This is the repository for data used in my master's thesis project "Evaluating species origins within tropical sky-islands arthropod communities", published in the Journal of Biogeography. This repository contains code for delimiting Operational Taxonomic Units (OTUs) using a Generalized Mixed Yule Coalescent method (GMYC) and CROP, estimate genetic and specific diversity, and run a null model. It also contains the sequences and trees needed to run the code. Here is a brief description of the files contained in this repo:
otus_delimitation. R code for delimiting OTUs using trees calculated in BEAST
diversity. R code for calculating genetic diversity, Fst and making haplotype networks. It also contains R code for calculatin beta diversity using OTUs
habitat. R code for identifying the habitat type of each specimen (branch) in each tree
EW_nullmodel. R code for making a null model with which I tested the east-west structure present in the TMVB
sequences_fasta. Contains all the sequences used in the project in fasta format. Sequences are grouped by order (e.g. Colepotera) and by OTUs
trees. Contains all the trees built in BEAST and used in this project.
OTUs. CSV file with a table of the number of individuals from each OTU (44 OTUs total) present in each mountain (7 mountains). This file is used for calculating a presence-absence matrix. Notice there is no OTU number 9, because this was found to be product of a sequencing error in downstream analyses and thus was deleted.
Software:
- BEAST, BEAUTI and treeanotator
- R libraries "splits", "ape", "MASS", "paran", "ape", "ade4", "adegenet", "diveRsity", "pegas", "vegan"
Data:
- Sequences in fasta format
- Ultrametric trees