Convergent evolution of noncoding elements associated with short tarsus length in birds

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 shor..., , , # Data from: Convergent evolution of noncoding elements associated with short tarsus length in birds

[https://doi.org/10.5061/dryad.2280gb63v](https://doi.org/10.5061/dryad.2280gb63v)

## Description of the data and file structure

1. 01_conserved_elems: Files for identifying conserved elements and ATACseq peak calls
2. 02_phyloacc: Input and results of phyloacc
3. 03_toga: Input and results of orthology identification using TOGA
4. 04_selection: Input and results for selection analyses
5. 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_galga...