Detecting hidden diversification shifts in models of trait-dependent speciation and extinction
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Abstract
The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.
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Failure to consider alternative models in which the background diversification rate changes across the tree explains support for trait-dependent diversification.
“The work of Beaulieu and O'Meara (Beaulieu et al. 2013;Beaulieu andO'Meara 2014, 2016) has illuminated important underlying reasons behind Rabosky and Goldberg's findings: the failure to consider alternative models in which the”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Beaulieu and O'Meara 2016
Accounting for background shifts in evolutionary regimes unrelated to the focal trait association is general and applies across comparative biology.
“We think that the solution proposed by Beaulieu and O'Meara (2016)-accounting for background shifts in evolutionary regimes unrelated to the focal trait association-is general and applies across comparative biology.”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Beaulieu and O'Meara (2016)
HSMs (following Beaulieu et al. 2013; Beaulieu and O'Meara 2016) are a potentially powerful, and widely applicable solution.
“For example, we highlighted in the introduction that we think HSMs (following Beaulieu et al. 2013;Beaulieu and O'Meara 2016) are a potentially powerful, and widely applicable solution, even though we did not consider these in detail here.”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Beaulieu and O'Meara 2016
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Research works printed but not linked: 8
- Beaulieu and Donoghue (2013). Specifically, we used HiSSE to locate and "paint" '#*! potential areas within Dipsidae that may be inflating the estimates of net diversification '$+! rates for achene lineages as a whole. We modified the original data set of Beaulieu and '$"! Donoghue (2013) in three important ways. First, we re-estimated the original molecular '$#! branch lengths using PAUP* (Swofford 2000), as opposed to relying on the branch '$$! lengths from the original RAxML (Stamatakis 2006) analysis, because PAUP* provides '$%! better optimization precision. Second, the molecular branch lengths were re-scaled in '$&! ! $"! support region: [0.179,0.221]. In fact, the model suggests that achene lineages not ')#! associated with the high diversification hidden state have a diversification rate that is ')$! indistinguishable from the non-achene diversification rate (r non-achene-= r achene-=0.059, ')%! support range: [0.049,0.068]). Non-achene lineages associated with the high ')&! diversification hidden state also show elevated diversification rates (r non-achene+ =0.158, ')'! support region: [0.138,0.185]), relative to the rate of the non-achene state with the other ')(! hidden state, suggesting strong rate heterogeneity even in Dipsidae lineages that bear '))! other fruit types. ')*! Character reconstructions identified two transitions to the hidden fast state in '*+! achene lineages, and thus a higher diversification rate: one shift occurred along the stem '*"! leading to crown Dipsacaceae and the other occurred along the stem leading to "core '*#! Valerianaceae" (the most inclusive clade that excludes Patrinia, Nardostachys, and '*$! Valeriana celtica) (Fig. 6). It is important to note that in the case of non-achene lineages, '*%! the model identified four shifts to the hidden fast state -one at the base of Caprifolieae '*&! (Lonicera, Symphoricarpus, Leycesteria, and Triosteum), and three within Viburnum '*'! (Fig. 6). The several shifts detected in Viburnum are noteworthy in that they correspond '*(! almost exactly with the inferred shifts detected in a more focused study of the genus that '*)! applied various models of diversification (Spriggs et al. 2015). '**! In regards to achene lineages, the general location of the inferred shifts is (++! intriguing, as they appear to coincide with specific clades that exhibit specialized (+"! structures related to achene dispersal. In Dipsacaceae, for example, there is tremendous (+#! diversity in the shape of the "epicalyx", a tubular structure that subtends the calyx and (+$! encloses the ovary (Donoghue et al. 2003; Carlson et al. 2009), which is often associated (+%! REFERENCES )''! Alexander H.K., Lambert A., Stadler T. 2015. Quantifying age-dependent extinction )'(! from species phylogenies. Systematic Biology In press. )')! doi:10.1093/sysbio/syv065. )'*! Alfaro M.E., Santini F., Brock C., Alamillo H., Dornbug A., Rabosky D.L., Carnevale )(+! G., Harmon L.J. 2009. Nine exceptional radiations plus high turnover explain )("! species diversity in jawed vertebrates. Proceedings of the National Academy of )(#! Sciences of the U.S.A. 106:13410-13414. ) · DOI
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Rethinking phylogenetic comparative methods
Uyeda, J. C., Zenil-Ferguson, R., & Pennell, M. W. (2018) · Systematic Biology · doi:10.1093/sysbio/syy031 · Cited by 313 · see citing works
- Authors
- Beaulieu, J. M., & O’Meara, B. C.
- Affiliations
- National Institute for Mathematical and Biological Synthesis (US)
- University of Tennessee at Knoxville (US)
- Corresponding author
- Beaulieu, Jeremy M.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-03-25
- Volume
- 65
- Issue
- 4
- Pages
- 583-601
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2951758813
- Cited by
- 579
- References
- 4
- Citations by year
- 2026: 69 · 2025: 60 · 2024: 56 · 2023: 58 · 2022: 72 · 2021: 57 · 2020: 56 · 2019: 63 · 2018: 44 · 2017: 28 · 2016: 13 · 2015: 2
- FWCI
- 34.81
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Systematic Biology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- hidden states, trait-dependent diversification, diversification rates, BiSSE, diversification rate shifts, clade diversity
- MeSH terms
- Classification, Models, Biological, Phenotype, Phylogeny, Biodiversity, Genetic Speciation, Extinction, Biological
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