Sub-Species Level Diversification and Phylogeny Reconstruction

A final phylogeny summarizes a longer history of births, mutations and extinctions. The simulator below follows that history through time and compares three views of the same run: individual lineages, coarsened taxa and a tree reconstructed from traits.

Each living lineage can produce a clonal daughter, produce a mutating daughter, or die. Event times follow a Gillespie simulation.^[1] A threshold on accumulated mutational steps groups lineages into named taxa. The parent can persist after producing a daughter, as in budding speciation.^[15] The threshold illustrates delayed species recognition; it does not implement the completion-rate models of protracted speciation.^[4][5]

Overview

• Diversification is an event-by-event process first, and only later a tree summary.
• Coarse-graining and extinction can make different fine-scale histories collapse into the same observed species-level pattern.
• A tree reconstructed from traits can disagree with a tree reconstructed from the event history for very ordinary reasons.
• The simulator makes those bottlenecks visible with time-resolved chronograms, a lineages-through-time panel, and a trait-space panel.

How to read the simulator

The six panels are arranged to move from process to summary. The first two show what is happening through time at the lineage and coarse-grained taxon levels; the next two show two different tree summaries of the same run; the last two summarize tempo and geometry.

• The chronograms keep event order explicit, so budding, persistence, and extinction are visible instead of being absorbed into a generic node-link picture.
• Scenario presets provide contrasting parameter settings. Reusing a seed makes a run reproducible, although changing parameters can also change how random draws are consumed.
• The Brownian and OU-like options give two contrasting ways to think about continuous traits: wandering versus constrained spread.
• Export a run as JSON or Newick for further analysis.

Leaf-pair r measures correlation between pairwise tip distances in the two trees. It describes distance agreement without testing topology.

The six panels

1. Full lineage chronogram. The fine-grained event history, including extinct and still-incidental lineages.
2. Coarsened species chronogram. The same history after you decide how many mutational steps count as “enough” to name a new species.
3. History tree. A tree summary of the coarsened record.
4. Trait tree. A reconstruction from observed trait distances.
5. Lineages through time. A quick sanity check on richness, extinction, and what survives into the observed layer.
6. Trait space. The geometry behind the trait tree. When panel 4 looks odd, this panel usually explains why.

From lineages to species

The Coarsen Level slider sets the threshold for recognizing a new taxon. At 0, every new lineage is promoted immediately. Higher values require more mutational steps, so several lineage events can belong to one species history.

Changing the threshold changes which branching events appear at the species level, even when the underlying lineage history stays fixed.

What extinction removes

Reconstructing a tree from surviving taxa removes extinct branches and their durations.^[2][3] Different complete histories can therefore yield the same extant tree. More generally, distinct speciation and extinction rate histories can have identical likelihoods for extant timetrees under birth–death models.^[14]

Toggle Prune extinct taxa to compare the complete simulated record with the history visible from surviving taxa.

Reconstructing relationships from traits

The trait tree uses observed characters to infer relationships. Brownian motion models unconstrained trait diffusion; the OU-like setting adds a pull toward a central value.^[11][12][13] Compare the two settings to see how trait dynamics affect reconstruction.

Tree disagreement has several biological sources. Gene trees can differ from species trees because of incomplete lineage sorting.^[9][10] Hybridization can require a network representation.^[6][7][8] These processes are outside this simulator, which focuses on budding, extinction, taxon thresholds and trait evolution.

Explore the simulator

1. High turnover. Switch to the turnover preset and compare the history tree to the trait tree. Compare how many extinct branches are absent from the extant summary.
2. Radiation. Use rapid radiation with coarsen level 1, then 3. Watch how the same event stream starts to look different as the species threshold changes.
3. Trait constraint. Keep the diversification settings fixed, flip from Brownian to OU-like, and look at the trait cloud. The geometry in panel 6 usually explains the stability or instability of panel 4.
4. Step mode. Press Step a dozen times instead of letting the animation run. The logic of the chronograms is easier to grasp when you watch events accumulate one by one.

EvoLab: the simulator project

The simulator in this post is EvoLab.

References

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3. Lambert A, Stadler T. 2013. Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies. Theor Popul Biol. 90:113–128. doi:10.1016/j.tpb.2013.10.002
4. Rosindell J, Cornell SJ, Hubbell SP, Etienne RS. 2010. Protracted speciation revitalizes the neutral theory of biodiversity. Ecol Lett. 13(6):716–727. doi:10.1111/j.1461-0248.2010.01463.x
5. Etienne RS, Rosindell J. 2012. Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Syst Biol. 61(2):204–213. doi:10.1093/sysbio/syr091
6. Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23(2):254–267. doi:10.1093/molbev/msj030
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8. Wen D, Yu Y, Nakhleh L. 2016. Bayesian inference of reticulate phylogenies under the multispecies network coalescent. PLoS Genet. 12(5):e1006006. doi:10.1371/journal.pgen.1006006
9. Maddison WP. 1997. Gene trees in species trees. Syst Biol. 46(3):523–536. doi:10.1093/sysbio/46.3.523
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11. Felsenstein J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am J Hum Genet. 25(5):471–492. PubMed: 4741844
12. Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat. 125(1):1–15. doi:10.1086/284325
13. Butler MA, King AA. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am Nat. 164(6):683–695. doi:10.1086/426002
14. Louca S, Pennell MW. 2020. Extant timetrees are consistent with a myriad of diversification histories. Nature. 580(7804):502–505. doi:10.1038/s41586-020-2176-1
15. Caetano DS, Quental TB. 2023. How important is budding speciation for comparative studies? Syst Biol. 72(6):1443–1453. doi:10.1093/sysbio/syad050