Why extinction estimates from extant phylogenies are so often zero

The ecology of plant extinctions

Extinctions occur when enough individual plants die without replacement to extirpate a population, and all populations are extirpated. While the ultimate drivers of plant extinctions are known, the proximate mechanisms at individual and population level are not. The fossil record supports climate change as the major driver until recently, with land-use change dominating in recent millennia. Climate change may regain its leading role later this century. Documented recent extinctions have been few and concentrated among narrow-range species, but population extirpations are frequent. Predictions for future extinctions often use flawed methods, but more than half of all plants could be threatened by the end of this century. We need targeted interventions tailored to the needs of each threatened species.

Fossils improve extinction-rate estimates under state-dependent diversification models

The effect of traits on diversification rates is a major topic of study in the fields of evolutionary biology and palaeontology. Many researchers investigating these macroevolutionary questions currently make use of the extensive suite of state-dependent speciation and extinction (SSE) models. These models were developed for, and are almost exclusively used with, phylogenetic trees of extant species. However, analyses considering only extant taxa are limited in their power to estimate extinction rates. Furthermore, SSE models can erroneously detect associations between neutral traits and diversification rates when the true associated trait is not observed. In this study, we examined the impact of including fossil data on the accuracy of parameter estimates under the binary-state speciation and extinction (BiSSE) model. This was achieved by combining SSE models with the fossilized birth-death process. We show that the inclusion of fossils improves the accuracy of extinction-rate estimates for analyses applying the BiSSE model in a Bayesian inference framework, with no negative impact on speciation-rate and state transition-rate estimates when compared with estimates from trees of only extant taxa. However, even with the addition of fossil data, analyses under the BiSSE model continued to incorrectly identify correlations between diversification rates and neutral traits.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.

Impact of evolutionary relatedness on species diversification and tree shape

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.

Challenges in estimating species' age from phylogenetic trees

Aim

Species age, the elapsed time since origination, can give insight into how species longevity might influence eco-evolutionary dynamics, which has been hypothesized to influence extinction risk. Traditionally, species' ages have been estimated from fossil records. However, numerous studies have recently used the branch lengths of time-calibrated phylogenies as estimates of the ages of extant species. This approach poses problems because phylogenetic trees only contain direct information about species identity at the tips and not along the branches. Here, we show that incomplete taxon sampling, extinction, and different assumptions about speciation modes can significantly alter the relationship between true species age and phylogenetic branch lengths, leading to high error rates. We found that these biases can lead to erroneous interpretations of eco-evolutionary patterns derived from comparing phylogenetic age and other traits, such as extinction risk.

Innovation

For bifurcating speciation, the default assumption in most analyses of species age, we propose a probabilistic approach based on the properties of a birth-death process to improve the estimation of species ages. Our approach can reduce the error by one order of magnitude under cases of high extinction and a high percentage of unsampled extant species.

Main conclusion

Our results call for caution in interpreting the relationship between phylogenetic ages and eco-evolutionary traits, as this can lead to biased and erroneous conclusions. We show that, under the assumption of bifurcating speciation, we can obtain unbiased approximations of species age by combining information from branch lengths with the expectations of a birth-death process.

Late Cretaceous ammonoids show that drivers of diversification are regionally heterogeneous

Palaeontologists have long sought to explain the diversification of individual clades to whole biotas at global scales. Advances in our understanding of the spatial distribution of the fossil record through geological time, however, has demonstrated that global trends in biodiversity were a mosaic of regionally heterogeneous diversification processes. Drivers of diversification must presumably have also displayed regional variation to produce the spatial disparities observed in past taxonomic richness. Here, we analyse the fossil record of ammonoids, pelagic shelled cephalopods, through the Late Cretaceous, characterised by some palaeontologists as an interval of biotic decline prior to their total extinction at the Cretaceous-Paleogene boundary. We regionally subdivide this record to eliminate the impacts of spatial sampling biases and infer regional origination and extinction rates corrected for temporal sampling biases using Bayesian methods. We then model these rates using biotic and abiotic drivers commonly inferred to influence diversification. Ammonoid diversification dynamics and responses to this common set of diversity drivers were regionally heterogeneous, do not support ecological decline, and demonstrate that their global diversification signal is influenced by spatial disparities in sampling effort. These results call into question the feasibility of seeking drivers of diversity at global scales in the fossil record.

Imbalanced speciation pulses sustain the radiation of mammals

The evolutionary histories of major clades, including mammals, often comprise changes in their diversification dynamics, but how these changes occur remains debated. We combined comprehensive phylogenetic and fossil information in a new "birth-death diffusion" model that provides a detailed characterization of variation in diversification rates in mammals. We found an early rising and sustained diversification scenario, wherein speciation rates increased before and during the Cretaceous-Paleogene (K-Pg) boundary. The K-Pg mass extinction event filtered out more slowly speciating lineages and was followed by a subsequent slowing in speciation rates rather than rebounds. These dynamics arose from an imbalanced speciation process, with separate lineages giving rise to many, less speciation-prone descendants. Diversity seems to have been brought about by these isolated, fast-speciating lineages, rather than by a few punctuated innovations.

The origin and speciation of orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

Genetic drift promotes and recombination hinders speciation on holey fitness landscapes

Dobzhansky and Muller proposed a general mechanism through which microevolution, the substitution of alleles within populations, can cause the evolution of reproductive isolation between populations and, therefore, macroevolution. As allopatric populations diverge, many combinations of alleles differing between them have not been tested by natural selection and may thus be incompatible. Such genetic incompatibilities often cause low fitness in hybrids between species. Furthermore, the number of incompatibilities grows with the genetic distance between diverging populations. However, what determines the rate and pattern of accumulation of incompatibilities remains unclear. We investigate this question by simulating evolution on holey fitness landscapes on which genetic incompatibilities can be identified unambiguously. We find that genetic incompatibilities accumulate more slowly among genetically robust populations and identify two determinants of the accumulation rate: recombination rate and population size. In large populations with abundant genetic variation, recombination selects for increased genetic robustness and, consequently, incompatibilities accumulate more slowly. In small populations, genetic drift interferes with this process and promotes the accumulation of genetic incompatibilities. Our results suggest a novel mechanism by which genetic drift promotes and recombination hinders speciation.

The macroevolutionary dynamics of activity pattern in mammals: Primates in context

Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.

The Major Features of Macroevolution

Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.

Analysis of intrinsic evolutionary factors leading to microendemic distributions in New Caledonian leaf beetles

Microendemicity, or the condition of some species having local ranges, is a relatively common pattern in nature. However, the factors that lead to this pattern are still largely unknown. Most studies addressing this issue tend to focus on extrinsic factors associated with microendemic distributions, such as environmental conditions, hypothesising a posteriori about underlying potential speciation mechanisms, linked or not to these conditions. Here, we use a multi-faceted approach mostly focusing on intrinsic factors instead, namely diversification dynamics and speciation modes in two endemic sibling genera of leaf beetles with microendemic distributions, Taophila and Tricholapita, in a microendemicity hotspot, New Caledonia. Results suggest that the diversification rate in this lineage slowed down through most of the Neogene and consistently with a protracted speciation model possibly combined with several ecological and environmental factors potentially adding rate-slowing effects through time. In turn, species accumulated following successive allopatric speciation cycles, possibly powered by marked geological and climatic changes in the region in the last 25 million years, with daughter species ranges uncorrelated with the time of speciation. In this case, microendemicity seems to reflect a mature state for the system, rather than a temporary condition for recent species, as suggested for many microendemic organisms.

Cross-disciplinary information for understanding macroevolution

Many different macroevolutionary models can produce the same observations. Despite efforts in building more complex and realistic models, it may still be difficult to distinguish the processes that have generated the biodiversity we observe. In this opinion we argue that we can make new progress by reaching out across disciplines, relying on independent data and theory to constrain macroevolutionary inference. Using mainly paleontological insights and data, we illustrate how we can eliminate less plausible or implausible models, and/or parts of parameter space, while applying comparative phylogenetic approaches. We emphasize that such cross-disciplinary insights and data can be drawn between many other disciplines relevant to macroevolution. We urge cross-disciplinary training, and collaboration using common-use databases as a platform for increasing our understanding.

Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae)

Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6-4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes - in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression - can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.

Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life

The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms.

The scaling of diversification rates with age is likely explained by sampling bias

Numerous phylogenetic studies reported the existence of a pervasive scaling relationship between the ages of extant eukaryotic clades and their estimated diversification rates. The causes of this age-rate-scaling (ARS), whether biological and/or artifactual, remain unresolved. Here we fit diversification models to thousands of eukaryotic time-calibrated phylogenies to explore multiple potential causes of the ARS including parameter non-identifiability, model inadequacy, biases in taxonomic practice, and an important and ubiquitous form of sampling bias-preferentially analyzing larger extant clades. We distinguish between two mechanism by which such sampling biases can cause an ARS: First, by favoring clades that happen to be unusually large merely by chance (i.e., due to the stochastic nature of the cladogenic process), thus leading to rate overestimation, and second, by favoring clades that have truly higher diversification rates. We find that, of the proposed explanations, only sampling biases are likely to contribute to the observed ARS. We develop methods for fully correcting for sampling bias mechanism 1, and find that despite these corrections a substantial ARS remains. We then confirm using simulations that preferring trees with truly higher rates (mechanism 2) likely explains this residual ARS. Since we do not have a completely unbiased sample of clades, including extinct ones, for phylogenetic analyses, it is difficult to demonstrate unambiguously that sampling biases are the sole cause of the ARS. Sampling biases are, however, a parsimonious and plausible explanation for this widely observed macroevolutionary pattern, and this has implications for how we interpret the distribution of diversification rate estimates in extant clades.

Protracted speciation under the state-dependent speciation and extinction approach

How long does speciation take? The answer to this important question in evolutionary biology lies in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently diverged lineages, we now have the lineage-level trees to answer these questions. However, we do not yet have an analytical tool for inferring speciation processes from these trees. What is needed is a model of speciation processes that generates both the trees and species identities of extant lineages. The model should allow calculation of the probability that certain lineages belong to certain species and have an evolutionary history consistent with the tree. Here, we propose such a model and test the model performance on both simulated data and real data. We show that maximum-likelihood estimates of the model are highly accurate and give estimates from real data that generate patterns consistent with observations. We discuss how to extend the model to account for different rates and types of speciation processes across lineages in a species group. By linking evolutionary processes on lineage level to species level, the model provides a new phylogenetic approach to study not just when speciation happened, but how speciation happened. [Micro–macro evolution; Protracted birth–death process; speciation completion rate; SSE approach.]

Ehrlich and Raven escape and radiate coevolution hypothesis at different levels of organization: Past and future perspectives

The classic paper by Ehrlich and Raven on coevolution will soon be 60 years old. Although they were not the first to develop the idea of coevolution, their thought-provoking paper certainly popularized this idea and inspired several generations of scientists interested in coevolution. Here, we describe some of their main contributions, quantitatively measure the impact of their seminal paper on different fields of research, and discuss how ideas related to their original paper might push the study of coevolution forward. To guide our discussion, we explore their original hypothesis into three research fields that are associated with distinct scales/levels of organization: (1) the genetic mechanisms underlying coevolutionary interactions; (2) the potential association between coevolutionary diversification and the organization of ecological networks; and (3) the micro- and macroevolutionary mechanisms and expected patterns under their hypothesis. By doing so, we discuss potentially overlooked aspects and future directions for the study of coevolutionary dynamics and diversification.

Evolutionary legacies in contemporary tetrapod imperilment

The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns - but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.

When adaptive radiations collide: Different evolutionary trajectories between and within island and mainland lizard clades

Oceanic islands are known as test tubes of evolution. Isolated and colonized by relatively few species, islands are home to many of nature's most renowned radiations from the finches of the Galápagos to the silverswords of the Hawaiian Islands. Despite the evolutionary exuberance of insular life, island occupation has long been thought to be irreversible. In particular, the presumed much tougher competitive and predatory milieu in continental settings prevents colonization, much less evolutionary diversification, from islands back to mainlands. To test these predictions, we examined the ecological and morphological diversity of neotropical Anolis lizards, which originated in South America, colonized and radiated on various islands in the Caribbean, and then returned and diversified on the mainland. We focus in particular on what happens when mainland and island evolutionary radiations collide. We show that extensive continental radiations can result from island ancestors and that the incumbent and invading mainland clades achieve their ecological and morphological disparity in very different ways. Moreover, we show that when a mainland radiation derived from island ancestors comes into contact with an incumbent mainland radiation the ensuing interactions favor the island-derived clade.

Biodiversity across space and time in the fossil record

The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.

Pulled Diversification Rates, Lineages-Through-Time Plots and Modern Macroevolutionary Modelling

Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth–death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticized such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here, we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations, we illustrate the characteristics of newly proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modeling, but they in no way suggest we should abandon diversification modeling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community. [Birth–death models; extinction; phylogenetics; speciation.]

Evolution: No extinction? No way!

The fossil record reveals rampant extinction. However, analyses of time-calibrated molecular phylogenies often find no extinction at all. A new paper shows that estimates of zero extinction are entirely incorrect and are caused by limitations of analysing phylogenies that sample only living species.