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Mesoraphidiidae is an extinct family of the order Raphidioptera with an evolutionary history that is largely unexplored. Here, we uncovered the evolutionary history of Mesoraphidiidae using phylogenetic comparative approaches, based on an updated morphological dataset, with an additional description of two new genera and species with distinct cephalic elongation, Dracoraphidia brachystigma gen. et sp. nov. and Teratocephala macrostigma gen. et sp. nov. from mid-Cretaceous Myanmar amber. Phylogenetic analysis shows their affinity to the subfamily Alloraphidiinae. Our results show that the radiation of species diversity and morphological disparity of Mesoraphidiidae dates back to the Lower Cretaceous and experienced a distinct peak approximately 130–118 million years ago (Ma). This timeframe aligns with the Cretaceous Terrestrial Revolution (KTR), a period from 125 to 80 Ma marked by the proliferation of flowering plants and their interactions with insects. The habitat preference of mesoraphidiid larvae to gymnosperm plants might have led to their extinction during the KTR, with the associated decline of gymnosperm diversity. Despite reduction in the occupation of morphospace by Mesoraphidiinae, there is surprising expansion of morphospace occupation by Alloraphidiinae in the Upper Cretaceous, possibly related to cephalic elongation, which may have enhanced pollen-feeding or predation ability, in response to extrinsic changes to biodiversity and ecosystems during the KTR. This study enriches our understanding of the macroevolution of snakeflies during the Mesozoic and provides new evidence for the impact of the KTR on insects. [ABSTRACT FROM AUTHOR]

Vertebrate evolution has been punctuated by three whole genome duplication events that have been implicated causally in phenotypic evolution, from the origin of phenotypic novelties to explosive diversification. Arguably, the most dramatic of these is the 3R whole genome duplication event associated with the origin of teleost fishes which comprise more than half of all living vertebrate species. However, tests of a causal relationship between whole genome duplication and teleost diversification have proven difficult due to the challenge of establishing the timing of these phenomena. Here we show, based on molecular clock dating of concatenated gene alignments, that the 3R whole genome duplication event occurred in the early–middle Permian (286.18 to 267.20 million years ago; Ma), 52.02 to 12.84 million years (Myr) before the divergence of crown-teleosts in the latest Permian–earliest Late Triassic (254.36 to 234.16 Ma) and long before the major pulses of teleost diversification in Ostariophysi and Percomorpha (56.37 to 100.17 Myr and at least 139.24 to 183.29 Myr later, respectively). The extent of this temporal gap between putative cause and effect precludes 3R as a deterministic driver of teleost diversification. However, these age constraints remain compatible with the expectations of a prolonged rediploidization process following whole genome duplication which, through the effects of chromosome rearrangement and gene loss, remains a viable mechanism to explain the evolution of teleost novelties and diversification. [ABSTRACT FROM AUTHOR]

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is well-preserved only in the early diverging stem-gnathostome heterostracans. However, its anatomy remains poorly understood. Here, we use X-ray microtomography to characterize the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). The apparatus is composed of 13 plates arranged approximately bilaterally, most of which articulate from the postoral plate. Our reconstruction shows that the oral plates were capable of rotating around the transverse axis, but likely with limited movement. It also suggests the nasohypophyseal organs opened internally, into the pharynx. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterized by a directional trend towards increasingly active food acquisition. [ABSTRACT FROM AUTHOR]

Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution. [ABSTRACT FROM AUTHOR]

Articulated natural assemblages contain direct evidence of the element numbers, morphologies, positions and structures for reconstructing the feeding apparatuses of conodont animals, but these kind of materials are very rare in fossil records. Here we report ten new conodont natural assemblages from Member II of the Guanling Formation in Luoping County, eastern Yunnan Province, southwestern China. These assemblages were obtained from the fossil-bearing layers of the Luoping Biota, dated to the early Middle Triassic Anisian stage (Pelsonian substage). These fossiliferous laminated limestones mainly consist of calcites and dolomites, with platy clay minerals and pyrites as subordinate components, indicating that the conodont assemblages were preserved in a lower energy and anoxic sedimentary environment. The new natural assemblages preserve the primary collapse orientations of the Nicoraella feeding apparatus from the Luoping Biota, showing the relative original positions of the S, M and P elements, that could be further used to refine the architecture of this apparatus in space variable M elements and the position unclear P1 elements. Integrating previously reported three-dimensional and bilaterally symmetrical fused clusters, we statistically analyze the size of the positional homogenous elements within different sized materials, in particular S4, S3, or S2 elements, indicates that elements ontogenic changes do not affect the apparatus architecture. Architecture of Nicoraella apparatus remains stable in the process of ontogeny, so our reconstructed model is credible. It is the first time that ample types of materials have been used to restore a conodont apparatus within one genus, namely natural assemblages (articulated and disarticulated), fused clusters (articulated, disarticulated, compressed, and relatively three-dimensional), and abundant discrete elements, respectively. These materials together record the most complete information on architecture in the gondolelloid apparatuses, thus enabling us to reconstruct a reliable fifteen-element apparatus and propose it as a standard template for gondolelloid apparatus reconstruction. [ABSTRACT FROM AUTHOR]

Analyses of morphological disparity can incorporate living and fossil taxa to facilitate the exploration of how phenotypic variation changes through time. However, taphonomic processes introduce non-random patterns of data loss in fossil data and their impact on perceptions of disparity is unclear. To address this, we characterize how measures of disparity change when simulated and empirical data are degraded through random and structured data loss. We demonstrate that both types of data loss can distort the disparity of clades, and that the magnitude and direction of these changes varies between the most commonly employed distance metrics and disparity indices. The inclusion of extant taxa and exceptionally preserved fossils mitigates these distortions and clarifies the full extent of the data lost, most of which would otherwise go uncharacterized. This facilitates the use of ancestral state estimation and evolutionary simulations to further control for the effects of data loss. Where the addition of such reference taxa is not possible, we urge caution in the extrapolation of general patterns in disparity from datasets that characterize subsets of phenotype, which may represent no more than the traits that they sample. [ABSTRACT FROM AUTHOR]

Galeaspids are extinct jawless relatives of living jawed vertebrates whose contribution to understanding the evolutionary assembly of the gnathostome bodyplan has been limited by absence of postcranial remains. Here, we describe Foxaspis novemura gen. et sp. nov., based on complete articulated remains from a newly discovered Konservat-Lagerstätte in the Early Devonian (Pragian, ∼410 Ma) of Guangxi, South China. F. novemura had a broad, circular dorso-ventrally compressed headshield, slender trunk and strongly asymmetrical hypochordal tail fin comprised of nine ray-like scale-covered digitations. This tail morphology contrasts with the symmetrical hypochordal tail fin of Tujiaaspis vividus , evidencing disparity in galeaspid postcranial anatomy. Analysis of swimming speed reveals galeaspids as moderately fast swimmers, capable of achieving greater cruising swimming speeds than their more derived jawless and jawed relatives. Our analyses reject the hypothesis of a driven trend towards increasingly active food acquisition which has been invoked to characterize early vertebrate evolution. [ABSTRACT FROM AUTHOR]

The ecological context of early vertebrate evolution has been characterized as a gradual shift from passive to more active feeding modes. This evolutionary scenario has been based largely on poorly constrained inferences of the feeding ecology of extinct stem-gnathostomes, among which heterostracans are the earliest. Pteraspidiform heterostracans possessed a feeding apparatus composed of rod-like oral plates with rows of rostrally facing denticles, previously interpreted as an adaptation for suspension feeding. Here, we test this hypothesis using computational fluid dynamics. We simulate water flow around 2D models consisting of rows of denticles both rostrally facing and reversed, to assess whether these orientations create recirculation patterns that are a hydrodynamic adaptation to suspension feeding. All tested models, independent of denticle orientation, show similar flow, velocity, and vorticity patterns. Recirculation patterns, highest velocity, and vorticity develop directly on top of the denticles and in spaces between the denticles. Therefore, we reject the hypothesis that denticle orientation is an adaptation for recirculation linked to suspension feeding. The denticles may instead have served to prevent material from lodging between the plates. [ABSTRACT FROM AUTHOR]

Analysis of a 458-million-year-old fossil fish reveals anatomical insights about the vertebrate skull and how skull organization evolved from that of ancestral early vertebrates to that of jawed vertebrates.Evolutionary clues from analysis of a 458-million-year-old fossil. [ABSTRACT FROM AUTHOR]

Osteostraci and Galeaspida are stem-gnathostomes, occupying a key phylogenetic position for resolving the nature of the jawless ancestor from which jawed vertebrates evolved more than 400 million years ago. Both groups are characterized by the presence of rigid headshields that share a number of common morphological traits, in some cases hindering the resolution of their interrelationships and the exact nature of their affinities with jawed vertebrates. Here, we explore the morphological and functional diversity of osteostracan and galeaspid headshields using geometric morphometrics and computational fluid dynamics to constrain the factors that promoted the evolution of their similar morphologies and informing on the ecological scenario under which jawed vertebrates emerged. Phylomorphospace, Mantel analysis and Stayton metrics demonstrate a high degree of homoplasy. Computational fluid dynamics reveals similar hydrodynamic performance among morphologically convergent species, indicating the independent acquisition of the same morphofunctional traits and, potentially, equivalent lifestyles. These results confirm that a number of the characters typically used to infer the evolutionary relationships among galeaspids, osteostracans and jawed vertebrates are convergent in nature, potentially obscuring understanding of the assembly of the gnathostome bodyplan. Ultimately, our results reveal that while the jawless relatives of the earliest jawed vertebrates were ecologically diverse, widespread convergence on the same hydrodynamic adaptations suggests they had reached the limits of their potential ecological diversity—overcome by jawed vertebrates and their later innovations. [ABSTRACT FROM AUTHOR]

Paired fins are a major innovation1,2 that evolved in the jawed vertebrate lineage after divergence from living jawless vertebrates3. Extinct jawless armoured stem gnathostomes show a diversity of paired body-wall extensions, ranging from skeletal processes to simple flaps4. By contrast, osteostracans (a sister group to jawed vertebrates) are interpreted to have the first true paired appendages in a pectoral position, with pelvic appendages evolving later in association with jaws5. Here we show, on the basis of articulated remains of Tujiaaspis vividus from the Silurian period of China, that galeaspids (a sister group to both osteostracans and jawed vertebrates) possessed three unpaired dorsal fins, an approximately symmetrical hypochordal tail and a pair of continuous, branchial-to-caudal ventrolateral fins. The ventrolateral fins are similar to paired fin flaps in other stem gnathostomes, and specifically to the ventrolateral ridges of cephalaspid osteostracans that also possess differentiated pectoral fins. The ventrolateral fins are compatible with aspects of the fin-fold hypothesis for the origin of vertebrate paired appendages6–10. Galeaspids have a precursor condition to osteostracans and jawed vertebrates in which paired fins arose initially as continuous pectoral–pelvic lateral fins that our computed fluid-dynamics experiments show passively generated lift. Only later in the stem lineage to osteostracans and jawed vertebrates did pectoral fins differentiate anteriorly. This later differentiation was followed by restriction of the remaining field of fin competence to a pelvic position, facilitating active propulsion and steering.Articulated remains of Tujiaaspis vividus reveal that galeaspids—extinct jawless vertebrates—had precursors to paired pectoral fins that consisted of paired, continuous pectoral–pelvic lateral fins that passively generated lift. [ABSTRACT FROM AUTHOR]

The ecological context of early vertebrate evolution is envisaged as a long-term trend towards increasingly active food acquisition and enhanced locomotory capabilities culminating in the emergence of jawed vertebrates. However, support for this hypothesis has been anecdotal and drawn almost exclusively from the ecology of living taxa, despite knowledge of extinct phylogenetic intermediates that can inform our understanding of this formative episode. Here we analyse the evolution of swimming speed in early vertebrates based on caudal fin morphology using ancestral state reconstruction and evolutionary model fitting. We predict the lowest and highest ancestral swimming speeds in jawed vertebrates and microsquamous jawless vertebrates, respectively, and find complex patterns of swimming speed evolution with no support for a trend towards more active lifestyles in the lineage leading to jawed groups. Our results challenge the hypothesis of an escalation of Palaeozoic marine ecosystems and shed light into the factors that determined the disparate palaeobiogeographic patterns of microsquamous versus macrosquamous armoured Palaeozoic jawless vertebrates. Ultimately, our results offer a new enriched perspective on the ecological context that underpinned the assembly of vertebrate and gnathostome body plans, supporting a more complex scenario characterized by diverse evolutionary locomotory capabilities reflecting their equally diverse ecologies. Modelling swim speed based on fin morphology in early vertebrates highlights complex evolutionary patterns in Palaeozoic marine ecosystems. [ABSTRACT FROM AUTHOR]

Simple Summary: All life is derived from a single common ancestor, whose descendants coevolved with the planet, shaping the structure of biodiversity and the physical processes that operate on Earth. This complex history cannot be inferred solely by studying the genomes of living organisms, nor through analysis of the fossil remains of their extinct relatives. Only a unified approach integrating living and extinct species and drawing from both genomic and anatomical evidence can achieve this aim. In this review, we highlight recent advances, challenges, and opportunities in this endeavour. These include the development of models for analysis of anatomical data; methods for combined analysis of fossil and living species, as well as anatomical and genomic data; and the combined estimation of evolutionary relationships, geographic range, and evolutionary rates. However, the application of such methods is limited by a shortage of expertise in taxonomy and comparative anatomy, which are skills required for the compilation of anatomical datasets. Whereas there is a common concern for the incompleteness of the fossil record, knowledge with respect to the comparative anatomy of living species is equally incomplete. We anticipate that the increased demand for an integrative phylogenetic approach to reconstruct the tree of life and evolutionary patterns and processes will encourage researchers to overcome these challenges with the aim of elucidating the complexities behind organismal evolution across broad taxonomic and time scales. The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms. [ABSTRACT FROM AUTHOR]

Understanding the relationship between form, function and diet in feeding structures is critical to constraining the roles of organisms in their ecosystem and adaptive responses to food resources. Yet, analysis of this relationship in invertebrates has been hampered by a reliance on descriptive and qualitative characterisation of the shapes of feeding structures. This has led to a lack of robust statistical analyses and overreliance on analogy and plausibility, especially for extinct taxa and animals that are hard to observe feeding.Here we test the efficacy of dental topographic metrics in quantification of form in invertebrate mandibles and assess their relationship with diet. Specifically, we analyse the mandibles of 45 species of extant orthopterans. Orthopterans' well‐constrained diets make them an ideal model system for our study.We find that topographic metrics applied to Orthoptera successfully recover the same relationship between dietary intractability and dental tool morphology as they do in mammals, and that combination of individual metrics in multivariate analysis most strongly captures this relationship. Furthermore, multivariate topographic metrics calibrated to the food consumed by mammals accurately predict dietary differences between orthopterans (82% taxa correctly assigned).Our results demonstrate that these metrics can be used in quantitative analysis and comparison of non‐homologous mouthparts to reliably investigate the relationship between diet, form and function of feeding tools across Bilateria. We anticipate that this will facilitate more rigorous ecological analysis of fossil and historical material, providing new methods to investigate adaptive responses and community‐level interactions through time. [ABSTRACT FROM AUTHOR]

High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1–3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the growing number of available genomes4. In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties5,6, and thus the timescale of placental mammal evolution remains contentious7–10. Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show that increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Palaeogene8 and show that crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Palaeocene/Eocene. Our Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. This approach can be used to address other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets.Bayesian analysis of datasets comprising genomes from multiple mammalian species can efficiently and precisely decipher their evolutionary timeline. [ABSTRACT FROM AUTHOR]

Embryo-like fossils from the early Ediacaran Weng'an biota provide a window of exceptional fossil preservation onto the period of life history in which molecular clocks estimate the fundamental animal lineages to have diverged. However, their diversity and biological affinities have proven controversial, because they are morphologically simple and, consequently, their interpretation lacks phylogenetic constraint. The subcellular structures preserved in these embryo-like fossils might help to understand their cytology, biology, and diversity, but the potential of these structures has not been fully realized, because detailed microscale physical and chemical investigations are lacking. Here, to remedy this deficiency, we performed a comprehensive study to characterize their micro- and ultra-structures as well as in-situ chemical components. Our results reveal three types of subcellular structure that differ in size, shape, and mineral components: (1) relatively small and spheroidal granules in embryo-like fossils with equal cell division pattern; (2) relatively large, spheroidal, or polygonal granules in embryo-like fossils with unequal and asynchronous cell division pattern; and (3) irregular multi-layered rim-bounded granules in embryo-like fossils with unequal and asynchronous cell division pattern. We propose that the three types may be rationalized to a single taphonomic pathway of preferential mineralization of the cell cytoplasm, preserving an external mould of subcellular granules. We followed the previous interpretation that the spheroidal and polygonal granules should be fossilized lipid droplets or yolk platelets. The distinction between these subcellular structures are largely the result of postmortem degradation processes such as autolysis. The widely preserved lipid droplets or yolk platelets within these Ediacaran embryo-like fossils are compatible with the interpretion of large yolky embryos with maternal nourishment and direct development. [ABSTRACT FROM AUTHOR]

Cladistic character matrices are routinely repurposed in analyses of morphological disparity. Unfortunately, the sampling of taxa and characters within such datasets reflects their intended application (to resolve phylogeny, rather than distinguish between phenotypes) resulting in tree shapes that often misrepresent broader taxonomic and morphological diversity. Here we use tree shape as a proxy to explore how sampling can affect perceptions of evolving morphological disparity. Through analyses of simulated and empirical data, we demonstrate that sampling can introduce biases in morphospace occupation between clades that are predicted by differences in tree symmetry and branch length distribution. Symmetrical trees with relatively long internal branches predict more expansive patterns of morphospace occupation. Conversely, asymmetrical trees with relatively short internal branches predict more compact distributions. Additionally, we find that long external branches predict greater phenotypic divergence by peripheral morphotypes. Taken together, our results caution against the uncritical repurposing of cladistic datasets in disparity analyses. However, they also demonstrate that when morphological diversity is proportionately sampled, differences in tree shape between clades can speak to genuine differences in morphospace occupation. While cladistic datasets may serve as a useful starting point, disparity datasets must attempt to achieve uniformity in lineage sampling across time and topology. Only when all potential sources of bias are accounted for can evolutionary phenomena be distinguished from artefactual signals. It must be accepted that the non‐uniformity of the fossil record may preclude representative sampling and, therefore, a faithful characterization of the evolution of morphological disparity. [ABSTRACT FROM AUTHOR]

The importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian total‐evidence dating methods, which use fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non‐random distribution of missing data. The impact of non‐random missing data on the accuracy and precision of clade age estimation is unknown. In an attempt to constrain the impact of taphonomy on tip‐calibrated dating analyses, we compared clade ages estimated from a very complete morphological matrix to ages estimated from the same matrix permuted to simulate the progressive loss of anatomical information resulting from taphonomic processes. We demonstrate that systematically distributed missing data negatively influence clade age estimates, but that successive stages within the taphonomic process introduce greater differences in age estimates, when compared to estimates obtained from untreated data. Despite these effects, the general influence of missing data is weak, presumably due to the compensatory effect of extensive morphological data from extant taxa. We suggest that, in the absence of models that can explicitly account for taphonomic processes, morphological datasets should be constructed to minimize the impact of taphonomy on divergence time estimation. [ABSTRACT FROM AUTHOR]

Cladistic datasets of morphological characters are comprised of observations that exhibit varying degrees of consistency with underlying phylogenetic hypotheses, reflecting the acquisition and retention of character states (highly consistent characters), or the convergent evolution and loss of character states (less consistent characters). The consistency between phylogenetic history and individual character histories has a bearing both on the evolutionary process and on the relative ease with which phylogenetic history may be inferred from morphological data. We surveyed 486 tetrapod morphological cladistic datasets to establish an empirical distribution of consistency among characters and datasets. Average dataset size has increased in the number of characters and taxa through time. The Consistency Index measure of homoplasy decreases as more characters are added but the most significant decreases result from the addition of taxa. Retention Index and Homoplasy Excess Ratio remain relatively constant with changes in taxa and character number. Our sampling of larger datasets confirms that the positive relationship between dataset size and homoplasy is primarily caused by an increase in taxa, not an increase in characters. Genealogies of cladistic data matrices for early vertebrates, scalidophorans and crocodilians, which have been modified in succession, show a trend of generally consistent quality through research time. Thus, we find no support for the widely shared conjecture that in the search for phylogenetic resolution, high quality phylogenetic characters are quickly exhausted, with subsequent research leading to the inclusion of potentially misleading characters exhibiting high levels of homoplasy. [ABSTRACT FROM AUTHOR]

Osteostraci and Galeaspida are stem-gnathostomes, occupying a key phylogenetic position for resolving the nature of the jawless ancestor from which jawed vertebrates evolved more than 400 million years ago. Both groups are characterized by the presence of rigid headshields that share a number of common morphological traits, in some cases hindering the resolution of their interrelationships and the exact nature of their affinities with jawed vertebrates. Here, we explore the morphological and functional diversity of osteostracan and galeaspid headshields using geometric morphometrics and computational fluid dynamics to constrain the factors that promoted the evolution of their similar morphologies and informing on the ecological scenario under which jawed vertebrates emerged. Phylomorphospace, Mantel analysis and Stayton metrics demonstrate a high degree of homoplasy. Computational fluid dynamics reveals similar hydrodynamic performance among morphologically convergent species, indicating the independent acquisition of the same morphofunctional traits and, potentially, equivalent lifestyles. These results confirm that a number of the characters typically used to infer the evolutionary relationships among galeaspids, osteostracans and jawed vertebrates are convergent in nature, potentially obscuring understanding of the assembly of the gnathostome bodyplan. Ultimately, our results reveal that while the jawless relatives of the earliest jawed vertebrates were ecologically diverse, widespread convergence on the same hydrodynamic adaptations suggests they had reached the limits of their potential ecological diversity—overcome by jawed vertebrates and their later innovations. [ABSTRACT FROM AUTHOR]

Morphological variation (disparity) is almost invariably characterized by two non‐mutually exclusive approaches: (1) quantitatively, through geometric morphometrics; and (2) in terms of discrete, 'cladistic', or categorical characters. Uncertainty over the comparability of these approaches diminishes the potential to obtain nomothetic insights into the evolution of morphological disparity and the few benchmarking studies conducted so far show contrasting results. Here, we apply both approaches to characterizing morphology in the stem‐gnathostome clade Osteostraci in order to assess congruence between these alternative methods as well as to explore the evolutionary patterns of the group in terms of temporal disparity and the influence of phylogenetic relationships and habitat on morphospace occupation. Our results suggest that both approaches yield similar results in morphospace occupation and clustering, but also some differences indicating that these metrics may capture different aspects of morphology. Phylomorphospaces reveal convergence towards a generalized 'horseshoe'‐shaped cranial morphology and two strong trends involving major groups of osteostracans (benneviaspidids and thyestiids), which probably reflect adaptations to different lifestyles. Temporal patterns of disparity obtained from categorical and morphometric approaches appear congruent, however, disparity maxima occur at different times in the evolutionary history of the group. The results of our analyses indicate that categorical and continuous data sets may characterize different patterns of morphological disparity and that discrepancies could reflect preservational limitations of morphometric data and differences in the potential of each data type for characterizing more or less inclusive aspects of overall phenotype. [ABSTRACT FROM AUTHOR]

Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori appear to be less reliable than a priori calibrated, timescales. [ABSTRACT FROM AUTHOR]

Timescales are of fundamental importance to evolutionary biology as they facilitate hypothesis tests of historical evolutionary processes. Through the incorporation of fossil occurrence data, the fossilized birth–death (FBD) process provides a framework for estimating divergence times using more paleontological data than traditional node calibration approaches have allowed. The inclusion of more data can refine evolutionary timescale estimates, but for many taxonomic groups it is computationally infeasible to include all available fossil occurrence data. Here, we utilize both empirical data and a simulation framework to identify approaches to subsampling fossil occurrence data that result in the most accurate estimates of divergence times. To achieve this we assess the performance of the FBD-Skyline model when implementing multiple approaches to incorporating subsampled fossil occurrence data. Our results demonstrate that it is necessary to account for all available fossil occurrence data to achieve the most accurate estimates of clade age. We show that this can be achieved if an empirical Bayes approach, accounting for fossil sampling through time, is applied to the FBD process. Random subsampling of occurrence data can lead to estimates of clade age that are incompatible with fossil evidence if no control over the affinities of fossil occurrences is enforced. Our results call into question the accuracy of previous divergence time studies incorporating the FBD process that have used only a subsample of all available fossil occurrence data. [ABSTRACT FROM AUTHOR]

The molecular clock provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/or to the nodes of a phylogeny. Tip‐calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphical horizons and it remains unclear how such age ranges should be interpreted to codify tip‐calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip‐calibrations. In particular, we focus on the effect of using tip‐calibrations defined using the oldest vs youngest stratigraphic occurrences, the full stratigraphical range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence‐time estimates and demonstrate that concentrating tip‐calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data were derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip‐dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating. [ABSTRACT FROM AUTHOR]

The apparatus composition and architecture of prioniodinin conodonts is poorly understood, largely because few prioniodinin taxa are represented by articulated oral feeding apparatuses (natural assemblages) in the fossil record, but also due to the highly variable gradational morphology of their constituent elements that makes apparatus reconstruction problematic. We describe here a natural assemblage of Erismodus quadridactylus (Stauffer), a prioniodinin, from the Sandbian (Late Ordovician) of North Dakota, USA. The assemblage demonstrates that the apparatus architecture of Erismodus is similar to those of late Palaeozoic prioniodinins namely, Kladognathus Rexroad and Hibbardella Bassler, but also has similarities with ozarkodinin apparatuses. In addition, there is evidence to suggest that E. quadridactylus shares topological similarities to balognathid architecture, with respect to the position of its inferred P elements. The apparatus composition and architecture presented here indicate that, at least with respect to the M–S array, an 'ozarkodinin‐type' bauplan is probably more widely representative across prioniodontids. The assemblage demonstrates that element morphotypes traditionally considered to lie within the S array are M elements, whereas others traditionally interpreted as P elements are found in the S array. These observations are used as a basis for refining concepts of element homology among prioniodinin conodonts and their closest relatives. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We reconstruct the apparatus architecture of the gondollelid conodont Nicoraella kockeli based on fused clusters from the early Middle Triassic (middle Anisian, Pelsonian) of Luoping County, east Yunnan Province, south‐west China. This material was characterized non‐invasively using synchrotron x‐ray tomographic microscopy and the ensuing data analysed using computed tomography, allowing us to infer the composition, homologies and architectural arrangement of elements within the apparatus. Much of the original three‐dimensional architecture of the apparatus is preserved and our apparatus reconstruction is the best characterized of any taxon within the superfamily Gondolelloidea. This allows us to test architectural models for gondolelloids and prioniodinins, more generally, as well as the functional interpretations based upon them. In particular, we reject a recent functional interpretation of the conodont feeding apparatus which was based on a biomechanically‐optimized inference of apparatus architecture in a close gondolelloid relative of Nicoraella. Nevertheless, our architectural model provides a foundation for future functional interpretations of gondolleloids and prioniodinins, more generally. [ABSTRACT FROM AUTHOR]

Summary: Unraveling the phylogenetic relationships between the four major lineages of terrestrial plants (mosses, liverworts, hornworts, and vascular plants) is essential for an understanding of the evolution of traits specific to land plants, such as their complex life cycles, and the evolutionary development of stomata and vascular tissue.Well supported phylogenetic hypotheses resulting from different data and methods are often incongruent due to processes of nucleotide evolution that are difficult to model, for example substitutional saturation and composition heterogeneity. We reanalysed a large published dataset of nuclear data and modelled these processes using degenerate‐codon recoding and tree‐heterogeneous composition substitution models.Our analyses resolved bryophytes as a monophyletic group and showed that the nonnonmonophyly of the clade that is supported by the analysis of nuclear nucleotide data is due solely to fast‐evolving synonymous substitutions.The current congruence among phylogenies of both nuclear and chloroplast analyses lent considerable support to the conclusion that the bryophytes are a monophyletic group. An initial split between bryophytes and vascular plants implies that the bryophyte life cycle (with a dominant gametophyte nurturing an unbranched sporophyte) may not be ancestral to all land plants and that stomata are likely to be a symplesiomorphy among embryophytes. [ABSTRACT FROM AUTHOR]

The Ediacaran macrofossil Charnia masoni Ford is perhaps the most iconic member of the Rangeomorpha: a group of seemingly sessile, frondose organisms that dominates late Ediacaran benthic, deep‐marine fossil assemblages. Despite C. masoni exhibiting broad palaeogeographical and stratigraphical ranges, there have been few morphological studies that consider the variation observed among populations of specimens derived from multiple global localities. We present an analysis of C. masoni that evaluates specimens from the UK, Canada and Russia, representing the largest morphological study of this taxon to date. We describe substantial morphological variation within C. masoni and present a new morphological model for this species that has significant implications both for interpretation of rangeomorph architecture, and potentially for existing taxonomic schemes. Previous reconstructions of Charnia include assumptions regarding the presence of structures seen in other rangeomorphs (e.g. an internal stalk) and of homogeneity in higher order branch morphology; observations that are not borne out by our investigations. We describe variation in the morphology of third and fourth order branches, as well as variation in gross structure near the base of the frond. The diagnosis of Charnia masoni is emended to take account of these new features. These findings highlight the need for large‐scale analyses of rangeomorph morphology in order to better understand the biology of this long‐enigmatic group. [ABSTRACT FROM AUTHOR]

To understand patterns and processes of the diversification of life, we require an accurate understanding of taxon interrelationships. Recent studies have suggested that analyses of morphological character data using the Bayesian and maximum likelihood Mk model provide phylogenies of higher accuracy compared to parsimony methods. This has proved controversial, particularly studies simulating morphology‐data under Markov models that assume shared branch lengths for characters, as it is claimed this leads to bias favouring the Bayesian or maximum likelihood Mk model over parsimony models which do not explicitly make this assumption. We avoid these potential issues by employing a simulation protocol in which character states are randomly assigned to tips, but datasets are constrained to an empirically realistic distribution of homoplasy as measured by the consistency index. Datasets were analysed with equal weights and implied weights parsimony, and the maximum likelihood and Bayesian Mk model. We find that consistent (low homoplasy) datasets render method choice largely irrelevant, as all methods perform well with high consistency (low homoplasy) datasets, but the largest discrepancies in accuracy occur with low consistency datasets (high homoplasy). In such cases, the Bayesian Mk model is significantly more accurate than alternative models and implied weights parsimony never significantly outperforms the Bayesian Mk model. When poorly supported branches are collapsed, the Bayesian Mk model recovers trees with higher resolution compared to other methods. As it is not possible to assess homoplasy independently of a tree estimate, the Bayesian Mk model emerges as the most reliable approach for categorical morphological analyses. [ABSTRACT FROM AUTHOR]

The morphology of the vertebrate lower jaw has been used to infer feeding ecology, with transformations in mandibular shape and structure likely to have facilitated the emergence of different feeding behaviours in vertebrate evolution. Here we present elliptical Fourier shape and principal component analyses, characterizing and comparing the disparity of jaw shape in early gnathostomes and their modern primitively aquatic counterparts. 83% of shape variation is summarized on the first three principal component axes and all component clades of early gnathostomes exhibit overlapping morphological variation. Non‐tetrapodomorph Palaeozoic sarcopterygians are more disparate than their extant counterparts whereas extant chondrichthyans are more disparate than their Palaeozoic counterparts. More generally, extant jawed fishes are more disparate than their Palaeozoic relatives largely because of the extensive shape variation exhibited by mandibles of extant actinopterygians. Only some areas of shape space vacated by Palaeozoic gnathostomes have been convergently refilled by living taxa. Characterization of theoretical jaw morphologies demonstrates that fewer than half of all possible shapes are realized by the jawed fishes that comprise our empirical dataset; many of these morphologies are realized by unrepresented terrestrial tetrapods, implying environmental constraint. Our results are incompatible with the early burst model of clade evolution and contradict the hypothesis that maximum disparity is reached early in the evolutionary history of jawed fishes. [ABSTRACT FROM AUTHOR]

The animal kingdom exhibits a great diversity of organismal form (i.e., disparity). Whether the extremes of disparity were achieved early in animal evolutionary history or clades continually explore the limits of possible morphospace is subject to continuing debate. Here we show, through analysis of the disparity of the animal kingdom, that, even though many clades exhibit maximal initial disparity, arthropods, chordates, annelids, echinoderms, and mollusks have continued to explore and expand the limits of morphospace throughout the Phanerozoic, expanding dramatically the envelope of disparity occupied in the Cambrian. The "clumpiness" of morphospace occupation by living clades is a consequence of the extinction of phylogenetic intermediates, indicating that the original distribution of morphologies was more homogeneous. The morphological distances between phyla mirror differences in complexity, body size, and species-level diversity across the animal kingdom. Causal hypotheses of morphologic expansion include time since origination, increases in genome size, protein repertoire, gene family expansion, and gene regulation. We find a strong correlation between increasing morphological disparity, genome size, and microRNA repertoire, but no correlation to protein domain diversity. Our results are compatible with the view that the evolution of gene regulation has been influential in shaping metazoan disparity whereas the invasion of terrestrial ecospace appears to represent an additional gestalt, underpinning the post-Cambrian expansion of metazoan disparity. [ABSTRACT FROM AUTHOR]

Here we use synchrotron tomography to characterise dental vasculature in the oldest known tooth-bearing sharks, Leonodus carlsi Mader, 1986 and Celtiberina maderi Wang, 1993. Three dimensional reconstruction of the vascular system and microstructure of both taxa revealed a complex and dense network of canals, including horizontal, ascending and secondary bifurcated canals, as well as histological features consistent with an osteodont histotype. However, L. carlsi and C. maderi also exhibit significant morphological differences, showing Leonodus a typical diplodont tooth morphology with a linguo-labially elongated base, that contrast with Celtiberina's teeth that show a single conical cusp curved lingually with a week developed flat base mesio-distally extended, perhaps reflecting distant relationship. These data are compatible with a pre-Devonian diversification of the two main tooth types traditionally recognised in Palaeozoic sharks (i.e., "cladodont" vs "diplodont"). Finally, our data demonstrate that existing dental classification schemes based on styles of vascularisation are over-simplified, especially when Palaeozoic taxa are considered. [ABSTRACT FROM AUTHOR]

microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparentwidespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animalmicroRNAomes, we reject the view thatmiRNA families are never lost, but they are rarely lost (92%are never lost). A small number of families account for a majority of losses (1.7% of families account for>45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation. [ABSTRACT FROM AUTHOR]

Rocks of the Ediacaran System (635–541 Ma) preserve fossil evidence of some of the earliest complex macroscopic organisms, many of which have been interpreted as animals. However, the unusual morphologies of some of these organisms have made it difficult to resolve their biological relationships to modern metazoan groups. Alternative competing phylogenetic interpretations have been proposed for Ediacaran taxa, including algae, fungi, lichens, rhizoid protists, and even an extinct higher‐order group (Vendobionta). If a metazoan affinity can be demonstrated for these organisms, as advocated by many researchers, they could prove informative in debates concerning the evolution of the metazoan body axis, the making and breaking of axial symmetries, and the appearance of a metameric body plan. Attempts to decipher members of the enigmatic Ediacaran macrobiota have largely involved study of morphology: comparative analysis of their developmental phases has received little attention. Here we present what is known of ontogeny across the three iconic Ediacaran taxa Charnia masoni, Dickinsonia costata and Pteridinium simplex, together with new ontogenetic data and insights. We use these data and interpretations to re‐evaluate the phylogenetic position of the broader Ediacaran morphogroups to which these taxa are considered to belong (rangeomorphs, dickinsoniomorphs and erniettomorphs). We conclude, based on the available evidence, that the affinities of the rangeomorphs and the dickinsoniomorphs lie within Metazoa. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte-tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin. [ABSTRACT FROM AUTHOR]