Homap/ostrich_PAR_analysis

The evolutionary maintenance of ancient recombining sex chromosomes in ostrich

Homa Papoli Yazdi¹, Colin Olito¹, Takeshi Kawakami, Per Unneberg, Mads F. Schou, Schalk W. P. Cloete, Bengt Hansson and Charlie K. Cornwallis

¹ These authors contributed equally to this work.

Abstract

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 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 female recombination rate in the heterogametic females, but not homogametic males. Genetic variation within the sex-linked region (π = 0.001) was significantly lower than the PAR, consistent with recombination cessation. Conversely, genetic variation across the PAR (π = 0.0016) was similar to the autosomes and dependent on local recombination rates, GC content and, to a lesser extent, gene density. The similarity of the PAR to autosomes is likely due to high recombination rates around the PAR boundary restricting genetic linkage with the sex-linked region (SLR) to only ~50Kb. The potential for alleles with antagonistic effects in males and females to drive chromosome degeneration is therefore limited, and while some regions of the PAR had divergent male-female allele frequencies, 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 accumulation of sexually antagonistic variation to generate selection for recombination cessation.

Repository structure and contents

• code
  This directory contains codes for processing and analysis of SNP data in each respective directory. Directory figures contains code for generating figures in the paper, statistical_analysis contains code for statistical analyses and simulation for codes used for coalescent simulations.

• data
  Contains processed data used for figure generation and statistical analyses.

• simulation_output
  Contains output of coalescent simulation after running the code in code/simulation

• software_module/R
  Contains frequently used modules in R scripts.

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