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Slowdowns in lineage accumulation are often observed in phylogenies of extant species. One explanation is the presence of ecological limits to diversity and hence to diversification. Previous research has examined whether and how species richness (SR) impacts diversification rates, but rarely considered the evolutionary relatedness (ER) between species, although ER can affect the degree of interaction between species, which likely sets these limits. To understand the influences of ER on species diversification and the interplay between SR and ER, we present a simple birth-death model in which the speciation rate depends on the ER. We use different metrics of ER that operate at different scales, ranging from branch/lineage-specific to clade-wide scales. We find that the scales at which an effect of ER operates yield distinct patterns in various tree statistics. When ER operates across the whole tree, we observe smaller and more balanced trees, with speciation rates distributed more evenly across the tips than in scenarios with lineage-specific ER effects. Importantly, we find that negative SR dependence of speciation masks the impact of ER on some of the tree statistics. Our model allows diverse evolutionary trajectories for producing imbalanced trees, which are commonly observed in empirical phylogenies but have been challenging to replicate with earlier models., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

While the theory of micro-evolution by natural selection assigns a crucial role to competition, its role in macroevolution is less clear. Phylogenetic evidence for a decelerating accumulation of lineages suggests a feedback of lineage diversity on diversification. However, does this feedback only occur between close relatives, or do distant relatives also influence each other's diversification? In other words: are there phylogenetic limits to this diversity-dependence? Islands form ideal systems to answer these questions because their boundedness facilitates an overview of all potential competitors. The DAISIE (Dynamic Assembly of Island biota through Speciation Immigration and Extinction) framework allows for testing the presence of diversity-dependence on islands given phylogenetic data on colonization and branching times. The current inference models in DAISIE assume that this diversity-dependence only applies within a colonizing clade, i.e., all mainland species can colonize and diversify independently from one another. We term this clade-specific (CS) diversity-dependence. Here we introduce a new DAISIE model that assumes that diversity-dependence applies to all island species of a taxonomic group regardless of their mainland ancestry, i.e., diversity-dependence applies both to species within the same clade and between different clades established by different mainland species. We call this island-wide (IW) diversity-dependence. We present a method to compute a likelihood for this model given phylogenetic data on colonization and branching events and use likelihood ratio bootstrapping to compare it to the likelihood of the CS model in order to overcome biases known for standard model selection. We apply it to the diversification of Eleutherodactylus frogs on Hispaniola. Across the Greater Antilles archipelago, this radiation shows repeated patterns of diversification in ecotypes that are similar across clades. This could be suggestive of overlapping niche space and hence between-clade interactions, i.e., IW diversity-dependence. But it could also be suggestive of only within-clade interactions because between-clade interactions would have blocked the same ecotype from re-appearing. We find that the CS model fits the data much better than the IW model, indicating that different colonizations while resulting in similar ecotypes, are sufficiently distinct to avoid interacting strongly. We argue that non-overlapping distributions between clades (both spatially and in terms of ecotypes) cannot be used as evidence of CS diversity-dependence, because this pattern may be a consequence of IW diversity-dependence. By contrast, by using phylogenetic data rather than distributional data our method does allow for inferring the phylogenetic limits to diversity-dependent diversification. We discuss possibilities for future extensions and applications of our modelling approach. [Adaptive radiation; birth-death model; Caribbean; diversity-dependence; Eleutherodactylus; island biogeography.]., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

The branching patterns of molecular phylogenies are generally assumed to contain information on rates of the underlying speciation and extinction processes. Simple birth-death models with constant, time-varying, or diversity-dependent rates have been invoked to explain these patterns. They have one assumption in common: all lineages have the same set of diversification rates at a given point in time. It seems likely, however, that there is variability in diversification rates across subclades in a phylogenetic tree. This has inspired the construction of models that allow multiple rate regimes across the phylogeny, with instantaneous shifts between these regimes. Several methods exist for calculating the likelihood of a phylogeny under a specified mapping of diversification regimes and for performing inference on the most likely diversification history that gave rise to a particular phylogenetic tree. Here, we show that the likelihood computation of these methods is not correct. We provide a new framework to compute the likelihood correctly and show, with simulations of a single shift, that the correct likelihood indeed leads to parameter estimates that are on average in much better agreement with the generating parameters than the incorrect likelihood. Moreover, we show that our corrected likelihood can be extended to multiple rate shifts in time-dependent and diversity-dependent models. We argue that identifying shifts in diversification rates is a nontrivial model selection exercise where one has to choose whether shifts in now-extinct lineages are taken into account or not. Hence, our framework also resolves the recent debate on such unobserved shifts. [Diversification; macroevolution; phylogeny; speciation]., (© The authors 2020. Published by Oxford University Press.)

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 upscaling 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 (DD) 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 DD 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, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends., (© 2020 The Authors. Evolution published by Wiley Periodicals LLC on behalf of The Society for the Study of Evolution.)

The emergence of new frameworks combining evolutionary and ecological dynamics in communities opens new perspectives on the study of speciation. By acknowledging the relative contribution of local and regional dynamics in shaping the complexity of ecological communities, metacommunity theory sheds a new light on the mechanisms underlying the emergence of species. Three integrative frameworks have been proposed, involving neutral dynamics, niche theory, and life history trade-offs respectively. Here, we review these frameworks of metacommunity theory to emphasise that: (1) studies on speciation and community ecology have converged towards similar general principles by acknowledging the central role of dispersal in metacommunities dynamics, (2) considering the conditions of emergence and maintenance of new species in communities has given rise to new models of speciation embedded in the metacommunity theory, (3) studies of diversification have shifted from relating phylogenetic patterns to landscapes spatial and ecological characteristics towards integrative approaches that explicitly consider speciation in a mechanistic ecological framework. We highlight several challenges, in particular the need for a better integration of the eco-evolutionary consequences of dispersal and the need to increase our understanding on the relative rates of evolutionary and ecological changes in communities., (© 2015 John Wiley & Sons Ltd/CNRS.)

Understanding the patterns of biodiversity through time and space is a challenging task. However, phylogeny-based macroevolutionary models allow us to account and measure many of the processes responsible for diversity buildup, namely speciation and extinction. The general latitudinal diversity gradient (LDG) is a well-recognized pattern describing a decline in species richness from the equator polewards. Recent macroecological studies in ectomycorrhizal (EM) fungi have shown that their LDG is shifted, peaking at temperate rather than tropical latitudes. Here we investigate this phenomenon from a macroevolutionary perspective, focusing on a well-sampled group of edible EM mushrooms from the genus Amanita-the Caesar's mushrooms, which follow similar diversity patterns. Our approach consisted in applying a suite of models including (1) nontrait-dependent time-varying diversification (Bayesian analysis of macroevolutionary mixtures [BAMM]), (2) continuous trait-dependent diversification (quantitative-state speciation and extinction [QuaSSE]), and (3) diversity-dependent diversification. In short, results give strong support for high speciation rates at temperate latitudes (BAMM and QuaSSE). We also find some evidence for different diversity-dependence thresholds in "temperate" and "tropical" subclades, and little differences in diversity due to extinction. We conclude that our analyses on the Caesar's mushrooms give further evidence of a temperate-peaking LDG in EM fungi, highlighting the importance and the implications of macroevolutionary processes in explaining diversity gradients in microorganisms., (© 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.)

Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion - often attributed to negative biotic interactions - are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure., (© 2015 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.)

Speciation is not instantaneous but takes time. The protracted birth-death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. ). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation., (© 2014 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.)

Phylogenetic trees show a remarkable slowdown in the increase of number of lineages towards the present, a phenomenon which cannot be explained by the standard birth-death model of diversification with constant speciation and extinction rates. The birth-death model instead predicts a constant or accelerating increase in the number of lineages, which has been called the pull of the present. The observed slowdown has been attributed to nonconstancy of the speciation and extinction rates due to some form of diversity dependence (i.e., species-level density dependence), but the mechanisms underlying this are still unclear. Here, we propose an alternative explanation based on the simple concept that speciation takes time to complete. We show that this idea of "protracted" speciation can be incorporated in the standard birth-death model of diversification. The protracted birth-death model predicts a realistic slowdown in the rate of increase of number of lineages in the phylogeny and provides a compelling fit to four bird phylogenies with realistic parameter values. Thus, the effect of recognizing the generally accepted fact that speciation is not an instantaneous event is significant; even if it cannot account for all the observed patterns, it certainly contributes substantially and should therefore be incorporated into future studies.

Understanding the maintenance and origin of biodiversity is a formidable task, yet many ubiquitous ecological patterns are predicted by a surprisingly simple and widely studied neutral model that ignores functional differences between species. However, this model assumes that new species arise instantaneously as singletons and consequently makes unrealistic predictions about species lifetimes, speciation rates and number of rare species. Here, we resolve these anomalies - without compromising any of the original model's existing achievements and retaining computational and analytical tractability - by modelling speciation as a gradual, protracted, process rather than an instantaneous event. Our model also makes new predictions about the diversity of 'incipient' species and rare species in the metacommunity. We show that it is both necessary and straightforward to incorporate protracted speciation in future studies of neutral models, and argue that non-neutral models should also model speciation as a gradual process rather than an instantaneous one.

Hubbell's neutral theory claims that ecological patterns such as species abundance distributions can be explained by a stochastic model based on simple assumptions. One of these assumptions, the point mutation assumption, states that every individual has the same probability to speciate. Etienne et al. have argued that other assumptions on the speciation process could be more realistic, for example, that every species has the same probability to speciate (Etienne, et al. in Oikos 116:241-258, 2007). They introduced a number of neutral community models with a different speciation process, and conjectured formulas for their stationary species abundance distribution. Here we study a generalised neutral community model, encompassing these modified models, and derive its stationary distribution, thus proving the conjectured formulas.

Understanding the processes that underlie biodiversity requires insight into the evolutionary history of the taxa involved. Accurate estimation of speciation, extinction, and diversification rates is a prerequisite for gaining this insight. Here, we develop a stochastic birth-death model of speciation and extinction that predicts the probability distribution of both extinct and extant numbers of species in a clade. We present two estimation methods based on this model given data on the number of extinct species (from the fossil record) and extant species (from diversity assessments): a multivariate method of moments approach and a maximum-likelihood approach. We show that, except for some special cases, the two estimation methods produce very similar estimates. This is convenient, because the usually preferred maximum-likelihood approach is much more computationally demanding, so the method of moments can serve as a proxy. Furthermore, we introduce a correction for possible bias that can arise by the mere fact that we will normally only consider extant clades. We find that in some cases the bias correction affects the estimates profoundly. Finally, we show how our model can be extended to incorporate incomplete preservation. Preservation rates can, however, not be reliably estimated on the basis of numbers of extant and extinct species alone.

Latimer et al. (Reports, 9 September 2005, p. 1722) used an approximate likelihood function to estimate parameters of Hubbell's neutral model of biodiversity. Reanalysis with the exact likelihood not only yields different estimates but also shows that two similar likelihood maxima for very different parameter combinations can occur. This reveals a limitation of using species abundance data to gain insight into speciation and dispersal.

The application of state-dependent speciation and extinction models to phylogenetic trees has shown an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. To explore whether assuming no dependence on traits leads to bias in inference on island dynamics, we extend an island biodiversity model, DAISIE (Dynamic Assembly of Islands through Speciation, Immigration, and Extinction) to include trait-dependent diversification simulations, and evaluate the robustness of the inference model which ignores this trait-dependence. Our results indicate that when the differences between colonization, extinction, and speciation rates between trait states are moderate, the model shows negligible error for a variety of island diversity metrics, suggesting that island diversity dynamics can be accurately estimated without the need to explicitly model trait dependence. We conclude that for many biologically realistic scenarios with trait-dependent diversification and colonization, this simple trait-less inference model is informative and robust to trait effects on colonization, speciation, and extinction. Nonetheless, our new simulation model may provide a useful tool for studying patterns of trait variation. [ABSTRACT FROM AUTHOR]

Vascular epiphytes form a diverse group of almost 30 000 species, yet theory concerning their community structure is still largely lacking. We therefore employed the simplest models of biodiversity, (near‐)neutral models, to generate hypotheses concerning their community structure. With recently developed tools for (near‐)neutral models we analyzed species abundance data from many samples in Central and South America which we divided into four metacommunities (Mesoamerica, Central America, Amazonia and Paraná), where for each metacommunity we considered two subsets differing in dispersal syndrome: an animal‐dispersed guild and a wind‐dispersed guild. We considered three models differing in the underlying speciation mode. Across all metacommunities, we found observed patterns to be indistinguishable from patterns generated by neutral or near‐neutral processes. Furthermore, we found that subdivision in different dispersal guilds was often supported, with recruitment limitation being stronger for animal‐dispersed species than for wind‐dispersed species. This is the first time that (near‐)neutral theory has been applied to epiphyte communities. Future efforts with additional data sets and more refined models are expected to further improve our understanding of community structure in epiphytes and will have to test the generality of our findings. [ABSTRACT FROM AUTHOR]

The latitudinal diversity gradient (LDG) is one of Earth's most iconic biodiversity patterns and still one of the most debated. Explanations for the LDG are often categorized into three broad pathways in which the diversity gradient is created by (1) differential diversification rates, (2) differential carrying capacities (ecological limits), or (3) differential time to accumulate species across latitude. Support for these pathways has, however, been mostly verbally expressed. Here, we present a minimal model to clarify the essential assumptions of the three pathways and explore the sensitivity of diversity dynamics to these pathways. We find that an LDG arises most easily from a gradient in ecological limits compared with a gradient in the time for species accumulation or diversification rate in most modeled scenarios. Differential diversification rates create a stronger LDG than ecological limits only when speciation and dispersal rates are low, but then the predicted LDG seems weaker than the observed LDG. Moreover, range dynamics may reduce an LDG created by a gradient in diversification rates or time for species accumulation, but they cannot reduce an LDG induced by differential ecological limits. We conclude that our simple model provides a null prediction for the effectiveness of the three LDG pathways and can thus aid discussions about the causal mechanisms underlying the LDG or motivate more complex models to confirm or falsify our findings. [ABSTRACT FROM AUTHOR]

Species diversification may be determined by many different variables, including the traits of the diversifying lineages. The state-dependent speciation and extinction (SSE) framework contains methods to detect the dependence of diversification on these traits. For the analysis of traits with multiple states, MuSSE (multiple-states dependent speciation and extinction) was developed. However, MuSSE and other SSE models have been shown to yield false positives, because they cannot separate differential diversification rates from dependence of diversification on the observed traits. The recently introduced method HiSSE (hidden-state-dependent speciation and extinction) resolves this problem by allowing a hidden state to affect diversification rates. Unfortunately, HiSSE does not allow traits with more than two states, and, perhaps more interestingly, the simultaneous action of multiple traits on diversification. Herein, we introduce an R package (SecSSE: several examined and concealed states-dependent speciation and extinction) that combines the features of HiSSE and MuSSE to simultaneously infer state-dependent diversification across two or more examined (observed) traits or states while accounting for the role of a possible concealed (hidden) trait. Moreover, SecSSE also has improved functionality when compared with its two "parents." First, it allows for an observed trait being in two or more states simultaneously, which is useful for example when a taxon is a generalist or when the exact state is not precisely known. Second, it provides the correct likelihood when conditioned on nonextinction, which has been incorrectly implemented in HiSSE and other SSE models. To illustrate our method, we apply SecSSE to seven previous studies that used MuSSE, and find that in five out of seven cases, the conclusions drawn based on MuSSE were premature. We test with simulations whether SecSSE sacrifices statistical power to avoid the high Type I error problem of MuSSE, but we find that this is not the case: for the majority of simulations where the observed traits affect diversification, SecSSE detects this. [ABSTRACT FROM AUTHOR]

Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking., Here, we simulate phylogenetic branching under linear negative diversity-dependent and diversity-independent models and estimate from the simulated phylogenies the maximum-likelihood parameters for three different conditionings - on survival of the birth-death process given the crown age, on tree size ( N) and on tree size given the crown age. We report the accuracy of recovering the simulation parameters and the reliability of the model selection based on the χ2 likelihood ratio test., Parameter estimate accuracy: Conditioning on survival given the crown age yields a severe bias of the carrying capacity K towards N and an upward bias of the speciation rate, particularly in clades where diversity-dependent feedbacks are still weak ( N « K). Conditioning on N yields an overestimate of K and an underestimate of speciation rate, particularly when saturation has been reached. Dual conditioning yields relatively unbiased parameter estimates on average, but the deviation from the true value for any single estimate may be large., Model selection reliability: The frequency of incorrectly rejecting a diversity-independent model when the simulation was diversity-independent (type I error) differs substantially from the significance level α used in the likelihood ratio test, rendering the likelihood ratio test inappropriate. The frequency of correctly rejecting the diversity-independent model when the simulation was diversity-dependent (power) is larger when the clade is closer to equilibrium and for conditioning on crown age., We conclude that conditioning on crown age has the best statistical properties overall, but caution that parameter estimates may be biased. To assess parameter uncertainty in future studies of diversity dependence on real data, we recommend parametric bootstrapping, examination of the likelihood surface and comparison of estimates across the types of conditioning. To assess model selection reliability, we discourage the use of the χ2 likelihood ratio test or AIC (which are equivalent in this case), but recommend a likelihood ratio test based on parametric bootstrap. We illustrate this method for the diversification of Dendroica warblers. [ABSTRACT FROM AUTHOR]

A correction is presented to the article "Estimating the duration of speciation from phylogenies" which appeared in the previous issue.

A major goal of island biogeography is to understand how island communities are assembled over time. However, we know little about the influence of variable area and ecological opportunity on island biotas over geological timescales. Islands have limited life spans, and it has been posited that insular diversity patterns should rise and fall with an island's ontogeny. The potential of phylogenies to inform us of island ontogenetic stage remains unclear, as we lack a phylogenetic framework that focuses on islands rather than clades. Here, we present a parsimonious island-centric model that integrates phylogeny and ontogeny into island biogeography and can incorporate a negative feedback of diversity on species origination. This framework allows us to generate predictions about species richness and phylogenies on islands of different ages. We find that peak richness lags behind peak island area, and that endemic species age increases with island age on volcanic islands. When diversity negatively affects rates of immigration and cladogenesis, our model predicts speciation slowdowns on old islands. Importantly, we find that branching times of in situ radiations can be informative of an island's ontogenetic stage. This novel framework provides a quantitative means of uncovering processes responsible for island biogeography patterns using phylogenies. [ABSTRACT FROM AUTHOR]