Use of Continuous Traits Can Improve Morphological Phylogenetics

Herbarium specimens reveal links between leaf shape of Capsella bursa-pastoris and climate

PREMISE

Studies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf shapes, quantifying variation in leaf shape and the effects of environmental factors on leaf shape has proven challenging.

METHODS

To investigate leaf shape variation in a species with inconsistently shaped leaves, we used geometric morphometric modeling and deterministic techniques to analyze approximately 500 digitized specimens of Capsella bursa-pastoris collected throughout the continental United States over 100 years. We generated a morphospace of the leaf shapes and modeled leaf shape as a function of environment and time.

RESULTS

Leaf shape variation of C. bursa-pastoris was strongly associated with temperature over its growing season, with lobing decreasing as temperature increased. While we expected to see changes in variation over time, our results show that the level of leaf shape variation was consistent over the 100 years.

CONCLUSIONS

Our findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation.

Do morphometric data improve phylogenetic reconstruction? A systematic review and assessment

BACKGROUND

Isolating phylogenetic signal from morphological data is crucial for accurately merging fossils into the tree of life and for calibrating molecular dating. However, subjective character definition is a major limitation which can introduce biases that mislead phylogenetic inferences and divergence time estimation. The use of quantitative data, e.g., geometric morphometric (GMM; shape) data can allow for more objective integration of morphological data into phylogenetic inference. This systematic review describes the current state of the field in using continuous morphometric data (e.g., GMM data) for phylogenetic reconstruction and assesses the efficacy of these data compared to discrete characters using the PRISMA-EcoEvo v1.0. reporting guideline, and offers some pathways for approaching this task with GMM data. A comprehensive search string yielded 11,123 phylogenetic studies published in English up to Oct 2023 in the Web of Science database. Title and abstract screening removed 10,975 articles, and full-text screening was performed for 132 articles. Of these, a total of twelve articles met final inclusion criteria and were used for downstream analyses.

RESULTS

Phylogenetic performance was compared between approaches that employed continuous morphometric and discrete morphological data. Overall, the reconstructed phylogenies did not show increased resolution or accuracy (i.e., benchmarked against molecular phylogenies) as continuous data alone or combined with discrete morphological datasets.

CONCLUSIONS

An exhaustive search of the literature for existing empirical continuous data resulted in a total of twelve articles for final inclusion following title/abstract, and full-text screening. Our study was performed under a rigorous framework for systematic reviews, which showed that the lack of available comparisons between discrete and continuous data hinders our understanding of the performance of continuous data. Our study demonstrates the problem surrounding the efficacy of continuous data as remaining relatively intractable despite an exhaustive search, due in part to the difficulty in obtaining relevant comparisons from the literature. Thus, we implore researchers to address this issue with studies that collect discrete and continuous data sets with directly comparable properties (i.e., describing shape, or size).

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

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

How many specimens make a sufficient training set for automated three-dimensional feature extraction?

Deep learning has emerged as a robust tool for automating feature extraction from three-dimensional images, offering an efficient alternative to labour-intensive and potentially biased manual image segmentation methods. However, there has been limited exploration into the optimal training set sizes, including assessing whether artficial expansion by data augmentation can achieve consistent results in less time and how consistent these benefits are across different types of traits. In this study, we manually segmented 50 planktonic foraminifera specimens from the genus Menardella to determine the minimum number of training images required to produce accurate volumetric and shape data from internal and external structures. The results reveal unsurprisingly that deep learning models improve with a larger number of training images with eight specimens being required to achieve 95% accuracy. Furthermore, data augmentation can enhance network accuracy by up to 8.0%. Notably, predicting both volumetric and shape measurements for the internal structure poses a greater challenge compared with the external structure, owing to low contrast differences between different materials and increased geometric complexity. These results provide novel insight into optimal training set sizes for precise image segmentation of diverse traits and highlight the potential of data augmentation for enhancing multivariate feature extraction from three-dimensional images.

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.

Herbarium specimens reveal links between Capsella bursa-pastoris leaf shape and climate

Studies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf margin features, quantifying leaf shape variation and the effects of environmental factors on leaf shape has proven challenging. To investigate leaf shape variation in species with inconsistent shapes, we analyzed approximately 500 digitized Capsella bursa-pastoris specimens collected throughout the continental U.S. over a 100-year period with geometric morphometric modeling and deterministic techniques. We generated a morphospace of C. bursa-pastoris leaf shapes and modeled leaf shape as a function of environment and time. Our results suggest C. bursa-pastoris leaf shape variation is strongly associated with temperature over the C. bursa-pastoris growing season, with lobing decreasing as temperature increases. While we expected to see changes in variation over time, our results show that level of leaf shape variation is consistent over the 100-year period. Our findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation.

Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data

The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type evolution have largely been limited to pairwise comparisons because we lack approaches to build cell phylogenies using model-based approaches. Here we approach the challenges of applying explicit phylogenetic methods to single-cell data by using principal components as phylogenetic characters. We infer a cell phylogeny from a large, comparative single-cell dataset of eye cells from five distantly related mammals. Robust cell type clades enable us to provide a phylogenetic, rather than phenetic, definition of cell type, allowing us to forgo marker genes and phylogenetically classify cells by topology. We further observe evolutionary relationships between diverse vessel endothelia and identify the myelinating and non-myelinating Schwann cells as sister cell types. Finally, we examine principal component loadings and describe the gene expression dynamics underlying the function and identity of cell type clades that have been conserved across the five species. A cell phylogeny provides a rigorous framework towards investigating the evolutionary history of cells and will be critical to interpret comparative single-cell datasets that aim to ask fundamental evolutionary questions.

Deep learning approaches to the phylogenetic placement of extinct pollen morphotypes

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

Seasonal and sex-specific changes in the gastrointestinal tracts of Peromyscus maniculatus

Functional traits are phenotypic characteristics that contribute to fitness of individuals in dynamic and changing environments. In mammals, both categorical and continuous (e.g., quantitative) functional traits have been extensively utilized as proxies for diet, locomotion, and other aspects of species ecology, but there has been less focus on form and function of soft tissues. This is particularly true for the digestive system, which varies in size and complexity across Class Mammalia and plays a major role in the energetics of species. To guide more effective utilization of gastrointestinal (GI) morphology as a functional proxy in small mammal ecology, we examined how GI tracts (lengths and masses of four GI sections) varied within a population of deer mice (Peromyscus maniculatus) in the Southern Appalachian Mountains of North Carolina, United States. We collected samples of adult P. maniculatus monthly for 1 year and measured GI tracts to quantify variation with respect to seasonality and trophic level, providing insight into plasticity in this soft tissue trait over time. We found that season had a significant effect on the total length and wet mass of the GI tract, with January mice having the longest GI tracts and lengths being shortest in the summer. The relative shortening of the GI tract in summer corresponded with a partial trophic increase detected by stable isotope signatures. GI length and wet mass also were affected by reproduction, but males and females responded in sex-specific ways to demands of reproduction, with reproductively active males having shorter and lighter GI tracts than nonreproductively active males. Our study provides proof-of-concept for understanding population-level plasticity in a rarely collected soft tissue trait, which may also be complementary to standard craniodental measurements as a functional dietary proxy to understand mammalian ecology and community assembly.

The predictive power of phylogeny on growth rates in soil bacterial communities

Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.

Fossil berries reveal global radiation of the nightshade family by the early Cenozoic

Fossil discoveries can transform our understanding of plant diversification over time and space. Recently described fossils in many plant families have pushed their known records farther back in time, pointing to alternative scenarios for their origin and spread. Here, we describe two new Eocene fossil berries of the nightshade family (Solanaceae) from the Esmeraldas Formation in Colombia and the Green River Formation in Colorado (USA). The placement of the fossils was assessed using clustering and parsimony analyses based on 10 discrete and five continuous characters, which were also scored in 291 extant taxa. The Colombian fossil grouped with members of the tomatillo subtribe, and the Coloradan fossil aligned with the chili pepper tribe. Along with two previously reported early Eocene fossils from the tomatillo genus, these findings indicate that Solanaceae were distributed at least from southern South America to northwestern North America by the early Eocene. Together with two other recently discovered Eocene berries, these fossils demonstrate that the diverse berry clade and, in turn, the entire nightshade family, is much older and was much more widespread in the past than previously thought.

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.

Classifying organisms and artefacts by their outline shapes

We often wish to classify objects by their shapes. Indeed, the study of shapes is an important part of many scientific fields, such as evolutionary biology, structural biology, image processing and archaeology. However, mathematical shape spaces are rather complicated and nonlinear. The most widely used methods of shape analysis, geometric morphometrics, treat the shapes as sets of points. Diffeomorphic methods consider the underlying curve rather than points, but have rarely been applied to real-world problems. Using a machine classifier, we tested the ability of several of these methods to describe and classify the shapes of a variety of organic and man-made objects. We find that one method, based on square-root velocity functions (SRVFs), outperforms all others, including a standard geometric morphometric method (eigenshapes), and that it is also superior to human experts using shape alone. When the SRVF approach is constrained to take account of homologous landmarks it can accurately classify objects of very different shapes. The SRVF method identifies a shortest path between shapes, and we show that this can be used to estimate the shapes of intermediate steps in evolutionary series. Diffeomorphic shape analysis methods, we conclude, now provide practical and effective solutions to many shape description and classification problems in the natural and human sciences.

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.

Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes

A substantial portion of biodiversity has evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multimarker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58 of 137 species and characterize major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data for 136 of 137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters not only can mask phylogenetic signals, but also are key for characterizing species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterizations.

Early cephalopod evolution clarified through Bayesian phylogenetic inference

BACKGROUND

Despite the excellent fossil record of cephalopods, their early evolution is poorly understood. Different, partly incompatible phylogenetic hypotheses have been proposed in the past, which reflected individual author's opinions on the importance of certain characters but were not based on thorough cladistic analyses. At the same time, methods of phylogenetic inference have undergone substantial improvements. For fossil datasets, which typically only include morphological data, Bayesian inference and in particular the introduction of the fossilized birth-death model have opened new possibilities. Nevertheless, many tree topologies recovered from these new methods reflect large uncertainties, which have led to discussions on how to best summarize the information contained in the posterior set of trees.

RESULTS

We present a large, newly compiled morphological character matrix of Cambrian and Ordovician cephalopods to conduct a comprehensive phylogenetic analysis and resolve existing controversies. Our results recover three major monophyletic groups, which correspond to the previously recognized Endoceratoidea, Multiceratoidea, and Orthoceratoidea, though comprising slightly different taxa. In addition, many Cambrian and Early Ordovician representatives of the Ellesmerocerida and Plectronocerida were recovered near the root. The Ellesmerocerida is para- and polyphyletic, with some of its members recovered among the Multiceratoidea and early Endoceratoidea. These relationships are robust against modifications of the dataset. While our trees initially seem to reflect large uncertainties, these are mainly a consequence of the way clade support is measured. We show that clade posterior probabilities and tree similarity metrics often underestimate congruence between trees, especially if wildcard taxa are involved.

CONCLUSIONS

Our results provide important insights into the earliest evolution of cephalopods and clarify evolutionary pathways. We provide a classification scheme that is based on a robust phylogenetic analysis. Moreover, we provide some general insights on the application of Bayesian phylogenetic inference on morphological datasets. We support earlier findings that quartet similarity metrics should be preferred over the Robinson-Foulds distance when higher-level phylogenetic relationships are of interest and propose that using a posteriori pruned maximum clade credibility trees help in assessing support for phylogenetic relationships among a set of relevant taxa, because they provide clade support values that better reflect the phylogenetic signal.

The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders

Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.

Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters

The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as "Ocadia" kehreri and "Ocadia" messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.

Relative tooth size, Bayesian inference, and Homo naledi

OBJECTIVES

Size-corrected tooth crown measurements were used to estimate phenetic affinities among Homo naledi (~335-236 ka) and 11 other Plio-Pleistocene and recent species. To assess further their efficacy, and identify dental evolutionary trends, the data were then quantitatively coded for phylogenetic analyses. Results from both methods contribute additional characterization of H. naledi relative to other hominins.

MATERIALS AND METHODS

After division by their geometric mean, scaled mesiodistal and buccolingual dimensions were used in tooth size apportionment analysis to compare H. naledi with Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, H. sapiens, and Pan troglodytes. These data produce equivalently scaled samples unaffected by interspecific size differences. The data were then gap-weighted for Bayesian inference.

RESULTS

Congruence in interspecific relationships is evident between methods, and with many inferred from earlier systematic studies. However, the present results place H. naledi as a sister taxon to H. habilis, based on a symplesiomorphic pattern of relative tooth size. In the preferred Bayesian phylogram, H. naledi is nested within a clade comprising all Homo species, but it shares some characteristics with australopiths and, particularly, early Homo.

DISCUSSION

Phylogenetic analyses of relative tooth size yield information about evolutionary dental trends not previously reported in H. naledi and the other hominins. Moreover, with an appropriate model these data recovered plausible evolutionary relationships. Together, the findings support recent study suggesting H. naledi originated long before the geological date of the Dinaledi Chamber, from which the specimens under study were recovered.

Accelerated Brain Shape Evolution Is Associated with Rapid Diversification in an Avian Radiation

AbstractNiche expansion is a critical step in the speciation process. Large brains linked to improved cognitive ability may enable species to expand their niches and forage in new ways, thereby promoting speciation. Despite considerable work on ecological divergence in brain size and its importance in speciation, relatively little is known about how brain shape relates to behavioral, ecological, and taxonomic diversity at macroevolutionary scales. This is due in part to inherent challenges with quantifying brain shape across many species. Here we present a novel, semiautomated approach for rapidly phenotyping brain shape using semilandmarks derived from X-ray computed microtomography scans. We then test its utility by parsing evolutionary trends within a diverse radiation of birds: kingfishers (Aves: Alcedinidae). Multivariate comparative analyses reveal that rates of brain shape evolution (but not beak shape) are positively correlated with lineage diversification rates. Distinct brain shapes are further associated with changes in body size and foraging behavior, suggesting both allometric and ecological constraints on brain shape evolution. These results are in line with the idea of brains acting as a "master regulator" of critical processes governing speciation, such as dispersal, foraging behavior, and dietary niche.

Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable

In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared-change parsimony performed similarly well as maximum likelihood, and both methods outperformed Wagner and Euclidean parsimony, neighbor-joining and UPGMA. Under an evolutionary model of isotropic Brownian motion, phylogeny can be estimated reliably if dimensionality is high, even with relatively unfavorable combinations of branch lengths. By contrast, if there is phenotypic integration such that most variation is concentrated in one or a few dimensions, the reliability of phylogenetic estimates is severely reduced. Evolutionary models with stabilizing selection also produce highly unreliable estimates, which are little better than picking a phylogenetic tree at random. To examine how these results apply to phylogenies with more than four taxa, we conducted further simulations with up to eight taxa, which indicated that the effects of dimensionality and phenotypic integration extend to more than four taxa, and that convergence among internal nodes may produce additional complications specifically for greater numbers of taxa. Overall, the simulations suggest that multidimensional data, under evolutionary models that are plausible for biological data, do not produce reliable estimates of phylogeny. [Brownian motion; gene expression data; geometric morphometrics; morphological integration; squared-change parsimony; phylogeny; shape; stabilizing selection.].

Insect morphometry is reproducible under average investigation standards

Morphometric research is being applied to a growing number and variety of organisms. Discoveries achieved via morphometric approaches are often considered highly transferable, in contrast to the tacit and idiosyncratic interpretation of discrete character states. The reliability of morphometric workflows in insect systematics has never been a subject of focused research, but such studies are sorely needed. In this paper, we assess the reproducibility of morphometric studies of ants where the mode of data collection is a shared routine.We compared datasets generated by eleven independent gaugers, that is, collaborators, who measured 21 continuous morphometric traits on the same pool of individuals according to the same protocol. The gaugers possessed a wide range of morphometric skills, had varying expertise among insect groups, and differed in their facility with measuring equipment. We used intraclass correlation coefficients (ICC) to calculate repeatability and reproducibility values (i.e., intra- and intergauger agreements), and we performed a multivariate permutational multivariate analysis of variance (PERMANOVA) using the Morosita index of dissimilarity with 9,999 iterations.The calculated average measure of intraclass correlation coefficients of different gaugers ranged from R = 0.784 to R = 0.9897 and a significant correlation was found between the repeatability and the morphometric skills of gaugers (p = 0.016). There was no significant association with the magnification of the equipment in the case of these rather small ants. The intergauger agreement, that is the reproducibility, varied between R = 0.872 and R = 0.471 (mean R = 0.690), but all gaugers arrived at the same two-species conclusion. A PERMANOVA test revealed no significant gauger effect on species identity (R 2 = 0.69, p = 0.58).Our findings show that morphometric studies are reproducible when observers follow the standard protocol; hence, morphometric findings are widely transferable and will remain a valuable data source for alpha taxonomy.

Systematic Redefinition of the Hypotricha (Alveolata, Ciliophora) Based on Combined Analyses of Morphological and Molecular Characters

The systematics of Hypotricha is one of the most puzzling problems in ciliate biology, having spanned numerous conflicting hypotheses with unstable relationships at various levels in molecular trees, for which the constant addition of newly discovered species has only increased the confusion. The hypotrichs comprise a remarkable morphologically diversified group of ciliates, and the phylogenetic potential of morphological traits is generally recognized. However, such characters were rarely used in phylogenetic reconstructions, and congruence with molecular data never assessed from simultaneous analyses. To properly reconciliate morphological and molecular information, maximum-likelihood and parsimony analyses of 79 morphological characters and 18S rDNA sequences were performed for 130 ingroup terminals, broadly sampled to represent the known hypotrich diversity. As result, well-supported and relatively stable clades were recovered, based on which the redefined Hypotricha comprises at least six higher taxa: The "arcuseriids", Holostichida, Parabirojimida, and the "amphisiellids", plus the two large clades Kentrurostylida nov. tax. (Hispidotergida nov. tax. and Simplicitergida nov. tax.) and Diatirostomata nov. tax. ("bistichellids", "kahliellids", Gonostomatida and Dorsomarginalia [Postoralida nov. tax. and Uroleptida]). Each taxon was circumscribed by synapomorphies, of which most were homoplastic, as the natural history of hypotrichs is portrayed by an outstanding quantity of convergences and reversions.

Gymnosiphon syceorosensis (Burmanniaceae), the second new species for the Philippines

A new holomycoheterotrophic member of Burmanniaceae, Gymnosiphon syceorosensis, is described from Mt. Hamiguitan located on the island of Mindanao, Philippines. This species differs from the recently named G. philippinensis from Cebu in a number of quantitative and qualitative characters. Phenetic (neighbor-joining) and phylogenetic (maximum parsimony) analyses of characters from Asian and Australian Gymnosiphon species were conducted and diagnostic taxonomic features were discussed. This new species appears to be most closely related to G. affinis J.J. Sm. from New Guinea but differs in a number of floral features including inner perianth lobe shape, stamen position in floral tube, and anther connective shape.

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.

Detecting Mosaic Patterns in Macroevolutionary Disparity

Evolutionary biologists have long sought to understand the full complexity in pattern and process that shapes organismal diversity. Although phylogenetic comparative methods are often used to reconstruct complex evolutionary dynamics, they are typically limited to a single phenotypic trait. Extensions that accommodate multiple traits lack the ability to partition multidimensional data sets into a set of mosaic suites of evolutionarily linked characters. I introduce a comparative framework that identifies heterogeneity in evolutionary patterns across large data sets of continuous traits. Using a model of continuous trait evolution based on the differential accumulation of disparity across lineages in a phylogeny, the approach algorithmically partitions traits into a set of character suites that best explains the data, where each suite displays a distinct pattern in phylogenetic morphological disparity. When applied to empirical data, the approach revealed a mosaic pattern predicted by developmental biology. The evolutionary distinctiveness of individual suites can be investigated in more detail either by fitting conventional comparative models or by directly studying the phylogenetic patterns in disparity recovered during the analysis. This framework can supplement existing comparative approaches by inferring the complex, integrated patterns that shape evolution across the body plan from disparate developmental, morphometric, and environmental sources of phenotypic data.

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.

Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods

BACKGROUND

In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods.

METHODS

We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure.

RESULTS

Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony.

Revealing paraphyly and placement of extinct species within Epischura (Copepoda: Calanoida) using molecular data and quantitative morphometrics

Epischura (Calanoida: Temoridae) is a Holarctic group of copepods serving important ecological roles, but it is difficult to study because of small range sizes of individual species and widespread distribution of the genus. This genus includes Tertiary relicts, some endemic to single, isolated lakes and can play major roles in unique ecosystems like Lakes Baikal and Tahoe. We present the first molecular and morphological analysis of Epischura that reveals their spatio-temporal evolutionary history. Morphological measurements of mandibles and genetics estimated phylogenetic relationships among all species represented in Epischura, including E. massachusettsensis, whose extinction status is of concern. Analyses used three gene regions for six previously unsequenced species to infer highly-resolved and well-supported phylogenies confirming a split between Siberian and North American species. Previously published age estimates and sequence data from broad taxonomic sampling of calanoid copepods estimated divergence times between the two Epischura groups. Divergence time estimates for Epischura were consistent with earlier molecular clock estimates and late-Miocene cooling events. Additionally, we provide the first taxonomically broad estimates of divergence times within Calanoida. The paraphyletic nature of the genus Epischura (and the family Temoridae) is apparent and requires the resurrection of the genus Epischurella (Smirnov, 1936) to describe the Siberian species.

A Systematist's Guide to Estimating Bayesian Phylogenies From Morphological Data

Phylogenetic trees are crucial to many aspects of taxonomic and comparative biology. Many researchers have adopted Bayesian methods to estimate their phylogenetic trees. In this family of methods, a model of morphological evolution is assumed to have generated the data observed by the researcher. These models make a variety of assumptions about the evolution of morphological characters, and these assumptions are translated into mathematics as parameters. The incorporation of prior distributions further allows researchers to quantify their prior beliefs about the value any one parameter can take. How to translate biological knowledge into mathematical language is difficult, and can be confusing to many biologists. This review aims to help systematics researchers understand the biological meaning of common models and assumptions. Using examples from the insect fossil record, I will demonstrate empirically what assumptions mean in concrete terms, and discuss how researchers can use and understand Bayesian methods for phylogenetic estimation.

Primitive Old World monkey from the earliest Miocene of Kenya and the evolution of cercopithecoid bilophodonty

Old World monkeys (Cercopithecoidea) are a highly successful primate radiation, with more than 130 living species and the broadest geographic range of any extant group except humans. Although cercopithecoids are highly variable in habitat use, social behavior, and diet, a signature dental feature unites all of its extant members: bilophodonty (bi: two, loph: crest, dont: tooth), or the presence of two cross-lophs on the molars. This feature offers an adaptable Bauplan that, with small changes to its individual components, permits its members to process vastly different kinds of food. Old World monkeys diverged from apes perhaps 30 million years ago (Ma) according to molecular estimates, and the molar lophs are sometimes incompletely developed in fossil species, suggesting a mosaic origin for this key adaptation. However, critical aspects of the group's earliest evolution remain unknown because the cercopithecoid fossil record before ∼18 Ma consists of only two isolated teeth, one from Uganda and one from Tanzania. Here we describe a primitive Old World monkey from Nakwai, Kenya, dated at ∼22 Ma, that offers direct evidence for the initial key steps in the evolution of the cercopithecoid dentition. The simple dentition and absence of bilophodonty in the Nakwai monkey indicate that the initial radiation of Old World monkeys was first characterized by a reorganization of basic molar morphology, and a reliance on cusps rather than lophs suggests frugivorous diets and perhaps hard object feeding. Bilophodonty evolved later, likely in response to the inclusion of leaves in the diet.

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.

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.

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.