Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data

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.

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.

Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny

Recently, many studies have addressed the performance of phylogenetic tree-building methods (maximum parsimony, maximum likelihood, and Bayesian inference), focusing primarily on simulated data. However, for discrete morphological data, there is no consensus yet on which methods recover the phylogeny with better performance. To address this lack of consensus, we investigate the performance of different methods using an empirical dataset for hexapods as a model. As an empirical test of performance, we applied normalized indices to effectively measure accuracy (normalized Robinson-Foulds metric, nRF) and precision, which are measured via resolution, one minus Colless' consensus fork index (1-CFI). Additionally, to further explore phylogenetic accuracy and support measures, we calculated other statistics, such as the true positive rate (statistical power) and the false positive rate (type I error), and constructed receiver operating characteristic plots to visualize the relationship between these statistics. We applied the normalized indices to the reconstructed trees from the reanalyses of an empirical discrete morphological dataset from extant Hexapoda using a well-supported phylogenomic tree as a reference. Maximum likelihood and Bayesian inference applying the k-state Markov (Mk) model (without or with a discrete gamma distribution) performed better, showing higher precision (resolution). Additionally, our results suggest that most available tree topology tests are reliable estimators of the performance measures applied in this study. Thus, we suggest that likelihood-based methods and tree topology tests should be used more often in phylogenetic tree studies based on discrete morphological characters. Our study provides a fair indication that morphological datasets have robust phylogenetic signal.

Phylogenetic congruence, conflict and consilience between molecular and morphological data

Morphology and molecules are important data sources for estimating evolutionary relationships. Modern studies often utilise morphological and molecular partitions alongside each other in combined analyses. However, the effect of combining phenomic and genomic partitions is unclear. This is exacerbated by their size imbalance, and conflict over the efficacy of different inference methods when using morphological characters. To systematically address the effect of topological incongruence, size imbalance, and tree inference methods, we conduct a meta-analysis of 32 combined (molecular + morphology) datasets across metazoa. Our results reveal that morphological-molecular topological incongruence is pervasive: these data partitions yield very different trees, irrespective of which method is used for morphology inference. Analysis of the combined data often yields unique trees that are not sampled by either partition individually, even with the inclusion of relatively small quantities of morphological characters. Differences between morphology inference methods in terms of resolution and congruence largely relate to consensus methods. Furthermore, stepping stone Bayes factor analyses reveal that morphological and molecular partitions are not consistently combinable, i.e. data partitions are not always best explained under a single evolutionary process. In light of these results, we advise that the congruence between morphological and molecular data partitions needs to be considered in combined analyses. Nonetheless, our results reveal that, for most datasets, morphology and molecules can, and should, be combined in order to best estimate evolutionary history and reveal hidden support for novel relationships. Studies that analyse only phenomic or genomic data in isolation are unlikely to provide the full evolutionary picture.

Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data

Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures-a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. [Bayesian inference, character dependency, character coding, distance metrics, morphological phylogenetics, maximum parsimony, performance, phylogenetic accuracy.].

Statistical evaluation of character support reveals the instability of higher-level dinosaur phylogeny

The interrelationships of the three major dinosaur clades (Theropoda, Sauropodomorpha, and Ornithischia) have come under increased scrutiny following the recovery of conflicting phylogenies by a large new character matrix and its extensively modified revision. Here, we use tools derived from recent phylogenomic studies to investigate the strength and causes of this conflict. Using maximum likelihood as an overarching framework, we examine the global support for alternative hypotheses as well as the distribution of phylogenetic signal among individual characters in both the original and rescored dataset. We find the three possible ways of resolving the relationships among the main dinosaur lineages (Saurischia, Ornithischiformes, and Ornithoscelida) to be statistically indistinguishable and supported by nearly equal numbers of characters in both matrices. While the changes made to the revised matrix increased the mean phylogenetic signal of individual characters, this amplified rather than reduced their conflict, resulting in greater sensitivity to character removal or coding changes and little overall improvement in the ability to discriminate between alternative topologies. We conclude that early dinosaur relationships are unlikely to be resolved without fundamental changes to both the quality of available datasets and the techniques used to analyze them.

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.

Molecular phylogenies map to biogeography better than morphological ones

Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees we show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees. These results have implications for understanding the distribution of homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses and the implications of analysing fossil groups for which molecular data are unavailable.

Using biogeographical and phylogenetic data, it is shown that molecular trees fit species geographical data better than trees inferred from morphology, and that these differences are not simply due to better tree resolution.

Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques

Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining long- and short-read next-generation sequencing techniques, highly accurate genomes were reconstructed, enabling detailed in silico genotyping. Thus, the strains could be assigned to the Tsiankovskii subgroup of the “TransEurAsia” clade, which is commonly found in this region. Their high genetic similarity suggests that the four strains are members of the endemic population whose progenitor was once introduced in the Ukraine and bordering regions. This study provides information on B. anthracis strains from a region where there is little knowledge of the local population, thereby adding to the picture of global B. anthracis genotype distribution. We also emphasize the importance of surveillance and prevention methods regarding anthrax outbreaks, as other studies predicted a higher number of cases in the future due to global warming.

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.

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.

Ancestral morphology of Ecdysozoa constrained by an early Cambrian stem group ecdysozoan

BACKGROUND

Ecdysozoa are the moulting protostomes, including arthropods, tardigrades, and nematodes. Both the molecular and fossil records indicate that Ecdysozoa is an ancient group originating in the terminal Proterozoic, and exceptional fossil biotas show their dominance and diversity at the beginning of the Phanerozoic. However, the nature of the ecdysozoan common ancestor has been difficult to ascertain due to the extreme morphological diversity of extant Ecdysozoa, and the lack of early diverging taxa in ancient fossil biotas.

RESULTS

Here we re-describe Acosmia maotiania from the early Cambrian Chengjiang Biota of Yunnan Province, China and assign it to stem group Ecdysozoa. Acosmia features a two-part body, with an anterior proboscis bearing a terminal mouth and muscular pharynx, and a posterior annulated trunk with a through gut. Morphological phylogenetic analyses of the protostomes using parsimony, maximum likelihood and Bayesian inference, with coding informed by published experimental decay studies, each placed Acosmia as sister taxon to Cycloneuralia + Panarthropoda-i.e. stem group Ecdysozoa. Ancestral state probabilities were calculated for key ecdysozoan nodes, in order to test characters inferred from fossils to be ancestral for Ecdysozoa. Results support an ancestor of crown group ecdysozoans sharing an annulated vermiform body with a terminal mouth like Acosmia, but also possessing the pharyngeal armature and circumoral structures characteristic of Cambrian cycloneuralians and lobopodians.

CONCLUSIONS

Acosmia is the first taxon placed in the ecdysozoan stem group and provides a constraint to test hypotheses on the early evolution of Ecdysozoa. Our study suggests acquisition of pharyngeal armature, and therefore a change in feeding strategy (e.g. predation), may have characterised the origin and radiation of crown group ecdysozoans from Acosmia-like ancestors.

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.

The origin of Rhinocerotoidea and phylogeny of Ceratomorpha (Mammalia, Perissodactyla)

Rhinoceroses have been considered to have originated from tapiroids in the middle Eocene; however, the transition remains controversial, and the first unequivocal rhinocerotoids appeared about 4 Ma later than the earliest tapiroids of the Early Eocene. Here we describe 5 genera and 6 new species of rhinoceroses recently discovered from the early Eocene to the early middle Eocene deposits of the Erlian Basin of Inner Mongolia, China. These new materials represent the earliest members of rhinocerotoids, forstercooperiids, and/or hyrachyids, and bridge the evolutionary gap between the early Eocene ceratomorphs and middle Eocene rhinocerotoids. The phylogenetic analyses using parsimony and Bayesian inference methods support their affinities with rhinocerotoids, and also illuminate the phylogenetic relationships and biogeography of Ceratomorpha, although some discrepancies are present between the two criteria. The nearly contemporary occurrence of various rhinocerotoids indicates that the divergence of different rhinocerotoid groups occurred no later than the late early Eocene, which is soon after the split between the rhinocerotoids and the tapiroids in the early early Eocene. However, the Bayesian tip-dating estimate suggests that the divergence of different ceratomorph groups occurred in the middle Paleocene.

Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations

Evolutionary inferences require reliable phylogenies. Morphological data have traditionally been analyzed using maximum parsimony, but recent simulation studies have suggested that Bayesian analyses yield more accurate trees. This debate is ongoing, in part, because of ambiguity over modes of morphological evolution and a lack of appropriate models. Here, we investigate phylogenetic methods using two novel simulation models-one in which morphological characters evolve stochastically along lineages and another in which individuals undergo selection. Both models generate character data and lineage splitting simultaneously: the resulting trees are an emergent property, rather than a fixed parameter. Standard consensus methods for Bayesian searches (Mki) yield fewer incorrect nodes and quartets than the standard consensus trees recovered using equal weighting and implied weighting parsimony searches. Distances between the pool of derived trees (most parsimonious or posterior distribution) and the true trees-measured using Robinson-Foulds (RF), subtree prune and regraft (SPR), and tree bisection reconnection (TBR) metrics-demonstrate that this is related to the search strategy and consensus method of each technique. The amount and structure of homoplasy in character data differ between models. Morphological coherence, which has previously not been considered in this context, proves to be a more important factor for phylogenetic accuracy than homoplasy. Selection-based models exhibit relatively lower homoplasy, lower morphological coherence, and higher inaccuracy in inferred trees. Selection is a dominant driver of morphological evolution, but we demonstrate that it has a confounding effect on numerous character properties which are fundamental to phylogenetic inference. We suggest that the current debate should move beyond considerations of parsimony versus Bayesian, toward identifying modes of morphological evolution and using these to build models for probabilistic search methods. [Bayesian; evolution; morphology; parsimony; phylogenetics; selection; simulation.].

Size matters: the effects of ontogenetic disparity on the phylogeny of Trematopidae (Amphibia: Temnospondyli)

Trematopids are a clade of terrestrial Permo-Carboniferous temnospondyl amphibians. The intrarelationships of this clade are poorly known. This is largely attributable to a substantial disparity in size between type specimens, which range from the small-bodied lectotype of Mattauschia laticeps (&lt; 4 cm skull length) to the large-bodied holotype of Acheloma cumminsi (&gt; 15 cm skull length). Inferred correlation of size disparity with ontogenetic disparity has led previous workers either to omit taxa in phylogenetic analyses or to forgo an analysis altogether. Here, I take a specimen-level approach and multiple subsampling permutations to explore the phylogeny of the Trematopidae as a case study for assessing the effects of ontogenetic disparity on phylogenetic reconstruction in temnospondyls. The various analyses provide evidence that ontogenetic disparity confounds the phylogenetic inference of trematopids but without a directional bias. Tree topologies of most permutations are poorly resolved and weakly supported, reflecting character conflict that results from the inability of the analyses to differentiate retained plesiomorphies from juvenile features. These findings urge caution in the interpretation of phylogenetic analyses for which ontogenetic disparity exists, but is unaccounted for, and provide a strong impetus for more directed exploration of the interplay of ontogeny and phylogeny across Temnospondyli.

Baltic amber members of the extant Micrillus–Scymbalium lineage of the Paederinae rove beetles (Coleoptera, Staphylinidae) and their systematic and ecological significance

Paederinae, a diverse subfamily of rove beetles (Staphylinidae), is poorly explored with an outdated subtribal and generic classification lacking proper phylogenetic perspective. Therefore, the discovery of two Baltic amber fossil specimens resembling the genera Micrillus and Scymbalium, which are particularly challenging in terms of systematics, called for a thorough analysis to infer their phylogenetic position and their ecological requirements. The fossils were examined with light microscopy supplemented by X-ray micro-computed tomography, and then scored into a Paederinae-specific matrix of 99 morphological characters, along with a broad sample of recent Paederinae and non-paederine outgroups. Morphological phylogenetic analyses were conducted, using Bayesian Inference and Maximum Parsimony. The obtained phylogeny confirmed that the genera Scymbalium and Micrillus form a lineage outside Lathrobiina; therefore, both genera are now classified as Lathrobiini incertae sedis pending a more inclusive phylogenetic work on Paederinae. The analysis firmly placed both fossils in that recent lineage, albeit rendering Micrillus paraphyletic with respect to Scymbalium. Without a more extensive analysis based on the revised world fauna, any systematic changes would be premature. Thus, the fossils are described as Micrillus electrus, sp. nov. and Scymbalium phaethoni, sp. nov. in accordance with the current diagnoses of both genera. Given that the recent species of Micrillus and Scymbalium are predominantly thermophilic and mainly confined to dry open landscapes in Africa, southern Eurasia and Australia, the finding of Baltic amber representatives implies the very diverse landscape and the equable (sub)tropical palaeoclimatic conditions of the Eocene amberiferous ‘forest’, the latter being the subject of continued debates.

Origin of horsetails and the role of whole-genome duplication in plant macroevolution

Whole-genome duplication (WGD) has occurred commonly in land plant evolution and it is often invoked as a causal agent in diversification, phenotypic and developmental innovation, as well as conferring extinction resistance. The ancient and iconic lineage of Equisetum is no exception, where WGD has been inferred to have occurred prior to the Cretaceous-Palaeogene (K-Pg) boundary, coincident with WGD events in angiosperms. In the absence of high species diversity, WGD in Equisetum is interpreted to have facilitated the long-term survival of the lineage. However, this characterization remains uncertain as these analyses of the Equisetum WGD event have not accounted for fossil diversity. Here, we analyse additional available transcriptomes and summarize the fossil record. Our results confirm support for at least one WGD event shared among the majority of extant Equisetum species. Furthermore, we use improved dating methods to constrain the age of gene duplication in geological time and identify two successive Equisetum WGD events. The two WGD events occurred during the Carboniferous and Triassic, respectively, rather than in association with the K-Pg boundary. WGD events are believed to drive high rates of trait evolution and innovations, but analysed trends of morphological evolution across the historical diversity of Equisetum provide little evidence for further macroevolutionary consequences following WGD. WGD events cannot have conferred extinction resistance to the Equisetum lineage through the K-Pg boundary since the ploidy events occurred hundreds of millions of years before this mass extinction and we find evidence of extinction among fossil polyploid Equisetum lineages. Our findings precipitate the need for a review of the proposed roles of WGDs in biological innovation and extinction survival in angiosperm and non-angiosperm lineages alike.

A relictual troglomorphic harvestman discovered in a volcanic cave of western Argentina: Otilioleptes marcelae, new genus, new species, and Otilioleptidae, new family (Arachnida, Opiliones, Gonyleptoidea)

The troglomorphic harvestman Otilioleptes marcelae gen. nov., sp. nov. from the basaltic cave Doña Otilia, Payunia region, Mendoza Province, Argentina, is described. Its systematic affinities were studied through cladistic and Bayesian analyses that included representatives of Gonyleptoidea; it was determined to represent a new monotypic family, Otilioleptidae fam. nov., occupying a basal position within the clade Laminata. This species shows accentuated troglomorphic traits, typical for troglobitic harvestmen: elongated appendages, depigmentation, reduction of eyes and fading of scutal sulci. Additionally, it almost lacks sexual dimorphism, the distal portion of coxa IV is not completely fused to the stigmatic segment, and penis morphology is remarkably divergent with other Laminata; these features cannot be attributed to cave adaptation and may reflect early lineage divergence. Otilioleptes marcelae is the first troglobitic gonyleptoid known from a lava tube. The xeric environments around the cave (Patagonian ecoregion) and the paleoenvironmental history of the area suggest the relictual character of O. marcelae. Scattered evidence supports a long time evolutionary scenario and a presumable relationship with the Chilean opiliofauna (especially with genus Osornogyndes). A comparative overview of all known troglobitic gonyleptoids is provided. The urgent need to protect this new species and its unique cave environment is emphasized.

The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition

Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.

Exploring the effects of character construction and choice, outgroups and analytical method on phylogenetic inference from discrete characters in extant crocodilians

Phylogenies for fossil taxa must be inferred from morphology, but accuracy of inference is questionable. Here, morphological characters for extant crocodilians are investigated to assess how to improve inference accuracy. The homoplasy of characters is assessed against a DNA-based phylogenetic tree. Cranial characters are significantly less homoplastic, but this result is perhaps confounded by research effort. Meristic characters are significantly more homoplastic and should be used with caution. Characters were reassessed first hand and documented. Those characters passing tests of robust construction are significantly less homoplastic. Suggestions are made for means to improve coding of discrete characters. Phylogenies inferred using only robust characters and a reassessed matrix, including corrected scorings, were not overall closer to the DNA tree, but did often place the gharial (Gavialis) in a position agreeing with or closer to it. The effects of the choice of analytical method were modest, but Bayesian analysis of the reassessed matrix placed Gavialis and Mecistops (slender-snouted crocodile) in DNA-concordant positions. Use of extant rather than extinct outgroups, even with the original matrix, placed Gavialis in a more DNA-concordant position, as did factoring out 3D skull shape. The morphological case for placement of Gavialis outside other extant crocodilians is arguably overstated, with many characters linked to skull shape.

Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony

Evolutionary origins of novel forms are often obscure because early and transitional fossils tend to be rare, poorly preserved, or lack proper phylogenetic contexts. We describe a new, exceptionally preserved enigmatic crab from the mid-Cretaceous of Colombia and the United States, whose completeness illuminates the early disparity of the group and the origins of novel forms. Its large and unprotected compound eyes, small fusiform body, and leg-like mouthparts suggest larval trait retention into adulthood via heterochronic development (pedomorphosis), while its large oar-like legs represent the earliest known adaptations in crabs for active swimming. Our phylogenetic analyses, including representatives of all major lineages of fossil and extant crabs, challenge conventional views of their evolution by revealing multiple convergent losses of a typical "crab-like" body plan since the Early Cretaceous. These parallel morphological transformations may be associated with repeated invasions of novel environments, including the pelagic/necto-benthic zone in this pedomorphic chimera crab.

Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets

Phylogenetic analysis aims to establish the true relationships between taxa. Different analytical methods, however, can reach different conclusions. In order to establish which approach best reconstructs true relationships, previous studies have simulated datasets from known tree topologies, and identified the method that reconstructs the generative tree most accurately. On this basis, researchers have argued that morphological datasets should be analysed by Bayesian approaches, which employ an explicit probabilistic model of evolution, rather than parsimony methods-with implied weights parsimony sometimes identified as particularly inaccurate. Accuracy alone, however, is an inadequate measure of a tree's utility: a fully unresolved tree is perfectly accurate, yet contains no phylogenetic information. The highly resolved trees recovered by implied weights parsimony in fact contain as much useful information as the more accurate, but less resolved, trees recovered by Bayesian methods. By collapsing poorly supported groups, this superior resolution can be traded for accuracy, resulting in trees as accurate as those obtained by a Bayesian approach. By contrast, equally weighted parsimony analysis produces trees that are less resolved and less accurate, leading to less reliable evolutionary conclusions.

Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock

Bayesian estimates of divergence times based on the molecular clock yield uncertainty of parameter estimates measured by the width of posterior distributions of node ages. For the relaxed molecular clock, previous works have reported that some of the uncertainty inherent to the variation of rates among lineages may be reduced by partitioning data. Here we test this effect for the purely morphological clock, using placental mammals as a case study. We applied the uncorrelated lognormal relaxed clock to morphological data of 40 extant mammalian taxa and 4,533 characters, taken from the largest published matrix of discrete phenotypic characters. The morphologically derived timescale was compared to divergence times inferred from molecular and combined data. We show that partitioning data into anatomical units significantly reduced the uncertainty of divergence time estimates for morphological data. For the first time, we demonstrate that ascertainment bias has an impact on the precision of morphological clock estimates. While analyses including molecular data suggested most divergences between placental orders occurred near the K-Pg boundary, the partitioned morphological clock recovered older interordinal splits and some younger intraordinal ones, including significantly later dates for the radiation of bats and rodents, which accord to the short-fuse hypothesis.

Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix

The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69-122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the "temnospondyl hypothesis" on the origin of Lissamphibia (TH) to be more parsimonious than the "lepospondyl hypothesis" (LH)-though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved-we document and justify all changes to the matrix-but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the "polyphyly hypothesis" (PH-R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid "nectrideans" and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Casineria, in which we tentatively identify a postbranchial lamina, emerges rather far from amniote origins in a gephyrostegid-chroniosuchian grade. Bayesian inference (Analysis EB, settings as in R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes (e.g. preaxial/postaxial polarity in limb development), and prospects for further improvement of this matrix. Even in its revised state, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates. Sufficient improvement will be laborious-but not difficult.

A new phylogenetic analysis of Phytosauria (Archosauria: Pseudosuchia) with the application of continuous and geometric morphometric character coding

Phytosauria is a clade of large, carnivorous, semi-aquatic archosauromorphs which reached its peak diversity and an almost global distribution in the Late Triassic (c. 230-201 Mya). Previous phylogenetic analyses of Phytosauria have either focused primarily on the relationships of specific subclades, or were limited in taxonomic scope, and no taxonomically comprehensive dataset is currently available. We here present the most taxonomically comprehensive cladistic dataset of phytosaurs to date, based on extensive first-hand study, identification of novel characters and synthesis of previous matrices. This results in an almost twofold increase in phylogenetic information scored per taxon over previous analyses. Alongside a traditional discrete character matrix, three variant matrices were analysed in which selected characters were coded using continuous and landmarking methods, to more rigorously explore phytosaur relationships. Based on these four data matrices, four tree topologies were recovered. Relationships among non-leptosuchomorph phytosaurs are largely consistent between these four topologies, whereas those of more derived taxa are more variable. Rutiodon carolinensis consistently forms a sister relationship with Angistorhinus. In three topologies Nicrosaurus nests deeply within a group of traditionally non-Mystriosuchini taxa, leading us to redefine Mystriosuchini by excluding Nicrosaurus as an internal specifier. Two distinct patterns of relationships within Mystriosuchini are present in the four topologies, distinguished largely by the variable position of Mystriosuchus. In two topologies Mystriosuchus forms the most basal clade in Mystriosuchini, whilst in the others it occupies a highly derived position within the Machaeroprosopus clade. 'Redondasaurus' is consistently recovered as monophyletic; however, it also nests within the Machaeroprosopus clade. The greatest impact on tree topology was associated with the incorporation of continuous data into our matrices, with landmark characters exerting a relatively modest influence. All topologies correlated significantly with stratigraphic range estimates. Topological variability in our results highlights clades in which further investigation may better elucidate phytosaur relationships.

Origin of Equisetum: Evolution of horsetails (Equisetales) within the major euphyllophyte clade Sphenopsida

PREMISE OF THE STUDY

Equisetum is the sole living representative of Sphenopsida, a clade with impressive species richness, a long fossil history dating back to the Devonian, and obscure relationships with other living pteridophytes. Based on molecular data, the crown group age of Equisetum is mid-Paleogene, although fossils with possible crown synapomorphies appear in the Triassic. The most widely circulated hypothesis states that the lineage of Equisetum derives from calamitaceans, but no comprehensive phylogenetic studies support the claim. Using a combined approach, we provide a comprehensive phylogenetic analysis of Equisetales, with special emphasis on the origin of genus Equisetum.

METHODS

We performed parsimony phylogenetic analyses to address relationships of 43 equisetalean species (15 extant, 28 extinct) using a combination of morphological and molecular characters.

KEY RESULTS

We recovered Equisetaceae + Neocalamites as sister to Calamitaceae + a clade of Angaran and Gondwanan horsetails, with the four groups forming a clade that is sister to Archaeocalamitaceae. The estimated age for the Equisetum crown group is mid-Mesozoic.

CONCLUSIONS

Modern horsetails are not nested within calamitaceans; instead, both groups have explored independent evolutionary trajectories since the Carboniferous. Diverse fossil taxon sampling helps to shed light on the position and relationships of equisetalean lineages, of which only a tiny remnant is present within the extant flora. Understanding these relationships and early character configurations of ancient plant clades as Equisetales provide useful tests of hypotheses about overall phylogenetic relationships of euphyllophytes and foundations for future tests of molecular dates with paleontological data.

A new lineage of Cretaceous jewel wasps (Chalcidoidea: Diversinitidae)

Jewel wasps (Hymenoptera: Chalcidoidea) are extremely species-rich today, but have a sparse fossil record from the Cretaceous, the period of their early diversification. Three genera and three species, Diversinitus attenboroughi gen. & sp. n., Burminata caputaeria gen. & sp. n. and Glabiala barbata gen. & sp. n. are described in the family Diversinitidae fam. n., from Lower Cretaceous Burmese amber. Placement in Chalcidoidea is supported by the presence of multiporous plate sensilla on the antennal flagellum and a laterally exposed prepectus. The new taxa can be excluded from all extant family level chalcidoid lineages by the presence of multiporous plate sensilla on the first flagellomere in both sexes and lack of any synapomorphies. Accordingly, a new family is proposed for the fossils and its probable phylogenetic position within Chalcidoidea is discussed. Morphological cladistic analyses of the new fossils within the Heraty et al. (2013) dataset did not resolve the phylogenetic placement of Diversinitidae, but indicated its monophyly. Phylogenetically relevant morphological characters of the new fossils are discussed with reference to Cretaceous and extant chalcidoid taxa. Along with mymarid fossils and a few species of uncertain phylogenetic placement, the newly described members of Diversinitidae are among the earliest known chalcidoids and advance our knowledge of their Cretaceous diversity.

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution

Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution (KTR) in which pollinators, herbivores and predators underwent explosive co-diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial. We used a Bayesian molecular dating method to analyse a dataset of 83 genes from 644 taxa and 52 fossil calibrations to explore the effect of different interpretations of the fossil record, molecular clock models, data partitioning, among other factors, on angiosperm divergence time estimation. Controlling for different sources of uncertainty indicates that the timescale of angiosperm diversification is much less certain than previous molecular dating studies have suggested. Discord between molecular clock and purely fossil-based interpretations of angiosperm diversification may be a consequence of false precision on both sides. We reject a post-Jurassic origin of angiosperms, supporting the notion of a cryptic early history of angiosperms, but this history may be as much as 121 Myr, or as little as 23 Myr. These conclusions remain compatible with palaeobotanical evidence and a more general KTR in which major groups of angiosperms diverged later within the Cretaceous, alongside the diversification of pollinators, herbivores and their predators.