Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster-Z Effect. To assess the magnitude and drivers of Faster-Z Evolution, we assembled six de novo transcriptomes, spanning 90 million years of avian evolution. Our analysis combines expression, sequence and polymorphism data with measures of sperm competition and promiscuity. In doing so, we present the first empirical evidence demonstrating the positive relationship between Faster-Z Effect and measures of promiscuity, and therefore variance in male mating success. Our results from multiple lines of evidence indicate that selection is less effective on the Z chromosome, particularly in promiscuous species, and that Faster-Z Evolution in birds is due primarily to genetic drift. Our results reveal the power of mating system and sexual selection in shaping broad patterns in genome evolution.
Sequence alignments used for divergence analysis
Contains 2649 phylip alignment files used to calculate divergence in PAML. Each phylip file contains cDNA sequence of the six species plus zebra finch outgroup. Orthogroups were aligned with PRANK v121218 using the orthologous Taeniopygia guttata cDNA (taeGut3.2.4.75) as an outgroup and specifying the following guidetree; (((A. cygnoides, A. platyrhynchos), (N. meleagris, (P. cristatus, (M. gallopavo, P. colchicus)))), T. guttata). APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus, TGU= Taeniopygia guttata.
SNP_6species_data.tgz
Polymorphism data for each of the six Galloanserae species
Contains a vcf file for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus. Polymorphism data was obtained by first mapping RNA-seq reads to orthogroups using the two pass alignment method of the STAR aligner with default parameters (Dobin et al. 2013). SNPs were called using varscan v2.3.6 (Koboldt et al. 2009; Koboldt et al. 2012) and Samtools (Li et al. 2009) following the recommendations of Quinn et al 2013 (Quinn et al. 2013).
SNP_6species_data.tgz
Sequences of Trinity contigs for each of the six Galloanserae species
Contains a fasta file of Trinity assembly contig sequences for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus.The left gonad and spleen were dissected separately from five males and five females of each species. The exceptions were P. colchicus, where six male gonad and spleen samples were collected, and M. gallopavo, where four male and two female spleens were collected. Samples were homogenzied and stored in RNAlater until preparation. We used the Animal Tissue RNA Kit (Qiagen) to extract RNA, and the samples were prepared and barcoded at The Wellcome Trust Centre for Human Genetics, University of Oxford using Illumina’s Multiplexing Sample Preparation Oligonucleotide Kit with an insert size of 280bp. RNA was sequenced on an Illumina HiSeq 2000. The data was quality assessed using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc) and filtered using Trimmomatic v0.22 (Lohse et al. 2012). Specifically, we removed reads containing adaptor sequences and trimmed reads if the sliding window average Phred score over four bases was <15 or if the leading/trailing bases had a Phred score <4. Reads were removed post filtering if either read pair was <25 bases in length. We constructed de novo transcriptome assemblies for each species using Trinity with default parameters (Grabherr et al. 2011).
Trinity_contigs_6species.tgz
RPKM data for each of the six Galloanserae species
Contains a file of RPKM expression data for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus. Gene expression was quantified using only adult gonad samples and estimated as reads per kilobase per million mappable reads (RPKM) using RSEM v1.1.21 with default parameters (Li and Dewey 2011).
RPKM_6species.tgz
