Codes & Datasets

Information on published codes and datasets is provided below, with direct links to their respective repositories

Codes

EvoPhylo

An R package: Pre- and Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics (version 0.3).

Preprint Tutorials GitHub repositoryCRAN repository

Co-develop with Noah Greifer and Stephanie Pierce for its first release, and with Joëlle Barido-Sottani for its upcoming expansion. EvoPhylo performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses.

Datasets

Constructing new phenotypic (i.e., morphological) or molecular datasets from scratch for phylogenetic and evolutionary analyses is a time consuming and painstaking process. However, these are the necessary foundations upon which all questions in evolutionary and comparative biology depend on. In my career, I have created guidelines for phenotypic dataset construction, brand new phenotypic datasets, as well as revised datasets for various groups of tetrapods, mostly on reptiles. I have also created molecular datasets using published sequence data, besides ongoing projects to extract and sequence whole genomic data. Some of these are detailed below with links to their repositories.

NEW datasets:

Amniota (morphological)

1st edition: Simões et al., 2022 (Science Advances). Dataset and analytical protocols available as Supplementary Information

Diapsida-Lepidosauria (morphological + nDNA/mDNA)

There have been several edits and expansions of this dataset by myself and others. Below I make reference to select (significant) expansions of this dataset that strictly follow the guidelines and empirical approach towards its construction (e.g., personal collection of phenotypic data).

1st edition: Simões et al., 2018 (Nature). Dataset and analytical protocols available as Supplementary Information

2nd edition: Garberoglio et al., 2019 (Science Advances): Dataset and analytical protocols available as Supplementary Information

3rd edition: Simões et al., 2020 (Nature Communications): Dataset and analytical protocols available in Harvard Dataverse

4th edition: Martínez et al., 2021 (Nature): Dataset and analytical protocols available in Harvard Dataverse

Sphenodontia (morphological)

1st edition: Simões et al., 2020 (BMC Biology): Dataset and analytical protocols available in Harvard Dataverse

2nd edition: Simões et al., 2022 (Communications Biology): Dataset and analytical protocols available in Harvard Dataverse

REVISED datasets:

Squamata (morphological)

Simões et al., 2017 (Cladistics): Character revisions and data re-scoring to the datasets of Conrad et al., 2008 and Gauthier et al., 2012: Dataset and analytical protocols available as Supplementary Information

Early Tetrapodomorpha (morphological)

Simões et al., 2021 (Nature Ecology and Evolution): Character revisions and additional taxa to the dataset from Cloutier et al., 2020 (Nature): Dataset and analytical protocols available in Harvard Dataverse