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120 results for “diversification rate”
Empirical and methodological challenges to the model-based inference of diversification rates in extinct clades
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Fast and accurate estimation of species-specific diversification rates using data augmentation
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Data from: Geophytism in monocots leads to higher rates of diversification
● Geophytes, plants with buds on underground structures, are found throughout the plant tree of life. These below ground structures allow plants to inhabit highly seasonal and disturbance-prone environments across ecosystems. Past researchers have hypothesized the bulbous, cormous and tuberous habits promote diversification, but this had yet to be tested. ● Using a comprehensive monocot data set of almost 13,000 taxa, we investigated the effects of the geophytic habit on diversification using both state-dependent and state-independent models. ● We found that geophytes exhibit increased rates of diversification relative to non-geophytes. State-dependent analyses recovered higher yet similar rates of diversification for bulbous, cormous and tuberous taxa compared to rhizomatous and non-geophytic taxa. However, the state-independent model returned no difference in rates among the different traits. ● Geophytism shows higher rates of diversification relative to non-geophytes but we find little support for the hypothesis that the evolution of the bulb, corm or tuber appears to provide a diversification increase relative to rhizomatous and non-geophytic taxa. Our broad scale analysis highlights the overall evolutionary importance of the geophytic habit (i.e., belowground bud placement). However, our results also suggest that belowground morphological diversity alone cannot explain this rate increase. In order to further test the evolutionary significance of these underground structures, future studies should consider them in combination with other biotic and abiotic factors.
Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
Data from: On the probabilities of branch durations and stratigraphic gaps in phylogenies of fossil taxa when rates of diversification vary over time
The time separating the first appearances of species from their divergences from related taxa affects assessments of macroevolutionary hypotheses about rates of anatomical or ecological change. Branch durations necessarily posit stratigraphic gaps in sampling within a clade over which we have failed to sample predecessors (ancestors) and over which there are no divergences leading to sampled relatives (sister taxa). The former reflects only sampling rates whereas the latter reflects sampling, origination and extinction rates. Because all three rates vary over time, the probability of a branch duration of any particular length will differ depending on when in the Phanerozoic that branch duration spans. Here, I present a birth death sampling model allowing interval to interval variation in diversification and sampling rates. Increasing either origination or sampling rates increases the probability of finding sister taxa that diverge both during and before intervals of high sampling/origination. Conversely, elevated extinction reduces the probability of divergences from sampled sister taxa before and during intervals of elevated extinction. In the case of total extinction, a Signor-Lipps will reduce expected sister-taxa leading up to the extinction, with the possible effect stretching back many millions of years when sampling is low. Simulations indicate that this approach provides reasonable estimates of branch duration probabilities under a variety of circumstances. Because our current probability models for describing morphological evolution are not as advanced as our methods for inferring diversification and sampling rates, branch duration priors allowing for time varying diversification and could be a potent tool for phylogenetic inference with fossil data.
Data from: Inferring diversification rate variation from phylogenies with fossils
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification — extinction rates in particular — can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. Our model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree. We implemented the model in BAMM, a computational framework that uses reversible jump Markov chain Monte Carlo to simulate a posterior distribution of macroevolutionary rate regimes conditional on the branching times and topology of a phylogeny. The implementation we describe can be applied to paleontological phylogenies, neontological phylogenies, and to phylogenies that include both extant and extinct taxa. We evaluate performance of the model on datasets simulated under a range of diversification scenarios. We find that speciation rates are reliably inferred in the absence of paleontological data. However, the inclusion of fossil observations substantially increases the accuracy of extinction rate estimates. We demonstrate that the inferences are relatively robust to at least some violations of model assumptions, including heterogeneity in preservation rates and misspecification of the number of occurrences in paleontological datasets.
Data from: A parametric method for assessing diversification rate variation in phylogenetic trees
Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification-rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification-rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data which showed that PRC has acceptable false positive rates and statistical power to detect rate variation. We apply the PRC method to the well-studied radiation of North American Plethodon salamanders, and support the inference that the large-bodied P. glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders.
Data from: Correlations of life-history and distributional-range variation with salamander diversification rates: evidence for species selection
Evolutionary biologists have long debated the relative influence of species selection on evolutionary patterns. As a test, we apply a statistical phylogenetic approach to evaluate the influence of traits related to species distribution and life-history characteristics on patterns of diversification in salamanders. We use independent contrasts to test trait-mediated diversification while accommodating phylogenetic uncertainty in relationships among all salamander families. Using a neontological data set, we find several species-level traits to be variable, heritable, and associated with differential success (i.e., higher diversification rates) at higher taxonomic categories. Specifically, the macroecological trait of small geographic-range size is strongly correlated with a higher rate of net diversification. We further consider the role that plasticity in life-history traits appears to fulfill in macroevolutionary processes of lineage divergence and durability. We find that pedotypy—wherein some, but not all, organisms of a species mature in the gilled form without metamorphosing—is also associated with higher net diversification rate than is the absence of developmental plasticity. Often dismissed as an insignificant process in evolution, we provide direct evidence for the role of species selection in lineage diversification of salamanders.
Data from: Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts
Estimates of diversification rates are invaluable for many macroevolutionary studies. Recently, an approach called BAMM (Bayesian Analysis of Macro-evolutionary Mixtures) has become widely used for estimating diversification rates and rate shifts. At the same time, several papers have concluded that estimates of net diversification rates from the method-of-moments (MS) estimators are inaccurate. Yet, no studies have compared the ability of these two methods to accurately estimate clade diversification rates. Here, we use simulations to compare their performance. We found that BAMM yielded relatively weak relationships between true and estimated diversification rates. This occurred because BAMM underestimated the number of rates shifts across each tree, and assigned high rates to small clades with low rates. Errors in both speciation and extinction rates contributed to these errors, showing that using BAMM to estimate only speciation rates is also problematic. In contrast, the MS estimators (particularly using stem group ages), yielded stronger relationships between true and estimated diversification rates, by roughly twofold. Furthermore, the MS approach remained relatively accurate when diversification rates were heterogeneous within clades, despite the widespread assumption that it requires constant rates within clades. Overall, we caution that BAMM may be problematic for estimating diversification rates and rate shifts.
Data from: FiSSE: A simple non-parametric test for the effects of a binary character on lineage diversification rates
It is widely assumed that phenotypic traits can influence rates of speciation and extinction, and several statistical approaches have been used to test for correlations between character states and lineage diversification. Recent work suggests that model-based tests of state-dependent speciation and extinction are sensitive to model inadequacy and phylogenetic pseudoreplication. We describe a simple non-parametric statistical test ("FiSSE") to assess the effects of a binary character on lineage diversification rates. The method involves computing a test statistic that compares the distributions of branch lengths for lineages with and without a character state of interest. The value of the test statistic is compared to a null distribution generated by simulating character histories on the observed phylogeny. Our tests show that FiSSE can reliably infer trait-dependent speciation on phylogenies of several hundred tips. The method has low power to detect trait-dependent extinction but can infer state-dependent differences in speciation even when net diversification rates are constant. We assemble a range of macroevolutionary scenarios that are problematic for likelihood-based methods, and we find that FiSSE does not show similarly elevated false positive rates. We suggest that non-parametric statistical approaches, such as FiSSE, provide an important complement to formal process-based models for trait-dependent diversification.
Data from: Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events
Background and Aims Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. Methods We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of individually analysed 48 tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. Key results Brassicaceae diverged 29.9 Mya during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. Conclusions The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant "pump" for continuous and high species diversification.
Data from: Investigating the timing of origin and evolutionary processes shaping regional species diversity: insights from simulated data and Neotropical butterfly diversification rates
Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence.
Data from: Phylogenies and diversification rates: variance cannot be ignored
A recent pair of articles published in the journal Evolution presented a test for assessing the validity of hierarchical macroevolutionary models. The premise of the test is to compare numerical point estimates of parameters from two levels of analysis; if the estimates differ, the hierarchical model is purportedly flawed. The articles in question (Meyer and Wiens 2017; Meyer et al. 2018) apply their proposed test to BAMM, a scientific software program that uses a Bayesian mixture model to estimate rates of evolution from phylogenetic trees. The authors use BAMM to estimate rates from large phylogenies (n > 60 tips) and they apply the method separately to subclades within those phylogenies (median size: n = 3 tips); they find that point estimates of rates differ between these levels and conclude that the method is flawed, but they do not test whether the observed differences are statistically meaningful. There is no consideration of sampling variation and its impact at any level of their analysis. Here, I show that numerical differences across groups that they report are fully explained by a failure to account for sampling variation in their point estimates. Variance in evolutionary rate estimates – from BAMM and all other methods – is an inverse function of clade size; this variance is extreme for clades with 5 or fewer tips (e.g., 70% of clades in the focal study). The articles in question rely on negative results that are easily explained by low statistical power to reject their preferred null hypothesis, and this low power is a trivial consequence of high variance in their point estimates. I describe additional mathematical and statistical mistakes that render the proposed testing framework invalid on first principles. Evolutionary rates are no different than any other population parameters we might wish to estimate, and biologists should use the training and tools already at their disposal to avoid erroneous results that follow from the neglect of variance.
Data from: Greater host breadth still not associated with increased diversification rate in the Nymphalidae – a response to Janz et al
In their technical comment, Janz et al. take issue with our recent study examining the association between host breadth and diversification rates in the brush footed butterflies (Lepidoptera: Nymphalidae) (Hamm and Fordyce 2015). Specifically, they are concerned that we misrepresent their "oscillation hypothesis" (OH) (Janz et al. 2016; Janz and Nylin 2008) and that one of our models was inadequate to test hypotheses regarding host breadth and diversification rate. Given our mutual interests in the macroevolutionary patterns of herbivorous insects, we appreciate the opportunity to respond to their concerns.
Fig. 1 in Diversification rates in Tardigrada indicate a decreasing tempo of lineage splitting regardless of reproductive mode
Fig. 1 Number of species/ entities delimited by tree-based and distance-based single-locus delimitation methods used in this study for three tardigrade groups: family Echiniscidae, family Macrobiotidae, genus Milnesium
Data from: Correlations of life-history and distributional-range variation with salamander diversification rates: evidence for species selection
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Data from: How well can we detect lineage-specific diversification-rate shifts? A simulation study of sequential AIC methods
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Data from: Greater host breadth still not associated with increased diversification rate in the Nymphalidae – a response to Janz et al
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The implications of interrelated assumptions on estimates of divergence times and rates of diversification
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Data from: Inferring diversification rate variation from phylogenies with fossils
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