DOI: 10.5061/dryad.gf1vhhmvd
title: Multiple mechanisms contribute to isolation-by-environment in the redheaded pine sawfly, Neodiprion lecontei

description: Isolation by environment (IBE) is a population genomic pattern that arises
 when ecological barriers reduce gene flow between populations. Although
 current evidence suggests IBE is common in nature, few studies have
 evaluated the underlying mechanisms that generate IBE patterns. In this
 study, we evaluate five proposed mechanisms of IBE (natural selection
 against immigrants, sexual selection against immigrants, selection against
 hybrids, biased dispersal, environment-based phenological differences)
 that may give rise to host-associated differentiation within a sympatric
 population of the redheaded pine sawfly, Neodiprion lecontei, a species
 for which IBE has previously been detected. We first characterize the
 three pine species used by N. lecontei at the site, finding morphological
 and chemical differences among the hosts that could generate divergent
 selection on sawfly host-use traits. Next, using morphometrics and ddRAD
 sequencing, we detect modest phenotypic and genetic differentiation among
 sawflies originating from different pines that is consistent with recent,
 in situ divergence. Finally, via a series of laboratory assays – including
 assessments of larval performance on different hosts, adult mate and host
 preferences, hybrid fitness, and adult eclosion timing – we find evidence
 that multiple mechanisms contribute to IBE in N. lecontei. Overall, our
 results suggest IBE can emerge quickly, possibly due to multiple
 mechanisms acting in concert to reduce migration between different
 environments.
description: ## README for "Multiple mechanisms contribute to
 isolation-by-environment in the redheaded pine sawfly, Neodiprion
 lecontei" ## All scripts can be found on Zenodo, and all data files
 are on Dryad. The two repositories share the same folder structure. This
 file gives an overview of both the scripts and data. #
 Host\_Phenotype\_IBE: This folder contains the scripts and data files used
 to perform the host plant characterization, morphological, and IBE
 analyses. # Authors: Catherine R. Linnen, Robin K. Bagley, Christopher J.
 Frost # The script folder contains the following file # -
 Host\_Phenotype\_IBE\_Scripts.R: R script with commented segments for
 performing the following analyses (in order of appearance): # - Analysis
 of host plant characteristics # - Needle width # - Volatile analysis # -
 Resin content analysis # - Analysis of ovipositor shape # - Analysis of
 IBE mechanisms # - Natural selection against immigrants # - Egg-to-cocoon
 survival # - Development time # - Cocoon weight (female and male) # -
 Sexual selection against immigrants # - Hybrid survival # - Dispersal bias
 # - No choice oviposition (host preference) # - Choice oviposition (host
 preference) # - Temporal isolation (adult eclosion) # The data folder
 contains the following files # - ALLNeedleWidth.csv: csv file containing
 needle width data for mature and seedling trees. # -
 pinus\_4species\_for\_NMDS.csv: csv file containing volatile VOC analyte
 measurements (in ng/min) for NMDS analysis. # - PSVresinFinal.csv: csv
 file containing resin content data. # - Labrearedcoordinates.csv: csv file
 containing (X,Y) coordinates for ovipositor landmarks # -
 Labrearedclassifier.csv: csv file containing identifying information (host
 and unique ID number), forewing lengths, # ovipositor lengths, and
 ovipositor widths. Note that for this file, cells containing with
 "NA" indicate # that forewing length was unable to be measured
 for that individual. # - EggToCocoonSurvival.csv: csv file containing
 family level egg-to-cocoon survival data. # -
 DevelopmentTime\_by\_individual.csv: csv file containing individual data
 for development time in days from egg to cocoon. # - CocoonWeights.csv:
 csv file containing individual weights for female and male cocoons. # -
 Mating\_outcomes\_SexualSelection.csv: csv file containing mate/no-mate
 outcomes of no-choice mating encounters. # - RI\_Fitness\_Survival.csv:
 csv file containing survival rates for hybrid and non-hybrid individuals.
 # - NoChoiceHostPref.csv: csv file containing yes/no eggs laid outcomes
 for no-choice oviposition assays. # - ChoiceHostPref.csv: csv file
 containing eggs laid outcomes for choice oviposition assays, including if
 females chose # their source host (Chose\_Natal). Note that for this
 dataset, cells containing "NA" indicate the female either did
 not # lay eggs before dying (Laid\_Eggs = 0), or represent a host that was
 not offered to that female (i.e., individual females # were only offered a
 choice between their source host and one alternative host; not both). # -
 2013\_cumulativeemergencebyhost.txt: text file containing daily cumulative
 eclosion proportion data per host for 2013. # -
 2014\_cumulativeemergencebyhost.txt: text file containing daily cumulative
 eclosion proportion data per host for 2014. # Admixture: This folder
 contains the scripts and data files used to perform Admixture population
 structure analysis. # The script folder contains the following file # -
 do\_Admixture.sh: bash script to run the Admixture analysis. # The data
 folder contains the following files # - Arb\_MAF0.05.vcf: VCF file used to
 prepare PLINK input files; contains genotype information. # -
 MAF\_Arb\_Admix.ped: PLINK PED format file containing genotype information
 for genotyped specimens. # - MAF\_Arb\_Admix.map: PLINK MAP format file
 containing identifying information for genotyped specimens. #
 Genomic\_FST: This folder contains the scripts and data files used to
 calculate FST values from ddRAD data. # Authors: Vitor C. Sousa, Catherine
 R. Linnen # The script folder contains the following files # -
 ALL\_computeFST\_from\_freq\_or\_genotypes.R: R script to compute FST
 between populations using Hudson's estimator. # - fstfunctions.R:
 supporting script to compute Neodiprion data to compute FST between
 populations using Hudson's estimator. # The data folder contains the
 following files # - Arb\_ALL.recode.GT: file containing individual
 genotype information for FST calculation. # - IndPop3\_alt.txt: file
 containing source host information for genotyped specimens.