Data from: A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

Detailed linkage and recombination rate maps are necessary to use the full
potential of genome sequencing and population genomic analyses. We used a
custom collared flycatcher 50 K SNP array to develop a high-density
linkage map with 37 262 markers assigned to 34 linkage groups in 33
autosomes and the Z chromosome. The best-order map contained 4215 markers,
with a total distance of 3132 cM and a mean genetic distance between
markers of 0.12 cM. Facilitated by the array being designed to include
markers from most scaffolds, we obtained a second-generation assembly of
the flycatcher genome that approaches full chromosome sequences (N50
super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to
and mostly ordered and oriented along chromosomes). We found that
flycatcher and zebra finch chromosomes are entirely syntenic but that
inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed
the organization within chromosomes, rates high enough for inversions to
potentially have been involved with many speciation events during avian
evolution. The mean recombination rate was 3.1 cM/Mb and correlated
closely with chromosome size, from 2 cM/Mb for chromosomes >100 Mb
to >10 cM/Mb for chromosomes <10 Mb. This size dependence
seemed entirely due to an obligate recombination event per chromosome; if
50 cM was subtracted from the genetic lengths of chromosomes, the rate per
physical unit DNA was constant across chromosomes. Flycatcher
recombination rate showed similar variation along chromosomes as chicken
but lacked the large interior recombination deserts characteristic of
zebra finch chromosomes.