Challenges in the estimation of extinction from molecular phylogenies: A response to Beaulieu and O'Meara

The origin and evolution of coral species richness in a marine biodiversity hotspot

The Coral Triangle (CT) region of the Indo-Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here, we use a time-calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model-based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the CT are lower than in surrounding regions, a result inconsistent with the long-standing center of origin hypothesis. Furthermore, endemism of coral species in the CT is low, and the CT endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the CT is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the CT requires protecting not just reefs within the hotspot, but also those in the surrounding areas.

Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia)

BACKGROUND

The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of dasyuromorphians and "dasyuromorphian-like" taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern dasyuromorphians.

RESULTS

Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5-13.1 MYA; composite 95% HPD: 9.5-15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4-8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species.

CONCLUSIONS

Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil dasyuromorphians, but future progress will require a much improved fossil record.

Approaches to Macroevolution: 2. Sorting of Variation, Some Overarching Issues, and General Conclusions

Approaches to macroevolution require integration of its two fundamental components, within a hierarchical framework. Following a companion paper on the origin of variation, I here discuss sorting within an evolutionary hierarchy. Species sorting-sometimes termed species selection in the broad sense, meaning differential origination and extinction owing to intrinsic biological properties-can be split into strict-sense species selection, in which rate differentials are governed by emergent, species-level traits such as geographic range size, and effect macroevolution, in which rates are governed by organism-level traits such as body size; both processes can create hitchhiking effects, indirectly causing the proliferation or decline of other traits. Several methods can operationalize the concept of emergence, so that rigorous separation of these processes is increasingly feasible. A macroevolutionary tradeoff, underlain by the intrinsic traits that influence evolutionary dynamics, causes speciation and extinction rates to covary in many clades, resulting in evolutionary volatility of some clades and more subdued behavior of others; the few clades that break the tradeoff can achieve especially prolific diversification. In addition to intrinsic biological traits at multiple levels, extrinsic events can drive the waxing and waning of clades, and the interaction of traits and events are difficult but important to disentangle. Evolutionary trends can arise in many ways, and at any hierarchical level; descriptive models can be fitted to clade trajectories in phenotypic or functional spaces, but they may not be diagnostic regarding processes, and close attention must be paid to both leading and trailing edges of apparent trends. Biotic interactions can have negative or positive effects on taxonomic diversity within a clade, but cannot be readily extrapolated from the nature of such interactions at the organismic level. The relationships among macroevolutionary currencies through time (taxonomic richness, morphologic disparity, functional variety) are crucial for understanding the nature of evolutionary diversification. A novel approach to diversity-disparity analysis shows that taxonomic diversifications can lag behind, occur in concert with, or precede, increases in disparity. Some overarching issues relating to both the origin and sorting of clades and phenotypes include the macroevolutionary role of mass extinctions, the potential differences between plant and animal macroevolution, whether macroevolutionary processes have changed through geologic time, and the growing human impact on present-day macroevolution. Many challenges remain, but progress is being made on two of the key ones: (a) the integration of variation-generating mechanisms and the multilevel sorting processes that act on that variation, and (b) the integration of paleontological and neontological approaches to historical biology.

Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models

Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA's numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that "unobserved rate shifts" appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the ${\sim}$20% of simulated trees in MEA's data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth-death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth.

Notes on the Statistical Power of the Binary State Speciation and Extinction (BiSSE) Model

The Binary State Speciation and Extinction (BiSSE) method is one of the most popular tools for investigating the rates of diversification and character evolution. Yet, based on previous simulation studies, it is commonly held that the BiSSE method requires phylogenetic trees of fairly large sample sizes (>300 taxa) in order to distinguish between the different models of speciation, extinction, or transition rate asymmetry. Here, the power of the BiSSE method is reevaluated by simulating trees of both small and large sample sizes (30, 60, 90, and 300 taxa) under various asymmetry models and root state assumptions. Results show that the power of the BiSSE method can be much higher, also in trees of small sample size, for detecting differences in speciation rate asymmetry than anticipated earlier. This, however, is not a consequence of any conceptual or mathematical flaw in the method per se but rather of assumptions about the character state at the root of the simulated trees and thus the underlying macroevolutionary model, which led to biased results and conclusions in earlier power assessments. As such, these earlier simulation studies used to determine the power of BiSSE were not incorrect but biased, leading to an overestimation of type-II statistical error for detecting differences in speciation rate but not for extinction and transition rates.

The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)

The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in driving diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 million yr. Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world's biodiversity.