The code in this repository accompany the paper:

Pervasive genomic signatures of local adaptation to altitude across highland specialist Andean hummingbird populations

Marisa C.W. Lim, Ke Bi, Christopher C. Witt, Catherine H. Graham, Liliana M. Davalos

Variant calling pipeline

Note: this pipeline uses scripts written by UC Berkeley MVZ/CGRL scientists.

1. Exon capture probe design: There were two probe design procedures - the first to capture previously identified candidate genes for high-altitude adaptation and the second to capture a 'random' set of exons across the entire hummingbird genome using the Anna's hummingbird (Calypte anna) as the reference.

2. Clean raw_reads_and assemble: Remove low quality reads, adapter sequences, PCR duplicates, and potential bacterial contaminant sequences; merge paired-end reads; and generate de novo assemblies as species-specific references

3. Read alignment: Map reads to species-specific reference assemblies and evaluate capture experiment (% reads retained after filtering but before alignment, length of mapped data, % of reads aligned to target region (specificity), % of targeted regions covered by at least one read (sensitivity), average coverage, variation in coverage, and % of sites retained at multiple coverage depths)

4. SNP calling: Call variants and filter loci with too much missing data, within 10bp of indels, that are not biallelic, and/or that have excessive heterozygosity

5. Population genomic analyses

• PCA
• Admixture
• Relatedness coefficient
• Gene flow estimates
  • Between population diversity (Fst, Dxy)
  • Isolation by distance - geodesic and least cost distance
• Within population diversity
• Estimating Effective Migration Surfaces (EEMS)
• Test for natural selection with Latent Factor Mixed Models (LFMM)
  • Call genotypes
  • LFMM