DOI: 10.5061/dryad.z8w9ghxt1
title: Host fragmentation reinforces dispersal limitation and lineage divergence in ectomycorrhizal fungi

description: Five types of datasets are provided: FASTA-formatted sequence data
 (xxx.fasta), model codes written in the Stan language (dModelxxx.stan),
 input data used for modeling (input_dataxxx.csv), tables showing the
 geographical distance from the study site and the genetic distance from
 each query sequence for every hit sequence (GeoDis_x_GenDis_xxx.csv), and
 the R commands used in this study (R-commands.R). Raw Illumina MiSeq
 sequencing data were processed and clustered into operational taxonomic
 units (OTUs) using Claident ver. 0.9.2024.06.10. The model codes and input
 data can be used to run the two-step binomial model, which estimates how
 many fungal OTUs detected at the study site are shared with each country
 or region.
description: # Host fragmentation reinforces dispersal limitation and lineage
 divergence in ectomycorrhizal fungi Dataset DOI:
 [10.5061/dryad.z8w9ghxt1](https://doi.org/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: *