Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts

Meyer, Andreas L. S.; Wiens, John J.

doi:10.1111/evo.13378

Cited by 91 publications

(100 citation statements)

References 56 publications

(134 reference statements)

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“…Results are shown using ε = 0.5, but all three values were used (Appendix S1, Tables S3 and S4 for tanagers and tortoises). Results were similar across different values, and simulations suggest that different values yield similar relationships between true and estimated stem‐based rates (Meyer & Wiens, ).…”

Section: Methodsmentioning

confidence: 70%

“…However, the crown‐group estimator cannot be used for monotypic genera (and these genera were excluded in the preceding analyses). Furthermore, the crown‐group estimator is generally less accurate in simulations (Meyer & Wiens, ). Therefore, we emphasize results based on stem‐group ages.…”

Section: Methodsmentioning

confidence: 99%

“…Furthermore, the ME estimator depends only on the age and richness of clades (i.e., young clades with many species will have higher estimated net diversification rates than older clades with fewer species), regardless of changes in instantaneous rates within clades (among subclades or over time). Simulations have now explicitly shown that heterogeneity in rates within clades need not impact the accuracy of the ME estimators (Meyer & Wiens, ). Variation in diversification rates over time might decouple richness and diversification (e.g., Kozak & Wiens, ), but our focus here is only on diversification rates.…”

Section: Methodsmentioning

confidence: 99%

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The Tortoise and the Finch: Testing for island effects on diversification using two iconic Galápagos radiations

Román‐Palacios

Wiens

2018

Journal of Biogeography

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Aims Islands are widely recognized as natural laboratories for evolutionary studies, but many questions about evolution on islands remain unresolved. Here we address two general questions from a macroevolutionary perspective. First, do lineages on islands have increased diversification rates relative to mainland lineages? Second, does the same geographical context (e.g., same archipelago) have similar effects on diversification in unrelated groups? We focused on Darwin's finches and Galápagos tortoises, two endemic radiations from the Galápagos Islands, and the larger families in which they are embedded. Location Global. Methods We estimated a new time‐calibrated phylogeny for tortoises (Testudinidae). Then, we examined their macroevolutionary patterns and compared them to those of Darwin's finches and relatives (Thraupidae), using a published thraupid tree. Specifically, we estimated and compared diversification rates between islands and the mainland and between the Galapagos Islands and all other regions, using clade‐based and species‐based approaches. Results Contrary to expectations, occurrence on islands in general did not significantly increase diversification rates in tanagers or tortoises. However, occurrence in the Galápagos Islands in particular was associated with increased speciation and diversification rates, and explained ~28% of the variation in diversification rates for thraupids and ~46% for testudinids. Both Darwin's finches and Galápagos tortoises were unique within each family in exhibiting the highest diversification rates. The congruence of these macroevolutionary patterns between both radiations supports a strong “place‐dependent” effect on diversification associated with the Galápagos. Finally, we found that Darwin's finches diversified ~2–8 times faster than Galápagos tortoises. Main conclusions Our results show that occurring on islands in general did not increase diversification rates in these clades, but occurrence in the Galápagos did. We also show that dramatic local‐scale differences in diversification rates between clades in the Galápagos parallel global‐scale differences in diversification rates between these families and between birds and turtles overall.

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Section: Methodsmentioning

confidence: 70%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

The Tortoise and the Finch: Testing for island effects on diversification using two iconic Galápagos radiations

Román‐Palacios

Wiens

2018

Journal of Biogeography

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“…2016; Rabosky 2017; Rabosky et al. 2017; Meyer and Wiens 2018). Therefore, we conducted clade specific diversification rate analyses with alternative approaches (to cross‐validate the BAMM results).…”

Section: Methodsmentioning

confidence: 99%

Climate and host‐plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

et al. 2018

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Using molecular phylogenetic data and methods we inferred divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host‐plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ∼53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred at the end of the Eocene (∼34 Ma). This contrasts with the overall deterioration in climate equability at the Eocene‐Oligocene boundary, but tracks the diversification of important host plant clades in temperate (higher) latitudes, leading to increased diversification rates in the weevil clades infesting temperate hosts. A third major phase of diversification is correlated with the rising temperatures of the Late Oligocene Warming Event (∼26.5 Ma); diversification rates then declined shortly after the Middle Miocene Climate Transition (∼14.9 Ma). Our results indicate that biotic and abiotic factors together explain the evolution of Ceutorhynchinae better than each of these drivers viewed in isolation.

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“…The diversification of turtle ants (genus Cephalotes), for example, can be characterized by an overall recent decline in speciation rates over time, but shows a positive rate shift coupled with body size evolution in a habitat-endemic clade (Price et al 2016). BAMM has recently been criticized as being highly sensitive to the selected rate shift prior (Moore et al 2016), and although these concerns have since been negated by the developers (Rabosky et al 2017), more concerns were raised regarding underestimation of rate shifts (Kodandaramaiah and Murali 2018) and overestimation of diversification rates by BAMM (Meyer and Wiens 2018). The absence of any major radiations and associated rate heterogeneity detectable by BAMM was therefore unexpected for such a species-rich group.…”

Section: Diversification Of Xylocopamentioning

confidence: 99%

Multiple origins of sexual dichromatism and aposematism within large carpenter bees

2018

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The evolution of reversed sexual dichromatism and aposematic coloration has long been of interest to both theoreticians and empiricists. Yet despite the potential connections between these phenomena, they have seldom been jointly studied. Large carpenter bees (genus Xylocopa) are a promising group for such comparative investigations as they are a diverse clade in which both aposematism and reversed sexual dichromatism can occur either together or separately. We investigated the evolutionary history of dichromatism and aposematism and a potential correlation of these traits with diversification rates within Xylocopa, using a newly generated phylogeny for 179 Xylocopa species based on ultraconserved elements (UCEs). A monochromatic, inconspicuous ancestor is indicated for the genus, with subsequent convergent evolution of sexual dichromatism and aposematism in multiple lineages. Aposematism is found to covary with reversed sexual dichromatism in many species; however, reversed dichromatism also evolved in non-aposematic species. Bayesian Analysis of Macroevolutionary Models (BAMM) did not show increased diversification in any specific clade in Xylocopa, whereas support from Hidden State Speciation and Extinction (HiSSE) models remained inconclusive regarding an association of increased diversification rates with dichromatism or aposematism. We discuss the evolution of color patterns and diversification in Xylocopa by considering potential drivers of dichromatism and aposematism.

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Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts

Cited by 91 publications

References 56 publications

The Tortoise and the Finch: Testing for island effects on diversification using two iconic Galápagos radiations

The Tortoise and the Finch: Testing for island effects on diversification using two iconic Galápagos radiations

Climate and host‐plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

Multiple origins of sexual dichromatism and aposematism within large carpenter bees

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