DOI: 10.5061/dryad.vhhmgqp19
title: Phalangeal Formula of Lepidosauria

description: Evolutionary tempo and mode summarize ancient and controversial subjects
 of theoretical biology such as gradualism, convergence, contingence,
 trends, and entrenchment. We employed an integrative methodological
 approach to explore the evolutionary tempo and mode of Lepidosaurian
 Phalangeal Formulae (PFs). This approach involves quantifying the
 frequencies of morphological changes along an evolutionary trajectory
 (ET). The five meristic characters encoded by PFs are particularly
 valuable in revealing evolutionary patterns, owing to their discrete
 nature and extensive documentation in the literature. Based on a
 pre-existing dataset of PFs from 649 taxa (35 Lepidosauria families,
 including fossils), from which there exists a unique repertoire of 53
 formulations, our approach simultaneously considers phenetic and
 phylogenetic data. This culminates in a diagram accounting for the
 phylogenetic dynamic of evolution traversing across different regions of
 morphospace. The method involves enumerating phenotypical options,
 reconstructing phenotypes across the phylogeny, projecting phenotypes onto
 a morphospace, and constructing a flow network from the frequency of
 evolutionary transitions between unique phenotypic conditions. This
 approach links Markovian chains and evolutionary trajectories to formally
 define parameters that describe the underlying transitions of
 morphological change. Among other results, we found that: (i) PF evolution
 exhibits a clear trend toward reduction in the phalangeal count, and that
 (ii) evolutionary change tends to occur significantly between
 morphologically similar PFs. Notwithstanding, although minor but not
 trivial, transitions between distant formulas jumps occur. Our results
 support a pluralistic view including stasis, gradualism, and saltationism
 discriminating their prevalence in a target character evolution.
description: The phalangeal formulae data set was compiled using information
 from specialized literature and own records from x‐rays, cleared and
 stained specimens, and dried osteological specimens. The sample included
 members of 33 extant families within Squamata belonging to every main
 clade (Gekkota, Scincoidea, Lacertoidea, Anguinomorpha, Iguania, and
 Serpentes), the extinct family Aigialosauridae (Anguimorpha), members of
 the Stem clades of extant representatives (Stem Gekkotan and Stem
 Serpentes) and members (both extinct and extant) of the squamatan sister
 group Rhynchocephalia (Sphenodontidae).
description: # *Phalangeal Formula of Lepidosauria: Dataset and Analysis* Authors:
 Fontanarrosa, Gabriela; Abdala, Virginia & Dos Santos, Daniel
 Andrés Corresponding author: Dos Santos, Daniel Andrés, e-mail:
 dadossantos@csnat.unt.edu.ar **Summary** The dataset pertains to the study
 of the evolutionary tempo and mode of Lepidosaurian Phalangeal Formulae
 (PFs). The study employs an integrative methodological approach that
 quantifies the frequencies of morphological changes along an evolutionary
 trajectory (ET). The dataset includes information on five meristic
 characters encoded by PFs, which are valuable for revealing evolutionary
 patterns due to their discrete nature and extensive documentation. PFs
 from 649 taxa were compiled, encompassing 35 Lepidosauria families,
 including fossils. The dataset is structured into R script files for
 analysis, a Lepidosaurian phylogeny assembled by Gabriela Fontanarrosa,
 phalangeal formulae of terminals with labels, and a transition matrix
 between hand configurations, developed by Daniels Andrés Dos Santos.
 **Description of the data and file structure** The dataset provided
 consists of several files, each serving a specific purpose in the analysis
 of Lepidosaurian Phalangeal Formulae (PFs) for exploring evolutionary
 tempo and mode. Here is a detailed description of each file: *Lepi.NEX*:
 This file contains a phylogenetic tree with 672 tips (terminal nodes) and
 671 internal nodes. *PFphylotips.rds* and *PF\_data.csv*: These files
 contain data on Lepidosaurian Phalangeal Formulae (PFs). PFphylotips.rds
 is an R data frame saved in RDS file format, while PF\_data.csv is the
 same data in CSV format. The data include information about the phalangeal
 formulas of terminals, which are crucial for understanding the
 morphological evolution of these taxa. Researchers can perform various
 analyses, such as frequency counts, transitions, and evolutionary trends
 based on these data. *redflujo.RData*: This file contains a matrix
 representing transitions among states of hand configurations related to
 unique phalangeal formulas. *Fontanarrosa\_el\_al\_JEB.R*: This annotated
 R script, dated August 23, 2023, provides supplementary material for the
 manuscript titled 'Modeling evolutionary tempo and mode using formal
 morphological spaces and Markov-chain principles.' It outlines an
 approach to explore the evolutionary tempo and mode of Lepidosaurian
 Phalangeal Formulae (PFs). The script begins by loading required packages
 and then reads a NEXUS file containing Lepidosaurian phylogeny and
 phalangeal formulas of terminals. Phenotypes throughout the phylogenetic
 tree are reconstructed, and the evolutionary paths of PFs are traced
 accordingly. The analysis employs a procedure based on geometric means to
 assign branch lengths, enabling the mapping of internal nodes within a
 pseudo-time window. The script constructs a flow network based on the
 frequency of evolutionary transitions between unique phenotypic
 conditions, creating an adjacency matrix and subsequently visualizing the
 network graph. It further generates aligned trajectories using dummy nodes
 and analyzes hitting times to measure the relative difficulty of
 evolutionary paths leading to different states. The script also explores
 phenotypic distances between pairs of states involved in simulated
 transitions and evaluates the mean number of visits for each state. Toward
 the end, the script combines phylogenetic (flow network) and phenetic
 (morphospace) information into a synthetic map of evolutionary change. It
 produces a level plot capturing the time necessary to reach any phenotypic
 option starting from the root condition, integrating morphospace data and
 observed or reconstructed hand configurations." Relationships Between
 Files: • The phylogenetic tree (Lepi.NEX) provides the evolutionary
 context for the analysis of PFs in Lepidosaurian species. •
 PFphylotips.rds and PF\_data.csv contain the actual phalangeal formula
 data, which can be analyzed using the methods outlined in the annotated R
 script (Fontanarrosa\_el\_al\_JEB.R). • The transitions among hand
 configurations (redflujo.RData) concern inferred evolutionary
 relationships among specific phalangeal formulas and can be further
 explored through a Markovian approach. **Sharing/Access information** The
 data provided here was already used by Fontanarrosa, Abdala, and Dos
 Santos, 2021
 (DOI:[10.1002/jez.b.23026](http://dx.doi.org/10.1002/jez.b.23026)) linked
 to the
 [GitHub](https://github.com/GFontanarrosa/Fontanarrosa-Abdala-Dos-Santos)[
 ](https://github.com/GFontanarrosa/Fontanarrosa-Abdala-Dos-Santos-JEB-2023)repository. Additionally, this data and code are hosted in the [GitHub ](https://github.com/GFontanarrosa/Fontanarrosa-Abdala-Dos-Santos-JEB-2023)repository.