DOI: 10.5061/dryad.hhmgqnkqb
title: Fitness consequences of structural variation inferred from a House Finch pangenome

description: Genomic structural variants (SVs) play a crucial role in adaptive
 evolution, yet their average fitness effects and characterization with
 pangenome tools are understudied in wild animal populations. We
 constructed a pangenome for House Finches, a model for studies of
 host-pathogen coevolution, using long-read sequence data on 16 individuals
 (32 de novo-assembled haplotypes) and one outgroup. We identified 643,207
 SVs larger than 50 base pairs, mostly (60%) involving repetitive elements,
 with reduced SV diversity in the eastern US as a result of its
 introduction by humans. The distribution of fitness effects of genome-wide
 SVs was estimated using maximum likelihood approaches and showed SVs in
 both coding and non-coding regions to be on average more deleterious than
 smaller indels or single nucleotide polymorphisms. Our reference-free
 pangenome facilitated the discovery of a 10-million-year-old,
 11-megabase-long pericentric inversion, whose genotype frequency increased
 steadily over the 25 years since House Finches were first exposed to the
 bacterial pathogen Mycoplasma gallispecticum and which showed
 signatures of balancing selection, capturing genes related to immunity and
 telomerase activity. We also observed shorter telomeres in populations
 with a greater number of years of exposure to Mycoplasma. Our
 study illustrates the utility of applying pangenome methods to wild animal
 populations, helps estimate the fitness effects of genome-wide SVs, and
 advances our understanding of adaptive evolution through structural
 variation.
description: The House Finch pangenome was constructed using <em>de
 novo</em> genome assemblies from 16 samples and a Common Rosefinch
 outgroup. A chromosome-level reference from the Vertebrate Genomes Project
 aided in establishing stable genomic coordinates for pangenomics analysis.
 The pangenome includes 35 haplotype assemblies and was constructed using
 the PanGenome Graph Builder (PGGB), which allows for a detailed
 representation of genomic variants across autosomes.
description: # Fitness consequences of structural variation inferred from a House Finch
 pangenome ## Overview This repository contains data files related to the
 pangenome analysis of House Finch genomes. The data includes: * **PGGB
 Pangenome Graph Files (.gfa)**: Pangenome graphs generated per chromosome
 using the PanGenome Graph Builder (PGGB). * **VCF File
 (`pggb_cleaned_final_noAT.vcf.gz`)**: A Variant Call Format (VCF) file
 containing variant information decomposed from the pangenome graphs (see
 methods in the paper). * **Processed Variant Information
 (`vcf_info_38chrs`)**: A data file containing detailed variant annotations
 and metrics. ### Processed Variant Information (`vcf_info_38chrs`) ####
 Column Descriptions 1. **CHROM**: Chromosome identifier where the variant
 is located. 2. **POS**: Position of the variant on the chromosome (1-based
 coordinate). 3. **REF**: Reference allele nucleotide(s) at the variant
 position. 4. **ALT**: Alternative allele nucleotide(s) at the variant
 position. 5. **N_allele**: Total number of alleles at the variant site
 (including REF and all ALT alleles). 6. **N_bp_ref**: Length (in base
 pairs) of the reference allele (REF). 7. **N_bp_diff**: Maximum difference
 in length (in base pairs) between the longest and shortest alleles at the
 variant site. 8. **type**: General classification of the variant based on
 allele lengths and differences: * **SNP**: Single Nucleotide Polymorphism
 (length REF = length ALT = 1 bp). * **MNP**: Multiple Nucleotide
 Polymorphism (length REF = length ALT, between 1 and 50 bp). * **INDEL**:
 Insertion or Deletion less than 50 bp (size difference between alleles
 &lt; 50 bp). * **SV**: Structural Variant (size difference ≥ 50 bp). *
 **SV_complex**: Complex Structural Variant not fitting standard criteria.
 9. **N_bp**: Length of the variant (in base pairs). For SNPs, `N_bp = 1`;
 for other variants, `N_bp = N_bp_diff`. 10. **invariants_HF**: Logical
 flag indicating whether the site is invariant among House Finch haplotypes
 (`TRUE` if invariant). 11. **ancestry_polarized**: Logical flag indicating
 whether the variant could be polarized using the outgroup genotype (Common
 Rosefinch haplotype 1). Polarization was limited to sites where the Common
 Rosefinch genotype was homozygous or had one allele missing (genotypes
 `0/0`, `1/1`, `0/.`, or `1/.`). 12. **DAC_west**: Derived Allele Count in
 the western House Finch population group. 13. **DAC_east**: Derived Allele
 Count in the eastern House Finch population group. 14. **DAC_all**:
 Derived Allele Count across all House Finch populations. 15.
 **Geno_RF_hap1**: Genotype of the outgroup (Common Rosefinch haplotype 1)
 used for ancestral allele determination. "." indicates missing
 data. 16. **MC_west**: Missing genotype counts in the western population
 group. 17. **MC_east**: Missing genotype counts in the eastern population
 group. 18. **MC_all**: Missing genotype counts across all populations. 19.
 **MC_ratio**: Ratio of missing genotypes across all populations (`MC_all /
 total number of haplotypes`). 20. **allele_count_West**: Number of unique
 alleles observed in the western population group. 21.
 **allele_count_East**: Number of unique alleles observed in the eastern
 population group. 22. **allele_count_All**: Number of unique alleles
 observed across all populations. 23. **subtype**: Detailed classification
 of the variant subtype based on size and ancestral allele (see Supporting
 Methods of the paper).