Dataset DOI: 10.5061/dryad.z8w9ghxt1

Description of the data and file structure

Datasets used for the study entitled "Host fragmentation promotes genetic divergence and speciation processes in ectomycorrhizal fungi". Following abbreviations are used here: the ribosomal RNA internal transcribed spacer (ITS) region, operational taxonomic units (OTUs), ectomycorrhizal (ECM) fungi, ectomycorrhizal Basidiomycota (ECMB), plant-saprotrophs/root-endophytes (PS/RE), and plant-saprotrophs (PS).

Files and variables

File:clustered_ITS.fasta

Description: FASTA format file comprising ITS sequences of respective fungal OTUs.

File:clustered_F_rbcL.fasta

Description: FASTA format file comprising rbcL forward sequences of respective plant OTUs.

File:clustered_R_rbcL.fasta

Description: FASTA format file comprising rbcL reverse sequences of respective plant OTUs.

dModel10ECM.stan

dModel1ECM.stan

dModel1PSRE.stan

dModel2ECM.stan

dModel2PSRE.stan

dModel3ECM.stan

dModel3PSRE.stan

dModel4ECM.stan

dModel4PSRE.stan

dModel5ECM.stan

dModel5PSRE.stan

dModel6ECM.stan

dModel6PSRE.stan

dModel7ECM.stan

dModel7PSRE.stan

dModel8ECM.stan

dModel8PSRE.stan

dModel9ECM.stan

Description: Stan model code describing the two-step bionomial model under the focal model used with the focal dataset. Four datasets are included: ECM (ectomycorrhizal fungi), ECMB (ectomycorrhizal Basidiomycota), PS/RE (plant saprotrophs/root endophytes), and PS (plant saprotrophs). Ten models (Model1–Model10) are available for the ECM and ECMB datasets, and eight models (Model1–Model8) are available for the PS/RE and PS datasets. This Stan code can be run in R using the rstan package by executing R scripts as shown in R-commands.R. Thereby, the appropriate input file (Input_data[threshold][dataset].csv) is fitted to the two-step binomial model.

File:GeoDis_x_GenDis_ECM.csv

Description: Table showing the geographical distance from the study site and the genetic distance from each ECM query sequence for every hit sequence

Variables

• Area: The geographic regions where the fungal materials corresponding to each hit sequences were collected
• Geo.dist:Geographical distance from the study site (km)
• Gen.dist:Genetic distance (p-distance) between query and hit sequence
• query:Name of query OTU
• Phylum:Phylum to which query OTU belongs

File:GeoDis_x_GenDis_PSRE.csv

Description: Table showing the geographical distance from the study site and the genetic distance from each PS/RE query sequence for every hit sequence

Variables

• Area: The geographic regions where the fungal materials corresponding to each hit sequences were collected
• Geo.dist:Geographical distance from the study site (km)
• Gen.dist:Genetic distance (p-distance) between query and hit sequence
• query:Name of query OTU
• Lifestyle:Lifestyle of query OTU
• Phylum:Phylum to which query OTU belongs

Input_data97ECM.csv

Input_data97ECMB.csv

Input_data97PS.csv

Input_data97PSRE.csv

Input_data98ECM.csv

Input_data98ECMB.csv

Input_data98PS.csv

Input_data98PSRE.csv

Input_data99ECM.csv

Input_data99ECMB.csv

Input_data99PS.csv

Input_data99PSRE.csv

Description: Input data used to analyze the focal dataset under the focal sequence-identity threshold. Four datasets are included: ECM (ectomycorrhizal fungi), ECMB (ectomycorrhizal Basidiomycota), PS/RE (plant saprotrophs/root endophytes), and PS (plant saprotrophs). Operational taxonomic units (OTUs) were clustered using three sequence-identity thresholds: 97%, 98%, and 99%.

Variables

• No: Row number
• Region:Focal geographical region
• Country:Focal country
• lat:Latitude
• lon:Longitude
• OTU:Total number of fungal ITS OTUs detected in the nucleotide sequence database
• Singleton:Number of singleton ITS OTUs detected in the nucleotide sequence database
• detected:Number of query OTUs for which highly similar hit sequences are available in public database
• Host1:Log transformation (log(x+1)) of Fagaceae species richness
• Host2:Log transformation (log(x+1)) of Dipterocarpaceae species richness
• Dist:Log transformation (log(x+1)) of geographical distance from the study site
• temp:Annual mean temperature of capital city (°C)
• prec:Annual accumulated precipitation of capital city (m)
• Sds:Standard deviations (in this order) of Host1, Host2, Dist, temp, and prec across 152 geographical regions for the ECM and ECMB datasets, and of Host1, Host2, Host3, Dist, temp, and prec across the same 152 geographical regions for the PS/RE and PS datasets.
• N:Number of total query OTUs in each dataset

Code/software

File:R-commands.R

Description: R format file describing commands used for the analyses.

Access information

Other publicly accessible locations of the data:

Data was derived from the following sources: