Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors

What else is dentition telling us? A new specimen-level phylogeny of Mesotheriidae (Mammalia, Notoungulata)

Mesotheriidae (Panperissodactyla, Notoungulata) are an extinct clade (early Oligocene-Pleistocene) of small to medium-sized herbivorous mammals that were widely distributed in South America. Although two subfamilies traditionally have been recognized (Trachytheriinae and Mesotheriinae), recent cladistic analyses based on discrete characters have indicated that "Trachytheriinae" is a paraphyletic assemblage. Given the availability of a large number of specimens and the fact that dental characters are the most common characters used in mesotheriid phylogenies, we performed specimen-level cladistic analyses combining discrete, continuous and geometric morphometrics-based dental characters. The aim was to: (1) include new scored morphological characters to solve the phylogenetic relationships of Mesotheriidae; (2) compare the results of the upper and lower dentition analyses as different character partitions and in combination, to establish phylogenetic hypotheses; and (3) trace the evolution of dental traits. Phylogenetic analyses employing characters of associated upper and lower dentitions recovered one most parsimonious tree with Archaeohyracidae (outgroup) as the sister group of Pan-Mesotheriidae (= Mesotheriidae; converted clade name), this latter composed of trachytheriines (stem-mesotheriine) + Mesotheriinae (converted clade name). Within Mesotheriinae, we recovered two main lineages phylogenetically defined here as Bolivarini and Pampaini (new clade names). Analyses of isolated upper and lower dentition sub-datasets each resulted in one most parsimonious tree congruent with the associated dentition. Our study emphasizes the use of geometric morphometrics characters to resolve additional clades in phylogenetic analyses, provides information on the evolution of size and morphology of teeth, and exposes specimen assignment issues at a taxonomic level. The integration of osteological characters might be crucial to further understanding the evolution of Mesotheriidae.

Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous)

Isolated spinosaurid teeth are relatively well represented in the Lower Cretaceous Wealden Supergroup of southern England, UK. Until recently it was assumed that these teeth were referable to Baryonyx, the type species (B. walkeri) and specimen of which is from the Barremian Upper Weald Clay Formation of Surrey. British spinosaurid teeth are known from formations that span much of the c. 25 Ma depositional history of the Wealden Supergroup, and recent works suggest that British spinosaurids were more taxonomically diverse than previously thought. On the basis of both arguments, it is appropriate to doubt the hypothesis that isolated teeth from outside the Upper Weald Clay Formation are referable to Baryonyx. Here, we use phylogenetic, discriminant and cluster analyses to test whether an isolated spinosaurid tooth (HASMG G369a, consisting of a crown and part of the root) from a non-Weald Clay Formation unit can be referred to Baryonyx. HASMG G369a was recovered from an uncertain Lower Cretaceous locality in East Sussex but is probably from a Valanginian exposure of the Hastings Group and among the oldest spinosaurid material known from the UK. Spinosaurid affinities are both quantitatively and qualitatively supported, and HASMG G369a does not associate with Baryonyx in any analysis. This supports recent reinterpretations of the diversity of spinosaurid in the Early Cretaceous of Britain, which appears to have been populated by multiple spinosaurid lineages in a manner comparable to coeval Iberian deposits. This work also reviews the British and global records of early spinosaurids (known mainly from dental specimens), and revisits evidence for post-Cenomanian spinosaurid persistence.

Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity

The fossilized birth-death (FBD) model is a naturally appealing way of directly incorporating fossil information when estimating diversification rates. However, an important yet often overlooked property of the original FBD derivation is that it distinguishes between two types of sampled lineages. Here we first discuss and demonstrate the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants. We then explore the benefits of including fossils, generally, by implementing and then testing two-types of FBD models, including one that converts a fossil set into stratigraphic ranges, in more complex likelihood-based models that assume multiple rate classes across the tree. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperforms analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. Similarly, we found that converting the fossil set to stratigraphic ranges, which is one way to remedy the effects of undercounting the number of k-type fossils, results in turnover rates and extinction fraction estimates that are generally underestimated. While fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.

Tip dating with fossil sites and stratigraphic sequences

Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies. Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through the use of uniform tip age priors. However, the use of tip age priors has the unwanted effect of decoupling the ages of fossils from the same fossil site. Here we introduce a new Markov Chain Monte Carlo (MCMC) proposal, which allows fossils from the same site to have linked ages, while still incorporating uncertainty in the age of the fossil site itself. We also include an extension, allowing fossil sites to be ordered in a stratigraphic column with age bounds applied only to the top and bottom of the sequence. These MCMC proposals are implemented in a new open-source BEAST2 package, palaeo. We test these new proposals on a dataset of early vertebrate fossils, concentrating on the effects on two sites with multiple acanthodian fossil taxa but wide age uncertainty, the Man On The Hill (MOTH) site from northern Canada, and the Turin Hill site from Scotland, both of Lochkovian (Early Devonian) age. The results show an increased precision of age estimates when fossils have linked tip ages compared to when ages are unlinked, and in this example leads to support for a younger age for the MOTH site compared with the Turin Hill site. There is also a minor effect on the tree topology of acanthodians. These new MCMC proposals should be widely applicable to studies that employ tip dating, particularly when the terminals are coded as individual specimens.

Exact Distribution of Divergence Times from Fossil Ages and Tree Topologies

Being given a phylogenetic tree of both extant and extinct taxa in which the fossil ages are the only temporal information (namely, in which divergence times are considered unknown), we provide a method to compute the exact probability distribution of any divergence time of the tree with regard to any speciation (cladogenesis), extinction, and fossilization rates under the Fossilized Birth–Death model. We use this new method to obtain a probability distribution for the age of Amniota (the synapsid/sauropsid or bird/mammal divergence), one of the most-frequently used dating constraints. Our results suggest an older age (between about 322 and 340 Ma) than has been assumed by most studies that have used this constraint (which typically assumed a best estimate around 310–315 Ma) and provide, for the first time, a method to compute the shape of the probability density for this divergence time. [Divergence times; fossil ages; fossilized birth–death model; probability distribution.]

A revision of the diagnosis and affinities of the metriorhynchoids (Crocodylomorpha, Thalattosuchia) from the Rosso Ammonitico Veronese Formation (Jurassic of Italy) using specimen-level analyses

Neptunidraco ammoniticus is a thalattosuchian crocodylomorph from the Rosso Ammonitico Veronese Formation (RAVF, Middle Jurassic) of northern Italy. Erected from one partial specimen, Neptunidraco is pivotal in reconstructing thalattosuchian evolution, being it the oldest known member of Metriorhynchidae. Two additional RAVF thalattosuchians have been referred to Neptunidraco. A revised diagnosis of N. ammoniticus is provided here. Using a well-sampled phylogenetic data set of Crocodylomorpha, the affinities of all three RAVF thalattosuchian specimens are investigated simultaneously for the first time using parsimony tree-search strategies and Bayesian inference using the Fossilized Birth-Death with Sampled Ancestor (FBDSA) model. The results of the alternative analyses are not consistent in the placement of the RAVF specimens. The holotype of N. ammoniticus is consequently referred to Metriorhynchidae incertae sedis. The first referred specimen is recovered in various alternative placements among Metriorhynchoidea. The third and most fragmentary specimen is recovered as a crocodylomorph of uncertain affinities in the parsimony analysis and in the undated Bayesian analysis, and a metriorhynchoid sister taxon of the second RAVF specimen in the tip-dated Bayesian analysis. Only a subset of the results in the parsimony-based analyses supports the referral of the latter two specimens to Neptunidraco. The unusually high rate of morphological divergence for the Neptunidraco branch, inferred in previous iterations of the Bayesian inference analyses but not recovered in the novel analysis, was likely an artifact of the a priori constraint of all RAVF thalattosuchians into a single taxonomic unit, and of the arbitrarily fixed tip-age priors for the terminal taxa. These results confirm the utility of specimen-level morphological analysis and of combined tree-search strategies for inferring the affinities and the inclusiveness of fragmentary but significant fossil taxa, and reinforce the importance of incorporating stratigraphic uncertainty as prior in tip-dated Bayesian inference analyses.

Evidence for Trait-Based Dominance in Occupancy among Fossil Taxa and the Decoupling of Macroecological and Macroevolutionary Success

Biological systems provide examples of differential success among taxa, from ecosystems with a few dominant species (ecological success) to clades that possess far more species than sister clades (macroevolutionary success). Macroecological success, the occupation by a species or clade of an unusually high number of areas, has received less attention. If macroecological success reflects heritable traits, then successful species should be related. Genera composed of species possessing those traits should occupy more areas than genera with comparable species richness that lack such traits. Alternatively, if macroecological success reflects autapomorphic traits, then generic occupancy should be a by-product of species richness among genera and occupancy of constituent species. We test this using Phanerozoic marine invertebrates. Although temporal patterns of species and generic occupancy are strongly correlated, inequality in generic occupancy typically is greater than expected. Genus-level patterns cannot be explained solely with species-level patterns. Within individual intervals, deviations between the observed and expected generic occupancy correlate with the number of lithological units (stratigraphic formations), particularly after controlling for geographic range and species richness. However, elevated generic occupancy is unrelated to or negatively associated with either generic geographic ranges or within-genus species richness. Our results suggest that shared traits among congeneric species encourage short-term macroecological success without generating short-term macroevolutionary success. A broad niche may confer high occupancy but does not necessarily promote speciation.

Inferring 'weak spots' in phylogenetic trees: application to mosasauroid nomenclature

Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the 'weak spots' in the phylogeny of mosasauroids, we revise the nomenclature of the 'traditionally' recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.