A genomic basis of vocal rhythm in birds

In this repository we provide processed data to reproduce the main results of the manuscript entitled "A genomic basis of vocal rhythm in birds"

The data should be used in combination with the scripts available at: [https://github.com/MatteoSebastianelli/Tinkerbird_SongGene]

We provide the following files:

1. MS_StabilityMaster_Tinkerbirds_SingleRecs_10Mar23.xlsx: dataset to perform the song stability analyses.
2. southern_africa_biallelic_snps_minDP4_MaxMiss20_MAF5.vcf.gz: ddRAD genomic data
3. tinkerbirds_merged_SNPs_biallelic_max-miss0.95_maf0.03_minmaxDP3.5_50.vcf.gz: whole-genome genomic data
4. MS_SouthernAfrica_ddRADS_95SympF_14Mar23.xlsx: spreadsheet containing parental ancestry of each sympatric female individual
5. MS_Tinkerbird138_Master_06Oct23.xlsx: main dataset containing mean phenotypic data and ancestry values for the 138 individuals sequenced at the whole-genome level.
6. Fst_average500kb_results_16Feb23.txt: Genome-wide Fst calculated in 500Kb windows used for Figure 2
7. LD_average500kb_results_16Feb23.txt: Genome-wide R2 (LD) calculated in 500Kb windows used for Figure 2
8. GC_CONTENT_500k.bed: GC content calculated in 500Kb windows used for Figure 2
9. REPEATS_500k__.bed: repeat content calculated in 500Kb windows used for Figure 2
10. SNPs_500k__.bed: SNP density content calculated in 500Kb windows used for Figure 2
11. gemma_ioi_Symp_17Nov22_max-miss0.95_maf0.03_minmaxDP3.5_50.assoc.txt: GEMMA output used for figures 3a, c
12. AS28702_AllChr_combined_ave_anc_pos.txt: raw data for Fig4b
13. AS39306_AllChr_combined_ave_anc_pos.txt: raw data for Fig4b
14. AS53235_AllChr_combined_ave_anc_pos.txt: raw data for Fig4b
15. tinkerbirds135_symp_chr25_thin2500.geno.ld.txt: raw data for FigS8
16. SourceData.xlsx: Raw data of all manuscript figures