15 files

A genomic basis of vocal rhythm in birds

posted on 2024-02-28, 20:41 authored by Matteo SebastianelliMatteo Sebastianelli, Sifiso M. LukheleSifiso M. Lukhele, Simona SecomandiSimona Secomandi, Stacey G. de Souza, Bettina Haase, Michaella Moysi, Christos Nikiforou, Alexander Hutfluss, Jacquelyn Mountcastle, Jennifer Balacco, Sarah Pelan, William Chow, Olivier Fedrigo, Colleen Downs, Ara Monadjem, Niels J Dingemanse, Erich D. Jarvis, Alan Brelsford, Bridgett VonHoldt, Alexander Kirschel

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: []

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


This study was possible thanks to funding from the European Regional Development Fund and the Republic of Cyprus through the Research and Innovation Foundation (Project: EXCELLENCE/0421/0301, ANGK), University of Cyprus Research Grant No. 8037P-25023 (ANGK), FP7 Marie Curie Reintegration Grant No. 268316 (ANGK), AG Leventis Foundation grants (MS, SML, MM, and SGdS) and American Ornithological Society covid relief fund (MS).


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