DOI: 10.5061/dryad.83bk3jb4d
title: An experimental test for ecologically dependent reproductive isolation across an avian migratory divide

description: Divergent adaptation can promote ecological speciation if hybrids have
 reduced fitness because they are poorly adapted to either parental niche.
 We tested for ecologically dependent, postzygotic isolation between two
 subspecies of Swainson’s thrushes, which form a migratory divide and
 hybrid zone in western North America. To do this, we translocated
 backcrossed and admixed birds from the hybrid zone into the range of each
 subspecies at the beginning of fall migration. We estimated a proxy for
 their survival on migration and migratory behaviour using automated radio
 tracking. Apparent survival of birds in the two environments did not
 depend on their genomic ancestry, suggesting that Swainson’s thrushes’
 divergent adaptation to different fall migration routes does not fit the
 classic model of ecological speciation. We propose an alternate scenario
 where ecological selection on migration may interact with intrinsic
 maladaptation in hybrids to produce reduced hybrid survival on migration.
 By translocating birds from the same genomic backgrounds into different
 environments, our experiment also allowed us to distinguish between the
 effects of environmental relative to genetic contributors to their
 migratory behaviour. We found evidence that both genetic and environmental
 factors influence migratory behaviour, as the effect of genomic ancestry
 on initial migratory trajectories depended on the start location for
 migration, but birds ultimately followed expected routes given their
 genomic ancestries.
description: # An experimental test for ecologically dependent reproductive isolation
 across an avian migratory divide #### motusTranslocatedBirds.csv * data
 for birds that were caught in the hybrid zone and translocated to Squamish
 (coastal) or Lillooet (inland) Column descriptions: * reference:
 Individual ID from banding sheets * name_in_vcf: Individual ID from vcf
 file * hiest_heterozygosity: Autosomal interspecific heterozygosity, based
 on AIMs * hiest_ancestry: Autosomal genomic ancestry, based on AIMs *
 release_site: Name of release site * capture_site: Name of capture site *
 release_year: Year tagged and released * sex_binary: Sex based on read
 counts from sex chromosomes * age_release: Age bird was tagged and
 released; HY = Hatch year * release_gps.n: GPS coordinate of release
 latitude * release_gps.w: GPS coordinate of release longitude *
 capture_gps.n: GPS coordinate of capture latitude * capture_gps.w: GPS
 coordinate of capture longitude * translocated: Translocation status; yes
 or no * motustagid ID number for Lotek radio tag registered with Motus *
 band: Bird band number * bander: Bander initials; HJ = Hannah Justen, KD =
 Kira Delmore * release_date: Date bird was released; format yyyy-mm-dd *
 releaseDay: Day of the year (1 = Jan 1) the bird was released *
 fall_releaseSite_bearing_tier1: Orientation in degrees, relative to
 release location, within 300 km of release location * survival: Binary
 estimate of survival (1 = survived, 0 = not survived) ####
 motusPembertonBirds.csv * data for birds that were caught and released in
 the hybrid zone Column descriptions: * reference: Individual ID from
 banding sheets * name_in_vcf: Individual ID from vcf file *
 hiest_heterozygosity: Autosomal interspecific heterozygosity, inferred
 with HIest * hiest_ancestry: Autosomal genomic ancestry, inferred with
 HIest * release_site: Name of release site * capture_site: Name of capture
 site * release_year: Year tagged and released * sex_binary: Sex based on
 read counts from sex chromosomes * age_release: Age bird was tagged and
 released; HY = Hatch year * release_gps.n: GPS coordinate of release
 latitude * release_gps.w: GPS coordinate of release longitude *
 capture_gps.n: GPS coordinate of capture latitude * capture_gps.w: GPS
 coordinate of capture longitude * translocated: Translocation status; yes
 or no * motustagid ID number for Lotek radio tag registered with Motus *
 band: Bird band number * bander: Bander initials; HJ = Hannah Justen, KD =
 Kira Delmore * release_date: Date bird was released; format yyyy-mm-dd *
 releaseDay: Day of the year (1 = Jan 1) the bird was released *
 fall_releaseSite_bearing_tier1: Orientation in degrees, relative to
 release location, within 300 km of release location * survival: Binary
 estimate of survival (1 = survived, 0 = not survived) ####
 motusDetections.filtered.csv * Motus radio station detections for all
 individuals included in the study Column descriptions: * hitID: ID
 associated with Motus detection * runID: ID associated with the Motus
 detection run * batchID: ID associated with a batch of Motus detections *
 ts: Time and date of detection * tsCorrected: Numerical time and date of
 detection * motustagid: ID number for Lotek radio tag registered with
 Motus * runLen: Run length for tag detection * tagProjID: Project ID
 associated with tag * mfg: Manufacturer ID * tagModel: Tag model name *
 tagLifespan: Lifespan of tag in days * pulseLen: Pulse length emitted by
 tag * tagDeployID: Deployment ID for tag * speciesID: Motus ID code for
 Swainson's thrush * tagDeployStart: Time and date of tag deployment *
 tagDeployEnd: Time and date tag will expire * tagDepLat: Latitude GPS for
 tag deployment * tagDepLon: Longitude GPS for tag deployment * fullID:
 Full ID for Motus tag registration * recvDeployID: Receiver station
 deployment ID * recvDeployLat: Receiver station latitude GPS *
 recvDeployLon: Receiver station longitude GPS * recv: Receiver station
 type * recvDeployName: Receiver station name * recvSiteName: Site name for
 receiver station * recvProjID: Project ID associated with the receiver *
 recvUtcOffset: Time zone difference from UTC of receiver * antType:
 Antenna type * antBearing: Antenna bearing * antHeight: Antenna height *
 speciesEN: Species name English * speciesFR: Species name French *
 speciesSci: Species name Scientific * speciesGroup: Species taxonomic
 group * tagProjName: Tag project name * recvProjName: Receiver project
 name * deployyear: Year tag was deployed * deploymonth: Month tag was
 deployed * deploydoy: Day of the year tag was deployed * detectyear: Year
 tag was detected * detectmonth: Month tag was detected * detectdoy: Day of
 the year tag was detected * detecttime: Time tag was detected * reference:
 Individual ID from banding sheets * name_in_vcf: Individual ID from vcf
 file * capture_site: Name of release site * release_site: Name of capture
 site * release_year: Year tagged and released * release_gps.n: GPS
 coordinate of release latitude * release_gps.w: GPS coordinate of release
 longitude * deployDay: Date bird was released; format yyyy-mm-dd * tsDay:
 Date bird was detected; format yyyy-mm-dd * tagDays: Number of days after
 tagging that the bird was detected #### SWTH_translocation.zip * code for
 statistical analysis of Swainson's thrush translocation experiment *
 input data: Motus detections (motusDetections.filtered.csv), ancestry
 & heterozygosity estimates (see SWTH_hiest.zip for bioinformatics
 pipeline), capture and release history metadata (motusPembertonBirds.csv
 & motusTranslocatedBirds.csv) * output results: model estimates of
 survival on migration and genetic x environment effects on migratory
 orientation; formatted figures * All data formatting and analyses run in R
 * required packages: tidyverse, sf, scico, rnaturalearth, geosphere, lme4,
 car, Matrix, marked **01_translocation_dataFormatting.Rmd** * formatting
 survival and phenotypic data from detections * basic data checks and
 visualization * making maps of detection data (Fig. 3A, Fig. 4)
 **02_translocation_analysis_orientation.Rmd** * analysis of migratory
 orientations * data checks and visualization * plotting orientation
 analysis outcome (Fig. 3C) **03_translocation_analysis_survival.R** * CJS
 model implementation * uses output from
 01_translocation_dataFormatting.Rmd
 **04_translocation_analysis_survival.Rmd** * visualizing output of CJS
 models (Fig. 2) * formatting CJS parameter and estimate tables * uses
 output from 03_translocation_analysis_survival.R #### SWTH_hiest.zip *
 bioinformatics pipeline for obtaining the highest ancestry estimates *
 Input sequences are publicly available via the NCBI Sequence Read Archive
 under BioProject Number PRJNA979932 * Required software: vcftools,
 bcftools, plink * Required R packages: HIest, tidyverse
 **01_vcf_to_hiestInput.sh** * process vcf to get divergent SNPs and allele
 counts for the ref panel and target hybrids * carry out data checks and
 quality filtering before selecting a final set of alleles
 **02_run_hiest.R** * data formatting in R, using output allele counts from
 01_vcf_to_highestInput.sh * Then run Hiest to estimate ancestry and
 heterozygosity