README:

Data stucture

Taxonomy:

This directory contains folders for each year of the Clements taxonomy.

• Clements_2021
• Clements_2022
• Clements_2023

Each taxonomy_year directory contains:

• OTT_crosswalk_YEAR.csv a CSV file mapping species from the Clements taxonomy for that taxonomy year to OpenTreeTaxonomy (OTT) identifiers (e.g. OTT_crosswalk_2021.csv). Also includes mapping from species in Clements to their Avibase id, and to the names for those taxa in the IOC World Bird List v14.1 , Birdlife/HBW 8, and the Howard and Moore v4 taxonomy"

• Column names and contents

  • TAXON_ORDER <- from Clements Checklist csv
  • SPECIES_CODE <- from Clements Checklist csv
  • TAXON_CONCEPT_ID <- Avibase id imported from Clements Checklist csv
  • PRIMARY_COM_NAME <- from Clements Checklist csv
  • SCI_NAME <- from Clements Checklist csv
  • ORDER1 <- from Clements Checklist csv
  • FAMILY <- from Clements Checklist csv
  • ott_id <- id for that species in OTT
  • ott_name <- name for that species in OTT
  • ott_tax_sources <- sources for that taxon name in OTT
  • ott_match_type <- how link was made from Clements name to OTT id. (may be 'canonical_match', 'synonym_match', 'new_taxon_addition', or 'NA' for no match, as well some other idiosyncratic match types for hand corrections)
  • H_M_name <- best match name or names in the Howard and Moore v4 taxonomy(if multiple names matched they are a semi-colon seperated list)
  • H_M_match_type <- how the the avibase taxon concepts map between the Clements and Howard and Moore names. One of 'concepts_match', 'child_of', 'parent_of', 'overlaps', or 'missing'.
  • Birdlife_name <- best match name or names in the Birdlife/HBW taxonomy(if multiple names matched they are a semi-colon seperated list)
  • Birdlife_match_type <- how the the avibase taxon concepts map between Clements and Birdlife names
  • IOC_name <- best match name or names in the Birdlife/HBW taxonomy(if multiple names matched they are a semi-colon seperated list)
  • IOC_match_type <- how the the avibase taxon concepts map between Clements and IOC names

• a taxon addition file capturing a suggested placement for species for which we do not yet have phylogenetic information

• a copy of the ebird taxonomy file for that year.

Trees:

This directory contains folders for each synth tree run, labelled by their version identifier (e.g. Aves_1.0)

The most recent tree is Aves_1.3 and that directory contains all of these files. (Older trees folders have some but not all of these files, and have a readme inculded in each folder)

Aves_1.3

For more details and code for how each of these files were generated see: https://github.com/McTavishLab/AvesTreeCode

• dates_citations.txt <-input studies used to estimate dates
• tree_citations.txt <- input studies used to estimate the phylogeny tree
• all_node_ages.json <- a json file storing the age estimates for each internal node in the phylogeny only tree, with the metadata about what input study suggested that node age.
• OpenTree_synth <- folder containing the direct outputs of OpenTree Synthesis (this is identical between Aves 1.2 and Aves 1.3)
  • This folder contains many nitty gritty internal synthesis outputs. These files are detailed in depth in the index.html file contained in the OpenTree synth folder
• A folder for each year of the Clements taxonomy folder:
  • phylo_only.tre <- OpenTree Id labeled tree including only tips with phylogenetic information
  • phylo_only_clements_labels.tre <- Clements labeled tree including only tips with phylogenetic information
  • phylo_only_clements_labels_ultrametric.tre <- ultrametric tree which is the input for the taxon addition step
  • taxon_addition_treeset.tre <- set of 100 complete trees from 100 stochastic taxon addition replicates
  • dated_rand_sample_clements.tre <- dated taxon addition tree cloud, 100 topologies from the taxon addition treeset using random selections from the node dates age for each dated node calibration. First line is a header line containing the text "trees", followed by one newick tree per line.
  • dated_mean_sample_clements.tre <- dated taxon addition tree cloud, 100 topologies from the taxon addition treeset using the mean node age for each node calibration. First line is a header line containing the text "trees", followed by one newick tree per line.
  • MCC_clements.tre <- Maximim clade credibility tree including all taxa in this version of the taxonomy summarized from the dated trees using random selections for the node calibrations. Labelled with Clements taxonomy labels.