DOI: 10.5061/dryad.xsj3tx9s6
title: Data from: Punctuated equilibria remains the dominant pattern of morphospecies origin in the fossil record: An analysis using the “persistence of ancestor” criterion

description: Punctuated Equilibria (PE) was presented 50 years ago as an alternative to
 the widespread assumption that most evolution proceeds by gradual phyletic
 change within lineages. Unfortunately, PE has been widely misunderstood,
 misrepresented, and unfairly dismissed since this first publication. We
 argue that much of this misunderstanding centers around a
 misinterpretation of the meaning of “mode,” and the significance of mode,
 properly understood, for how we understand macroevolutionary processes. PE
 proposed that most morphospecies do not show significant anagenetic trends
 through their stratigraphic ranges, and that most new morphospecies that
 are recognized arise via cladogenesis. To the degree that this is true,
 most exploration of disparity-space must be associated with cladogenesis.
 We surveyed a sample of the recent paleontological literature to assess
 the frequency with which new morphospecies appear in the fossil record via
 anagenesis vs cladogenesis using a persistence of ancestor criterion and
 found the overwhelmingly dominant mode of species origin to be
 cladogenesis. This is a valuable but underutilized approach to this
 problem, which could be exploited with more studies of species-level
 phylogenies of fossil taxa. Combined with the conclusions of other studies
 that stasis or non-directional change is common, this finding of the
 dominance of cladogenesis affirms that PE is very much alive, and of
 substantial significance for understanding macroevolutionary
 patterns. 
description: # Punctuated equilibria remains the dominant pattern of morphospecies
 origin in the fossil record: An analysis using the “persistence of
 ancestor” criterion
 [https://doi.org/10.5061/dryad.xsj3tx9s6](https://doi.org/10.5061/dryad.xsj3tx9s6) ## Description of the data and file structure This supplemental file is the result of a literature review of phylogenies which contain stratigraphic information to assess the relative frequency of anagenesis vs cladogenesis (evolutionary mode). Additional information on the data table is provided in the table caption file. ### Files and variables #### File: Table\_S1.xlsx **Description:**  ##### Examination of the same papers studied in text Table 1 applying strict criteria of taxon co-occurrence. Table S1 readme. This table contains the counts used in Anderson and Allmon, “Punctuated equilibria remains the dominant pattern of morphospecies origin in the fossil record: An analysis using the “persistence of ancestor” criterion,” for a strict interpretation analysis which does not assume temporal coincidence of co-occurring taxa unless these taxa are demonstrated to have necessarily overlapped in temporal range by cladistic arrangement or boundary-crossing. **Caption**: Table S1. Examination of the same papers using strict criteria of taxon co-occurrence. Boundary-crossing taxa are those known to co-occur because they are both present above and below the same stratigraphic/temporal boundary used in the examined study (and therefore had to be contemporaneous at least at the boundary). Other cladogenetic pairs are inferred from examination of tree topology. Co-occurring species in the same temporal bin were treated as non-contemporaneous without these additional criteria for demonstrating temporal association (*i.e.* each species was inferred to have existed instantaneously and not at the same time as others presented as occurring in the same unit). For each case the minimum number of species arising via cladogenesis using a persistence of ancestor criterion is presented (the maximum number of ambiguous cases in each tree due to phylogenetic uncertainty are resolved as cases of anagenesis). (The following terminals were ignored as being out of the timeframe of investigation for the included study, were missing stratigraphic information, or the text indicated potential synonymy of material included as a terminal was possible: Alvarez & del Rio 2020,  *R. ninfasiensis*; Becker et al., (2013), species of Stephanorhinus and Ceratotherium which were not included by Becker et al. (2013) in the presented phylogeny did not have accompanying stratigraphic information; Kligman et al., 2021, multiple extant Sphenodon taxa; Tabuce et al. 2020, Numidotherium sp. Material). **Column Descriptions:** * Phylogeny source: The paper from which an example phylogeny used in the study was drawn. - General Clade: A description of the type of organism under study at broad taxonomic resolution. * Specific Clade: The name of the clade under consideration or the taxa which define it. - Habitat type: Whether the taxa in the study are Marine, Terrestrial, or Aquatic (freshwater and/or marine). * Earliest time: Age of the oldest unit considered in the study. This may be an age, stage, zone, or period depending on how stratigraphic ages were given in a particular study. - Latest time: Age of the youngest unit considered in the study. This may be an age, stage, zone, or period depending on how stratigraphic ages were given in a particular study. * Age unit evaluated: The level of resolution of temporal binning we used to evaluate species occurrences in our (Anderson and Allmon) study. - Unit of study resolution: The resolution or resolution(s) which were referred to in the considered studies. * Range of resolutions used in the study: Some studies had different levels of resolution in different portions of their stratigraphic ranges or a range of resolutions was provided. This is reflected in this column. - Maximum reported in the same unit: The number of species found in the temporal unit with the highest species diversity for a given study. * Number of species spanning multiple intervals: The total number of species which were boundary-crossers for a given study at the age unit evaluated in our analysis. - Notes: Notes on assumptions made in the strict analysis or about whether specimens co-occurred in a specific locality or were described as co-temporal but potentially from different sites. * Boundary crossing or co-extant pairs: The number of species which had to have been contemporaneous because they crossed a common stratigraphic boundary. - Minimum possible cladogenetic (Topology + BC): The absolute minimum number of species which originated through cladogenesis in the study, even assuming in most cases species found in the same stratigraphic interval were ephemeral and did not co-occur unless logically required. This requirement could come from mutually crossing the same stratigraphic boundary (BC) or from how ghost ranges required from tree topology necessitated cladogenetic events. * Minimum portion of cladogenesis possible: Of all species in the clade under consideration, what portion of them necessarily arose via cladogenesis rather than anagenesis. - Average minimum proportion of each clade originating by cladogenesis: Across all examined studies, what was the average proportion of species that necessarily originated via cladogenesis. * Median proportion originating by cladogenesis: Across all examined studies, what was the median proportion of species that necessarily originated via cladogenesis.