Data from: Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution

Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE

Date Published: February 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.4gv50

 

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Title Sequence alignments used for divergence analysis
Downloaded 3 times
Description 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.
Download SNP_6species_data.tgz (36.85 Mb)
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Title Polymorphism data for each of the six Galloanserae species
Downloaded 1 time
Description 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).
Download SNP_6species_data.tgz (36.85 Mb)
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Title Sequences of Trinity contigs for each of the six Galloanserae species
Downloaded 1 time
Description 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).
Download Trinity_contigs_6species.tgz (1.386 Gb)
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Title RPKM data for each of the six Galloanserae species
Downloaded 1 time
Description 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).
Download RPKM_6species.tgz (49.97 Mb)
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When using this data, please cite the original publication:

Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE (2015) Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution. Molecular Ecology 24(6): 1218-1235. http://dx.doi.org/10.1111/mec.13113

Additionally, please cite the Dryad data package:

Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE (2015) Data from: Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4gv50
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