Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
- 1. University of Groningen
- 2. Center for Environmental Economics in Montpellier in Montpellier*
- 3. University of Stirling
Description
One of the primary goals of macroevolutionary biology has been to explain general trends in long-term diversity patterns, including whether such patterns correspond to an up-scaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity-dependent diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time-dependence without diversity-dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time-dependent, but diversity-independent model that matches the expected diversity through time of a diversity-dependent model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity-dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity-dependence. We advocate that tests encompassing additional data, e.g., traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
Notes
As described in Methods, the data archived here were produced from functions in R package DDD.
Instead of calling the DDD functions mentioned above directly, the first author developed and used a utility R package for the project, called "DDvTDtools", that calls DDD functions and manages their input and output in a standard way. The package is available on GitHub (https://github.com/TheoPannetier/DDvTDtools), and can be cloned from there or installed from within R (remotes::install_github("TheoPannetier/DDvTDtools")). For instructions on how to run the simulations and obtain the maximum likelihood parameter estimates, I refer to the README.md file of this package.
Simulated trees are stored in files with the pattern simXX-PARA.RData, where XX is the model name (DD or TD) and PARA a four-digit code specifying parameter values (see ReadMe.txt for more details)
The results of the maximum likelihood procedure are stored in data frames, in files with the pattern simXX_optimYY_PARA_INITK.rds, where YY is the name of the model fitted to a tree (DD or TD, can be the same or different as XX), and INITK specifies initial parameter values (see ReadMe.txt for more details)
Data for empirical phylogenies follow the same naming pattern; simulated trees are stored in files with pattern simXX_FAMILY_FROM.RData, and the results of maximum likelihood are stored in files with pattern FAMILY_simXX_optimYY_FROM.rds, where FAMILY is the name of a family of birds or mammals, and FROM specifies which values the trees were simulated with (see ReadMe.txt for more details).
Funding provided by: Nederlandse Organisatie voor Wetenschappelijk Onderzoek
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100003246
Award Number:
Funding provided by: Faculty of Natural Sciences, University of Stirling*
Crossref Funder Registry ID:
Award Number:
Funding provided by: Faculty of Natural Sciences, University of Stirling
Crossref Funder Registry ID:
Files
ReadMe.txt
Files
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md5:3a26b4a447019a04032c0a634cb0263c
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46.8 kB | Download |
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md5:763fefe27d903c15733cd512132e7ce1
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44.2 kB | Download |
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md5:2acc3c12d10ddf12979758105812e2b5
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46.8 kB | Download |
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md5:491883f3b79e5e9cd9d90ed80524510a
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47.0 kB | Download |
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md5:ae84f651cd3f1b55f59f17d0409654aa
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48.2 kB | Download |
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md5:2005d8e200aa183004b4735d4a775713
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45.8 kB | Download |
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md5:d5a55829ffa21588c05cc42d8d4c1907
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46.2 kB | Download |
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md5:4739111f0976cfd00ac69a3ed4dbc101
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38.4 kB | Download |
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md5:c5e19a7637017259763f9ed0085f13de
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46.0 kB | Download |
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md5:dcf10a250061727f365dd3bce41da12f
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40.7 kB | Download |
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md5:9663e25d84f5d1861b19738c9141709c
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44.8 kB | Download |
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md5:37480c9218027b8cb5796bfdc8feb81c
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46.3 kB | Download |
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md5:63d0a9f0a125e7537ee99f4d94c554f6
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46.7 kB | Download |
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md5:0f0db8d6e6049ba3b32b084e0692c6b7
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30.8 kB | Download |
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md5:7d3023821f8b37d0173dc30c4d9b8bea
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46.7 kB | Download |
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md5:fffb116a92941f1d05d722f0b33198cd
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32.4 kB | Download |
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md5:3707951dfceffb6306b50d3f94db7828
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45.4 kB | Download |
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md5:c75094415f507c809bc6dc5d4504c4ed
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48.3 kB | Download |
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md5:b58befb59bd38b1788f058456bce57d2
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46.6 kB | Download |
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md5:9650aa58fe060fa6ff696a0199b45680
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46.7 kB | Download |
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md5:96ed077c537678265d9207b4ae0edb27
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29.9 kB | Download |
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md5:663f4a81b25c0e2611f965965b3b3c4f
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47.3 kB | Download |
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md5:fb10cd31d89d3d53d051a0f2b11ba4d5
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46.8 kB | Download |
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md5:ef029456ab30b2385d3bb5db4a6ba340
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30.7 kB | Download |
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md5:63cdf4e3b6e3fc91a2afaf5fca6a6232
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47.1 kB | Download |
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md5:da531a2dd1f08e63f1114c68b8e4b92b
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46.0 kB | Download |
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md5:3ec9ca0e0bf5610ac65cf76856d9af78
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46.9 kB | Download |
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md5:f99edd2803856d1daba2a5a307e2c14a
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42.8 kB | Download |
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md5:ef2d25caad549667daa9726db4850165
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47.3 kB | Download |
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md5:2d3f75aff60d6ddac2915213a7e287e8
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43.2 kB | Download |
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md5:6b8ddc277e93c99259279b1fefb8a6d4
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46.7 kB | Download |
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md5:27a05ec52db17d4e231515c594c40219
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46.7 kB | Download |
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md5:be811f287c3ddbe7157df1d3912ef209
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44.8 kB | Download |
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md5:66672fc5b5754be2ff526c86cbeb4495
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8.8 MB | Download |
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md5:59670e21fe2e0fc83eabc48625210626
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9.4 MB | Download |
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md5:9d9496fedcd7931d3abb2f8fabb75981
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1.2 MB | Download |
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md5:abedcbef714218449bb4e858df73bc6b
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922.7 kB | Download |
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md5:31917e60089c0a5acd96772e6b1bd44a
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419 Bytes | Download |
Additional details
Related works
- Is derived from
- https://github.com/TheoPannetier/DDvTDtools (URL)
- https://cran.r-project.org/web/packages/DDD/index.html (URL)