation runs. The expected probability was calculated by a simulation following the model in [61]. The model assumes random accumulation of point mutations at a rate of 10−9/site/generation and that gene conversion occurs at a given rate c per site (see [61] for details). The red, green, and blue solid lines represent simulation results of SDs of 1kb, 10kb, and 100kb when c=0, and the green-dashed lines represent results of a 10-kb SD when c={1,3,5}×10−8 with an average tract length of 1kb (1/Q=0.1 in [61]) representing low, intermediate, and high gene conversion rates. The vertical gray lines approximately correspond to the divergence between human and chimpanzee, orangutan, and macaque.
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5. Figure I
Illustration of how duplicates diverge in the presence of gene conversion. The green bars represent regions within the segmental duplications (SDs) that are undergoing gene conversion. Regions undergoing gene conversion gradually decrease due to large indels or the accumulation of mutations. (A) Scenario where the termination of gene conversion occurs randomly throughout the SD. Regions undergoing gene conversion in each species differ, although they are not entirely independent due to their shared history. (B) Scenario where selection favors ongoing gene conversion in specific regions (blue bar) due to some functional constraint. The continuation and termination of gene conversion is not random, and the same region likely retains high similarity in each species.
Trends in Genetics  , DOI: ( /j.tig )
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