Data from: Convergent evolution of noncoding elements associated with short tarsus length in birds
Data files
Feb 25, 2025 version files 36.37 GB
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01_conserved_elems.tar.gz
225.91 MB
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02_phyloacc.tar.gz
2.97 GB
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03_toga.tar.gz
15.95 GB
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04_selection.tar.gz
2.85 GB
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05_popgen.tar.gz
14.37 GB
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README.md
2.92 KB
Abstract
Background
Convergent evolution is the independent evolution of similar traits in unrelated lineages across the Tree of Life. Various genomic signatures can help identify cases of convergent evolution at the molecular level, including changes in substitution rate in the same genes or gene networks. In this study, utilizing tarsus measurements of ~5400 species of birds, we identify independent shifts in tarsus length and use both comparative genomic and population genetic data to identify convergent evolutionary changes among focal clades with shifts to shorter optimal tarsus length.
Results
Using a newly generated, comprehensive and broadly accessible set of 932,467 avian conserved non-exonic elements (CNEEs) and a whole-genome alignment of 79 birds, we find strong evidence for convergent acceleration in short-tarsus clades among 14,422 elements. Analysis of 9854 protein-coding genes, however, yielded no evidence of convergent patterns of positive selection. Accelerated elements in short-tarsus clades are concentrated near genes with functions in development, with the strongest enrichment associated with skeletal system development. Analysis of gene networks support convergent changes in regulation of broadly homologous limb developmental genes and pathways.
Conclusions
Our results highlight the important role of regulatory elements undergoing convergent acceleration in convergent skeletal traits and are consistent with previous studies showing the roles of regulatory elements and skeletal phenotypes.
https://doi.org/10.5061/dryad.2280gb63v
Description of the data and file structure
- 01_conserved_elems: Files for identifying conserved elements and ATACseq peak calls
- 02_phyloacc: Input and results of phyloacc
- 03_toga: Input and results of orthology identification using TOGA
- 04_selection: Input and results for selection analyses
- 05_popgen: VCFs and results for population resequencing analysis
Files and variables
File: 01_conserved_elems.tar.gz
Description:
- Bmel_Z.fa > Extra scaffolds added to the Brachypodius atriceps genome
- cactus_tree.txt > The guide tree used for the alignment
- five files for each of the 5 databases mapped to galgal7b and filtered
- ratites_merged_sized.bed
- Hum2chick_CNEE_merged_NCBI.bed
- vocal_merged_sized.bed
- conserved_all_phastcon_filt.bed
- conserved_tgut_galgal7_filt.bed
- conserved_elements_all.txt > The combined and annotated list of conserved elements
- final_data_filtered.txt > The final filtered list of conserved elements
- atac > All files for the individual ATACseq calls
- atac_all_annot.txt > The annotated final list of ATACseq calls
- emu_hindlimb_HH18.bed > The emu ATACseq call for hindlimb HH18 stage
File: 02_phyloacc.tar.gz
Description:
Files needed to run phyloacc are in 3 folders for the macrochromosomes, microchromosomes, and Z chromosome:
- *.mod > The neutral rate including the associated tree
- *.fa > The concatenated alignment and their respective coordinates
PhyloAcc output files are as such:
- elem_lik_filt.txt > Marginal log-likelihoods output of phyloacc
- M* > Maximum log-likelihood configurations of latent state Z under null, accelerated and full model
- rate_postZ_M*.txt > Posterior median of different rates
- accelerated_elements_all_m2.txt > Accelerated elements in the short-tarsus broad and short-tarsus specific datasets
- loci_accl_genes_m2.txt > Overlap of accelerated elements and closest genes
- all_enrich_m2.txt > Results of GO enrichment analysis
- meme > Results of motif search
File: 03_toga.tar.gz
Description: Each folder contains the output for the TOGA runs to get orthology-based annotations of the genomes
File: 04_selection.tar.gz
Description:
- absrel > Results of absrel run and other selection analysis
- degenotate_bulbul > results of degenotate for bulbul
- degenotate_swallow > results of degenotate for swallows
- all_accl_*_stats.txt > input and results of MK test
File: 05_popgen.tar.gz
Description: Polarized vcf files for bulbuls and swallows
Code/software
All codes needed to analyze the results and replicate study is present in https://subirshakya.github.io/projects_rmarkdown/