Description
Local adaptation can occur at small spatial scales relative to the dispersal capacity of species. Alpine ecosystems have sharp environmental clines that offer an opportunity to investigate the effects of fine scale shifts in species’ niche breadth on adaptive genetic processes. Here we examine two grasshopper species endemic to the Australian Alps (Kosciuscola spp.) that differ in elevational niche breadth; one broader, K. usitatus (1400-2200m), and one narrower, K. tristis (1600-2000m). We examine signatures of selection with respect to environmental and morphological variables in two mountain regions using FST outlier tests and environmental association analyses (EAA) applied to Single Nucleotide Polymorphism data (K. usitatus: 9,017 SNPs, n = 130; K. tristis: 7,363 SNPs, n = 135). Stronger genetic structure was found in the more narrowly distributed K. tristis, which showed almost twice the number of SNPs under putative selection (10.8%) compared with K. usitatus (5.3%). When examining SNPs in common across species (n = 3,058), 260 SNPs (8.5%) were outliers shared across species, and these were mostly associated with elevation, a proxy for temperature, suggesting parallel adaptive processes in response to climatic drivers. Additive polygenic scores (an estimate of the cumulative signal of selection across all candidate loci) were non-linearly and positively correlated with elevation in both species. However, a steeper correlation in K. tristis indicated a stronger signal of spatially varying selection towards higher elevations. Our study illustrates that the niche breadth of co-occurring and related species distributed along the same environmental cline is associated with differences in patterns of microgeographic adaptation.
Methods
Sampling was undertaken for two weeks in late February to early March of 2017. Three transects ranging from 1400-2200m in elevation were sampled within each of two mountain regions, Thredbo and Guthega within Kosciuszko National Park in New South Wales. DNA was extracted from the tissue of one femur per collected specimen at the Diversity Arrays Technology sequencing facility, Canberra (DArTseq). A modified double-digest RAD sequencing protocol was used to generate data at DArTseq. SNPs were further filtered using the Radiator r package.
Usage Notes
Files: K.usitatus_9017_SNPs.ped, K.usitatus_9017_SNPs.map
Genotype information of 130 individuals of Kosciuscola usitatus analysed at 9,017 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers
File: K.usitatus_3321_SNPs.str
File with 3,321 SNPs and 130 individuals, used to analyse pairwise Fst, genetic structure, isolation by distance and spatial autocorrelation analyses for Kosciuscola usitatus. The file is STRUCTURE formatted. Missing values are coded as -9
File: K.usitatus_envt_data.csv
Environmental data information used to detect signatures of selection (EAA analysis, pRDA and RDA).
pop= population information representing the area of collection for each individual
transect= transect information for each individual
location= Location
individual= unique name of individual
elevation= elevation in meter above sea level
FPC= Foliage Projective Cover (%)
precipseas = precipitation seasonality
roughness = terrain roughness
FZ = number of frost days
bd = soil bulk density
ph = soil ph
femur length = measured in mm
sex = sex per individual, binary coded: male = 0, female = 1
Files: K.tristis_7363_SNPS.ped, K.tristis_7363_SNPS.map
Genotype information of a total of 135 individuals of Kosciuscola usitatus analysed at 7,363 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers
File: K.tristis_3566_SNPS.str
File with 3,566 SNPs and 135 individuals, used to analyse pairwise Fst, genetic structure, isolation by distance and spatial autocorrelation analyses for Kosciuscola tristis. The file is STRUCTURE formatted. Missing values are coded as -9
File: K.tristis_envt_data
Environmental data information used to detect signatures of selection (EAA analysis, pRDA and RDA).
pop= population information representing the area of collection for each individual
transect= transect information for each individual
location= Location
individual= unique name of individual
elevation= elevation in meter above sea level
FPC= Foliage Projective Cover (%)
precipseas = precipitation seasonality
roughness = terrain roughness
FZ = number of frost days
bd = soil bulk density
ph = soil ph
femur length = measured in mm
sex = sex per individual, binary coded: male = 0, female = 1
File: Whole_data_3058_SNPs.ped, Whole_data_3058_SNPs.map
Genotype information of 266 individuals (129 K. usitatus, 137 K. tristis) analysed at 3,058 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers
File: Whole_data_2143_SNPs.str
File with 2,143 SNPs and 266 individuals, used to perform genetic structure analysis for the common dataset for the two species. The file is STRUCTURE formatted. Missing values are coded as -9
Methods
Sampling was undertaken for two weeks in late February to early March of 2017. Three transects ranging from 1400-2200m in elevation were sampled within each of two mountain regions, Thredbo and Guthega within Kosciuszko National Park in New South Wales. DNA was extracted from the tissue of one femur per collected specimen at the Diversity Arrays Technology sequencing facility, Canberra (DArTseq). A modified double-digest RAD sequencing protocol was used to generate data at DArTseq. SNPs were further filtered using the Radiator r package.
Usage Notes
Files: K.usitatus_9017_SNPs.ped, K.usitatus_9017_SNPs.map
Genotype information of 130 individuals of Kosciuscola usitatus analysed at 9,017 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers
File: K.usitatus_3321_SNPs.str
File with 3,321 SNPs and 130 individuals, used to analyse pairwise Fst, genetic structure, isolation by distance and spatial autocorrelation analyses for Kosciuscola usitatus. The file is STRUCTURE formatted. Missing values are coded as -9
File: K.usitatus_envt_data.csv
Environmental data information used to detect signatures of selection (EAA analysis, pRDA and RDA).
pop= population information representing the area of collection for each individual
transect= transect information for each individual
location= Location
individual= unique name of individual
elevation= elevation in meter above sea level
FPC= Foliage Projective Cover (%)
precipseas = precipitation seasonality
roughness = terrain roughness
FZ = number of frost days
bd = soil bulk density
ph = soil ph
femur length = measured in mm
sex = sex per individual, binary coded: male = 0, female = 1
Files: K.tristis_7363_SNPS.ped, K.tristis_7363_SNPS.map
Genotype information of a total of 135 individuals of Kosciuscola usitatus analysed at 7,363 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers
File: K.tristis_3566_SNPS.str
File with 3,566 SNPs and 135 individuals, used to analyse pairwise Fst, genetic structure, isolation by distance and spatial autocorrelation analyses for Kosciuscola tristis. The file is STRUCTURE formatted. Missing values are coded as -9
File: K.tristis_envt_data
Environmental data information used to detect signatures of selection (EAA analysis, pRDA and RDA).
pop= population information representing the area of collection for each individual
transect= transect information for each individual
location= Location
individual= unique name of individual
elevation= elevation in meter above sea level
FPC= Foliage Projective Cover (%)
precipseas = precipitation seasonality
roughness = terrain roughness
FZ = number of frost days
bd = soil bulk density
ph = soil ph
femur length = measured in mm
sex = sex per individual, binary coded: male = 0, female = 1
File: Whole_data_3058_SNPs.ped, Whole_data_3058_SNPs.map
Genotype information of 266 individuals (129 K. usitatus, 137 K. tristis) analysed at 3,058 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers
File: Whole_data_2143_SNPs.str
File with 2,143 SNPs and 266 individuals, used to perform genetic structure analysis for the common dataset for the two species. The file is STRUCTURE formatted. Missing values are coded as -9
| Date made available | 10 Jun 2022 |
|---|---|
| Publisher | Macquarie University |
Keywords
- Biological sciences