A Likelihood-Based Method for Testing for Nonstochastic Variation of Diversification Rates in Phylogenies

McConway, Kevin; Sims, Hallie J.

doi:10.1554/03-110

Cited by 11 publications

(29 citation statements)

References 56 publications

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“…We place more emphasis here on the results derived from the likelihood-based shift statistics because of the problems associated with the power, accuracy and independence of the Slowinski-Guyer test (McConway and Sims 2004;Moore et al 2004). Despite the lack of previous formal statistical analyses, earlier studies have proposed a number of mechanisms that may have driven radiations within at least some of the clades.…”

Section: Discussionmentioning

confidence: 99%

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Bats, Clocks, and Rocks: Diversification Patterns in Chiroptera

2005

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Abstract. Identifying nonrandom clade diversification is a critical first step toward understanding the evolutionary processes underlying any radiation and how best to preserve future phylogenetic diversity. However, differences in diversification rates have not been quantitatively assessed for the majority of groups because of the lack of necessary analytical tools (e.g., complete species-level phylogenies, estimates of divergence times, and robust statistics which incorporate phylogenetic uncertainty and test appropriate null models of clade growth). Here, for the first time, we investigate diversification rate heterogeneity in one of the largest groups studied thus far, the bats (Mammalia: Chiroptera). We use a recent, robust statistical approach (whole-tree likelihood-based relative rate tests) on complete dated species-level supertree phylogenies. As has been demonstrated previously for most other groups, among-lineage diversification rate within bats has not been constant. However, we show that bat diversification is more heterogeneous than in other mammalian clades thus far studied. The whole-tree likelihood-based relative rates tests suggest that clades within the families Phyllostomidae and Molossidae underwent a number of significant changes in relative diversification rate. There is also some evidence for rate shifts within Pteropodidae, Emballonuridae, Rhinolophidae, Hipposideridae, and Vespertilionidae, but the significance of these shifts depends on polytomy resolution within each family. Diversification rate in bats has also not been constant, with the largest diversification rate shifts occurring 30-50 million years ago, a time overlapping with the greatest number of shifts in flowering plant diversification rates.

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Section: Discussionmentioning

confidence: 99%

“…Additionally, diversification statistics have also improved (e.g., McConway and Sims 2004;Moore et al 2004), incorporating more appropriate null models of clade growth and phylogenetic uncertainty (e.g., different topologies and unresolved nodes) into analyses (e.g., Chan and Moore 2005).…”

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confidence: 99%

Bats, Clocks, and Rocks: Diversification Patterns in Chiroptera

2005

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“…A popular approach has been to compare the relative sizes of sister groups using nonparametric sign tests, for example, in studies of insect phytophagy (Mitter et al 1988), plant latex and resin canals (Farrell et al 1991), floral nectar spurs (Hodges 1997), and flower symmetry (Sargent 2004). Alternatively, parametric approaches make it possible to identify unusually large clades by fitting data to predictions of null models of stochastic cladogenesis, and this can increase the statistical power associated with trait correlations (Slowinski and Guyer 1993;Sims and McConway 2003;McConway and Sims 2004).…”

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confidence: 99%

“…Despite this, general methods for detecting shifts in diversification rate on phylogenies can be used to associate an inferred rate shift with the origin of the trait of interest. These use stochastic branching models to evaluate the observed data, either the distribution of clade sizes on a phylogenetic tree (e.g., Slowinski and Guyer 1989;Sanderson and Donoghue 1994;Sims and McConway 2003;McConway and Sims 2004;Moore et al 2004), or the distribution of the number of lineages through time (e.g., Nee et al 1992Nee et al , 1994Paradis 1997). The dichotomy of approaches has led to them being termed topological and temporal methods, respectively (Chan and Moore 2002).…”

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confidence: 99%

Detecting the Historical Signature of Key Innovations Using Stochastic Models of Character Evolution and Cladogenesis

Ree¹

2005

Evolution

132

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Abstract. Phylogenetic evidence for biological traits that increase the net diversification rate of lineages (key innovations) is most commonly drawn from comparisons of clade size. This can work well for ancient, unreversed traits and for correlating multiple trait origins with higher diversification rates, but it is less suitable for unique events, recently evolved innovations, and traits that exhibit homoplasy. Here I present a new method for detecting the phylogenetic signature of key innovations that tests whether the evolutionary history of the candidate trait is associated with shorter waiting times between cladogenesis events. The method employs stochastic models of character evolution and cladogenesis and integrates well into a Bayesian framework in which uncertainty in historical inferences (such as phylogenetic relationships) is allowed. Applied to a well-known example in plants, nectar spurs in columbines, the method gives much stronger support to the key innovation hypothesis than previous tests. The tempo of evolution is a subject of general interest to evolutionary biologists, from nucleotide mutation rates within populations to the proliferation of branches on the tree of life. At the macroevolutionary level, key innovation hypotheses (Sanderson and Donoghue 1994) have been put forth to explain unusual disparities in species number between clades. A key innovation is commonly regarded as a biological trait that promotes lineage diversification via mechanisms that increase the rate of speciation and/or decrease the rate of extinction (e.g., Hodges and Arnold 1995). (Hereafter, ''diversification'' will be used to convey the net change in clade diversity as a result of speciation and extinction.) Changes in the rate of lineage diversification are expected to leave an imprint in the phylogeny of the affected species, underscoring the importance of historical inference in studies of evolutionary innovations.Key innovation hypotheses are most frequently studied by correlation, which measures the degree to which multiple origins of a trait are associated with clades of unusual size. Correlations are appealing because they use phylogenetically independent datapoints, typically comparisons of sister clades, to demonstrate a general, repeatable effect on diversity by the candidate trait. Increasing the sample size in this way reduces the potential impact of other factors that affect diversification rate. A popular approach has been to compare the relative sizes of sister groups using nonparametric sign tests, for example, in studies of insect phytophagy (Mitter et al. 1988), plant latex and resin canals (Farrell et al. 1991), floral nectar spurs (Hodges 1997), and flower symmetry (Sargent 2004). Alternatively, parametric approaches make it possible to identify unusually large clades by fitting data to predictions of null models of stochastic cladogenesis, and this can increase the statistical power associated with trait correlations (Slowinski and Guyer 1993;Sims and McConway 2003;McConway and Sims 2004).I...

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“…For example, modern sister comparison methods, such as diversity contrast tests, now consider the numerical values of species richness across clades (opposed to the qualitative sign of the difference only – as in sign tests) (Barraclough, Harvey, & Nee, , ; Sargent, ; Wiegmann, Mitter, & Farrell, ). Modern sister‐clade comparison methods also use maximum likelihood to estimate null hypotheses (McConway & Sims, ; Paradis, ) and to account for stem length biases (Käfer & Mousset, ). Given a well‐resolved phylogeny, a collection of likelihood‐based methods is also available to explicitly model lineage diversification through time (e.g.…”

Section: Introductionmentioning

confidence: 99%

Do latex and resin canals spur plant diversification? Re‐examining a classic example of escape and radiate coevolution

et al. 2019

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The association between increased lineage diversification rates and the evolution of latex and resin canals is widely cited as a paradigmatic example of Ehrlich and Raven’s ‘escape‐and‐radiate’ hypothesis of co‐evolution. However, it has been over a quarter‐century since the original study, and updates to phylogenetic comparative methods, plant molecular systematics, and phenotypic data warrant a reassessment of this classic finding. We gathered data on latex and resin canals across 345 families and 986 genera of vascular plants and conducted a multi‐scale test of the association between these traits and lineage diversification rates. At a broad scale (across clades), we used sister‐clade comparisons to test whether 28 canal‐bearing clades had higher net diversification rates than their canal‐lacking sister clades. At a finer scale (within clades), we used ancestral state reconstructions and phylogenetic models of lineage diversification rates to examine the relationship between trait evolution and the timing of diversification rate shifts in two better‐characterized clades – Araceae and Papaveraceae. At both scales of our analyses we found poor support for the predicted relationship between diversification and the evolution of latex and resin canals. Follow‐up analyses clarified that the qualitative change between our results and those of the Farrell et al.’s classic study is not the result of different phylogenetic comparative methods. Instead, the differences are attributable to updates to plant systematic hypotheses and new data on laticifers and resin canal presence/absence. Synthesis. Our updated study reveals that there is no longer strong evidence for latex or resin canals as general, consistently replicable drivers of species diversity across plants. However, we cannot rule out a relationship in all groups. We therefore argue that theoretical and empirical work aimed at understanding ecological factors that condition ‘escape‐and‐radiate’ dynamics will allow for more nuanced tests of the hypothesis in the future.

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A Likelihood-Based Method for Testing for Nonstochastic Variation of Diversification Rates in Phylogenies

Cited by 11 publications

References 56 publications

Bats, Clocks, and Rocks: Diversification Patterns in Chiroptera

Bats, Clocks, and Rocks: Diversification Patterns in Chiroptera

Detecting the Historical Signature of Key Innovations Using Stochastic Models of Character Evolution and Cladogenesis

Do latex and resin canals spur plant diversification? Re‐examining a classic example of escape and radiate coevolution

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