DOI: 10.5061/dryad.pnvx0k6sx
title: The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich

description: Sex chromosomes have evolved repeatedly across the tree of life and often
 exhibit extreme size dimorphism due to genetic degeneration of the
 sex-limited chromosome (e.g. the W chromosome of some birds and Y
 chromosome of mammals). However, in some lineages, ancient sex-limited
 chromosomes have escaped degeneration. Here, we study the evolutionary
 maintenance of sex chromosomes in the ostrich (Struthio camelus), where
 the W remains 65% the size of the Z chromosome, despite being more than
 100 million years old. Using genome-wide resequencing data, we show that
 the population-scaled recombination rate of the pseudoautosomal region
 (PAR) is higher than similar-sized autosomes and is correlated with
 pedigree-based recombination rate in the heterogametic females, but not
 homogametic males. Genetic variation within the sex-linked region (SLR) (π
 = 0.001) was significantly lower than in the PAR, consistent with
 recombination cessation. Conversely, genetic variation across the PAR (π =
 0.0016) was similar to that of autosomes and dependent on local
 recombination rates, GC content, and to a lesser extent, gene density. In
 particular, the region close to the SLR was as genetically diverse as
 autosomes, likely due to high recombination rates around the PAR boundary
 restricting genetic linkage with the SLR to only ~50Kb. The potential for
 alleles with antagonistic fitness effects in males and females to drive
 chromosome degeneration is therefore limited. While some regions of the
 PAR had divergent male-female allele frequencies, suggestive of sexually
 antagonistic alleles, coalescent simulations showed this was broadly
 consistent with neutral genetic processes. Our results indicate that the
 degeneration of the large and ancient sex chromosomes of the ostrich may
 have been slowed by high recombination in the female PAR, reducing the
 scope for the accumulation of sexually antagonistic variation to generate
 selection for recombination cessation.
description: Blood samples of
 <em>Struthio</em> <em>camelus</em>
 were obtained
 from Western Cape
 Department of Agriculture’s ostrich research facility in Oudtshoorn, South
 Africa. Since 1995, individuals have been bred in pairs at the research
 facility to create pedigrees. At the time of sampling, the pedigrees
 contained 1531 males and 2067 females. We selected 5 males and 5 females
 for sequencing using the program PedMine. PedMine identifies individuals with most
 distant links within pedigrees allowing the maximum amount of genetic
 diversity in populations to be sampled. All procedures were approved by
 the Departmental Ethics Committee for Research on Animals (DECRA) of the
 Western Cape Department of Agriculture, reference no. AP/BR/O/SC14.
 Samples were sequenced at
 Science for Life Laboratory, the National Genomics Infrastructure, using paired end with
 126 base pairs on Illumina HiSeq 2500, following manufacturer's
 protocol. Reads were
 trimmed with cutadapt version 2.10 and then mapped to the optical map improved
 reference genome
 (<em>Struthio_camelus.20130116.OM.fa.masked</em>) with bwa
 version 0.7.17.r1188.
 Duplicates were marked with Picard MarkDuplicate. Variant calling was performed with GATK version
 4.1.4.1 following best practice procedures developed at the Broad
 Institute. The GATK
 HaplotypeCaller was run individually on each sample to generate GVCF
 output. GVCF files for all samples were imported to a GenomicsDB
 datastore, followed by genotyping with GATK GenotypeGVCFs to produce a
 final raw variant call set. Several filtering steps were performed on the
 raw call set to obtain the final call set of high quality. Biallelic SNPs
 were selected with GAKT SelectVariants and filtered with GATK
 VariantFilteration using best practice options QUAL &lt; 30,
 QualByDepth (QD) &lt; 2.0, RMSMappingQuality (MQ) &lt; 40.0,
 MappingQualityRankSumTest (MQRankSum) &lt; -12.5, FisherStrand (FS)
 &gt; 60.0, ReadPosRankSumTest &lt; -8.0 and StrandOddsRatio (SOR)
 &gt; 3.0. We removed
 variants overlapping with repeats annotated by the aves repeat library
 using BEDTools intersect.
 We filtered SNPs with more than twice the average coverage (&gt;70
 reads) and less than 5 reads per site. SNPs in the SLR in females are
 expected to occur only as haploid. However, heterozygous SNPs in the SLR
 in females can occur either due to genotyping error or due to the
 divergence of the Z and W sequences in the gametologous
 region. We therefore filtered the heterozygous SNPs in
 females in the SLR.