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.
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.
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.