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  • Recent Climate Change and Historical Population Structure Predict Spatial Patterns of Admixture Between Two Host‐Specialised Pine Sawfly Species
Title: Recent Climate Change and Historical Population Structure Predict Spatial Patterns of Admixture Between Two Host‐Specialised Pine Sawfly Species
ABSTRACT Human disturbance can have profound effects on biodiversity, including increasing hybridization between reproductively isolated species. One approach for understanding how human activity affects hybridization dynamics is to evaluate correlations between disturbance (e.g., urbanisation, temperature change) and hybridization. Because variation in hybridization can also arise from historical factors unrelated to recent human disturbance, it is essential to account for population structure to avoid spurious correlations. Here, we combine environmental and high‐coverage whole‐genome resequencing data to investigate how human disturbance and population structure affect hybridization dynamics between a pair of pine sawflies adapted to different pines,Neodiprion leconteiandNeodiprion pinetum. We find thatN. leconteiandN. pinetumexhibit strikingly different patterns of population structure, which we hypothesise stem from differences in host use. We also find that recent admixture is both asymmetric and geographically variable. Linear regression analyses reveal that admixture proportion is predicted by indirect human disturbance (i.e., climate change) and not direct human disturbance (e.g., urbanisation) in bothN. leconteiandN. pinetum. Lastly, inN. pinetum, we find evidence of a spurious association between admixture and direct human disturbance that disappears when regression models account for population structure via inclusion of genetic principal component scores as covariates. Together, our data suggest that indirect human disturbance and population structure both contribute to geographic variation in admixture betweenN. leconteiandN. pinetum. Our study also highlights the importance of adequately controlling for population structure when attempting to identify environmental predictors (human disturbance‐related or not) of hybridization.  more » « less
Award ID(s):
2348574 1750946
PAR ID:
10668763
Author(s) / Creator(s):
 ;  
Publisher / Repository:
Wiley
Date Published:
Journal Name:
Molecular Ecology
Volume:
34
Issue:
24
ISSN:
0962-1083
Page Range / eLocation ID:
e70183
Format(s):
Medium: X
Associated Dataset(s):
View Associated Dataset(s) >>
Sponsoring Org:
National Science Foundation
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We also find that recent\n admixture is both asymmetric and geographically variable. Linear\n regression analyses reveal that admixture proportion is predicted by\n indirect human disturbance (i.e., climate change) and not direct human\n disturbance (e.g., urbanization) in both N. lecontei and N. pinetum.\n Lastly, in N. pinetum, we find evidence of a spurious association between\n admixture and direct human disturbance that disappears when regression\n models account for population structure via inclusion of genetic principal\n component scores as covariates. Together, our data suggest that indirect\n human disturbance and population structure both contribute to geographic\n variation in admixture between N. lecontei and N. pinetum. Our study also\n highlights the importance of adequately controlling for population\n structure when attempting to identify environmental predictors (human\n disturbance-related or not) of hybridization."],"TechnicalInfo":["# Recent climate change and historical population structure predict\n spatial patterns of admixture between two host-specialized pine sawfly\n species Dataset DOI: [10.5061/dryad.kh18932jw](10.5061/dryad.kh18932jw) ##\n Description of the data and file structure To perform all analyses, run\n scripts provided in the order indicated in the folder/script name (i.e.,\n "01*" to "07*"). NOTE: for all bash scripts (*.sh),\n you will have to modify them to run on your cluster. However, the program\n commands should work as long as you are using the same version of the\n program (program versions indicated in the Materials and Method section of\n the manuscript). ### Files and variables #### File:\n Glover_Linnen_dryad.zip **Description:**  Input files required to run\n analyses are provided: 1.\n "allsites_LecPineHetr_filtered_ExclIndvs_minQ20_AllImbHom_refilter_bcftools_norm.vcf.gz" - required for ABBA-BABA analysis ("06_ABBA-BABA" folder); vcf file contains variant and invariant sites for all *N. lecontei*, *N. pinetum*, and *N. hetricki* individuals included in analysis 2. "snps_LecPine_filtered_ExclIndvs_MAF05_minQ20_AllImbHom_refilter_pruned_bcftools_norm.vcf.gz" - required for ADMIXTURE ("03_ADMIXTURE" folder) and principal component analysis (PCA) for both species combined ("04_run_pcas.sh" script) analyses; vcf file contains linkage-pruned SNPs for all *N. lecontei* and *N. pinetum* individuals included in analyses (i.e., contaminated/putative haploid male individuals removed) 3. "snps_LecOnly_filtered_ExclIndvs_MAF05_minQ20_AllImbHom_refilter_pruned_bcftools_norm.vcf.gz" - required for PCA for *N. lecontei* only analysis ("04_run_pcas.sh" script"); vcf file contains linkage-pruned SNPs for all *N. lecontei* individuals included in analysis (i.e., contaminated/putative haploid male individuals removed) 4. "snps_PineOnly_noHybrid_filtered_ExclIndvs_MAF05_minQ20_AllImbHom_refilter_pruned_bcftools_norm.vcf.gz" - required for PCA for *N. pinetum *only analysis ("04_run_pcas.sh" script"); vcf file contains linkage-pruned SNPs for all *N. pinetum *individuals included in analysis (i.e., contaminated/putative haploid male individuals and F1 hybrid called *N. pinetum* at time of collection due to being collected on white pine removed) 5. "fulldata_LecPine.csv", "fulldata_LecOnly.csv", "fulldata_PineOnly.csv" - full/compiled data for all *N. lecontei* and *N. pinetum* individuals together, all *N. lecontei* individuals, and all *N. pinetum* individuals included in downstream analyses, respectively. These files are required to run the "05_plot_PCAs_ADMIXTURE.R" and "07_run_models.R" scripts. Description of columns in the *.csv files (#5) above (each row represents an individual sawfly): 1. "ind" = unique individual identifier assigned by the sequencing center (Admera Health) 2. 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