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Adaptive introgression of the beta-globin cluster in two Andean waterfowl

Citation

Graham, Allie; McCracken, Kevin (2021), Adaptive introgression of the beta-globin cluster in two Andean waterfowl, Dryad, Dataset, https://doi.org/10.5061/dryad.bnzs7h4b4

Abstract

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.

Methods

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 et al, 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.

Usage Notes

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) Heredity (https://doi.org/10.5061/dryad.kd08516).

ST_YBP_HIF_no_indels_tags.0.inds.missing.no.invariable.recode.vcf

The combined ST-YBP VCF file for the HIF-pathway, with indels removed.

ST_YBP_HBA_no_indels_tags.0.inds.missing.no.invariable.recode.vcf

The combined ST-YBP VCF file for the alpha-globin complex, with indels removed.

ST_YBP_Hb_no_indels_tags.0.inds.missing.no.invariable.recode.vcf

The combined ST-YBP VCF file for the beta-globin complex, with indels removed.

Corresponding SET files for Dsuite execution:

SETS_Hb.txt

SETS_HIF.txt