Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN, Griffith SC, McVean G, Przeworski M.

Science. 2015 Nov 20;350(6263):928-32. doi:10.1126/science.aad0843

Stable recombination hotspots in birds.

Recombination maps obtained from genome sequences of 24 zebra finches and 20 long-tail finches, in which SNP Haplotypes were inferred from phase-informative reads and family phasing. Recombination rates estimated as ρ = 26.2/kb and 14.0/kb, respectively (0.14 cM/Mb in both species). 3—4000 Hotspots “operationally defined them as regions that are at least 2 kb in length; have at least five times the background recombination rate as estimated across the 80 kb of sequence surrounding the region; and are statistically supported as hotspots by a likelihood ratio test” (18). “73% of zebra finch hotspots (...) were detected as shared between the two species.” “Hotspots in the zebra finch and long-tailed finch genomes are enriched near transcription start sites (TSSs), transcription stop sites (TESs), and CpG islands (CGIs), with close to half of all hotspots occurring within 3 kb of one of these features.” “Median recombination rates across and within chromosomes vary over nearly six orders of magnitude (...) with regions of elevated recombination near telomeres and large intervening deserts.