* Department of Ecology and Evolution, University of Chicago; Institute of Zoology, National Taiwan University, Taipei, Taiwan; and
Department of Biological Sciences, University of South Carolina, Columbia
Correspondence: E-mail: whli{at}uchicago.edu.
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Abstract |
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Key Words: pseudoautosomal region recombination rate mutation rate nucleotide substitution
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Introduction |
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It has also been observed that recombination, or more precisely gene conversion, is GC biased, promoting mutations from A and T to G and C (Brown and Jiricny 1988, 1989; Eyre-Walker 1993; Perry and Ashworth 1999; Fullerton, Bernardo Carvalho, and Clark 2001; Montoya-Burgos, Boursot, and Galtier 2003; Marais 2003). Again, the strength of bias has not been well established and needs further investigation. For the same reason as above, the Fxy gene in Mus is suitable for addressing this issue. For the above two purposes, we have sequenced parts of introns 1, 2, and 3 (non-PAR located) and parts of introns 4 through 7 (PAR-located) in M. m. musculus, M. m. domesticus, M. spretus, and M. caroli. In addition, we have also used published data from PAR and non-PAR regions in mammals to address the above two issues.
To pursue the present study, it is useful to know the origin of the partially PAR-located Fxy gene in the Mus genus. Montoya-Burgos, Boursot, and Galtier (2003) proposed that a duplication of Fxy occurred and one copy moved to be partially inside the PAR region in the common ancestor of M. spretus and M. musculus. In this study, we found no evidence for either the proposed duplication or the presence of a partially PAR-located Fxy gene in M. spretus. Thus, the sliding of Fxy into the PAR probably occurred in the ancestor of M. musculus.
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Methods |
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Evolutionary Analysis
Sequences were aligned using ClustalW (Thompson et al. 1997). The neighbor-joining method (Saitou and Nei 1987) and the Kimura two-parameter model of sequence evolution, as implemented in MEGA version 2 (Kumar et al. 2001), were used to infer the phylogeny of Mus Fxy.
To estimate the frequency of mutations in different lineages (Gojobori, Li, and Graur 1982; Li, Wu, and Luo 1984), the sequence of the ancestor was inferred at the phylogenetic node joining M. musculus, M. spretus, and M. caroli (outgroup). This method reconstructs an ancestral nucleotide sequence by assigning bases (A, G, C, or T) to the ancestral node based on the least number of changes along all lineages of a phylogeny that can account for the present-day nucleotide sequence differences. We use this simple method because the sequences under study are highly similar.
The assembled human genomic sequence (Golden Path alignment version hg16; repeat-masked) and recombination rate data (Kong et al. 2002) for all autosomes were obtained from the UCSC Genome Browser. The human autosomal sequence was divided into nonoverlapping bins of size 1 Mb (including repeats) and recombination rates (cM/Mb) assigned. Repetitive sequences were then removed for computing GC%.
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Results and Discussion |
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With no evidence of Fxy_PAR in M. spretus, the movement of Fxy into the PAR occurred after the divergence of M. spretus and M. musculuslikely before the diversification of the M. musculus lineage (Perry and Ashworth 1999). Also, in the absence of a duplication of Fxy in the Mus lineages, there is no need to invoke a gene loss and a translocation of Fxy to explain Fxy_PAR in M. musculus, as proposed by Montoya-Burgos, Boursot, and Galtier (2003). It is more likely that the PAR has slid along the X chromosome in the lineage leading to M. musculus.
Mutagenicity of Recombination
In Mouse
The introns sequenced were divided into two groups, roughly the first half (intron 1 to first-half of intron 3; 2,307 sites sequenced) and the second half (intron 4 to intron 6; 2,378 sites sequenced). Only the second half in M. m. domesticus (dom) and M. m. musculus (mus) is in the PAR.
To compare the rate of nucleotide substitutions in different regions and taxa, we constructed two neighbor-joining trees for the two halves of the Fxy gene (fig. 2). The total branch length between M. caroli (car) and M. spretus (spr) is 0.0163 + 0.0077 + 0.0043 = 0.0283 for the first half (fig. 2A) and 0.0580 for the second half (fig. 2B). Therefore, the second half has evolved two times faster than the first half. On the other hand, the total branch length between dom and mus is 0.0030 for the first half and 0.0150 (five times higher) for the second half. Therefore, we may infer that because of a very high recombination rate in the PAR, the substitution rate in the Mus PAR introns has increased 5/2 = 2.5 times.
We now consider a second estimate. From figure 2, we computed the average branch length from the common ancestral node of spr, dom, and mus to the tips of dom and mus as 0.0071 + (0.0015 + 0.0015)/2 = 0.0086 for the first half and 0.0821 for the second half. The estimated substitution rate for the second half is now 9.5 times faster than that for the first half. Therefore, we may infer that the high recombination rate in the second half has increased the substitution rate by 9.5/2 = 4.8-fold. As in the above estimate, this estimate assumes that the non-PAR second half has evolved two times faster than the first half. This estimate should be taken with caution for two reasons. First, the ratio 0.0821/0.0086 = 9.5 could have been inflated because the denominator is small, so that a small error can be easily amplified. Second, it assumes that the second half has been in the PAR since the divergence between the spr lineage and the dom-mus lineage, which may not be true.
A third estimate was obtained by comparing the branch length (0.0329) from the common node of spr, dom, and mus with spr and comparing the average branch length (0.0821) from the same common node with dom and mus. This comparison gives a ratio of 2.5 for the increase in substitution rate because of the increase in recombination rate. Again, this estimate assumes that the second half has been in the PAR since the divergence between the spr and the dom-mus lineages. Despite this assumption, it might not be an underestimate because in the first half (fig. 2A) the average branch length (0.0071 + 0.0015 = 0.0086) for the dom-mus lineage is twice as long as that for the spr lineage (0.0043), suggesting the possibility of a faster clock in the dom-mus lineage than in the spr lineage.
From the above three estimates, we suggest that the increase in recombination rate in the PAR has, on average, increased the substitution rate in the PAR introns by twofold to fivefold. A very liberal upper bound is 10, which is obtained from the above second estimate (9.5) without dividing it by 2.
In Human
A weak effect of recombination on mutation rate was found in two recent studies of XG (Filatov and Gerrard 2003; Yi et al. 2004), a gene that straddles the PAB in human and apes (Rappold 1993; Lien et al. 2000). Filatov and Gerrard (2003) also studied two additional genes located in the human and ape PAR that did show twofold and threefold increases in the number of substitutions compared with the genomic average (3%) between human and orangutan. However, their analysis of X-linked and autosomal regions in human and orangutan showed no evidence of an association between mutation rate and recombination rate.
In this study, three data sets (Filatov and Gerrard 2003; Filatov 2004; Yi et al. 2004) were pooled along with the available sex-averaged recombination rates in human (Kong et al. 2002), and the human/orangutan intron divergences were correlated with recombination rates (fig. 3). For the PAR and X-linked regions, the influence of recombination rate on the substitution rate is fairly weak; that is, slope = 0.22% substitutions per cM/Mb (fig. 3A), whereas for the autosomal regions, there is no correlation and a slope of approximately 0.0 (fig. 3A).
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Increase of GC Content with Recombination Rate
We inferred lineage-specific mutations in each segment sequenced and found that PAR introns have a higher rate of change from A or T (0.1081 or 0.1110) than from G or C (0.0370 or 0.0302; [table 1, and see also table 1 in Supplementary Material online]). This trend is not apparent in any of the non-PAR regions. Also, using additional sites for the comparison between M. m. musculus and M. m. domesticus revealed an average GC% of 44.3 in the PAR versus 37.2 in the non-PAR. Both results support a GC bias in the PAR (Filatov and Gerrard 2003; Filatov 2004; Yi et al. 2004).
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One possibility for the difference in slope between the above two data sets is that the effect of recombination on GC% is not linear. However, we did a logistic transformation of the GC values in the human PAR and X-linked regions and obtained a similar regression line. Another possibility is that the recombination rate changes with time, so that the current rate may be different from the rate in the past. A third possibility is that the effect of recombination varies among chromosomes. In this case, the two slopes (0.7 and 2.3) can represent a lower and an upper bound of the effect of recombination on GC%. A value closer to the upper bound seems more reasonable because the window size was large and not as sensitive to past changes in the pattern of recombination along the chromosomes. Galtier (2004) proposed that past events that shifted part of the PAR into a non-PAR region can lead to a great reduction in recombination rate and a slow rate of change in GC%. Under this situation, the effects of recombination near the PAB could be underestimated. If this is true, the upper bound is closer to the truth because our lower bound was estimated from regions surrounding the PAB.
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Conclusions |
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Acknowledgements |
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Footnotes |
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References |
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