The influence of GC-biased gene conversion on nonadaptive sequence evolution in short introns of Drosophila melanogaster.

Population genetic inference of selection on the nucleotide sequence level often proceeds by comparison to a reference sequence evolving only under mutation and population demography. Among the few candidates for such a reference sequence is the 5' part of short introns (5SI) in Drosophila. In addition to mutation and population demography, however, there is evidence for a weak force favoring GC bases, likely due to GC-biased gene conversion (gBGC), and for the effect of linked selection. Here, we use polymorphism and divergence data of Drosophila melanogaster to detect and describe the forces affecting the evolution of the 5SI. We separately analyze mutation classes, compare them between chromosomes, and relate them to recombination rate frequencies. GC-conservative mutations seem to be mainly influenced by mutation and drift, with linked se- lection mostly causing differences between the central and the peripheral (i.e., telomeric and cen- tromeric) regions of the chromosome arms. Comparing GC-conservative mutation patterns between autosomes and the X chromosome, showed differences in mutation rates, rather than linked selec- tion, in the central chromosomal regions after accounting for differences in effective populations sizes. On the other hand, GC-changing mutations show asymmetric site frequency spectra, indi- cating the presence of gBGC, varying among mutation classes and in intensity along chromosomes, but approximately equal in strength in autosomes and the X chromosome.