Closing the gap between rocks and clocks using total-evidence dating

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.

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.

Two Notorious Nodes: A Critical Examination of Relaxed Molecular Clock Age Estimates of the Bilaterian Animals and Placental Mammals

The popularity of relaxed clock Bayesian inference of clade origin timings has generated several recent publications with focal results considerably older than the fossils of the clades in question. Here, we critically examine two such clades: the animals (with a focus on the bilaterians) and the mammals (with a focus on the placentals). Each example displays a set of characteristic pathologies which, although much commented on, are rarely corrected for. We conclude that in neither case does the molecular clock analysis provide any evidence for an origin of the clade deeper than what is suggested by the fossil record. In addition, both these clades have other features (including, in the case of the placental mammals, proximity to a large mass extinction) that allow us to generate precise expectations of the timings of their origins. Thus, in these instances, the fossil record can provide a powerful test of molecular clock methodology, and why it goes astray, and we have every reason to think these problems are general. [Cambrian explosion; mammalian evolution; molecular clocks.].

Skyline Fossilized Birth-Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating

Several total-evidence dating studies under the fossilized birth-death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed "deep root attraction (DRA)." For two specific data sets, involving divergence time estimation for the early radiations of ants, bees, and wasps (Hymenoptera) and of placental mammals (Eutheria), it has been shown that the DRA effect can be greatly reduced by accommodating the fact that extant species in these trees have been sampled to maximize diversity, so-called diversified sampling. Unfortunately, current methods to accommodate diversified sampling only consider the extreme case where it is possible to identify a cut-off time such that all splits occurring before this time are represented in the sampled tree but none of the younger splits. In reality, the sampling bias is rarely this extreme and may be difficult to model properly. Similar modeling challenges apply to the sampling of the fossil record. This raises the question of whether it is possible to find dating methods that are more robust to sampling biases. Here, we show that the skyline FBD (SFBD) process, where the diversification and fossil-sampling rates can vary over time in a piecewise fashion, provides age estimates that are more robust to inadequacies in the modeling of the sampling process and less sensitive to DRA effects. In the SFBD model we consider, rates in different time intervals are either considered to be independent and identically distributed or assumed to be autocorrelated following an Ornstein-Uhlenbeck (OU) process. Through simulations and reanalyses of Hymenoptera and Eutheria data, we show that both variants of the SFBD model unify age estimates under random and diversified sampling assumptions. The SFBD model can resolve DRA by absorbing the deviations from the sampling assumptions into the inferred dynamics of the diversification process over time. Although this means that the inferred diversification dynamics must be interpreted with caution, taking sampling biases into account, we conclude that the SFBD model represents the most robust approach currently available for addressing DRA in total-evidence dating.

Integrating Fossil Flowers into the Angiosperm Phylogeny Using Molecular and Morphological Evidence

Fossils are essential to infer past evolutionary processes. The assignment of fossils to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish fossil affinities has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level data set of 30 floral traits for 1201 extant species that were sampled to capture the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches and showed minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils agrees with previously suggested relationships, but for others, a new placement is inferred. We also identified fossils that are well supported within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future analyses combining molecular and morphological evidence, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of divergence times and the temporal evolution of morphological traits. [Angiosperms; fossil flowers; phylogenetic uncertainty; RoguePlots.].

Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process

Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].

Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools

Time-calibrated phylogenetic trees are a tremendously powerful tool for studying evolutionary, ecological, and epidemiological phenomena. Such trees are predominantly inferred in a Bayesian framework, with the phylogeny itself treated as a parameter with a prior distribution (a "tree prior"). However, we show that the tree "parameter" consists, in part, of data, in the form of taxon samples. Treating the tree as a parameter fails to account for these data and compromises our ability to compare among models using standard techniques (e.g., marginal likelihoods estimated using path-sampling and stepping-stone sampling algorithms). Since accuracy of the inferred phylogeny strongly depends on how well the tree prior approximates the true diversification process that gave rise to the tree, the inability to accurately compare competing tree priors has broad implications for applications based on time-calibrated trees. We outline potential remedies to this problem, and provide guidance for researchers interested in assessing the fit of tree models. [Bayes factors; Bayesian model comparison; birth-death models; divergence-time estimation; lineage diversification].

Systematics of Miocene apes: State of the art of a neverending controversy

Hominoids diverged from cercopithecoids during the Oligocene in Afro-Arabia, initially radiating in that continent and subsequently dispersing into Eurasia. From the Late Miocene onward, the geographic range of hominoids progressively shrank, except for hominins, which dispersed out of Africa during the Pleistocene. Although the overall picture of hominoid evolution is clear based on available fossil evidence, many uncertainties persist regarding the phylogeny and paleobiogeography of Miocene apes (nonhominin hominoids), owing to their sparse record, pervasive homoplasy, and the decimated current diversity of this group. We review Miocene ape systematics and evolution by focusing on the most parsimonious cladograms published during the last decade. First, we provide a historical account of the progress made in Miocene ape phylogeny and paleobiogeography, report an updated classification of Miocene apes, and provide a list of Miocene ape species-locality occurrences together with an analysis of their paleobiodiversity dynamics. Second, we discuss various critical issues of Miocene ape phylogeny and paleobiogeography (hylobatid and crown hominid origins, plus the relationships of Oreopithecus) in the light of the highly divergent results obtained from cladistic analyses of craniodental and postcranial characters separately. We conclude that cladistic efforts to disentangle Miocene ape phylogeny are potentially biased by a long-branch attraction problem caused by the numerous postcranial similarities shared between hylobatids and hominids-despite the increasingly held view that they are likely homoplastic to a large extent, as illustrated by Sivapithecus and Pierolapithecus-and further aggravated by abundant missing data owing to incomplete preservation. Finally, we argue that-besides the recovery of additional fossils, the retrieval of paleoproteomic data, and a better integration between cladistics and geometric morphometrics-Miocene ape phylogenetics should take advantage of total-evidence (tip-dating) Bayesian methods of phylogenetic inference combining morphologic, molecular, and chronostratigraphic data. This would hopefully help ascertain whether hylobatid divergence was more basal than currently supported.

Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches

There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.

Disease-causing human viruses: novelty and legacy

About 270 viruses are known to infect humans. Some of these viruses have been known for centuries, whereas others have recently emerged. During their evolutionary history, humans have moved out of Africa to populate the world. In historical times, human migrations resulted in the displacement of large numbers of people. All these events determined the movement and dispersal of human-infecting viruses. Technological advances have resulted in the characterization of the genetic variability of human viruses, both in extant and in archaeological samples. Field studies investigated the diversity of viruses hosted by other animals. In turn, these advances provided insight into the evolutionary history of human viruses back in time and defined the key events through which they originated and spread.

Incrementing and clarifying the diversity and early evolution of termites (Blattodea: Isoptera)

The past diversity of Isoptera is relatively poorly documented. Many early-diverging families are only represented today by relicts of their Mesozoic and Cenozoic richness. Therefore, the onset of their evolutionary history and the transitions between families, or even between subsocial and eusocial ways of life, remain difficult to decipher and require additional fossil occurrences. Here, we report the oldest worker/pseudergate trapped in amber and a new Mastotermitidae, both from Hkamti amber. We document a diverse assemblage of species representing early-diverging families from the ‘Mid’-Cretaceous of Myanmar, including two new genera and four new species in as many different genera: Anisotermes bourguignoni sp. nov., Longitermes pulcher gen. et sp. nov., Magnifitermes krishnai gen. et sp. nov. and Mastotermes myanmarensis sp. nov. These descriptions provide significant morphological evidence to discuss the placement of the genus Anisotermes, confidently place the new genera and confirm the monophyly of Mastotermitidae. The diversity of Cretaceous isopterans, in light of the biology of their extant representatives, is used to discuss palaeoecological implications and highlights the radiation of early diverged Isoptera in the complex Cretaceous ecosystem. The validity of the species Meiatermes cretacicus is discussed.

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

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

Phylogenomics reveals the origin of mammal lice out of Afrotheria

Mammals host a wide diversity of parasites. Lice, comprising more than 5,000 species, are one group of ectoparasites whose major lineages have a somewhat patchwork distribution across the major groups of mammals. Here we explored patterns in the diversification of mammalian lice by reconstructing a higher-level phylogeny of these lice, leveraging whole genome sequence reads to assemble single-copy orthologue genes across the genome. The evolutionary tree of lice indicated that three of the major lineages of placental mammal lice had a single common ancestor. Comparisons of this parasite phylogeny with that for their mammalian hosts indicated that the common ancestor of elephants, elephant shrews and hyraxes (that is, Afrotheria) was the ancestral host of this group of lice. Other groups of placental mammals obtained their lice via host-switching out of these Afrotherian ancestors. In addition, reconstructions of the ancestral host group (bird versus mammal) for all parasitic lice supported an avian ancestral host, indicating that the ancestor of Afrotheria acquired these parasites via host-switching from an ancient avian host. These results shed new light on the long-standing question of why the major groups of parasitic lice are not uniformly distributed across mammals and reveal the origins of mammalian lice.

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.

Sustained high rates of morphological evolution during the rise of tetrapods

The fish-to-tetrapod transition is one of the most iconic events in vertebrate evolution, yet fundamental questions regarding the dynamics of this transition remain unresolved. Here, we use advances in Bayesian morphological clock modelling to reveal the evolutionary dynamics of early tetrapodomorphs (tetrapods and their closest fish relatives). We show that combining osteological and ichnological calibration data results in major shifts on the time of origin of all major groups of tetrapodomorphs (up to 25 million years) and that low rates of net diversification, not fossilization, explain long ghost lineages in the early tetrapodomorph fossil record. Further, our findings reveal extremely low rates of morphological change for most early tetrapodomorphs, indicating widespread stabilizing selection upon their 'fish' morphotype. This pattern was broken only by elpistostegalians (including early tetrapods), which underwent sustained high rates of morphological evolution for ~30 Myr during the deployment of the tetrapod body plan.

Bayesian Morphological Clock versus Parsimony: An insight into the relationships and dispersal events of postvacuum Cricetidae (Rodentia, Mammalia)

Establishing an evolutionary timeline is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution and diversification. However, the tree of life is pruned by extinction and molecular data cannot be gathered for extinct lineages. Until recently methodological challenges have prevented the application of tip-dating Bayesian approaches in morphology-based fossil-only datasets. Herein, we present a morphological dataset for a group of cricetid rodents to which we apply an array of methods fairly new in palaeontology that can be used by palaeontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, time-calibrated and non-calibrated Bayesian inference phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods outperform parsimony in the case of our dataset, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes and diversification in cricetids.

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

Evolutionary models account for either population- or species-level processes but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth–death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.[Caninae; fossilized birth–death; molecular clock; multispecies coalescent; phylogenetics; species trees.]

Fossils improve phylogenetic analyses of morphological characters

Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth-death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.

Molecular and morphological clocks for estimating evolutionary divergence times

BACKGROUND

Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.

RESULTS

We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as  some intermediate nodes may show large time differences between these two types of data.

CONCLUSIONS

Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution

Quantifying speciation times during human evolution is fundamental as it provides a timescale to test for the correlation between key evolutionary transitions and extrinsic factors such as climatic or environmental change. Here, we applied a total evidence dating approach to a hominin phylogeny to estimate divergence times under different topological hypotheses. The time-scaled phylogenies were subsequently used to perform ancestral state reconstructions of body mass and phylogenetic encephalization quotient (PEQ). Our divergence-time estimates are consistent with other recent studies that analysed extant species. We show that the origin of the genus Homo probably occurred between 4.30 and 2.56 million years ago. The ancestral state reconstructions show a general trend towards a smaller body mass before the emergence of Homo, followed by a trend towards a greater body mass. PEQ estimations display a general trend of gradual but accelerating encephalization evolution. The obtained results provide a rigorous temporal framework for human evolution.

Fossil data support a pre-Cretaceous origin of flowering plants

Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve this discrepancy, we developed a Bayesian method to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity. Our results indicate that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group. We report a marked increase in lineage accumulation from 125 to 72 million years ago, supporting Darwin's hypothesis of a rapid Cretaceous angiosperm diversification. Our results demonstrate that a pre-Cretaceous origin of angiosperms is supported not only by molecular clock approaches but also by analyses of the fossil record that explicitly correct for incomplete sampling.

Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid-Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artifact that might be detrimental for total-evidence dating: "bare-branch attraction," namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information. [Bare-branch attraction; ichneumonids; fossils; morphological matrix; phylogeny; RoguePlots.].

Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a central role in cholesterol homeostasis in humans as a major regulator of LDLR levels. PCSK9 is an intriguing protease in that it does not act by proteolysis but by preventing LDLR recirculation from endosomes to the plasma membrane. This, and the inexistence of any other proteolytic substrate but itself could suggest that PCSK9 is an exquisite example of evolutionary fine-tuning. However, the gene has been lost in several mammalian species, and null alleles are present (albeit at low frequencies) in some human populations without apparently deleterious health effects, raising the possibility that the PCSK9 may have become dispensable in the mammalian lineage. To address this issue, we systematically recovered, assembled, corrected, annotated and analysed publicly available PCSK9 sequences for 420 eutherian species to determine the distribution, frequencies, mechanisms and timing of PCSK9 pseudogenization events, as well as the evolutionary pressures underlying the preservation or loss of the gene. We found a dramatic difference in the patterns of PCSK9 retention and loss between Euarchontoglires—where there is strong pressure for gene preservation—and Laurasiatheria, where multiple independent events have led to PCSK9 loss in most species. These results suggest that there is a fundamental difference in the regulation of cholesterol metabolism between Euarchontoglires and Laurasiatheria, which in turn has important implications for the use of Laurasiatheria species (e.g. pigs) as animal models of human cholesterol-related diseases.

Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

BACKGROUND

The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored.

RESULTS

Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group.

CONCLUSIONS

We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study

Reconstructing the tree of life is an essential task in evolutionary biology. It demands accurate phylogenetic inference for both extant and extinct organisms, the latter being almost entirely dependent on morphological data. While parsimony methods have traditionally dominated the field of morphological phylogenetics, a rapidly growing number of studies are now employing probabilistic methods (maximum likelihood and Bayesian inference). The present-day toolkit of probabilistic methods offers varied software with distinct algorithms and assumptions for reaching global optimality. However, benchmark performance assessments of different software packages for the analyses of morphological data, particularly in the era of big data, are still lacking. Here, we test the performance of four major probabilistic software under variable taxonomic sampling and missing data conditions: the Bayesian inference-based programs MrBayes and RevBayes, and the maximum likelihood-based IQ-TREE and RAxML. We evaluated software performance by calculating the distance between inferred and true trees using a variety of metrics, including Robinson-Foulds (RF), Matching Splits (MS), and Kuhner-Felsenstein (KF) distances. Our results show that increased taxonomic sampling improves accuracy, precision, and resolution of reconstructed topologies across all tested probabilistic software applications and all levels of missing data. Under the RF metric, Bayesian inference applications were the most consistent, accurate, and robust to variation in taxonomic sampling in all tested conditions, especially at high levels of missing data, with little difference in performance between the two tested programs. The MS metric favored more resolved topologies that were generally produced by IQ-TREE. Adding more taxa dramatically reduced performance disparities between programs. Importantly, our results suggest that the RF metric penalizes incorrectly resolved nodes (false positives) more severely than the MS metric, which instead tends to penalize polytomies. If false positives are to be avoided in systematics, Bayesian inference should be preferred over maximum likelihood for the analysis of morphological data.

A test of Generalized Bayesian dating: A new linguistic dating method

In current practice, when dating the root of a Bayesian language phylogeny the researcher is required to supply some of the information beforehand, including a distribution of root ages and dates for some nodes serving as calibration points. In addition to the potential subjectivity that this leaves room for, the problem arises that for many of the language families of the world there are no available internal calibration points. Here we address the following questions: Can a new Bayesian framework which overcomes these problems be introduced and how well does it perform? The new framework that we present is generalized in the sense that no family-specific priors or calibration points are needed. We moreover introduce a way to overcome another potential source of subjectivity in Bayesian tree inference as commonly practiced, namely that of manual cognate identification; instead, we apply an automated approach. Dates are obtained by fitting a Gamma regression model to tree lengths and known time depths for 30 phylogenetically independent calibration points. This model is used to predict the time depths of both the root and the internal nodes for 116 language families, producing a total of 1,287 dates for families and subgroups. It turns out that results are similar to those of published Bayesian studies of individual language families. The performance of the method is compared to automated glottochronology, which is an update of the classical method of Swadesh drawing upon automated cognate recognition and a new formula for deriving a time depth from percentages of shared cognates. It is also compared to a third dating method, that of the Automated Similarity Judgment Program (ASJP). In terms of errors and correlations with known dates, ASJP works better than the new method and both work better than automated glottochronology.

Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles

The origin of phenotypic diversity among higher clades is one of the most fundamental topics in evolutionary biology. However, due to methodological challenges, few studies have assessed rates of evolution and phenotypic disparity across broad scales of time to understand the evolutionary dynamics behind the origin and early evolution of new clades. Here, we provide a total-evidence dating approach to this problem in diapsid reptiles. We find major chronological gaps between periods of high evolutionary rates (phenotypic and molecular) and expansion in phenotypic disparity in reptile evolution. Importantly, many instances of accelerated phenotypic evolution are detected at the origin of major clades and body plans, but not concurrent with previously proposed periods of adaptive radiation. Furthermore, strongly heterogenic rates of evolution mark the acquisition of similarly adapted functional types, and the origin of snakes is marked by the highest rates of phenotypic evolution in diapsid history.

Phylogenomics indicates the "living fossil" Isoetes diversified in the Cenozoic

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process

Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.

Reconstructing the ancestral phenotypes of great apes and humans (Homininae) using subspecies-level phylogenies

Owing to their close affinity, the African great apes are of interest in the study of human evolution. Although numerous researchers have described the ancestors we share with these species with reference to extant great apes, few have done so with phylogenetic comparative methods. One obstacle to the application of these techniques is the within-species phenotypic variation found in this group. Here, we leverage this variation, modelling common ancestors using ancestral state reconstructions (ASRs) with reference to subspecies-level trait data. A subspecies-level phylogeny of the African great apes and humans was estimated from full-genome mitochondrial DNA sequences and used to implement ASRs for 14 continuous traits known to vary between great ape subspecies. Although the inclusion of within-species phenotypic variation increased the phylogenetic signal for our traits and improved the performance of our ASRs, whether this was done through the inclusion of subspecies phylogeny or through the use of existing methods made little difference. Our ASRs corroborate previous findings that the last common ancestor of humans, chimpanzees and bonobos was a chimp-like animal, but also suggest that the last common ancestor of humans, chimpanzees, bonobos and gorillas was an animal unlike any extant African great ape.

Cyanobacteria evolution: Insight from the fossil record

Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.

Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds

Recently, comprehensive morphological datasets including nearly all the well-recognized Mesozoic birds became available, making it feasible for statistically rigorous methods to unveil finer evolutionary patterns during early avian evolution. Here, we exploited the advantage of Bayesian tip dating under relaxed morphological clocks to estimate both the divergence times and evolutionary rates while accounting for their uncertainties. We further subdivided the characters into six body regions (i.e. skull, axial skeleton, pectoral girdle and sternum, forelimb, pelvic girdle and hindlimb) to assess evolutionary rate heterogeneity both along the lineages and across partitions. We observed extremely high rates of morphological character changes during early avian evolution, and the clock rates are quite heterogeneous among the six regions. The branch subtending Pygostylia shows an extremely high rate in the axial skeleton, while the branches subtending Ornithothoraces and Enantiornithes show notably high rates in the pectoral girdle and sternum and moderately high rates in the forelimb. The extensive modifications in these body regions largely correspond to refinement of the flight capability. This study reveals the power and flexibility of Bayesian tip dating implemented in MrBayes to investigate evolutionary dynamics in deep time.

Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating

Confidence in molecular dating analyses has grown with the increasing sophistication of the methods. Some problematic cases where molecular dates disagreed with paleontological estimates appear to have been resolved with a growing agreement between molecules and fossils. But we cannot relax just yet. The growing analytical sophistication of many molecular dating methods relies on an increasingly large number of assumptions about evolutionary history and processes. Many of these assumptions are based on statistical tractability rather than being informed by improved understanding of molecular evolution, yet changing the assumptions can influence molecular dates. How can we tell if the answers we get are driven more by the assumptions we make than by the molecular data being analyzed?

Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters

Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modeled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population “noise”) and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are high. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analyzed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times.

Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the group

Flying squirrels are the only group of gliding mammals with a remarkable diversity and wide geographical range. However, their evolutionary story is not well known. Thus far, identification of extinct flying squirrels has been exclusively based on dental features, which, contrary to certain postcranial characters, are not unique to them. Therefore, fossils attributed to this clade may indeed belong to other squirrel groups. Here we report the oldest fossil skeleton of a flying squirrel (11.6 Ma) that displays the gliding-related diagnostic features shared by extant forms and allows for a recalibration of the divergence time between tree and flying squirrels. Our phylogenetic analyses combining morphological and molecular data generally support older dates than previous molecular estimates (~23 Ma), being congruent with the inclusion of some of the earliest fossils (~36 Ma) into this clade. They also show that flying squirrels experienced little morphological change for almost 12 million years.

Mammals can walk, hop, swim and fly; a few, like marsupial sugar gliders or colugos, can even glide. With 52 species scattered across the Northern hemisphere, flying squirrels are by far the most successful group that adopted this way of going airborne. To drift from tree to tree, these small animals pack their own ‘parachute’: a membrane draping between their lower limbs and the long cartilage rods that extend from their wrists. Tiny specialized wrist bones, which are unique to flying squirrels, help to support the cartilaginous extensions.

The origin of flying squirrels is a point of contention: while most genetic studies point towards the group splitting from tree squirrels about 23 million years ago, the oldest remains – mostly cheek teeth – suggest the animals were already soaring through forests 36 million years ago. However, recent studies show that the dental features used to distinguish between gliding and non-gliding squirrels may actually be shared by the two groups.

In 2002, the digging of a dump site in Barcelona unearthed a peculiar skeleton: first a tail and two thigh bones, big enough that the researchers thought it could be the fossil of a small primate. In fact, and much to the disappointment of paleoprimatologists, further excavating revealed that it was a rodent. As the specimen – nearly an entire skeleton – was being prepared, paleontologists insisted that all the ‘dirt’ attached to the bones had to be carefully screen-washed. From the mud emerged the minuscule specialized wrist bones: the primate-turned-rodent was in fact Miopetaurista neogrivensis, an extinct flying squirrel.

Here, Casanovas-Vilar et al. describe the 11.6 million years old fossil, the oldest ever found. The wrist bones reveal that the animal belongs to the group of flying squirrels that have large sizes. Evolutionary analyses that combined molecular and paleontological data demonstrated that flying squirrels evolved from tree squirrels as far back as 31 to 25 million years ago, and possibly even earlier. In addition, the results show that Miopetaurista is closely related to Petaurista, a modern group of giant flying squirrels. In fact, their skeletons are so similar that the large species that currently inhabit the tropical and subtropical forests of Asia could be considered living fossils.

Molecular and paleontological data are often at odds, but this fossil shows that they can be reconciled and combined to retrace history. Discovering older fossils, or even transitional forms, could help to retrace how flying squirrels took a leap from the rest of their evolutionary tree.

Bayesian placement of fossils on phylogenies using quantitative morphometric data

Jointly developing a comprehensive tree of life from living and fossil taxa has long been a fundamental goal in evolutionary biology. One major challenge has stemmed from difficulties in merging evidence from extant and extinct organisms. While these efforts have resulted in varying stages of synthesis, they have been hindered by their dependence on qualitative descriptions of morphology. Though rarely applied to phylogenetic inference, traditional and geometric morphometric data can improve these issues by generating more rigorous ways to quantify variation in morphological structures. They may also facilitate the rapid and objective aggregation of large morphological datasets. I describe a new Bayesian method that leverages quantitative trait data to reconstruct the positions of fossil taxa on fixed reference trees composed of extant taxa. Unlike most formulations of phylogenetic Brownian motion models, this method expresses branch lengths in units of morphological disparity, suggesting a new framework through which to construct Bayesian node calibration priors for molecular dating and explore comparative patterns in morphological disparity. I am hopeful that the approach described here will help to facilitate a deeper integration of neo- and paleontological data to move morphological phylogenetics further into the genomic era.

The soft explosive model of placental mammal evolution

BACKGROUND

Recent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal diversification, but typically place this event some 10-20 million years earlier than the Paleocene fossils, among apparently more "primitive" mammal faunas.

RESULTS

However, current models of molecular evolution do not adequately account for parallel rate changes, and result in dramatic divergence underestimates for large, long-lived mammals such as whales and hominids. Calibrating among these taxa shifts the rate model errors deeper in the tree, inflating interordinal divergence estimates. We employ simulations based on empirical rate variation, which show that this "error-shift inflation" can explain previous molecular dating overestimates relative to fossil inferences. Molecular dating accuracy is substantially improved in the simulations by focusing on calibrations for taxa that retain plesiomorphic life-history characteristics. Applying this strategy to the empirical data favours the soft explosive model of placental evolution, in line with traditional palaeontological interpretations - a few Cretaceous placental lineages give rise to a rapid interordinal diversification following the 66 Ma Cretaceous-Paleogene boundary mass extinction.

CONCLUSIONS

Our soft explosive model for the diversification of placental mammals brings into agreement previously incongruous molecular, fossil, and ancestral life history estimates, and closely aligns with a growing consensus for a similar model for bird evolution. We show that recent criticism of the soft explosive model relies on ignoring both experimental controls and statistical confidence, as well as misrepresentation, and inconsistent interpretations of morphological phylogeny. More generally, we suggest that the evolutionary properties of adaptive radiations may leave current molecular dating methods susceptible to overestimating the timing of major diversification events.

Mass extinction in tetraodontiform fishes linked to the Palaeocene-Eocene thermal maximum

Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene-Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic.

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity.

Use of Continuous Traits Can Improve Morphological Phylogenetics

The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modeling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modeling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters. The often subjective nature of discrete character coding can generate discordant results that are rooted in individual researchers' subjective interpretations. Employing continuous measurements to infer phylogenies may alleviate some of these issues. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behavior is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative or supplement to discrete characters for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from simulated continuous and discrete characters. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk when simulated under unbounded Brownian motion, and equal performance when simulated under an Ornstein-Uhlenbeck model. Continuous characters also perform reasonably well in the presence of covariance between sites. I argue that inferring phylogenies directly from continuous traits may be benefit efforts to maximize phylogenetic information in morphological data sets by preserving larger variation in state space compared to many discretization schemes. I also suggest that the use of continuous trait models in phylogenetic reconstruction may alleviate potential concerns of discrete character model adequacy, while identifying areas that require further study in this area. This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference.