The fossilized birth-death process for coherent calibration of divergence-time estimates

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'.

The Fossilized Birth-Death Model Is Identifiable

Time-dependent birth-death sampling models have been used in numerous studies to infer past evolutionary dynamics in different biological contexts, for example,  speciation and extinction rates in macroevolutionary studies, or effective reproductive number in epidemiological studies. These models are branching processes where lineages can bifurcate, die, or be sampled with time-dependent birth, death, and sampling rates, generating phylogenetic trees. It has been shown that in some subclasses of such models, different sets of rates can result in the same distributions of reconstructed phylogenetic trees, and therefore, the rates become unidentifiable from the trees regardless of their size. Here, we show that widely used time-dependent fossilized birth-death (FBD) models are identifiable. This subclass of models makes more realistic assumptions about the fossilization process and certain infectious disease transmission processes than the unidentifiable birth-death sampling models. Namely, FBD models assume that sampled lineages stay in the process rather than being immediately removed upon sampling. The identifiability of the time-dependent FBD model justifies using statistical methods that implement this model to infer the underlying temporal diversification or epidemiological dynamics from phylogenetic trees or directly from molecular or other comparative data. We further show that the time-dependent FBD model with an extra parameter, the removal after sampling probability, is unidentifiable. This implies that in scenarios where we do not know how sampling affects lineages, we are unable to infer this extra parameter together with birth, death, and sampling rates solely from trees.

Cladistic estimates of evolutionary rates focused on palaeontological datasets using TNT

We describe a protocol for estimating evolutionary rates from phylogenetic trees based on parsimony character optimization. The rate estimation is conducted through a TNT script and the results are analysed in a script for the software environment R. The TNT script allows analysing multiple optimal topologies, considering optimization ambiguity, and alternative time-calibrations or pre-calibrated trees. The R script summarizes estimated rates on a consensus tree and plots the variation of evolutionary rates through time, jointly with the phylogenetic diversity and a new metric (clade completeness index) that measures the distribution of missing data along the tree. We present results for simulated and empirical analyses, and evaluate the impact of missing data and alternative calibration methods in rate estimates. We found that while missing data can lower the nominal values of evolutionary rates, the overall pattern of rate variation through time remained robust. Empirical cases highlight different scenarios, such as datasets in which peaks of evolutionary rates can be coupled or decoupled from diversification dynamics (phylogenetic diversity) and cases in which missing data may influence the variation of estimated evolutionary rates. We conclude with recommendations for using this protocol and interpreting the results of parsimony-based rate estimates.

Accounting for sampling heterogeneity suggests a low paleolatitude origin for dinosaurs

Dinosaurs dominated Mesozoic terrestrial ecosystems for ∼160 million years, but their biogeographic origin remains poorly understood. The earliest unequivocal dinosaur fossils appear in the Carnian (∼230 Ma) of southern South America and Africa, leading most authors to propose southwestern Gondwana as the likely center of origin. However, the high taxonomic and morphological diversity of these earliest assemblages suggests a more ancient evolutionary history that is currently unsampled. Phylogenetic uncertainty at the base of Dinosauria, combined with the subsequent appearance of dinosaurs throughout Laurasia in their early evolutionary history, further complicates this picture. Here, we estimate the distribution of early dinosaurs and their archosaurian relatives under a phylogenetic maximum likelihood framework, testing alternative topological arrangements and incorporating potential abiotic barriers to dispersal into our biogeographic models. For the first time, we include spatiotemporal sampling heterogeneity in these models, which frequently supports a low-latitude Gondwanan origin for dinosaurs. These results are best supported when silesaurids are constrained as early-diverging ornithischians, which is likely because this topology accounts for the otherwise substantial ornithischian ghost lineage, explaining the group's absence from the fossil record prior to the Early Jurassic. Our results suggest that the archosaur radiation also took place within low-latitude Gondwana following the end-Permian extinction before lineages dispersed across Pangaea into ecologically and climatically distinct provinces during the Late Triassic. Mesozoic terrestrial vertebrates are under-sampled at low paleolatitudes, and our findings suggest that heterogeneous sampling has hitherto obscured the true paleobiogeographic origin of dinosaurs and their kin.

Phylogenomic resolution of lampreys reveals the recent evolution of an ancient vertebrate lineage

Jawless vertebrates once dominated Palaeozoic waters, but just two lineages have persisted to the present day: lampreys and hagfishes. Living lampreys are a relatively small clade, with just over 50 species described, but knowledge of their evolutionary relationships has always been based on either a few mitochondrial genes or a small number of taxa. Biogeographers have noted the disjunct antitropical distribution of living lamprey families. Here, we present a comprehensive phylogenomic analysis of living and fossil lampreys, sampling 36 species with phylogenomic data and 46 in total with genetic data. We present new divergence time estimates based on comprehensive nuclear data and analysis of their diversification dynamics. Our analysis indicates a central role for extreme global warming during the Late Cretaceous Cenomanian-Turonian Boundary Event as a likely cause for the antitropical distribution of living lampreys, and a notable increase in lineage diversification in Northern Hemisphere lampreys during the Miocene corresponding with a period of global cooling.

A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa

The reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154 to 1036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe-iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil-calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.

Dinosaur palaeoneurology: an evolving science

Our fascination with dinosaur brains and their capabilities essentially began with the first dinosaur discovery. The history of this study is a useful reflection of palaeoneurology as a whole and its relationship to a more inclusive evolutionary neuroscience. I argue that this relationship is imbued with high heuristic potential, but one whose realization requires overcoming certain constraints. These constraints include the need for a stable phylogenetic framework, methods for efficient and precise endocast construction, and fossil researchers who are steeped in a neuroscience perspective. The progress that has already been made in these areas sets the stage for a more mature palaeoneurology-not only one capable of being informed by neuroscience discoveries but one that drives such discoveries. I draw from work on the size, shape, behavioural correlates and developmental role of the dinosaur brain to outline current advances in dinosaur palaeoneurology. My examples largely are taken from theropods and centre on questions related to the origin of birds and their unique locomotory capabilities. The hope, however, is that these exemplify the potential for study in other dinosaur groups, and for utilizing the dinosaur-bird lineage as a parallel model on a par with mammals for studying encephalization.

Reticulate evolution: Detection and utility in the phylogenomics era

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.

PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, thanks to its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This article describes the features of PhyloJunction-which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models-and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.

Deep-time origin of tympanic hearing in crown reptiles

The invasion of terrestrial ecosystems by tetrapods (c. 375 million years [Ma]) represents one of the major evolutionary transitions in the history of life on Earth. The success of tetrapods on land is linked to evolutionary novelties. Among these, the evolution of a tympanic ear contributed to mitigating the problem of an impedance mismatch between the air and the fluid embedding sound-detecting hair cells in the inner ear.1,2,3 Pioneering studies advocated that similarities in the tympanic ear of tetrapods could only result from a single origin of this structure in the group,4,5 an idea later challenged by paleontological and developmental data.4,6,7,8 Current evidence suggests that this sensory structure evolved independently in amphibians, mammals, and reptiles,1,6 but it remains uncertain how many times tympanic hearing originated in crown reptiles.9,10 We combine developmental information with paleontological data to evaluate the evolution of the tympanic ear in reptiles from two complementary perspectives. Phylogenetically informed ancestral reconstruction analyses of a taxonomically broad sample of early reptiles point to the presence of a tympanic membrane as the ancestral condition of the crown group. Consistently, comparative analyses using embryos of lizards and crocodylians reveal similarities, including the formation of the tympanic membrane within the second pharyngeal arch, which has been previously reported for birds. Therefore, both our developmental and paleontological data suggest a single origin for the tympanic middle ear in the group, challenging the current paradigm of multiple acquisitions of tympanic hearing in living reptiles.

Shifts in Chromosome Evolution Rates Shape the Karyotype Patterns of Leafcutting Ants

Trait evolution has become a central focus in evolutionary biology, with phylogenetic comparative methods offering a framework to study how and why traits vary among species. Identifying variations in trait evolution rates within phylogenies is important for uncovering the mechanisms behind these differences. Karyotype variation, which is substantial across eukaryotic organisms, plays an essential role in species diversification. This study investigates karyotype variation within the leafcutting ant clade, focusing on chromosome number and morphology. We aim to determine whether karyotypic traits are phylogenetically dependent and how different evolutionary models explain karyotype diversity. Previous models have been insufficient in explaining these variations. To address these gaps, we employ modern phylogenetic methods to assess the impact of chromosomal fissions and fusions on karyotype evolution. By evaluating various evolutionary models-particularly the Brownian motion model, which suggests neutral chromosomal changes-we pursue for the further understanding the mode and tempo of karyotype evolution in ants. Our research examines how shifts in chromosomal change rates contribute to divergence among leafcutting ant species and assesses the role of chromosomal changes in the clade's evolutionary trajectory. Comparative analysis of leafcutting ant ideograms suggests that shared karyotype traits are strongly related to species relationships. This implies that karyotype diversification in leafcutting ants follows a phylogenetic trajectory at varying rates, with differences in karyotype traits reflecting the evolutionary distance between lineages. Particularly, the increase in the chromosome number of Acromyrmex is likely due to fission rearrangements rather than demi or polyploidization. We discuss and provide insights into the mechanisms driving karyotype variation and its implications for leafcutting ant diversification.

Phylogenetic and taxonomic revisions of Jurassic sea stars support a delayed evolutionary origin of the Asteriidae

Background

The superorder Forcipulatacea is a major clade of sea stars with approximately 400 extant species across three orders (Forcipulatida, Brisingida, Zorocallida). Over the past century, the systematics of Forcipulatacea have undergone multiple revisions by various authors, with some considering numerous families such as Asteriidae, Zoroasteridae, Pedicellasteridae, Stichasteridae, Heliasteridae, Labidiasteridae, and Neomorphasteridae, while others recognized only two families (i.e., Asteriidae and Zoroasteridae). Recent molecular analyses have shown the artificial nature of some of these groupings. Notably, four well-supported clades (Zorocallida, Brisingida, Stichasteridae, and Asteriidae) emerged from a synthesis of morphological and molecular evidence. The majority of extinct forcipulatacean species have been placed in modern families. However, many of these fossil species are in need of revision, especially those species placed within the Asteriidae, the largest of all forcipulatacean families.

Methods

In light of recent advancements in forcipulatacean systematics, we comprehensively reassess six well-preserved Jurassic forcipulatacean taxa, including the earliest crown-group members from the Hettangian (∼201.4 Ma), and also describe two new Jurassic genera, Forbesasterias gen. nov. and Marbleaster gen. nov. We assembled the largest and most comprehensive phylogenetic matrix for this group, sampling 42 fossil and extant forcipulatacean species for 120 morphological characters. To infer phylogenetic relationships and construct an evolutionary timeline for the diversification of major clades, we conducted a Bayesian tip-dating analysis incorporating the fossilized birth-death process. A total of 13 fossil species were sampled in our analysis, including six taxonomically revaluated herein, two recently reappraised species from the Jurassic, and five additional species from the Cretaceous and Miocene.

Results

Contrary to prior assumptions, our results indicate that none of the Jurassic taxa investigated belong to Asteriidae or any other modern families, and instead represent stem-forcipulatids. Furthermore, our phylogenetic results suggest that Asteriidae likely originated during the late Cretaceous. Our findings highlight a greater early diversity within the Forcipulatacea than previously presumed, challenging existing perceptions of the evolutionary history of this significant clade of marine invertebrates.

Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation

Models have always been central to inferring molecular evolution and to reconstructing phylogenetic trees. Their use typically involves the development of a mechanistic framework reflecting our understanding of the underlying biological processes, such as nucleotide substitutions, and the estimation of model parameters by maximum likelihood or Bayesian inference. However, deriving and optimizing the likelihood of the data is not always possible under complex evolutionary scenarios or even tractable for large datasets, often leading to unrealistic simplifying assumptions in the fitted models. To overcome this issue, we coupled stochastic simulations of genome evolution with a new supervised deep-learning model to infer key parameters of molecular evolution. Our model is designed to directly analyze multiple sequence alignments and estimate per-site evolutionary rates and divergence without requiring a known phylogenetic tree. The accuracy of our predictions matched that of likelihood-based phylogenetic inference when rate heterogeneity followed a simple gamma distribution, but it strongly exceeded it under more complex patterns of rate variation, such as codon models. Our approach is highly scalable and can be efficiently applied to genomic data, as we showed on a dataset of 26 million nucleotides from the clownfish clade. Our simulations also showed that the integration of per-site rates obtained by deep learning within a Bayesian framework led to significantly more accurate phylogenetic inference, particularly with respect to the estimated branch lengths. We thus propose that future advancements in phylogenetic analysis will benefit from a semi-supervised learning approach that combines deep-learning estimation of substitution rates, which allows for more flexible models of rate variation, and probabilistic inference of the phylogenetic tree, which guarantees interpretability and a rigorous assessment of statistical support.

The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics

Phylogenetic trees establish a historical context for the study of organismal form and function. Most phylogenetic trees are estimated using a model of evolution. For molecular data, modeling evolution is often based on biochemical observations about changes between character states. For example, there are 4 nucleotides, and we can make assumptions about the probability of transitions between them. By contrast, for morphological characters, we may not know a priori how many characters states there are per character, as both extant sampling and the fossil record may be highly incomplete, which leads to an observer bias. For a given character, the state space may be larger than what has been observed in the sample of taxa collected by the researcher. In this case, how many evolutionary rates are needed to even describe transitions between morphological character states may not be clear, potentially leading to model misspecification. To explore the impact of this model misspecification, we simulated character data with varying numbers of character states per character. We then used the data to estimate phylogenetic trees using models of evolution with the correct number of character states and an incorrect number of character states. The results of this study indicate that this observer bias may lead to phylogenetic error, particularly in the branch lengths of trees. If the state space is wrongly assumed to be too large, then we underestimate the branch lengths, and the opposite occurs when the state space is wrongly assumed to be too small.

Genetic diversity of the largest African mole-rat genus, Bathyergus. One, two or four species?

Recent advances in sequencing technology and phylogenetic methods allow us to solve puzzling taxonomic questions using detailed analyses of genetic diversity of populations and gene flow between them. The genus of solitary-living dune mole-rat, Bathyergus, is quite unique among six genera of African mole-rats. The animals are by far the largest and the only scratch digging mole-rat genus possessing a skull less adapted to digging, grooved upper incisors, and more surface locomotor activity. Most authors recognize two species of dune mole-rats, B. suillus and B. janetta, but according to others, the genus is monotypic. In addition, recent molecular studies have revealed cryptic genetic diversity and suggested the existence of up to four species. In our study, we used mitochondrial and genome-wide nuclear data collected throughout the distribution of the genus to investigate the number of species. In agreement with previous studies, we found Bathyergus to be differentiated into several distinct lineages, but we also found evidence for a degree of gene flow between some of them. Furthermore, we confirmed that B. janetta is nested within B. suillus, making the latter paraphyletic and we documented an instance of local mitochondrial introgression between these two nominal species. Phylogeographic structure of the genus was found to be very shallow. Although traditionally dated to the Miocene, we found the first split within the genus to be much younger estimated to 0.82 Ma before present. Genealogical distinctiveness of some lineages was very low, and the coancestry matrix showed extensive sharing of closely related haplotypes throughout the genus. Accordingly, Infomap clustering on the matrix showed all populations to form a single cluster. Overall, our study tends to support the existence of only one species of Bathyergus namely, B. suillus. Environmental niche modelling confirmed its dependence on sandy soils and the preference for soils with relatively high carbon content. Bayesian skyline plots indicate recent population decline in the janetta lineage, probably related to global environmental change.

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.

Comparative Population Genomics of Arctic Sled Dogs Reveals a Deep and Complex History

Recent evidence demonstrates genomic and morphological continuity in the Arctic ancestral lineage of dogs. Here, we use the Siberian Husky to investigate the genomic legacy of the northeast Eurasian Arctic lineage and model the deep population history using genome-wide single nucleotide polymorphisms. Utilizing ancient dog-calibrated molecular clocks, we found that at least two distinct lineages of Arctic dogs existed in ancient Eurasia at the end of the Pleistocene. This pushes back the origin of sled dogs in the northeast Siberian Arctic with humans likely intentionally selecting dogs to perform different functions and keeping breeding populations that overlap in time and space relatively reproductively isolated. In modern Siberian Huskies, we found significant population structure based on how they are used by humans, recent European breed introgression in about half of the dogs that participate in races, moderate levels of inbreeding, and fewer potentially harmful variants in populations under strong selection for form and function (show, sled show, and racing populations of Siberian Huskies). As the struggle to preserve unique evolutionary lineages while maintaining genetic health intensifies across pedigreed dogs, understanding the genomic history to guide policies and best practices for breed management is crucial to sustain these ancient lineages and their unique evolutionary identity.

Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock

Relaxing the molecular clock using models of how substitution rates change across lineages has become essential for addressing evolutionary problems. The diversity of rate evolution models and their implementations are substantial, and studies have demonstrated their impact on divergence time estimates can be as significant as that of calibration information. In this review, we trace the development of rate evolution models from the proposal of the molecular clock concept to the development of sophisticated Bayesian and non-Bayesian methods that handle rate variation in phylogenies. We discuss the various approaches to modeling rate evolution, provide a comprehensive list of available software, and examine the challenges and advancements of the prevalent Bayesian framework, contrasting them to faster non-Bayesian methods. Lastly, we offer insights into potential advancements in the field in the era of big data.

Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)

Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of evolution. Values for all model parameters need to be evaluated as well. Modern statistical methods involve not just the estimation of a tree, but also solutions to more complex models involving fossil record information and other data sources. Markov chain Monte Carlo (MCMC) is a leading method for approximating the posterior distribution of parameters in a mathematical model. It is deployed in all Bayesian phylogenetic tree estimation software. While many researchers use MCMC in phylogenetic analyses, interpreting results and diagnosing problems with MCMC remain vexing issues to many biologists. In this manuscript, we will offer an overview of how MCMC is used in Bayesian phylogenetic inference, with a particular emphasis on complex hierarchical models, such as the fossilized birth-death (FBD) model. We will discuss strategies to diagnose common MCMC problems and troubleshoot difficult analyses, in particular convergence issues. We will show how the study design, the choice of models and priors, but also technical features of the inference tools themselves can all be adjusted to obtain the best results. Finally, we will also discuss the unique challenges created by the incorporation of fossil information in phylogenetic inference, and present tips to address them.

Bayesian tip-dated phylogeny and biogeography of Cissampelideae (Menispermaceae): Mitigating the effects of homoplastic morphological characters

The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.

A macroevolutionary analysis of European Late Upper Palaeolithic stone tool shape using a Bayesian phylodynamic framework

Phylogenetic models are commonly used in palaeobiology to study the patterns and processes of organismal evolution. In the human sciences, phylogenetic methods have been deployed for reconstructing ancestor-descendant relationships using linguistic and material culture data. Within evolutionary archaeology specifically, phylogenetic analyses based on maximum parsimony and discrete traits dominate, which sets limitations for the downstream role cultural phylogenies, once derived, can play in more elaborate analytical pipelines. Recent methodological advances in Bayesian phylogenetics, however, now allow us to infer evolutionary dynamics using continuous characters. Capitalizing on these developments, we here present an exploratory analysis of cultural macroevolution of projectile point shape evolution in the European Final Palaeolithic and earliest Mesolithic (approx. 15 000-11 000 BP) using a Bayesian phylodynamic approach and the fossilized birth-death process model. This model-based approach leaps far beyond the application of parsimony, in that it not only produces a tree, but also divergence times, and diversification rates while incorporating uncertainties. This allows us to compare rates to the pronounced climatic changes that occurred during our time frame. While common in cultural evolutionary analyses of language, the extension of Bayesian phylodynamic models to archaeology arguably represents a major methodological breakthrough.

Tropical Origin, Global Diversification, and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny

The processes responsible for the formation of Earth's most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea) and investigate the role of time, macroevolutionary processes, and biome-shift dynamics in shaping the LDG in this ancient insect superfamily. We used process-based biogeographic models to jointly infer ancestral ranges and speciation times and to characterize within-biome dispersal and biome-shift dynamics across the cosmopolitan distribution of Coenagrionoidea. We also investigated temporal and biome-dependent variation in diversification rates. Our results uncover a tropical origin of pond damselflies and featherlegs ~105 Ma, while highlighting the uncertainty of ancestral ranges within the tropics in deep time. Even though diversification rates have declined since the origin of this clade, global climate change and biome-shifts have slowly increased diversity in warm- and cold-temperate areas, where lineage turnover rates have been relatively higher. This study underscores the importance of biogeographic origin and time to diversify as important drivers of the LDG in pond damselflies and their relatives, while diversification dynamics have instead resulted in the formation of ephemeral species in temperate regions. Biome-shifts, although limited by tropical niche conservatism, have been the main factor reducing the steepness of the LDG in the last 30 Myr. With ongoing climate change and increasing northward range expansions of many damselfly taxa, the LDG may become less pronounced. Our results support recent calls to unify biogeographic and macroevolutionary approaches to improve our understanding of how latitudinal diversity gradients are formed and why they vary across time and among taxa.

Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least 7 and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. [Brachyura; convergent evolution; crustaceans; divergence times; fossil calibration; molecular phylogeny; terrestrialization; threshold model.].

New insights into the early morphological evolution of sea turtles by re-investigation of Nichollsemys baieri, a three-dimensionally preserved fossil stem chelonioid from the Campanian of Alberta, Canada

The early evolution of Pan-Chelonioidea (sea turtles) is poorly understood. This is in part due to the rarity of undeformed skulls of definitive early stem chelonioids. In this work, we redescribe the holotype of Nichollsemys baieri using µCT scans and segmentations of the skull. This fossil is the best 3D preserved skull of any Campanian sea turtle, and includes partial "soft tissue" preservation. Nichollsemys is morphologically similar but clearly distinct from Toxochelys spp., and both show a mosaic of plesiomorphic and derived chelonioid features. The internal cranial anatomy documents the presence of derived characters in Nichollsemys baieri that are absent in Toxochelys spp., such as the loss of the epipterygoids and the rod-like shape of the rostrum basisphenoidale. Among the numerous plesiomorphic characters is the presence of a splenial bone, which was unnoticed before. An updated phylogenetic analysis retrieves Nichollsemys baieri as a non-protostegid early stem chelonioid in a slightly more crownward position than Toxochelys latiremis. Our phylogeny includes macrobaenids and protostegids as pan-chelonioids, and we find unorthodox results for dermochelyids. Thus, although Nichollsemys baieri provides important new insights into the early morphological evolution of sea turtles, much work remains to be done. As a completely 3D preserved specimen, we included Nichollsemys baieri into a recent landmark-based skull shape dataset of turtles. Morphospace analysis reveals an intermediate position between cryptodires and crown chelonioids. Based on these data, we also predict that Nichollsemys baieri was still capable of neck retraction, constraining the loss of this trait to more crownward pan-chelonioids.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-024-00323-8.

Convergent evolution of giant size in eurypterids

Eurypterids-Palaeozoic marine and freshwater arthropods commonly known as sea scorpions-repeatedly evolved to remarkable sizes (over 0.5 m in length) and colonized continental aquatic habitats multiple times. We compiled data on the majority of eurypterid species and explored several previously proposed explanations for the evolution of giant size in the group, including the potential role of habitat, sea surface temperature and dissolved sea surface oxygen levels, using a phylogenetic comparative approach with a new tip-dated tree. There is no compelling evidence that the evolution of giant size was driven by temperature or oxygen levels, nor that it was coupled with the invasion of continental aquatic environments, latitude or local faunal diversity. Eurypterid body size evolution is best characterized by rapid bursts of change that occurred independently of habitat or environmental conditions. Intrinsic factors played a major role in determining the convergent origin of gigantism in eurypterids.

The trunk replaces the longer mandible as the main feeding organ in elephant evolution

The long-trunked elephantids underwent a significant evolutionary stage characterized by an exceptionally elongated mandible. The initial elongation and subsequent regression of the long mandible, along with its co-evolution with the trunk, present an intriguing issue that remains incompletely understood. Through comparative functional and eco-morphological investigations, as well as feeding preference analysis, we reconstructed the feeding behavior of major groups of longirostrine elephantiforms. In the Platybelodon clade, the rapid evolutionary changes observed in the narial region, strongly correlated with mandible and tusk characteristics, suggest a crucial evolutionary transition where feeding function shifted from the mandible to the trunk, allowing proboscideans to expand their niches to more open regions. This functional shift further resulted in elephantids relying solely on their trunks for feeding. Our research provides insights into how unique environmental pressures shape the extreme evolution of organs, particularly in large mammals that developed various peculiar adaptations during the late Cenozoic global cooling trends.

Testing extinction events and temporal shifts in diversification and fossilization rates through the skyline Fossilized Birth-Death (FBD) model: The example of some mid-Permian synapsid extinctions

In the last decade, the Fossilized Birth-Death (FBD) process has yielded interesting clues about the evolution of biodiversity through time. To facilitate such studies, we extend our method to compute the probability density of phylogenetic trees of extant and extinct taxa in which the only temporal information is provided by the fossil ages (i.e. without the divergence times) in order to deal with the piecewise constant FBD process, known as the "skyline FBD", which allows rates to change between pre-defined time intervals, as well as modelling extinction events at the bounds of these intervals. We develop approaches based on this method to assess hypotheses about the diversification process and to answer questions such as "Does a mass extinction occur at this time?" or "Is there a change in the fossilization rate between two given periods?". Our software can also yield Bayesian and maximum-likelihood estimates of the parameters of the skyline FBD model under various constraints. These approaches are applied to a simulated dataset in order to test their ability to answer the questions above. Finally, we study an updated dataset of Permo-Carboniferous synapsids to get additional insights into the dynamics of biodiversity change in three clades (Ophiacodontidae, Edaphosauridae and Sphenacodontidae) in the Pennsylvanian (Late Carboniferous) and Cisuralian (Early Permian), and to assess support for end-Sakmarian (or Artinskian) and end-Cisuralian mass extinction events discussed in previous studies.

A new abelisaurid dinosaur from the end Cretaceous of Patagonia and evolutionary rates among the Ceratosauria

Gondwanan dinosaur faunae during the 20 Myr preceding the Cretaceous-Palaeogene (K/Pg) extinction included several lineages that were absent or poorly represented in Laurasian landmasses. Among these, the South American fossil record contains diverse abelisaurids, arguably the most successful groups of carnivorous dinosaurs from Gondwana in the Cretaceous, reaching their highest diversity towards the end of this period. Here we describe Koleken inakayali gen. et sp. n., a new abelisaurid from the La Colonia Formation (Maastrichtian, Upper Cretaceous) of Patagonia. Koleken inakayali is known from several skull bones, an almost complete dorsal series, complete sacrum, several caudal vertebrae, pelvic girdle and almost complete hind limbs. The new abelisaurid shows a unique set of features in the skull and several anatomical differences from Carnotaurus sastrei (the only other abelisaurid known from the La Colonia Formation). Koleken inakayali is retrieved as a brachyrostran abelisaurid, clustered with other South American abelisaurids from the latest Cretaceous (Campanian-Maastrichtian), such as Aucasaurus, Niebla and Carnotaurus. Leveraging our phylogeny estimates, we explore rates of morphological evolution across ceratosaurian lineages, finding them to be particularly high for elaphrosaurine noasaurids and around the base of Abelisauridae, before the Early Cretaceous radiation of the latter clade. The Noasauridae and their sister clade show contrasting patterns of morphological evolution, with noasaurids undergoing an early phase of accelerated evolution of the axial and hind limb skeleton in the Jurassic, and the abelisaurids exhibiting sustained high rates of cranial evolution during the Early Cretaceous. These results provide much needed context for the evolutionary dynamics of ceratosaurian theropods, contributing to broader understanding of macroevolutionary patterns across dinosaurs.

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.

Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses

Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.

Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters

Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.

Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the 'woody clade' in Saxifragales

BACKGROUND

The "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence.

RESULTS

Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected.

CONCLUSIONS

Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.

Jurassic shuotheriids show earliest dental diversification of mammaliaforms

Shuotheriids are Jurassic mammaliaforms that possess pseudotribosphenic teeth in which a pseudotalonid is anterior to the trigonid in the lower molar, contrasting with the tribosphenic pattern of therian mammals (placentals, marsupials and kin) in which the talonid is posterior to the trigonid1-4. The origin of the pseudotribosphenic teeth remains unclear, obscuring our perception of shuotheriid affinities and the early evolution of mammaliaforms1,5-9. Here we report a new Jurassic shuotheriid represented by two skeletal specimens. Their complete pseudotribosphenic dentitions allow reidentification of dental structures using serial homology and the tooth occlusal relationship. Contrary to the conventional view1,2,6,10,11, our findings show that dental structures of shuotheriids can be homologized to those of docodontans and partly support homologous statements for some dental structures between docodontans and other mammaliaforms6,12. The phylogenetic analysis based on new evidence removes shuotheriids from the tribosphenic ausktribosphenids (including monotremes) and clusters them with docodontans to form a new clade, Docodontiformes, that is characterized by pseudotribosphenic features. In the phylogeny, docodontiforms and 'holotherians' (Kuehneotherium, monotremes and therians)13 evolve independently from a Morganucodon-like ancestor with triconodont molars by labio-lingual widening their posterior teeth for more efficient food processing. The pseudotribosphenic pattern passed a cusp semitriangulation stage9, whereas the tribosphenic pattern and its precursor went through a stage of cusp triangulation. The two different processes resulted in complex tooth structures and occlusal patterns that elucidate the earliest diversification of mammaliaforms.

Comparative Genomics Reveal Phylogenetic Relationship and Chromosomal Evolutionary Events of Eight Cervidae Species

Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the single-copy orthologous genes sequences, providing new insights into the phylogeny of Cervidae, particularly the phylogenetic relationship among sika deer, red deer, wapiti and Tarim red deer. Gene family analysis revealed contractions in the olfactory receptor gene family and expansions in the histone gene family across eight Cervidae species. Furthermore, synteny analysis was used to explore the chromosomal evolutionary events of Cervidae species, revealing six chromosomal fissions during the evolutionary process from Bovidae to Cervidae. Notably, specific chromosomal fusion events were found in four species of Cervus, and a unique chromosomal fusion event was identified in Muntiacus reevesi. Our study further completed the phylogenetic relationship within the Cervidae and demonstrated the feasibility of inferring species phylogeny at the whole-genome level. Additionally, our findings on gene family evolution and the chromosomal evolutionary events in eight Cervidae species lay a foundation for comprehensive research of the evolution of Cervidae.

Disparity of cycad leaves dispels the living fossil metaphor

The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists. Here, we use a recent phylogenetic framework and an improved character matrix to reconstruct the Disparity Through Time for cycad leaves using a Principal Coordinate Analysis and employing Pre-Ordination Ancestral State Reconstruction to test the impact of sampling on the results. Our analysis shows that the cycad leaf morsphospace expanded up to the present, with numerous shifts in its general positioning, independently of sampling biases. Moreover, they also show that Zamiaceae expanded rapidly in the Early Cretaceous and continued to expand up to the present, while now-extinct clades experienced a slow contraction from their peak in the Triassic. We also show that rates of evolution were constantly high up to the Early Cretaceous, and then experienced a slight decrease in the Paleogene, followed by a Neogene acceleration. These results show a much more dynamic history for cycads, and suggest that the 'living fossil' metaphor is actually a hindrance to our understanding of their macroevolution.

Tip dating and Bayes factors provide insight into the divergences of crown bird clades across the end-Cretaceous mass extinction

The origin of crown birds (Neornithes) remains contentious owing to conflicting divergence time hypotheses obtained from alternative sources of data. The fossil record suggests limited diversification of Neornithes in the Late Mesozoic and a substantial radiation in the aftermath of the Cretaceous-Palaeogene (K-Pg) mass extinction, approximately 66 Ma. Molecular clock studies, however, have yielded estimates for neornithine origins ranging from the Early Cretaceous (130 Ma) to less than 10 Myr before the K-Pg. We use Bayes factors to compare the fit of node ages from different molecular clock studies to an independent morphological dataset. Our results allow us to reject scenarios of crown bird origins deep in the Early Cretaceous, as well as an origin of crown birds within the last 10 Myr of the Cretaceous. The scenario best supported by our analyses is one where Neornithes originated between the Early and Late Cretaceous (ca 100 Ma), while numerous divergences within major neoavian clades either span or postdate the K-Pg. This study affirms the importance of the K-Pg on the diversification of modern birds, and the potential of combined-evidence tip-dating analyses to illuminate recalcitrant 'rocks versus clocks' debates.

Locomotion and the early Mesozoic success of Archosauromorpha

The Triassic was a time of ecological upheaval as life recovered from the Permian-Triassic mass extinction. Archosauromorphs were a key component of the recovery, diversifying substantially during the Triassic and encompassing the origins of dinosaurs, pterosaurs and crocodylomorphs. Here, we explore the evolution of locomotion in Archosauromorpha to test whether dinosaurs show any distinctive locomotory features that might explain their success. We implement geometric morphometrics on limb bone shapes and use limb ratios to calculate bipedality and cursoriality metrics. We find that the Avemetatarsalia (dinosaurs, pterosaurs and relatives) exhibit more variable limb form and limb ratios than any other group, indicating a wider range of locomotory modes. The earliest avemetatarsalians were bipedal and cursorial, and their range of form increased through the Triassic with notable diversification shifts following extinction events. This is especially true of dinosaurs, even though these changes cannot be discriminated from a stochastic process. By contrast, the Pseudosuchia (crocodilians and relatives) were more restricted in limb form and locomotor mode with disparity decreasing through time, suggesting more limited locomotor adaptation and vulnerability to extinction. Perhaps the greater locomotor plasticity of dinosaurs gave them a competitive advantage in the changing climates of the Late Triassic.

Embracing uncertainty: The way forward in plant fossil phylogenetics

Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the fossil record in phylogenetic trees offers to our understanding of macroevolutionary processes and dynamics and the possibility that the inclusion of fossil taxa could lead to more accurate phylogenetic hypotheses. The plant fossil record presents some challenges to its integration in a phylogenetic framework. Phylogenies including plant fossils often retrieve uncertain relationships with low support, or lack of resolution. This low support is due to the pervasiveness of morphological convergence among plant organs and the fragmentary nature of many plant fossils, and it is often perceived as a fundamental weakness reducing the utility of plant fossils in phylogenetics. Here I discuss the importance of uncertainty in morphological phylogenetics and how we can identify important information from different patterns and types of uncertainty. I also review a set of methodologies that can allow us to understand the causes underpinning uncertainty and how these practices can help us to further our knowledge of plant fossils. I also propose that a new visual language, including the use of networks instead of trees, represents an improvement on the old visualization based on consensus trees and more adequately serves phylogeneticists working with plant fossils. This set of methods and visualization tools represents an important way forward in a fundamental field for our understanding of the evolutionary history of plants.

A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade

Background

Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group.

Methods

Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data.

Results

Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.

Diversification dynamics of a common deep-sea octocoral family linked to the Paleocene-Eocene thermal maximum

The deep-sea has experienced dramatic changes in physical and chemical variables in the geological past. However, little is known about how deep-sea species richness responded to such changes over time and space. Here, we studied the diversification dynamics of one of the most diverse octocorallian families inhabiting deep sea benthonic environments worldwide and sustaining highly diverse ecosystems, Primnoidae. A newly dated species-level phylogeny was constructed to infer their ancestral geographic locations and dispersal rates initially. Then, we tested whether their global and regional (the Southern Ocean) diversification dynamics were mediated by dispersal rate and abiotic factors as changes in ocean geochemistry. Finally, we tested whether primnoids showed changes in speciation and extinction at discrete time points. Our results suggested primnoids likely originated in the southwestern Pacific Ocean during the Lower Cretaceous ∼112 Ma, with further dispersal after the physical separation of continental landmasses along the late Mesozoic and Cenozoic. Only the speciation rate of the Southern Ocean primnoids showed a significant correlation to ocean chemistry. Moreover, the Paleocene-Eocene thermal maximum marked a significant increase in the diversification of primnoids at global and regional scales. Our results provide new perspectives on the macroevolutionary and biogeographic patterns of an ecologically important benthic organism typically found in deep-sea environments.

Deep learning approaches to the phylogenetic placement of extinct pollen morphotypes

The phylogenetic interpretation of pollen morphology is limited by our inability to recognize the evolutionary history embedded in pollen features. Deep learning offers tools for connecting morphology to phylogeny. Using neural networks, we developed an explicitly phylogenetic toolkit for analyzing the overall shape, internal structure, and texture of a pollen grain. Our analysis pipeline determines whether testing specimens are from known species based on uncertainty estimates. Features from specimens with uncertain taxonomy are passed to a multilayer perceptron network trained to transform these features into predicted phylogenetic distances from known taxa. We used these predicted distances to place specimens in a phylogeny using Bayesian inference. We trained and evaluated our models using optical superresolution micrographs of 30 extant Podocarpus species. We then used trained models to place nine fossil Podocarpidites specimens within the phylogeny. In doing so, we demonstrate that the phylogenetic history encoded in pollen morphology can be recognized by neural networks and that deep-learned features can be used in phylogenetic placement. Our approach makes extinction and speciation events that would otherwise be masked by the limited taxonomic resolution of the fossil pollen record visible to palynological analysis.

A Palaeogene stem crotaphytid (Aciprion formosum) and the phylogenetic affinities of early fossil pleurodontan iguanians

Pleurodonta is an ancient, diverse clade of iguanian lizard distributed primarily in the Western Hemisphere. Although the clade is a frequent subject of systematic research, phylogenetic resolution among the major pleurodontan clades is elusive. That uncertainty has complicated the interpretations of many fossil pleurodontans. I describe a fossil skull of a pleurodontan lizard from the Palaeogene of Wyoming that was previously allocated to the puzzling taxon Aciprion formosum, and provide an updated morphological matrix for iguanian lizards. Phylogenetic analyses using Bayesian inference demonstrate that the fossil skull is the oldest and first definitive stem member of Crotaphytidae (collared and leopard lizards), establishing the presence of that clade in North America during the Palaeogene. I also discuss new or revised hypotheses for the relationships of several early pleurodontans. In particular, I examine potential evidence for crown-Pleurodonta in the Cretaceous of Mongolia (Polrussia), stem Pleurodonta in the Cretaceous of North America (Magnuviator) and a stem anole in the Eocene of North America (Afairiguana). I suggest that the placement of the fossil crotaphytid is stable to the uncertain phylogeny of Pleurodonta, but recognize the dynamic nature of fossil diagnosis and the potential for updated systematic hypotheses for the other fossils analysed here.

Burma Terrane Amber Fauna Shows Connections to Gondwana and Transported Gondwanan Lineages to the Northern Hemisphere (Araneae: Palpimanoidea)

Burmese amber is a significant source of fossils that documents the mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma Terrane, which broke away from Gondwana and later collided with Asia, although the timing is disputed. Palpimanoidea is a dispersal-limited group that was a dominant element of the Mesozoic spider fauna, and has an extensive fossil record, particularly from Burmese amber. Using morphological and molecular data, evolutionary relationships of living and fossil Palpimanoidea are examined. Divergence dating with fossils as terminal tips shows timing of diversification is contemporaneous with continental breakup.Ancestral range estimations show widespread ancestral ranges that divide into lineages that inherit different Pangean fragments, consistent with vicariance. Our results suggest that the Burmese amber fauna has ties to Gondwana due to a historical connection in the Early Cretaceous, and that the Burma Terrane facilitated biotic exchange by transporting lineages from Gondwana into the Holarctic in the Cretaceous.

PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction - which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models - and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.

A Silurian pseudocolonial pterobranch

Pterobranchs, a major group of the phylum Hemichordata, first appear in the fossil record during the Cambrian,1 and there are more than 600 fossil genera dominated by the mainly planktic graptolites of the Paleozoic, which are widely used as zone fossils for correlating sedimentary rock sequences.2 Pterobranchs are rare today; they are sessile marine forms represented by Rhabdopleura, which is considered the only living graptolite, and Cephalodiscus. Unlike their sister taxon, the colonial graptolites, cephalodiscids are pseudocolonial.3,4 Here, we describe a problematic fossil from the Silurian (Pridoli) Bertie Group of Ontario (420 mya), a sequence of near-shore sediments well known for its remarkably preserved diversity of eurypterids (sea scorpions).5 The fossil, Rotaciurca superbus, a new genus and species, was familiarly known as Ezekiel's Wheel,5 with reference to the unusual circular arrangement of the tubes that compose it. The structure and arrangement of the tubes identify Rotaciurca as a pterobranch, and phylogenetic analysis groups it with the cephalodiscids. We place it in a new family Rotaciurcidae to distinguish it from Cephalodiscidae. A large structure associated with the tubes is interpreted as a float, which would distinguish Rotaciurca as the only known planktic cephalodiscid-thus cephalodiscids, like the graptolites, invaded the water column. This mode of life reflects the rarity of pseudocolonial macroinvertebrates in planktic ocean communities, a role occupied by the tunicates (Chordata) known as salps today. Our estimates of divergence times, the first using relaxed total-evidence clocks, date the origins of both hemichordates and pterobranchs to the earliest Cambrian (Fortunian).

Dating the evolution of the complex thalloid liverworts (Marchantiopsida): total-evidence dating analysis supports a Late Silurian-Early Devonian origin and post-Mesozoic morphological stasis

Divergence times based on molecular clock analyses often differ from those derived from total-evidence dating (TED) approaches. For bryophytes, fossils have been excluded from previous assessments of divergence times, and thus, their utility in dating analyses remains unexplored. Here, we conduct the first TED analyses of the complex thalloid liverworts (Marchantiopsida) that include fossils and evaluate macroevolutionary trends in morphological 'diversity' (disparity) and rates. Phylogenetic analyses were performed on a combined dataset of 130 discrete characters and 11 molecular markers (sampled from nuclear, plastid and mitochondrial genomes). Taxon sampling spanned 56 extant species - representing all the orders within Marchantiophyta and extant genera within Marchantiales - and eight fossil taxa. Total-evidence dating analyses support the radiation of Marchantiopsida during Late Silurian-Early Devonian (or Middle Ordovician when the outgroup is excluded) and that of Ricciaceae in the Middle Jurassic. Morphological change rate was high early in the history of the group, but it barely increased after Late Cretaceous. Disparity-through-time analyses support a fast increase in diversity until the Middle Triassic (c. 250 Ma), after which phenotypic evolution slows down considerably. Incorporating fossils in analyses challenges previous assumptions on the affinities of extinct taxa and indicates that complex thalloid liverworts radiated c. 125 Ma earlier than previously inferred.

The time and place of origin of South Caucasian languages: insights into past human societies, ecosystems and human population genetics

This study re-examines the linguistic phylogeny of the South Caucasian linguistic family (aka the Kartvelian linguistic family) and attempts to identify its Urheimat. We apply Bayesian phylogenetics to infer a dated phylogeny of the South Caucasian languages. We infer the Urheimat and the reasons for the split of the Kartvelian languages by taking into consideration (1) the past distribution ranges of wildlife elements whose names can be traced back to proto-Kartvelian roots, (2) the distribution ranges of past cultures and (3) the genetic variations of past and extant human populations. Our best-fit Bayesian phylogenetic model is in agreement with the widely accepted topology suggested by previous studies. However, in contrast to these studies, our model suggests earlier mean split dates, according to which the divergence between Svan and Karto-Zan occurred in the early Copper Age, while Georgian and Zan diverged in the early Iron Age. The split of Zan into Megrelian and Laz is widely attributed to the spread of Georgian and/or Georgian speakers in the seventh-eighth centuries CE. Our analyses place the Kartvelian Urheimat in an area that largely intersects the Colchis glacial refugium in the South Caucasus. The divergence of Kartvelian languages is strongly associated with differences in the rate of technological expansions in relation to landscape heterogeneity, as well as the emergence of state-run communities. Neolithic societies could not colonize dense forests, whereas Copper Age societies made limited progress in this regard, but not to the same degree of success achieved by Bronze and Iron Age societies. The paper also discusses the importance of glacial refugia in laying the foundation for linguistic families and where Indo-European languages might have originated.

Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity

The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.