DOI: 10.5061/dryad.bnzs7h4b4
title: Adaptive introgression of the beta-globin cluster in two Andean waterfowl

description: Introgression of alleles has emerged as an important avenue for genetic
 adaptation in both plant and animal populations. In vertebrates,
 adaptation to hypoxic high-altitude environments involves the coordination
 of multiple molecular and cellular mechanisms, including selection on the
 Hypoxia-Inducible Factor (HIF) pathway and the blood-O2 transport protein
 hemoglobin (Hb). In two Andean duck species, a striking DNA sequence
 similarity reflecting identity by descent is present across the ~20 kb
 b-globin cluster including both embryonic (HBE) and adult (HBB) paralogs,
 though it was yet untested whether this is due to independent parallel
 evolution or adaptive introgression. In this study, we find that identical
 amino acid substitutions in the b-globin cluster that increase Hb-O2
 affinity have likely resulted from historical interbreeding between
 high-altitude populations of two different distantly-related species. We
 examined the direction of introgression and discovered that the species
 with a deeper mtDNA divergence that colonized high altitude earlier in
 history (Anas flavirostris) transferred adaptive genetic variation to the
 species with a shallower divergence (A. georgica) that likely colonized
 high altitude more recently possibly following the range shift into a
 novel environment. As a consequence, the species that received these
 b-globin variants through hybridization might have adapted to the
 high-altitude environment more quickly through acquiring beneficial
 alleles from the new, hybrid-origin variation, leading to faster
 evolution.
description: A custom pipeline (https://github.com/amgraham07) was created to
 remove orphan sequences and assemble sequences against the α-globin
 (NW_004678373, scaffold 2065) and β-globin (NW_004682656, scaffold 6035)
 sequences of the mallard reference, using BWA v0.7.15 (Li and Durbin, 2009). The
 Samtools package v1.3.1, including BCFtools v.1.3.1 (Li<i> et al</i>,
 2009) was then used to create a VCF file and to
 provide assembly statistics (i.e., bp-by-bp coverage). These programs used
 in the pipeline called SNP variants against the mallard reference,
 including indels (insertion/deletion); however, indels were excluded in
 the final dataset as were sites with missing data.
description: Included in this repository are VCF files the contain 40
 individuals from both Speckled Teal (ST) and Yellow-billed Pintail
 (YBP). Individual species HIF-pathway files can be found on an additional
 Dryad repository associated with Graham and McCracken (2019)
 <em>Heredity</em> (https://doi.org/10.5061/dryad.kd08516). <strong>ST_YBP_HIF_no_indels_tags.0.inds.missing.no.invariable.recode.vcf</strong> The combined ST-YBP VCF file for the HIF-pathway, with indels removed. <strong>ST_YBP_HBA_no_indels_tags.0.inds.missing.no.invariable.recode.vcf</strong> The combined ST-YBP VCF file for the alpha-globin complex, with indels removed. <strong>ST_YBP_Hb_no_indels_tags.0.inds.missing.no.invariable.recode.vcf</strong> The combined ST-YBP VCF file for the beta-globin complex, with indels removed. Corresponding SET files for Dsuite execution: <strong>SETS_Hb.txt</strong> <strong>SETS_HIF.txt</strong>