DATASET
MS_StabilityMaster_Tinkerbirds_SingleRecs_10Mar23.xlsx (29.54 MB)
.GZ
southern_africa_biallelic_snps_minDP4_MaxMiss20_MAF5.vcf.gz (141.87 MB)
DATASET
MS_SouthernAfrica_ddRADS_95SympF_14Mar23.xlsx (21.64 kB)
DATASET
MS_Tinkerbird138_Master_06Oct23.xlsx (51.98 kB)
TEXT
GC_CONTENT_500k.bed (67.31 kB)
TEXT
REPEATS_500k_%.bed (82.56 MB)
TEXT
SNPs_500k_%.bed (407.33 MB)
TEXT
Fst_average500kb_results_16Feb23.txt (124.24 kB)
TEXT
LD_average500kb_results_16Feb23.txt (171.28 kB)
TEXT
gemma_ioi_Symp_17Nov22_max-miss0.95_maf0.03_minmaxDP3.5_50.assoc.txt (2.27 GB)
TEXT
AS28702_AllChr_combined_ave_anc_pos.txt (407.73 MB)
TEXT
AS39306_AllChr_combined_ave_anc_pos.txt (480.89 MB)
TEXT
AS53235_AllChr_combined_ave_anc_pos.txt (435.76 MB)
DATASET
SourceData.xlsx (355.76 MB)
TEXT
tinkerbirds135_symp_chr25_thin2500.geno.ld.txt (1.12 GB)
1/0
A genomic basis of vocal rhythm in birds
dataset
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 KirschelIn 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:
- MS_StabilityMaster_Tinkerbirds_SingleRecs_10Mar23.xlsx: dataset to perform the song stability analyses.
- southern_africa_biallelic_snps_minDP4_MaxMiss20_MAF5.vcf.gz: ddRAD genomic data
- tinkerbirds_merged_SNPs_biallelic_max-miss0.95_maf0.03_minmaxDP3.5_50.vcf.gz: whole-genome genomic data
- MS_SouthernAfrica_ddRADS_95SympF_14Mar23.xlsx: spreadsheet containing parental ancestry of each sympatric female individual
- MS_Tinkerbird138_Master_06Oct23.xlsx: main dataset containing mean phenotypic data and ancestry values for the 138 individuals sequenced at the whole-genome level.
- Fst_average500kb_results_16Feb23.txt: Genome-wide Fst calculated in 500Kb windows used for Figure 2
- LD_average500kb_results_16Feb23.txt: Genome-wide R2 (LD) calculated in 500Kb windows used for Figure 2
- GC_CONTENT_500k.bed: GC content calculated in 500Kb windows used for Figure 2
- REPEATS_500k__.bed: repeat content calculated in 500Kb windows used for Figure 2
- SNPs_500k__.bed: SNP density content calculated in 500Kb windows used for Figure 2
- gemma_ioi_Symp_17Nov22_max-miss0.95_maf0.03_minmaxDP3.5_50.assoc.txt: GEMMA output used for figures 3a, c
- AS28702_AllChr_combined_ave_anc_pos.txt: raw data for Fig4b
- AS39306_AllChr_combined_ave_anc_pos.txt: raw data for Fig4b
- AS53235_AllChr_combined_ave_anc_pos.txt: raw data for Fig4b
- tinkerbirds135_symp_chr25_thin2500.geno.ld.txt: raw data for FigS8
- SourceData.xlsx: Raw data of all manuscript figures
