Conservation of fundamental mutation and recombination parameters between mammals and zebra finch

Most of our understanding of the fundamental processes of mutation and recombination stems from a handful of disparate model organisms and pedigree studies of mammals, with little known about other vertebrates. To gain a broader comparative perspective, we focused on the zebra finch (Taeniopygia castanotis), which, like other birds, differs from mammals in its karyotype (which includes many micro-chromosomes), in the mechanism by which recombination events are specified, and possibly in the developmental timing of sex differentiation. We collected genome sequences from three generation pedigrees that provide information about 80 meioses, inferring 202 single-point de novo mutations, 1,174 crossovers, and 273 non-crossovers. On that basis, we estimated a sex-averaged mutation rate of 0.000000005 per base pair per generation, on par with mammals that have a similar generation time. Also as in mammals, we found a paternal germline mutation bias at later stages of gametogenesis (of 1.7 to 1) but no discernible difference between sexes in early development. Focusing on macro-chromosomes, the sex-averaged crossover rate (1.05 cM/Mb) is again similar to values in mammals, as is the spatial distribution of crossovers, with an enrichment near telomeres; in contrast, non-crossover rates are more uniformly distributed. On micro-chromosomes, sex-averaged crossover rates are substantially higher (4.21 cM/Mb), and events more uniformly distributed, as expected from crossover assurance. At a finer scale, recombination events overlap CpG islands more often than expected by chance, as expected in the absence of PRDM9. Despite differences in the mechanism by which recombination is directed to the genome and the presence of many micro-chromosomes, the degree of GC-biased gene conversion (estimated to be 0.59), the mean non-crossover conversion tract length (about 23 bp), and the non-crossover to crossover ratio (7.4:1) are all comparable to those reported in primates and mice. The conservation of mutation and recombination properties from zebra finch to mammals suggest that these processes evolve under stabilizing selection.