This repository contains data, code, and supplementary information for the paper:
Hoban, ML, Williams, JT, 2019. Cirripectes matatakaro, a new species of combtooth blenny from the Central Pacific, illuminates the origins of the Hawaiian fish fauna (in review)
- cirripectes.Rproj -- RStudio project for code and analyses
- cirripectes_genetic_stats.R -- calculate genetic summary statistics
- cirripectes_map.R -- create distribution map (requires google API key / billing)
- cirripectes_pca.R -- calculate and plot principal components analysis (PCA)
- cirripectes_tree_beast.R -- format and display divergence timetree
- this is left over from a previous version of the paper
- cirripectes_tree_mrbayes.R -- format and display COI phylogeny
- cirripectes_specimens.xlsx -- morphological specimen data
- new_sp_occurrence.csv -- geographical occurrence data for C. matatakaro returned from google geocoding algorithm
- 'lon': longitude
- 'lat': latitude
- 'type': location type
- 'loctype': basis of geocode calculation
- 'address': text description of location
- 'north': northern bounding latitude
- 'south': southern bounding latitude
- 'east': eastern bounding longitude
- 'west': western bounding longitude
- samples.tab -- sequencee/specimen data for haplotype network construction
- 'id': sequence identifier
- 'species': species
- 'island','country','region': locality information
- variolosus-vanderbilti-geocoded.csv -- specimen occurrence data from GBIF with geocoded locations (where coordinates where lacking)
- see GBIF.org for file format
- PartitionFinder_output.txt -- best partitioned substitution model scenario (AICc) output from PartitionFinder
- jModelTest2_output.txt -- best nonpartitioned substitution model scenario (AICc) output from jModelTest2
- cirripectes-684-reduced.nex -- MrBayes input file / NEXUS alignment
- partitioned substitution model (see below)
- cirripectes-684-reduced.nex.con.tre -- COI phylogeny tree file (current, used)
- outgroup: Plagiotremus tapeinosoma
- MrBayes MCMC run: 2e8 generations, 20% burn-in
- partitioned substitution model
- codon 1: GTR+G
- codon 2: F81+G
- codon 3: GTR+I+G
- cirripectes-HKY-nonpartitioned.tre -- COI phylogeny tree file (secondary)
-this is a secondary analysis using a nonpartitioned substitution model
- outgroup: Plagiotremus tapeinosoma
- MrBayes MCMC run: 2e7 generations, 20% burn-in
- substitution mode: HKY+I+G
- treebuild2.nex.con.tre -- COI phylogeny tree file
- this is retained from a previous version of the manuscript
- outgroup: Exallias brevis
- MrBayes MCMC run: 3e7 generations, 20% burn-in
- substitution model: GTR+I+G
- vanderbilti-redhead-coi.fasta -- COI sequence data for C. vanderbilti and C. matatakaro
- variolosus-redhead.fasta -- COI sequence data for C. variolosus and C. matatakaro