DOI: 10.5061/dryad.2256f38
title: Data from: The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function

description: An underexplored question in evolutionary genetics concerns the extent to
 which mutational bias in the production of genetic variation influences
 outcomes and pathways of adaptive molecular evolution. In the genomes of
 at least some vertebrate taxa, an important form of mutation bias involves
 changes at CpG dinucleotides: If the DNA nucleotide cytosine (C) is
 immediately 5’ to guanine (G) on the same coding strand, and if the C is
 methylated, then C→T and G→A mutations occur at an elevated rate relative
 to mutations at non-CpG sites. Here we examine experimental data from case
 studies in which it has been possible to identify the causative
 substitutions that are responsible for adaptive changes in the functional
 properties of vertebrate hemoglobin (Hb). Specifically, we examine the
 molecular basis of convergent increases in Hb-O2 affinity in high-altitude
 birds. Using a data set of experimentally verified, affinity-enhancing
 mutations in the Hbs of highland avian taxa, we tested whether causative
 changes are enriched for mutations at CpG dinucleotides relative to the
 frequency of CpG mutations among all possible missense mutations. The
 tests revealed that a disproportionate number of causative amino acid
 replacements were attributable to CpG mutations, demonstrating that
 mutation bias can influence outcomes of molecular adaptation.
description: # README for supplementary data from Storz, et al. This is the main README
 file for the supplementary data package for the study of CpG bias in avian
 hemoglobin adaptation by Storz, et al., entitled "The role of
 mutation bias in adaptive molecular evolution: insights from convergent
 changes in protein function" (10.1098/rstb.2018.0238). # EXPLANATION
 Based on prior work, Storz, et al. provide a summary of experimentally
 validated changes in hemoglobin affinity associated with altitude
 adaptation in 35 pairs of closely related low- and high-altitude bird
 populations. The authors report on a statistically significant association
 of CpG mutation hotspots with these adaptive changes. This supplementary
 data package provides a script and data files that reproduce the main
 results by processing the primary data, recomputing the null expectations,
 and conducting statistical tests. The data also may be useful to
 researchers carrying out meta-analyses of cases in which adaptation can be
 traced to specific molecular changes. # DESCRIPTION OF FILES The files are
 all text files, including sequence alignment files in FASTA format, tables
 in csv (comma-separated values) format, and an R-MarkDown script: *
 altitude_pairs_changes_2018-09-13.csv (primary data file describing
 validated changes) * altitude_pairs_changes_meta.csv (data definition file
 for above) * hb_CpG_analysis.Rmd (script to process data, calculate null
 models, carry out tests) * alpha-globin_ancestral_seqs.fas (reconstructed
 ancestral Hb alpha A sequences) * beta-globin_ancestral_seqs.fas
 (reconstructed ancestral Hb beta sequences) * README.txt (this file) # HOW
 TO OBTAIN THE CONTENTS The contents of this package are available from
 Dryad () or from the authors
 (see TECHNICAL SUPPORT). # SOFTWARE REQUIREMENTS The files are all text
 files readable with a text editor. The csv (comma-separated values) files
 can be opened with Excel and a variety of other tools. The script is
 written in R-markdown and is best used in RStudio. The code chunks in the
 Rmd file also can be copied and pasted into an R environment. # VALIDATION
 The hb_CpG_analysis.Rmd script will generate
 script_output/altitude_pairs_obs_exp.csv (null expectations and counts)
 and script_output/test_results.csv (P values). The contents of these files
 can be compared with values reported in the manuscript. Use the following
 assertions to validate the integrity of the files and the correctness of
 processing without the Rmd script: * each FASTA file has exactly 35
 ancestral CDS sequences, one for each pair * there are no gaps in the
 sequences * the main data file describes 10 paths with 6, 3, 3, 2, 2, 2,
 1, 1, 1, 1 events * there are 6 G to S (Gly to Ser) changes at site 83 in
 HBB * the HBA change from A to V at site 63 is in a CpG context * the HBA
 change from P to A at site 119 is not in a CpG context # TECHNICAL SUPPORT
 For questions about data processing and statistical analysis, contact
 Arlin Stoltzfus (). For questions about experimental
 data and natural history of the bird species, contact Jay Storz
 (). # STATEMENT OF RIGHTS AND DISCLAIMER The
 authors release the data and scripts in this package into the public
 domain, with no warranty, under a Creative Commons Zero (CC0 1.0) license.