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