Brian Raney | bioRxiv Science

bioRxiv2015

Stable recombination hotspots in birds

Although the DNA-binding protein PRDM9 plays a critical role in the specification of meiotic recombination hotspots in mice and apes, it appears to be absent from many vertebrate species, including birds. To learn about the determinants of fine-scale recombination rates and their evolution in natural populations lacking PRDM9, we inferred fine-scale recombination maps from population resequencing data for two bird species, the zebra finch Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda, whose divergence is on par with that between human and chimpanzee. We find that both bird species have hotspots, and these are enriched near CpG islands and transcription start sites. In sharp contrast to what is seen in mice and apes, the hotspots are largely shared between the two species, with indirect evidence of conservation extending across bird species tens of millions of years diverged. These observations link the evolution of hotspots to their genetic architecture, suggesting that in the absence of PRDM9 binding specificity, accessibility of the genome to the cellular recombination machinery, particularly around functional genomic elements, both enables increased recombination and constrains its evolution.

Evolutionary Biology↗

bioRxiv2014

Alignathon: A competitive assessment of whole genome alignment methods.

BackgroundMultiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark datasets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole genome alignment (WGA).\n\nResultsUsing the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments, and assessments were performed collectively after all the submissions were received. Three datasets were used: two of simulated primate and mammalian phylogenies, and one of 20 real fly genomes. In total 35 submissions were assessed, submitted by ten teams using 12 different alignment pipelines.\n\nConclusionsWe found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable difference in the alignment quality of differently annotated regions, and found few tools aligned the duplications analysed. We found many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all datasets, submissions and assessment programs for further study, and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.

Bioinformatics↗