DOI: 10.5061/dryad.dr7sqvb6n
title: Simulations modelling the effect of budding speciation on phylogenies

description: Paleobiologists have long sought to explain how alternative modes of
 speciation, including budding and bifurcating cladogenesis, shape patterns
 of evolution. Methods introduced over the past decade have paved the way
 for a renewed enthusiasm for exploring modes of speciation in the fossil
 record. However, the field does not yet have a strong intuition for how
 ancestor-descendant relationships, especially those that arise from
 budding speciation, might influence the shape of trees reconstructed for
 fossil or living clades. We developed a simulation approach based on
 classic paleobiological theory to ask what proportion of ancestral nodes
 in paleontological phylogenies are expected to correspond to sampled
 lineages under a range of preservational regimes. We compared our
 simulated results to empirical estimates of absolute fossil record
 completeness gathered from the literature and found that many fossilized
 clades of marine invertebrates are likely to display upwards of 80%
 sampled ancestors. Under a primarily budding model, phylogenies where 100%
 of the internal nodes correspond to named species are very possible for
 well-sampled clades at local and regional scales. We also leveraged our
 simulation approach to ask how budding might shape extant clades. We found
 that the ancestral signature of budding causes rampant hard polytomies in
 extant clades. Our results highlight how budding can yield dramatic and
 unrecognized effects on phylogenetic reconstruction of clades of both
 living and extinct organisms.
description: # Simulations modelling the effect of budding speciation on phylogenies
 [https://doi.org/10.5061/dryad.dr7sqvb6n](https://doi.org/10.5061/dryad.dr7sqvb6n) ## Description of the data and file structure **completeness.csv** - completeness estimates for each fossil clade examined. Columns are: `Taxon`: Name of the clade `Completeness`: Estimate of completeness, expressed as a percentage of total taxa inferred to have been sampled by the dataset, among all of the taxa that are inferred to have existed throughout the history of the clades. `Level`: Taxonomic level at which the clade was sampled. All clades examined here were sampled either at the species or genus level. `Scale`: Approximate estimation of the geographic scale at which the clade was sampled. Some were sampled globally, while others were sampled locally, at a single or small handful of nearby locality(ies) `Epoch`: Geological interval for which the clade was sampled. "All" means that the clade was sampled over its entire existence. `Reference`: Literature reference from which the completeness estimate (or FreqRat used to estimate completeness) was harvested. **foote_sepkoski_freqrats.csv** - range-frequency ratios reported by Foote and Sepkoski (1999) and interpreted as preservation probabilities. these are used to estimate completeness in the terms expressed for the other datasets by integrating over a range of possible extinction rates.  Columns are: `Taxon`: Name of the clade `Upper`: Upper bound of completeness estimates derived and reported by Foote and Sepkoski (1999). `Lower`: Lower bound of completeness estimates derived and reported by Foote and Sepkoski (1999). `Level`: Taxonomic level at which the clade was sampled. All clades examined here were sampled either at the species or genus level. `Scale`: Approximate estimation of the geographic scale at which the clade was sampled. Some were sampled globally, while others were sampled locally, at a single or small handful of nearby locality(ies) `Epoch`: Geological interval for which the clade was sampled. "All" means that the clade was sampled over its entire existence. `Reference`: Literature reference from which the completeness estimate (or FreqRat used to estimate completeness) was harvested. ## Code/Software Included python scripts can be used to rerun simulations and generate plots for budding and bifurcating speciation as well as for the extant polytomy analyses and empirical estimation of completeness metrics from the Foote and Sepkoski FreqRat data. ## Description of scripts sim_range_completeness.py -- simulates phylogenies and calculates the proportion of sampled ancestors after stochastically sampling the simulated trees using a Poisson model of fossil preservation. calc_completeness.py -- functions to calculate completeness of fossil clades using several approaches, including Foote and Raup 'FreqRat' (1996) and Solow and Smith (1997) equations. calc_foote_sepkoski_completeness.py -- script to marginalize over extinction rates to estimate completeness using values from Foote and Sepkoski (1999). ### simulate phylogenetic tree replicates and produce figure 3 plots #### budding python sim_range_completeness.py bud #### bifurcating python sim_range_completeness.py bif ### transform foote and sepkoski (1999) completeness values python calc_foote_sepkoski_completeness.py foote_sepkoski_freqrats.csv This will print the estimated completenesses to the terminal. These values, plus the other estimates taken directly from the literature, are compiled in the csv 'completeness.csv', which also includes references for each completeness estimate. These values can then be plotted in R using the script plot_completeness.R ### estimate polytomies in simulated "extant" clades and plot results (this produces figure 5) python get_timeslice_polytomies.py ### Additional scripts/modules (all are dependencies) node.py -- python module containing the basis of the tree object used for simulations tree_reader.py -- python module for reading and writing phylogenetic trees to files distributions.py -- python module implementing several statistical distributions. these are used for the stochastic birth-death simulations. bd_fast.py -- implementation of the birth-death and sampling model. Functions in this module are called from sim_range_completenesses.py and get_timeslice_polytomies.py **supp.pdf** -- additional PDF file of the supplemental information file containing supplemental figures (Figures S1-6) table (Table S1), and references. ### References Foote, M. and Raup, D.M., 1996. Fossil preservation and the stratigraphic ranges of taxa. *Paleobiology*, *22*(2), pp.121-140. Foote, M. and Sepkoski Jr, J.J., 1999. Absolute measures of the completeness of the fossil record. Nature, 398(6726), pp.415-417. Solow, A.R. and Smith, W., 1997. On fossil preservation and the stratigraphic ranges of taxa. *Paleobiology*, *23*(3), pp.271-277.