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

Abstract

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.

Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff (Phylloscopus collybita abietinus/tristis) hybrid zone

“…The range for individual samples was 1.6–4.3 Gb after filtering out bases with Q ‐scores <30 using ConDeTri (Smeds & Künstner, 2011), in total 113 Gb. The quality‐filtered nuclear sequence reads were mapped to the Ficedula albicollis genome sequence (Ellegren et al., 2012; Kawakami et al., 2014) using the Burrows–Wheeler algorithm as implemented in the software BWA (version 0.5.9, Li & Durbin, 2010). SAMtools (Li et al., 2009) was used to convert files to BAM format and to visually inspect some of the alignments.…”

Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

“…The BLAST+ utility (Camacho et al, 2009) was used to match loci in our study with chromosomal locations in the Zebra Finch (Taeniopygia guttata) genome, which is possible because of strong patterns of synteny in birds (Kawakami et al, 2014). Although we are able to match loci to chromosomes, there have been many intrachromosomal recombination events (for example, inversions; Kawakami et al 2014) precluding locating the position of a locus on a chromosome.…”

“…Although we are able to match loci to chromosomes, there have been many intrachromosomal recombination events (for example, inversions; Kawakami et al 2014) precluding locating the position of a locus on a chromosome. Although this is true, we mapped all loci and fixed differences to Zebra Finch chromosomal location to explore potential clustering of genetic variation (Supplementary Information 4).…”

“…All regressions with the reduced data sets showed similar, statistically significant results to those of the full data set (results not shown). Due to the observed relationships, we also investigated the relationship between chromosomal average recombination rates (data from Ficedula; Kawakami et al, 2014) and genetic differentiation and diversity. Here, we observed a negative relationship between recombination rates and genetic differentiation (R 2 = 0.514, Po0.001; Figure 6) and a positive relationship between recombination rates and genetic diversity in both the northern (R 2 = 0.507, Po0.001) and southern (R 2 = 0.387, Po0.001) lineages.…”

“…With new methods for obtaining reduced-representation libraries of the genome (for example, restriction digest-based methods, Miller et al, 2007 andultraconserved elements, Faircloth et al, 2012) for many individuals, phylogeographic studies may contain thousands of loci with dozens of individuals sampled. In songbirds, strong patterns of interchromosomal synteny (Kawakami et al, 2014), the published genome of the Zebra Finch (Taeniopygia guttata; Warren et al, 2010) and thousands of genetic markers across the genome allow the opportunity to investigate not only phylogeographic structure in a clade well known for its high levels of geographic differentiation (Manthey et al, 2011a), but also diversity and differentiation across chromosomes (Manthey and Spellman, 2014).…”