Phalangeal Formula of Lepidosauria
Data files
Nov 03, 2023 version files 28.37 KB
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PF_data.csv
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README.md
Abstract
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.
README: 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) linked to the GitHub repository.
Additionally, this data and code are hosted in the GitHub repository.
Methods
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).