DOI: 10.5061/dryad.hx3ffbgpf
title: Genetic parallelism underlying repeated bill divergence in Island Scrub-Jays (<em>Aphelocoma insularis</em>) increases at higher genetic levels of organization

description: Whether the same genes underlie parallel adaptive trait evolution remains
 an open question in biology. The degree of parallelism is expected to
 increase at higher hierarchical levels due to the hierarchical nature of
 the genetic basis of traits (i.e., single nucleotide polymorphisms (SNPs)
 to genes to pathways to phenotype), which genomic approaches can help
 elucidate. Previous research shows a large degree of variation in the
 extent to which phenotypic parallelism shares the same genetic mechanisms
 in nature. Here, we analyzed the degree of genetic parallelism underlying
 repeated divergence in bill morphology of Island Scrub-Jays (Aphelocoma
 insularis), across three naturally replicated pine-oak ecotones on Santa
 Cruz Island, California, USA. We analyzed 66,503 SNPs generated using
 restriction site-associated DNA sequencing (RADseq) in 161 Island
 Scrub-Jays to identify candidate SNPs associated with environmental
 variation and divergence in bill morphology. We then examined signatures
 of parallelism in genomic regions containing candidate SNPs and the
 associated pathways. We found little evidence for parallelism at the SNP
 or gene level, but substantial parallelism at the pathway level. Our
 results support the view that the degree of genetic parallelism underlying
 convergent evolution depends on the genetic level of organization being
 analyzed.
description: # Genetic parallelism underlying repeated bill divergence in Island
 Scrub-Jays (*Aphelocoma insularis*) increases at higher genetic levels of
 organization
 [https://doi.org/10.5061/dryad.hx3ffbgpf](https://doi.org/10.5061/dryad.hx3ffbgpf) ## Description of the data and file structure This repository contains the bulk of the files needed to run the code, except for the raw fasta files for the bioinformatics scripts. Data was generated using BestRAD sequencing.  ### Files and variables #### File: chapter_2_individuals_plate_key_final.csv **Description:** metadata for the samples denoting genomic libraries ##### Variables * file_name: raw file name from the sequencer * tissue_number: Colorado State University tissue identifier * library: which genomic library individuals were sequenced in. Each library was a plate of 93 individuals and 3 duplicates.  #### File: ISSJ.ZEFIcorr.csv **Description:** Coordinates of Zebra Finch genome relative to the California Scrub-Jay aligned Island Scrub-Jay reads. Completed using SatsumaSynteny ##### Variables * ZEFI_CHROM: Zebra finch chromosome number * ZEFIPOS: Zebra Finch locus position * CHROM: California Scrub-Jay scaffold * POS: California Scrub-Jay position * SNP_ID for California Scrub-Jay aligned Island Scrub-Jay loci #### File: issj_ZEFI_ordered_imputed_Beagle_snp_pos.txt **Description:** Coordinates of Zebra Finch genome for SNP IDs. Needed to reference SNPs back to their Zebra Finch chromosome  ##### Variables * Column 1: "chromosome", Zebra Finch Chromosome number * Column 2: "ZEFIPOS", Zebra Finch Chromosome locus position  * Column 3: "snp_id", Zebra Finch SNP ID #### File: issj_CASJ_radiator_filtered.vcf **Description:**  Unimputed filtered dataset of California Scrub-Jay aligned Island Scrub-Jay reads in .vcf format.  #### File: issj_ZEFI_ordered_imputed_Beagle_neutral.vcf **Description:** BEAGLE imputed filtered dataset of California Scrub-Jay aligned Island Scrub-Jay reads in .vcf format.  ## Code/software 001-bioinformatics scripts final -- copy of scripts used in bioinformatic processing of raw Island Scrub-Jay sequence data.  0015 California Scrub-Jay bioinformatics -- scripts used to complete alignment to California scrub jay reference genome 002- Chapter 2 neutral pop gen final -- scripts used to conduct neutral population genetics.  003- identification of parallel selection by habitat --scripts used to complete genotype-by-environment analyses for all three pine oak ecotones 004- characterization of loci underlying variation in morphology final --scripts used to complete genome-wide association analyses for all three pine oak ecotones 006- genomic parallelism in ISSJ -- RMarkdown detailing use of PAUP to look at phylogenetic history of the jays (but wound up relying on previous results by Langin et al. 2015, because the PAUP didn't add anything that we didn't already know) and genetic parallelism analysis using AFVAPER ## Access information Other publicly accessible locations of the data: * California Scrub-Jay reference genome [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/536/675/GCA_028536675.1_bAphCal1.0.hap1/GCA_028536675.1_bAphCal1.0.hap1_genomic.fna.gz](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/536/675/GCA_028536675.1_bAphCal1.0.hap1/GCA_028536675.1_bAphCal1.0.hap1_genomic.fna.gz) * Zebra Finch reference genome [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/957/565/GCF_003957565.2_bTaeGut1.4.pri/GCF_003957565.2_bTaeGut1.4.pri_genomic.fna.gz](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/957/565/GCF_003957565.2_bTaeGut1.4.pri/GCF_003957565.2_bTaeGut1.4.pri_genomic.fna.gz)