DOI: 10.5061/dryad.8sf7m0cpq
title: Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species

description: We present evidence for and investigate potential mechanisms driving
 habitat-linked genetic divergence within a bird species endemic to a
 single 250 km2 island. The island scrub-jay (Aphelocoma insularis)
 exhibits microgeographic divergence in bill morphology across pine-oak
 ecotones on Santa Cruz Island, California (USA) similar to adaptive
 differences described in mainland congeners over much larger geographic
 scales. To test whether individuals exhibit genetic differentiation
 related to habitat type and divergence in bill length, we genotyped over
 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay
 males from across Santa Cruz Island using restriction site-associated DNA
 sequencing (RADseq). Neutral landscape genomic analyses revealed that
 genome-wide genetic differentiation was primarily related to geographic
 distance and differences in habitat composition. We also found 168
 putatively adaptive loci associated with habitat type using multivariate
 redundancy analysis (RDA) while controlling for spatial effects. Finally,
 two genome-wide association analyses revealed a polygenic basis to
 variation in bill length with multiple loci detected in or near genes
 known to affect bill morphology in other birds. Our findings support the
 hypothesis that divergent selection at microgeographic scales can cause
 adaptive divergence in the presence of ongoing gene flow.
description: <strong>Aphelocoma insularis RAD-sequencing and
 genotyping</strong> We generated RADseq libraries for adult male
 Island Scrub-jays using the restriction
 enzyme <em>SbfI. </em>We then sequenced 100 bp single-end reads on two Illumina
 HiSeq 2500 lanes at the Genomics Core Facility at the University of
 Oregon. Sequenced reads were quality‐filtered and demultiplexed, and
 individual barcodes were removed using STACKS version 2.3b pipeline. We
 aligned sequences to the Florida scrub-jay (<em>Aphelocoma
 coerulescens</em>) draft reference genome using BWA-MEM. We used the
 default settings of ref_map.pl in STACKS to identify SNPs and exported the
 raw SNP matrix using the “populations” module of
 STACKS.  Bioinformatic pipeline code available in:
 001-bioinformatics_scripts_final.Rmd,
 radiator_script_150_ISSJ.R <strong>Filtered VCF file for neutral popualtion
 genetics  </strong> Additional filtering was performed using the RADIATOR
 package. Filters are summarized in supplemental Table S1.  We mapped
 scaffolds to individual chromosomes of the Zebra Finch genome and imputed
 missing data using BEAGLE and putatively adaptive loci identified by
 PCADAPT were removed. VCF containes 3,342 SNPs from 123
 individuals. ISSJ.ZF.ordered_imputed_BEAGLE_neutral.vcf Circuitscape resistance file: ISSJ_resistance_data.csv <strong>Filtered VCF file for genotype-by-environment association and genome-wide association  </strong> VCF without putatively adaptive loci removed and containes 3,345 SNPs. ISSJ.ZF.ordered_imputed_BEAGLE.vcf Individual sampling locality data and habitat composition is available in: issj_filtered.csv, ISSJ_environmental_data_final.csv Associated files for GWA analyses: tguttata_gene_ensembl.csv, ISSJ.ZFcorr.csv, Beagle_imputed_GWAS.assoc.txt GEA code: 200–Identification_of_Population_Structure_Associated_with_Habitat_final.Rmd GWA code: 300-Identification_of_loci_Underlying_Variation_in_Morphology_final_bedops.Rmd