Dataset DOI: 10.5061/dryad.v15dv4283

Description of the data and file structure

# Supplementary Data for the manuscript titled: "From setae to scales: Burmese amber fossils reveal the Early Cretaceous innovation of body coverings in scaly crickets."

The dataset comprises the following components:

1. Tree files and corresponding R scripts necessary for ancestral state reconstruction;

2. Phylogenetic morphospace tree files with associated R scripts;

3. TNT and NEX format files used for phylogenetic analysis

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The Ancestral_state_reconstruction folder contains the following files:

1. morphology.nex.con.tre.phy (phylogenetic tree file based on tip-dating using the morphological matrix)

2. total.nex.con.tre.phy (phylogenetic tree file based on total-evidence matrix)

3. time_tree.R (R script for visualizing divergence time trees)

4. morphology_ancestral.R (R script for ancestral state reconstruction of body covering states using the phylogeny based on morphological data)

5. total_ancestral.R (R script for ancestral state reconstruction of body covering states using the total-evidence phylogeny)

6. distribution_ancestral_morph.R (R script for ancestral state reconstruction of body covering distribution using the phylogeny based on

morphological data)

7. distribution_ancestral_total.R (R script for ancestral state reconstruction of body covering distribution using the total-evidence phylogeny)

For ancestral state reconstruction analysis, either script can be used by modifying the input tree file accordingly.

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The Phylogenetic_morphospace folder contains the following files:

1. ages.txt (age information for taxa)

2. char_dependent.txt (trait dependencies for the HSJ method)

3. morphology.nex.con.tre.phy (a phylogenetic tree file based on tip-dating using the morphological matrix)

4. total.nex.con.tre.phy (a phylogenetic tree file based on total-evidence matrix)

5. morphology_char.nex (the morphological character matrix)

6. morphospace_morphology.R (R script for phylogenetic morphospace and related analyses)

To perform phylogenetic morphospace analysis, simply modify the input tree file as needed.

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The phylogenetic_analysis folder contains the following files:

1. morphology_with_time.nex (the morphological matrix for tip-dating analysis)

2. morphology_without_time.nex (the morphological matrix for bayesian inference)

3. total_evidence.nex （the total evidence matrix for tip-dating analysis)

4. tnt.tnt (the morphological matrix for TNT)

Files and variables

File: script-2025.09.22.zip

Description: including phylogenetic matrices, tree files, R scripts for ancestral state reconstruction and phylogenetic morphospace analyses, and TNT input files

Code/software

R v4.3.1

The R scripts provided in the ‘Ancestral_state_reconstruction’ and ‘Phylogenetic_morphospace’ folders can be run in R or RStudio. They load the input tree files (e.g., ‘morphology.nex.con.tre.phy’) and perform ancestral state reconstructions (using maximum likelihood or stochastic mapping) and phylogenetic morphospace projections. Users should modify the file paths in the scripts to match their local directory structure.

MrBayes v3.2.7

Used for Bayesian phylogenetic inference under the Mk model with gamma-distributed rate variation and fossil tip-dating. Input files: ‘morphology_with_time.nex’, ‘total_evidence.nex’ (formatted with MrBayes blocks).

TNT 1.6

Used for maximum parsimony analysis of the morphological dataset. Input file: ‘tnt.tnt’ (contains character matrix and analysis commands).