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PREMISE Fossils provide fundamental evidence of the evolutionary processes that crafted today's biodiversity and consequently for understanding life on Earth. We report the finding of Myrtaceidites eucalyptoides pollen grains preserved within the anthers of a 52-million-year-old Eucalyptus flower collected at Laguna del Hunco locality of Argentinean Patagonia and discuss its implications in understanding the evolutionary history of the iconic Australian genus Eucalyptus. METHODS Pollen grains were extracted from the flower's anthers and were then observed under light microscopy and scanning electron microscopy. The phylogenetic position of the fossil was investigated by adding pollen data to a previously published total-evidence matrix and analyzing it using parsimony. RESULTS We erect the species Eucalyptus xoshemium for the fossil flower. Pollen extracted from E. xoshemium belongs to the species Myrtaceidites eucalyptoides, which, until now, was only known as dispersed pollen. The numerous pollen grains recovered from the single flower allowed estimation of M. eucalyptoides' variability. Results of the phylogenetic analysis reinforce the position of this fossil within crown group Eucalyptus. CONCLUSIONS The discovery of these pollen grains within a Patagonian Eucalyptus fossil flower confirms the hypothesis that Myrtaceidites eucalyptoides represents fossil pollen in the Eucalyptus lineage, extends the geographic and stratigraphic fossil pollen record, and supports an earlier age for crown-group eucalypts.

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

Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.]

—Species in the genus Coccoloba are trees, shrubs, and lianas present in low elevation tropical and sub-tropical forests. Since 1756, well over 400 taxa have been described for Coccoloba. Coccoloba species are natively distributed throughout the New World in a variety of habitats. Despite being distributed throughout the Neotropics, the concentration of Coccoloba species in a given area varies considerably, with four centers of diversity for the genus: southern and coastal Brazil, the West Indies, Mesoamerica, and Amazonia. We here present the first molecular phylogeny of Coccoloba and use this phylogeny to investigate geographic patterns of diversity within the genus. The topology of the phylogeny and the closest related genera to Coccoloba suggest a Mesoamerican origin for the genus. The South American species are recovered as the crown group of the phylogeny with one instance of a separate migration event from Mesoamerica to South America. Coccoloba species in Mesoamerica and the Caribbean show little to no geographic pattern to their diversification. Mesoamerica and the Caribbean are best considered as one phytogeographic region for Coccoloba.

One of the most remarkable differences between Paleogene penguins and their living relatives is the shape and length of their beaks. Many of the Eocene and Oligocene penguins have a thin and elongated spear-like bill, which contrasts with the proportionally shorter and more robust bill of most living species. These differences suggest an important shift in their feeding strategies. This study explores the morphological disparity on the skull of penguins, emphasizing bill morphology and it relationship with feeding habits. For this, the skulls of 118 species of aquatic birds, including 21 fossil and living penguins, were analyzed using two-dimensional geometric morphometric. The results show that, unlike what has been reported for modern birds overall, in penguins and Aequornithes, bill elongation is related to a reduction of the braincase. The discriminant analysis shows that there are significant differences between penguins that feed near or far from the coast and between those that consume nectonic and planktonic prey, identifyingMadrynornisas the only extinct form with a possibly planktonic diet. Additionally, it is clear that Paleogene penguins occupy a region of morphospace unexplored by most diving birds, with the western grebe being their closest modern analogue. This is consistent with the hypothesis that giant penguins hunted by harpooning and not by biting as living forms do, signaling a significant change in the habits of those birds leading to the emergence of their crown group.

We study the systematics and evolutionary history of the Afrotropical butterfly genus Mylothris (Lepidoptera: Pieridae) based on six gene regions (COI, EF1a, GAPDH, MDH, RpS5 and wingless). We find that the genus can be placed into five species groups, termed the jacksoni, elodina, rhodope, agathina and hilara groups. Within these species groups, we find that many species show very little genetic differentiation based on the markers we sequenced, suggesting they have undergone rapid and recent speciation. Based on secondary calibrations, we estimate the age of the crown group of Mylothris to be about 16 million years old, but that many of the species level divergences have happened in the Pleistocene. We infer that the clade has its origin in the forests of the Eastern part of Central Africa, and has spread out from there to other regions of Africa.

Funding Information: We thank Guido W. Grimm, Orleans, France for commenting an earlier version of this manuscript, and two anonymous reviewers for their suggestions to improve this manuscript. Publisher Copyright: © 2021 The Authors The fossil record of Lythrum is scarce and every new find brings an extra piece of the puzzle to the obscure phytogeographic history of this genus. Lythrum pollen is unique and has the potential to be recognized in palynological assemblages. Therefore, the few pre-Holocene fossil records are all pollen described from North America, Russia, and Europe. The European records are both most numerous and geologically younger than those from other parts of the Northern Hemisphere. Earliest European Lythrum pollen records are of late Miocene age and parallel to starting crown group radiation in the Eurasian clade of Lythrum. European Miocene to Pliocene Lythrum pollen morphology is comparable to that of extant species. Interestingly, the late Miocene expansion of Lythrum into Europe coincides with the decline of Decodon, and Lythrum appears to replace Decodon in late Neogene fossil palynological assemblages. publishersversion published

The Cretaceous–Paleogene (K–Pg) mass extinction 66 million years ago was characterized by a worldwide ecological catastrophe and rapid species turnover. Large‐scale devastation of forested environments resulting from the Chicxulub asteroid impact likely influenced the evolutionary trajectories of multiple clades in terrestrial environments, and it has been hypothesized to have biased survivorship in favour of nonarboreal lineages across the K–Pg boundary. Here, we evaluate patterns of substrate preferences across the K–Pg boundary among crown group mammals, a group that underwent rapid diversification following the mass extinction. Using Bayesian, likelihood, and parsimony reconstructions, we identify patterns of mammalian ecological selectivity that are broadly similar to those previously hypothesized for birds. Models based on extant taxa indicate predominant K–Pg survivorship among semi‐ or nonarboreal taxa, followed by numerous independent transitions to arboreality in the early Cenozoic. However, contrary to the predominant signal, some or all members of total‐clade Euarchonta (Primates + Dermoptera + Scandentia) appear to have maintained arboreal habits across the K–Pg boundary, suggesting ecological flexibility during an interval of global habitat instability. We further observe a pronounced shift in character state transitions away from plesiomorphic arboreality associated with the K–Pg transition. Our findings are consistent with the hypothesis that predominantly nonarboreal taxa preferentially survived the end‐Cretaceous mass extinction, and emphasize the pivotal influence of the K‐Pg transition in shaping the early evolutionary trajectories of extant terrestrial vertebrates., We explore the evolution of mammal ecology across the end‐Cretaceous mass extinction event, 66 million years ago. Our results suggest that nonarboreal mammals were selectively favored across this mass extinction event, congruent with the hypothesis that forest communities were devastated in the aftermath of the asteroid impact at the end of the Cretaceous.

We describe new fossils from the late Eocene of Mongolia, which show that the crane-like Eogruidae and Ergilornithidae are stem group representatives of the Struthioniformes (ostriches). Currently, both taxa are unanimously assigned to the neognathous Gruiformes (cranes and allies). However, ergilornithids show a progressive reduction of the second toe, and a few earlier authors likened these birds to ostriches, which are the only extant birds with just 2 toes. So far, eogruids and ergilornithids were mainly known from hindlimb bones from the Cenozoic of Asia, and here we provide important new data on the skeletal anatomy of these birds. A partial skull exhibits characteristic features of palaeognathous birds, and ostriches in particular. In its distinctive shape, it furthermore closely resembles the skull of the Eocene palaeognathous Palaeotididae, which are here also considered to be stem group representatives of the Struthioniformes. A femur from the late Eocene of Mongolia likewise corresponds to that of ostriches in derived traits, whereas cervical vertebrae exhibit features of neognathous birds. The fossils suggest that true ostriches (crown group Struthionidae) originated in Asia, and the Neognathae-like morphology of some bones opens a new perspective on the evolution of skeletal characteristics of palaeognathous birds. LAY SUMMARY Even though various fossil ostriches (Struthioniformes) have been described from late Cenozoic deposits, the early evolutionary history of these birds has remained elusive. Ostriches are the only extant birds with only 2 toes, but a didactyl condition also occurs in the Ergilornithidae from the Cenozoic of Asia. These fossil birds have so far mainly been known from hindlimb bones and are currently assigned to the Gruiformes (cranes and allies). Here we describe new fossils from the late Eocene of Mongolia, which corroborate earlier assumptions that the Ergilornithidae as well as the closely related Eogruidae are struthioniform birds. The fossils suggest that true ostriches originated in Asia and their unusual character mosaic opens a new perspective on the evolution of skeletal characteristics of palaeognathous birds.

Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.

The Drosophila montium species group is a clade of 94 named species, closely related to the model species D. melanogaster. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times within the montium species group, and its relative divergence time from D. melanogaster. To assess the robustness of our phylogenetic inferences, we use 3 non-overlapping sets of 20 single-copy coding sequences and analyze all 60 genes with both Bayesian and maximum likelihood methods. Our analyses support monophyly of the group. Apart from the uncertain placement of a single species, D. baimaii, our analyses also support the monophyly of all seven subgroups proposed within the montium group. Our phylograms and relative chronograms provide a highly resolved species tree, with discordance restricted to estimates of relatively short branches deep in the tree. In contrast, age estimates for the montium crown group, relative to its divergence from D. melanogaster, depend critically on prior assumptions concerning variation in rates of molecular evolution across branches, and hence have not been reliably determined. We discuss methodological issues that limit phylogenetic resolution - even when complete genome sequences are available - as well as the utility of the current phylogeny for understanding the evolutionary and biogeographic history of this clade.

The origin of amniotes was a key event in vertebrate evolution, enabling tetrapods to break their ties with water and invade terrestrial environments. Two pivotal clades of early tetrapods, the diadectomorphs and the seymouriamorphs, have played an unsurpassed role in debates about the ancestry of amniotes for over a century, but their skeletal morphology has provided conflicting evidence for their affinities. Using high-resolution X-ray microcomputed tomography, we reveal the three-dimensional architecture of the well preserved endosseous labyrinth of the inner ear in representative species belonging to both groups. Data from the inner ear are coded in a new cladistic matrix of stem and primitive crown amniotes. Both maximum parsimony and Bayesian inference analyses retrieve seymouriamorphs as derived non-crown amniotes and diadectomorphs as sister group to synapsids. If confirmed, this sister group relationship invites re-examination of character polarity near the roots of the crown amniote radiation. Major changes in the endosseous labyrinth and adjacent braincase regions are mapped across the transition from non-amniote to amniote tetrapods, and include: a ventral shift of the cochlear recess relative to the vestibule and the semicircular canals; cochlear recess (primitively housed exclusively within the opisthotic) accommodated within both the prootic and the opisthotic; development of a distinct fossa subarcuata. The inner ear of seymouriamorphs foreshadows conditions of more derived groups, whereas that of diadectomorphs shows a mosaic of plesiomorphic and apomorphic traits, some of which are unambiguously amniote-like, including a distinct and pyramid-like cochlear recess.

Premise of research. Fern fronds are common in Late Paleozoic and Mesozoic strata. Large tri- or multipinnate fronds are mainly preserved as impression/compressions, while anatomically preserved sp...

Astragalus, a highly diverse genus of flowering plants with its highest center of diversity in West Asia, is a classic example of rapid species-level radiation and adaptation to a diversity of habitats throughout the world. We examined the historical biogeography of Astragalus using molecular dating and ancestral area reconstruction to understand how past climate changes, geographical patterns and transition in life history have provoked diversification of Astragalus. Our results suggest that Astragalus probably originated during the middle Miocene in West Asia, underwent rapid diversification, subsequently and repeatedly expanded its range in the Mediterranean region, and later to North America through West Europe. This distribution range was also extended toward central and eastern Asia from the Middle Miocene to Pleistocene. Several climatic and geological processes during the Miocene-Pliocene may be implicated in the diversification of the major Astragalus clades. In particular, the annual lineages, which are important elements in the Mediterranean flora of Africa and Europe and in the deserts of southwest to central Asia, have arisen in response to progressing aridity from the late Miocene onwards (between 8.6 Ma and 2.98 Ma). Diversification rate analyses indicate three rapid and recent diversification events, one at c. 11 Ma in the clade that groups most of the Astragalus s.s. (all except the Ophiocarpus sister lineage), one at c. 5 Ma in the crown group of the Hypoglottis clade, including herbaceous annual and perennial species, and the most recent one at c. 3 Ma in the spiny cushion forming Astracantha clade. Our study highlights the complexity of processes and factors shaping diversifications in Astragalus; a complex interaction among climatic modifications providing opportunities for diversification and likely coincident with the evolution of key morphological and physiological adaptations.

We describe a nearly complete, three‐dimensionally preserved skull of a new albatross species from the late Pliocene (3.0–3.4 million years ago) Tangahoe Formation of New Zealand. Aldiomedes angustirostris, n. gen. et sp. has only about 90% of the length of the skull of the smallest extant albatross and is the geologically youngest record of a small‐sized albatross known to date. The new species is characterized by a mediolaterally compressed beak, which is not found in any living albatross. The small size and some cranial features of A. angustirostris indicate that, in spite of its comparatively young geological age, the new species was not part of crown group Diomedeidae. We hypothesize that A. angustirostris was more piscivorous than extant albatrosses, which predominantly feed on squid. The reasons for the extinction of smaller‐sized albatrosses are elusive but may be related to changes in seabird fauna during the Pliocene epoch, which witnessed the radiation of various non‐procellariiform seabird groups.

Micropeltidaceae species are flyspeck fungi which have been subjected to few systematic studies. We re-examined 27 genera which were accepted in the Micropeltidaceae and re-described them based on herbaria materials and protologues. Based on morphology and phylogenetic investigations, we transfer Micropeltidaceae to a new order, Micropeltidales (Lecanoromycetes). Genera with bluish or greenish upper walls (Dictyopeltella, Dictyothyriella, Dictyothyrina, Dictyothyrium, Haplopeltheca, Micropeltis, Scolecopeltidium and Stomiopeltopsis) are accepted in the new taxonomic concept for Micropeltidaceae. A molecular clock approach estimated the divergence time of the Micropeltidaceae crown group at 130 (165–104) Mya, which also supports its rank as an order (diverging from 220–100 Mya). The evolutionary histories between Micropeltidaceae species and host plants are interpreted by cophylogenetic analyses calibrated by their divergence times. The result indicates that the diversification of Angiospermae (130–80 Mya) fosters the formation of genera of Micropeltidaceae mainly via cospeciation events, and this codivergent period would be an important reference when establishing generic boundaries of epifoliar fungi.

Floristic similarities between European and Asian mountain ranges have long been recognized, and the hypothesis that European mountain plant taxa immigrated from Asian mountain areas has been confirmed by several molecular phylogenetic analyses. Callianthemum contains ca. 14 species, of which ca. 11 are distributed in Asia and three in Europe. A molecular phylogenetic analysis of the genus using ITS and four plastid DNA sequences (matK, rpL32–trnL intergenic spacer, trnL–trnF intergenic spacer, trnV–ndhC intergenic spacer) revealed that the genus reached Europe twice, with C. coriandrifolium representing one, and C. anemonoides and C. kernerianum a second lineage. Support for C. anemonoides and C. kernerianum as sister species is weak. The crown group ages of the C. coriandrifolium lineage (median 2.2 million years) and of the C. anemonoides/C. kernerianum lineage (median 1.62 million years) are similar and place their immigration to Europe in the Quaternary. Analysis of climatic data shows that C. coriandrifolium grows in colder climate than C. anemonoides/C. kernerianum and that the climatic niches of the three European species are different considering all climatic variables analyzed.

The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events], info:eu-repo/semantics/published

The eusporangiate marattialean ferns represent an ancient radiation with a rich fossil record but limited modern diversity in the tropics. The long evolutionary history without close extant relatives has confounded studies of the phylogenetic origin, rooting and timing of marattialean ferns. Here we present new complete plastid genomes of six marattialean species and compiled a plastid genome dataset representing all of the currently accepted marattialean genera. We further supplemented this dataset by compiling a large dataset of mitochondrial genes and a phenotypic data matrix covering both extant and extinct representatives of the lineage. Our phylogenomic and total-evidence analyses corroborated the postulated position of marattialean ferns as the sister to leptosporangiate ferns, and the position of Danaea as the sister to the remaining extant marattialean genera. However, our results provide new evidence that Christensenia is sister to Marattia and that M. cicutifolia actually belongs to Eupodium. The apparently highly reduced rate of molecular evolution in marattialean ferns provides a challenge for dating the key phylogenetic events with molecular clock approaches. We instead applied a parsimony-based total-evidence dating approach, which suggested a Triassic age for the extant crown group. The modern distribution can best be explained as mainly resulting from vicariance following the breakup of Pangaea and Gondwana. We resolved the fossil genera Marattiopsis, Danaeopsis and Qasimia as members of the monophyletic family Marattiaceae, and the Carboniferous genera Sydneia and Radstockia as the monophyletic sister of all other marattialean ferns.

Background Ecdysozoa are the moulting protostomes, including arthropods, tardigrades, and nematodes. Both the molecular and fossil records indicate that Ecdysozoa is an ancient group originating in the terminal Proterozoic, and exceptional fossil biotas show their dominance and diversity at the beginning of the Phanerozoic. However, the nature of the ecdysozoan common ancestor has been difficult to ascertain due to the extreme morphological diversity of extant Ecdysozoa, and the lack of early diverging taxa in ancient fossil biotas. Results Here we re-describe Acosmia maotiania from the early Cambrian Chengjiang Biota of Yunnan Province, China and assign it to stem group Ecdysozoa. Acosmia features a two-part body, with an anterior proboscis bearing a terminal mouth and muscular pharynx, and a posterior annulated trunk with a through gut. Morphological phylogenetic analyses of the protostomes using parsimony, maximum likelihood and Bayesian inference, with coding informed by published experimental decay studies, each placed Acosmia as sister taxon to Cycloneuralia + Panarthropoda—i.e. stem group Ecdysozoa. Ancestral state probabilities were calculated for key ecdysozoan nodes, in order to test characters inferred from fossils to be ancestral for Ecdysozoa. Results support an ancestor of crown group ecdysozoans sharing an annulated vermiform body with a terminal mouth like Acosmia, but also possessing the pharyngeal armature and circumoral structures characteristic of Cambrian cycloneuralians and lobopodians. Conclusions Acosmia is the first taxon placed in the ecdysozoan stem group and provides a constraint to test hypotheses on the early evolution of Ecdysozoa. Our study suggests acquisition of pharyngeal armature, and therefore a change in feeding strategy (e.g. predation), may have characterised the origin and radiation of crown group ecdysozoans from Acosmia-like ancestors.

The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92–113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders. [biogeography; concatenation; Liphistiidae; molecular dating; summary coalescent; UCEs.]

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages. Deutsche Forschungsgemeinschaft BR5039/3-1 National Science Foundation ANT-0551969, ANT-0440577 Ministerio de Economía y Competitividad POL2006-06399/CGL, CTM2012-39350- C02-01 Antarctic Science AA3010 National Science Foundation IOS-1552610

Although dissimilar in their overall appearance and life habits, the praying mantises (Mantodea) and cockroaches (Blattodea, including their eusocial relatives, the termites [Isoptera]) are grouped within the clade Dictyoptera, based on – among other significant characteristics – the laying of eggs in a compound structure called an ootheca. The origin of the Dictyoptera and the currently recognized taxa within is, however, a controversial topic among entomologists. This has resulted from disparities in the divergence age estimates obtained from phylogenetic analyses based on molecular data together with the limited and controversial fossil evidence attributable to these groups. Here, we report two new oothecae ichnospecies found in a Carnian (237 to 227 mya. lowermost Upper Triassic) deposit from Argentina. Morphological comparisons and Scanning Electron Microscope and X-ray Energy Dispersive Spectroscopy analyses of fossil and extant oothecae of mantises and cockroaches were performed in an attempt to solve their systematic placement within Dictyoptera and fossil allies, such as †Alienoptera. In addition to being the earliest known record of oothecae, this discovery moves the origin of this specialized reproductive strategy back by 100 million years. As direct fossil evidence, these specimens provide an important calibration and reference point that can inform future research on the origins and timing of diversification of the Dictyoptera. Fil: Cariglino, Barbara. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina Fil: Lara, Maria Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Centro de Ecología Aplicada del Litoral. Universidad Nacional del Nordeste. Centro de Ecología Aplicada del Litoral; Argentina Fil: Zavattieri, Ana Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; Argentina

International audience; The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups—holocephalans and elasmobranchs—have played a pivotal role in the formation of evolutionary hypotheses targeting major cranial structures such as the jaws and pharynx. However, despite the advent of digital dissections as a means of easily visualizing and sharing the results of anatomical studies in three dimensions, information on the musculoskeletal systems of the chondrichthyan head remains largely limited to traditional accounts, many of which are at least a century old. Here, we use synchrotron tomographic data to carry out a digital dissection of a holocephalan and an elasmobranch widely used as model species: the elephantfish, Callorhinchus milii, and the small‐spotted catshark, Scyliorhinus canicula. We describe and figure the skeletal anatomy of the head, labial, mandibular, hyoid, and branchial cartilages in both taxa as well as the muscles of the head and pharynx. In Callorhinchus, we make several new observations regarding the branchial musculature, revealing several previously unreported or ambiguously characterized muscles, likely homologous to their counterparts in the elasmobranch pharynx. We also identify a previously unreported structure linking the pharyngohyal of Callorhinchus to the neurocranium. Finally, we review what is known about the evolution of chondrichthyan cranial muscles from their fossil record and discuss the implications for muscle homology and evolution, broadly concluding that the holocephalan pharynx is likely derived from a more elasmobranch‐like form which is plesiomorphic for the chondrichthyan crown group. This dataset has great potential as a resource, particularly for researchers using these model species for zoological research, functional morphologists requiring models of musculature and skeletons, as well as for palaeontologists seeking comparative models for extinct taxa.

Ladybirds (family Coccinellidae) are one of the most diverse groups of beetles and globally comprise over 6000 species. Despite their scientific and economic significance, the taxonomy of Coccinellidae remains unstable, and we still know little about their evolutionary history. By using a small number of genes, previous phylogenetic analyses have not reliably resolved the relationships among major ladybird lineages. In this study, we sequenced 94 nuclear protein-coding genes for 214 species of Coccinellidae and 14 outgroups, covering 90 genera and 35 tribes. We found that nucleotide compositional heterogeneity is present among ladybird tribes so that phylogenetic inference at the amino acid level is more reliable than at the DNA level. Based on the maximum likelihood analyses of the amino acid dataset, we recognize three subfamilies in Coccinellidae: Microweiseinae, Monocoryninae stat. nov., and Coccinellinae. The subfamily relationships are strongly supported as (Microweiseinae, (Monocoryninae stat. nov., Coccinellinae)). The tribes of ladybirds are mostly monophyletic, except Ortaliini, Sticholotidini, Scymnini, and Coccidulini. The phylogenetic relationships among tribes of Coccinellinae are still not well resolved, with many nodes weakly supported. Our divergence time analysis suggests that the crown group of extant lady beetles arose in the Early Cretaceous ~ 143 million years ago (Mya) and experienced a rapid diversification during the Late Cretaceous (120–70 Mya). We hypothesize that the boom of angiosperms in the Late Cretaceous promoted the diversification of herbivorous Sternorrhyncha insects, especially aphids, which in turn drove the rapid radiation of predatory lady beetles. In summary, our work provides a comprehensive time-calibrated phylogeny of Coccinellidae that provides a sound framework for revising their classification and understanding the origin of their biodiversity.

In the present study, a series of phylogenetic analyses of morphological, molecular, and combined morphological-molecular datasets were conducted to investigate the relationships of 23 extant and 44 fossil caniforme genera, in order to test the phylogenetic position of putative stem pinniped Puijila within a comprehensive evolutionary framework. With Canis as an outgroup, a Bayesian Inference analysis employing tip-dating of a combined molecular-morphological (i.e., Total Evidence) dataset recovered a topology in which musteloids are the sister group to a monophyletic pinniped clade, to the exclusion of ursids, and recovered Puijila and Potamotherium along the stem of Pinnipedia. A similar topology was recovered in a parsimony analysis of the same dataset. These results suggest the pinniped stem may be expanded to include additional fossil arctoid taxa, including Puijila, Potamotherium, and Kolponomos. The tip-dating analysis suggested a divergence time between pinnipeds and musteloids of ~45.16 million years ago (Ma), though a basal split between otarioids and phocids is not estimated to occur until ~26.52 Ma. These results provide further support for prolonged freshwater and nearshore phases in the evolution of pinnipeds, prior to the evolution of the extreme level of aquatic adaptation displayed by extant taxa. Ancestral character state reconstruction was used to investigate character evolution, to determine the frequency of reversals and parallelisms characterizing the three extant clades within Pinnipedia. Although the phylogenetic analyses did not directly provide any evidence of parallel evolution within the pinniped extant families, it is apparent from the inspection of previously-proposed pinniped synapomorphies, within the context of a molecular-based phylogenetic framework, that many traits shared between extant pinnipeds have arisen independently in the three clades. Notably, those traits relating to homodonty and limb-bone specialization for aquatic locomotion appear to have multiple origins within the crown group, as suggested by the retention of the plesiomorphic conditions in early-diverging fossil members of the three extant families. Thus, while the present analysis identifies a new suite of morphological synapomorphies for Pinnipedia, the frequency of reversals and other homoplasies within the clade limit their diagnostic value.

The first comprehensive timetree is presented for phytoplasmas, a diverse group of obligate intracellular bacteria restricted to phloem sieve elements of vascular plants and tissues of their hemipteran insect vectors. Maximum likelihood-based phylogenetic analysis of DNA sequence data from the 16S rRNA and methionine aminopeptidase (map) genes yielded well resolved estimates of phylogenetic relationships among major phytoplasma lineages, 16Sr groups and known strains of phytoplasmas. Age estimates for divergences among two major lineages of Mollicutes based on a previous comprehensive bacterial timetree were used to calibrate an initial 16S timetree. A separate timetree was estimated based on the more rapidly-evolving map gene, with an internal calibration based on a recent divergence within two related 16Sr phytoplasma subgroups in group 16SrV thought to have been driven by the introduction of the North American leafhopper vector Scaphoideus titanus Ball into Europe during the early part of the 20th century. Combining the resulting divergence time estimates into a final 16S timetree suggests that evolutionary rates have remained relatively constant overall through the evolution of phytoplasmas and that the origin of this lineage, at ~641 million years ago (Ma), preceded the origin of land plants and hemipteran insects. Nevertheless, the crown group of phytoplasmas is estimated to have begun diversifying ~316 Ma, roughly coinciding with the origin of seed plants and Hemiptera. Some phytoplasma groups apparently associated with particular plant families or insect vector lineages generally arose more recently than their respective hosts and vectors, suggesting that vector-mediated host shifts have been an important mechanism in the evolutionary diversification of phytoplasmas. Further progress in understanding macroevolutionary patterns in phytoplasmas is hindered by large gaps in knowledge of the identity of competent vectors and lack of data on phytoplasma associations with non-economically important plants.

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.

PREMISE OF THE STUDY Recent clarification of the distribution of Marattiales through time provides the impetus for "total evidence" phylogenetic analyses of a major fern clade with a rich fossil record. These analyses serve as empirical tests for results from systematic analyses of living species and also of the belief that relationships among living species accurately reflect the overall pattern of phylogeny for clades with an extensive fossil record and a large percentage of extinction. METHODS Species of living and fossil Marattiaceae are analyzed employing a "total evidence approach" via maximum parsimony. Analyses were conducted using TNT implemented through WinClada. KEY RESULTS Systematic analyses of living species and of living + extinct species provide roughly concordant topologies for living taxa. However, living species of Marattiales are only one component of a much larger clade with two major subclades. One consists of Psaroniaceae and extends through time to at least the Early Cretaceous. The other consists of Marattiaceae and includes all living species. Various analyses support the generic-level clades of living species from earlier analyses, but the arrangement of such clades varies from analysis to analysis. CONCLUSIONS Marattiales is a monophyletic group that is extremely common in late Paleozoic and early Mesozoic deposits, with a stem group Psaroniaceae and a crown group Marattiaceae. Because Marattiaceae represents only a small component of overall marattialean diversity, living species alone neither account for evolutionary changes within the clade over time, nor accurately reflect the overall pattern of marattialean fern phylogeny.

The origins, evolutionary history and diversification of the Australian butterfly fauna are poorly known and uncertain. Two competing hypotheses have been proposed to explain the occurrence of butterflies on this isolated continental landmass. The common view is that all Australian butterflies entered the continent relatively recently from the northern hemisphere via Southeast Asia and/or mainland New Guinea (i.e. northern dispersal origin hypothesis). The alternative view is that part or all of the Australian butterfly fauna ultimately evolved in remnant or Southern Gondwana when Australia was connected to South America through Antarctica (i.e. Southern Gondwanan origin hypothesis). However, robust phylogenies with strong support for monophyly are lacking for the majority of Australian endemic butterfly lineages, thereby precluding determination of their systematic relationships and hence their geographic origins. Here, we use molecular data to reconstruct phylogenetic relationships of the globally distributed butterfly subtribe Coenonymphina (Satyrinae: Satyrini). This group represents a major component of the butterfly fauna of the wider Australasian region, with 19 genera and 71 species endemic to the region. Dating estimates extrapolated from secondary calibration sources indicate that the subtribe arose c. 48 Ma (95% credibility interval, 52–42 Ma), and the crown group first diverged in the Eocene (c. 44 Ma, 95% credibility interval 51–37 Ma). Rapid speciation events subsequently followed around the Eocence–Oligocene boundary, resulting in a near-hard polytomy comprising short basal branches with nodes that are difficult to resolve. Based on strongly supported phylogenetic relationships and estimates of divergence times, we conclude that the group probably had its origin in the fragment of Southern Gondwana consisting of Australia, Antarctica and South America. However, we are unable to rule out the northern dispersal scenario, particularly as Coenonymphina are closely related to a set of predominantly Asian lineages. Dispersal and extinction events following the final break-up of Gondwana have played a pivotal role in shaping the extant distributions of the group. (Less)

Aim: To infer divergence times and historical biogeography of the cosmopolitan lycophyte family Lycopodiaceae. Location: Worldwide. Methods: We generated time‐calibrated phylogenies of the Lycopodiaceae based on six regions of chloroplast DNA using a node‐dating approach implemented in beast with eight fossil calibrations. To investigate effects of among‐lineage substitution rate heterogeneity on divergence time estimation, we compared the performance of two relaxed clock models: an uncorrelated lognormal clock model and a random local clock (RLC) model. The historical biogeography of the family was inferred using two Bayesian models implemented in BioGeoBEARS. Results: Divergence time estimates for major groups of the Lycopodiaceae obtained using the two substitution clock models differed substantially, and the RLC model was a better fit. The Lycopodiaceae crown group age is estimated to be late Devonian, and most deep divergence events date to the Carboniferous, with most extant species diversity accumulating during the Cenozoic. The timing of divergences of major clades in the Lycopodiaceae corresponds to the breakup of the Pangaean and Gondwanan supercontinents. Long‐distance dispersal events are relatively common, but generally do not appear to be followed by subsequent radiations. Main conclusions: Accounting for among‐lineage substitution rate heterogeneity improves divergence time estimates for the Lycopodiaceae. The family has a deep evolutionary history, and continent‐scale vicariance events in the Mesozoic appear to have been associated with major cladogenesis events, with long‐distance dispersal playing a relatively minor role.

Chiliadenus is a small genus in the Inuleae (Asteraceae), consisting of ten species with allopatric distributions along the southern edge of the Mediterranean Sea. The different species have restricted areas of distribution, with only one being more widely distributed. The first molecular phylogenetic study of the genus with complete sampling, as well as a biogeographic analysis of the origin and biogeographic patterns leading to the current diversity of Chiliadenus is presented. Results confirm Chiliadenus as monophyletic and placed as sister to Dittrichia. The ancestor of Chiliadenus is dated to have diverged from that of Dittrichia around 5.45 Ma ago, coinciding with the Messinian salinity crisis, whereas the Chiliadenus crown group is dated to 2.29 Ma, around 3 million years later. Ancestral area reconstructions show the crown group to likely have originated in the area around Morocco and northwestern Algeria, which is also the area where the early divergences have occurred. Chiliadenus has then later diverged and dispersed over the Mediterranean to its current distribution. The evolution of the Chiliadenus crown group coincides with the onset of the Mediterranean climate, and its evolution may be connected to the subsequent climatic changes.

Apiosphaeria guaranitica, the causal agent of brown crust disease of several bignoniaceous hosts, among them Handroanthus and Tabebuia species, has been traditionally placed in Phyllachoraceae, based exclusively on morphological studies, without supporting molecular evidence. Here, we provide molecular data for the link between sexual and asexual states of the fungus and elucidate the phylogeny of A. guaranitica. The multilocus phylogenetic analyses employed sequences from the 18S subunit (18S), 28S subunit (28S), and nuclear internal transcribed spacers (ITS1-5.8S-ITS2 = ITS) of the nuc rDNA, second-largest subunit of RNA polymerase II (RPB2), and translation elongation factor 1-α (TEF1) genetic loci. Estimates of the divergence time of this lineage were supported by fossil calibration (FC) and secondary calibration (SC) strategies. Our results indicate a natural placement of Apiosphaeria within Diaporthaceae (Diaporthales), where it represents an ancient lineage of the crown group of Diaporthaceae, diverging during the late Paleocene at 61.15 (FC) and 60.63 (SC) million years ago. This divergence time estimate within Diaporthales is based on Spataporthe taylori, a diaporthaceous fossil.

A new species of the Marattialean fern frond Rothwellopteris is proposed for specimens preserving both morphology and anatomy from the Wuchiapingian–Changshingian (late Permian) aged Xuanwei Formation of South China. Fronds are at least bipinnate and bear falcate, pecopteroid pinnules with a thin lamina. The penultimate pinna rachis has a polycyclic vascular system with endarch primary xylem and longer vascular bundles located abaxially in a single radial row, and shorter vascular bundles adaxially arranged in two radial rows, with a vascular bundle sheath of sclerenchyma cells. Ground tissue comprises parenchyma cells and numerous secretory ducts. Features of the new species suggest that it was adapted for mesomorphy, while the previously recognized species Rothwellopteris pecopteroides was adapted for xeromorphy or was a sun-leaf. Like R. pecopteroides, the new species displays a mosaic of morphological and anatomical features characteristic of both the Paleozoic family Psaroniaceae and the extant family Marattiaceae; we interpret it to be a member of the evolutionary stem-group from which stratigraphically younger Marattiaceae evolved. Our findings show that the stem- to crown-group transition within Marattiales commenced before the end of the Permian and that a greater diversity of transitional forms can now be recognized from the late Permian and include the genera Compsopteris, Rothwellopteris, Tietea and Tuvichapteris.

Cololejeuneinae is the largest subtribe of the liverwort family Lejeuneaceae and the crown group of the family. The species often grow on the surfaces of living leaves and twigs or in swiftly running waters and many of them possess neotenic gametophytes, considered an adaptation to these extreme habitats. We describe a new, epiphyllous genus and species in Cololejeuneinae from the Western Cordillera of Ecuador, Reinerantha foliicola Gradst. & R.L.Zhu. Analysis of combined molecular datasets with parsimony, maximum likelihood and Bayesian methods revealed Reinerantha in a sister relationship to the large pantropical genus Diplasiolejeunea. Reinerantha differs from Diplasiolejeunea in leaf segmentation, epidermal wall thickening, stylus, male bracts and perianth keels, and is morphologically more similar to the genus Tuyamaella. In the molecular analysis, however, Reinerantha and Tuyamaella were resolved in different clades and not closely related. Tuyamaella is shown to be restricted to Asia; the report of Tuyamaella from South America (Peru) was erroneous and a case of mislabeling.

Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of post-polyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an inter-tribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere. The reconstructed ancestral allopolyploid genome (n = 15) originated probably in north-eastern Asia or western North America during the Late Miocene (c. 10.6 - 7 million years ago) and reached the Australian mainland via long-distance dispersal. In Australia, the allotetraploid genome diverged into at least three main subclades exhibiting different levels of PPD and diversity: 1.25-fold descending dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial Arabidella (3 species), 1.5-fold DD of n = 15 → n = 10 in the perennial Pachycladon (11 spp.), and 2.1 to 3.75-fold DD of n = 15 → n = 7 - 4 in the largely annual crown group genera (42 spp. in 15 genera). These results are among the first to demonstrate multi-speed genome evolution in taxa descending from a common allopolyploid ancestor. It is suggested that clade-specific PPD can operate at different rates and efficacies, and can be tentatively linked to life histories and the extent of taxonomic diversity. This article is protected by copyright. All rights reserved.

With approximately 25 endemic species, the genus Pyrus (pears) is highly diverse in the Caucasus ecoregion. The majority of Caucasian pears inhabit xerophytic open woodlands or similar habitats, to which they display morphological adaptations, such as narrow leaves. The other species, both Caucasian and non-Caucasian taxa, mainly inhabit mesophytic forests and display broad leaves. Using a representative taxon sampling of Pyrus from the Caucasus, Europe and Asia, we reconstruct phylogenetic relationships in the genus based on multiple plastid regions. We also estimate the divergence times of major clades in Pyrus, reconstruct the evolution of leaf shapes, and discuss the emergence of xeromorphic leaf traits. Our results confirm the monophyly of Pyrus and the existence of two major clades: (a) an E Asian clade with a crown group age of 15.7 (24.02–8.37 95% HPD) My, and (b) a W Eurasian clade that comprises species from Europe, SW Asia and the Caucasus and that displays a slightly younger crown group of 12.38 (19.02–6.41 95% HPD) My. The existing infrageneric classification of Pyrus was found partially incongruent with the inferred phylogenetic trees. Several currently accepted species were not recovered as monophyletic, indicating that current species limits require re-evaluation. Ancestral character state reconstructions revealed several independent transitions from broad- to narrow-shaped leaves in Pyrus, probably via intermediate-shaped leaves.

Aim The historical biogeography of the species-rich flowering plant genus Goniothalamus (c. 130 species) and the wider Annonaceae tribe Annoneae is investigated to evaluate hypotheses regarding the processes underlying tropical intercontinental disjunctions (‘long-distance dispersal [LDD]’ versus ‘boreotropics’) and floristic exchange between biodiversity hotspots in tropical Asia. Location Tropics, tropical Asia. Methods Divergence time estimation was based on plastid DNA sequence data (c. 10 kb; 164 Annonaceae accessions, including 65 Goniothalamus species) using an uncorrelated lognormal relaxed clock model and two fossil calibrations. Likelihood ancestral range estimation was performed using dispersal-extinction-cladogenesis models with and without time-stratified dispersal constraints. Results The boreotropics model incorporating high chances for intercontinental dispersal during 68–34 Ma fitted the data significantly better than LDD models enforcing low intercontinental dispersal rates. Multiple vicariance events were identified in Annoneae including at the Annoneae crown node (57–49 Ma, Africa/S+N America), and the Disepalum-Asimina split (27–24 Ma, Asia/N America). A wide ancestral range in continental SE Asia, W and E Malesia was inferred at the Goniothalamus crown node (24–21 Ma). Several dispersal events from continental SE Asia/W Malesia were identified in the Miocene: two north-eastwards to the Philippines, one eastwards to the Sahul Shelf and two westwards to India. Main conclusions The boreotropics hypothesis provides a well-supported, plausible explanation for the disjunctions and dispersal–vicariance patterns in tribe Annoneae. The wide distribution inferred at the Goniothalamus crown node indicates that its ancestors already bridged the marine gap between the Sunda and Sahul Shelves by LDD or rafting on tectonic plate microfragments. Dispersal across long-standing water bodies in Malesia occurred multiple times from the early Miocene as marine gaps decreased following tectonic plate convergence and land emergence. Substantially older crown group divergence estimates compared with previous studies indicate that hypotheses of rapid recent radiation in Goniothalamus must be rejected.

Albatross fossils have been collected from the late Oligocene Lincoln Creek Formation and the early/middle Miocene Astoria Formation near the townsite of Knappton, Pacific County, Washington (USA). The albatross from the Lincoln Creek Formation, Diomedavus knapptonensis, n. gen. et sp., is smaller than all extant albatrosses and represents the oldest published fossil albatross from the North Pacific Basin. Diomedavus knapptonensis is clearly distinguished from extant albatrosses in several osteological features; some are likely plesiomorphic, supporting a phylogenetic position outside the crown group. The unusual shape of the deltopectoral crest of the humerus suggests that D. knapptonensis also differed from extant albatrosses in its flight performance. A partial skeleton from the Astoria Formation likely represents another new albatross species; however, it is not named because there is no overlap with the skeletal elements of other fossil Diomedeidae. This species, here informally termed the “...

Although both the Yanliao and Jehol vertebrate assemblages are known for exceptional preservation of feathered dinosaurs, mammals, pterosaurs, lizards, salamanders, and fish, the Early Cretaceous Jehol Biota also contains birds, choristoderes, frogs, and turtles that are currently lacking in the Jurassic Yanliao Biota. The vertebrate assemblages of the Yanliao and Jehol biotas are very distinct from each other, with the salamander Liaoxitriton being the sole unquestionably shared taxon on generic level. Both assemblages contain mainly stem relatives of major clades of extant vertebrates, with all genera and species extinct. Crown group taxa are restricted to some fishes, salamanders, frogs, and turtles. In addition to its much greater taxonomic diversity, the Jehol vertebrate assemblage also shows a greater body size variation among dinosaurs, pterosaurs, and mammals (three major vertebrate groups shared by the two biotas); however, members of these groups are generally small in the Yanliao Biota. The Jehol aquatic vertebrates also show a much greater diversity, characterized by many large-sized forms such as acipenseriforms and choristoderes, possibly indicating growing and more expanded ecological adaptations of the Jehol vertebrates. The relatively greater biodiversity of pterosaurs in the Yanliao Biota as compared to that in the Jehol Biota was due possibly to the lack of birds as a competitor then. Birds in the Jehol Biota had occupied much of the similar ecological niches (forest, lakes etc.) with more sophisticated and refined flight capability. The Yanliao dinosaurs that were dominated by maniraptorans are either paravians or closely related species, possibly indicating that northeastern China could be an origin center of the earliest birds, consistent with the previous hypothesis that this area was probably also the origin and diversification center for many other biological groups. The flourishing time of the Jehol Biota (125 Ma) appears to be coincident with the peak of the destruction of the North China Craton, and the flourishing time of the Yanliao Biota (160 Ma) is coincident with the initiation time of the destruction of the North China Craton or the beginning of the subduction of the Paleo-Pacific plate underneath the Asian continent that resulted a series of tectonic and palaeogeographic and palaeoenvironmental changes, confirming the co-evolution between the two biotas and their geological and palaeoenvironmental background. The frequent volcanic activities during the formation of both the Yanliao and Jehol biotas not only provided much nutrient to the lakes, but also were critical for the exceptional soft tissue preservation of the two lagerstatten. The cold temperature or the fluctuation of temperature during the Middle Jurassic–Late Jurassic transition might be related to the first appearance of feathered dinosaurs and haired pterosaurs. The cold interval during the Early Cretaceous Jehol Biota could possibly partially explain the presence of many feathered dinosaurs including some large-sized theropods.

After the demise of many fish taxa including xenacanth sharks before the Late Triassic, non-marine fish faunas reappeared in Australia the mid-Jurassic in the East Gondwana component of Pangaea with one new chondrichthyan occurring in the Late Jurassic freshwater Talbragar Lagerstatten near Gulgong, New South Wales. The Kimmeridgian Talbragar Fossil Fish Bed unit yields a Jehol-type fauna and flora, with a variety of bony fishes as well as this first-known Jurassic shark in Australasia. The new taxon is based on a partial skeleton lacking a head but with at least partial fins and scales. The latter might be from a hybodontiform or synechodontiform shark or even a crown group neoselachian. From the inferred palaeogeography, this was one of the most southerly living chondrichthyans of the time.

Potentilleae, one of ten tribes of the Rosaceae, are mainly distributed in alpine regions of the northern hemisphere. The taxonomy of Potentilleae has been challenging due to extensive hybridization, polyploidization and/or apomixis characterizing several genera of Potentilleae, such as Alchemilla, Argentina and Potentilla. To help clarify relationships within Potentilleae, a phylogenetic analysis of the tribe with an emphasis on the polyphyletic genus Sibbaldia was conducted using nuclear ribosomal ITS and ETS and the plastid trnL-F and trnS-G spacer regions. In agreement with previous phylogenetic analyses, three major clades were identified in the present study–the subtribe Fragariinae, the genera Argentina and Potentilla. The 15 species of Sibbaldia were recovered in five distinct clades: three in subtribe Fragariinae, one in Argentina and the last in Potentilla. The recently established genus Chamaecallis, comprising a single species formerly treated in Sibbaldia that has intermediate floral character states with respect to Fragariinae and Potentilla, was recovered as sister to Drymocallis. Morphological character state reconstruction indicated that a reduction in the number of stamens (≤10) is a derived character state that has arisen multiple times in Potentilleae. Molecular dating analyses agreed with previously published estimates and suggested that crown group Potentilleae arose in the Middle to Late Eocene, with most generic-level divergences occurring in the Oligocene and Miocene.

Interest in the origin and evolution of Equus dates back to over a century, but there is still no consensus on the definition of the genus or its phylogenetic position. We review the placement of Equus within several phylogenetic frameworks and present a phylogenetic analysis of derived Equini, including taxa referred to Equus, Haringtonhippus, Dinohippus, Astrohippus, Hippidion, and Boreohippidion. A new, morphology-based phylogenetic tree was used as an initial hypothesis for discussing what taxa Equus encompasses, using four criteria previously used to define the genus category in mammals: phylogenetic gaps, uniqueness of adaptive zone, crown group definition, and divergence time. According to the phylogenetic gaps criterion, Equus encompasses clade 6 (Ha. francisci = E. francisci, E. conversidens, E. quagga, E. hemionus, E. mexicanus, E. ferus, E. occidentalis, and E. neogeus) based on morphological synapomorphies. Equus is assigned to clade 6, or possibly clade 7, according to the uniqueness of adaptive zone criterion. The crown group criterion places Equus at clade 6. Based on the time-calibrated phylogeny of Equini, the divergence time criterion suggests that Equus encompasses clade 9. This clade comprises all taxa traditionally assigned to Equus analyzed in our study, including the eight taxa listed above as well as E. stenonis, E. idahoensis, and E. simplicidens; the latter two are sometimes referred to the subgenus Plesippus and the former to the subgenus Allohippus. With the exception of the divergence time criterion, the results of our evaluation are congruent in identifying clade 6 as the most suitable position for Equus. The taxonomic implications of delimiting Equus to clade 6 in our phylogenetic tree include elevation of Allohippus and Plesippus to generic rank, assignment of a new genus to “Dinohippus” mexicanus, and synonymy of Haringtonhippus with Equus.

The subclass Corallinophycidae is the only group of red algae characterized by the presence of calcite crystals in their cell walls. Except for the Rhodogorgonales, the remaining orders - collectively called corallines - are diverse and widely distributed, having calcified cell walls and highly variable morphology. Corallines constitute the group with the richest fossil record among marine algae. In the present study, we investigate the evolutionary history of the subclass Corallinophycidae and provide a time-calibrated phylogeny to date the radiation of the crown group and its main lineages. We use a multi-locus dataset with an extensive taxon sampling and comprehensive collection of fossil records, carefully assigned to corallines, to reconstruct a time-calibrated phylogeny of this subclass. Our molecular clock analyses suggest that the onset of crown group diversification of Corallinophycidae started in the Lower Jurassic and sped up in the Lower Cretaceous. The divergence time of the oldest order Sporolithales is estimated in the Lower Cretaceous followed by the remaining orders. We discuss the long period of more than 300 million years between the early Paleozoic records attributed to the stem group of Corallinophycidae and the radiation of the crown group. Our inferred phylogeny yields three highly-supported suprageneric lineages for the order Corallinales; we confirm the family Mastophoraceae and amend circumscription of the families Corallinaceae and Lithophyllaceae. These three families are distinguished by a combination of vegetative and reproductive features. In light of the phylogeny, we discuss the evolutionary trends of eleven morphological characters. In addition, we also highlight homoplasious characters and selected autapomorphies emerging in particular taxa. ispartof: MOLECULAR PHYLOGENETICS AND EVOLUTION vol:150 ispartof: location:United States status: published

The attine ants are a monophyletic lineage that switched to fungus farming ca. 55–60 MYA. They have become a model for the study of complex symbioses after additional fungal and bacterial symbionts were discovered, but their abdominal endosymbiotic bacteria remain largely unknown. Here, we present a comparative microbiome analysis of endosymbiotic bacteria spanning the entire phylogenetic tree. We show that, across 17 representative sympatric species from eight genera sampled in Panama, abdominal microbiomes are dominated by Mollicutes, α‐ and γ‐Proteobacteria, and Actinobacteria. Bacterial abundances increase from basal to crown branches in the phylogeny reflecting a shift towards putative specialized and abundant abdominal microbiota after the ants domesticated gongylidia‐bearing cultivars, but before the origin of industrial‐scale farming based on leaf‐cutting herbivory. This transition coincided with the ancestral single colonization event of Central/North America ca. 20 MYA, documented in a recent phylogenomic study showing that almost the entire crown group of the higher attine ants, including the leaf‐cutting ants, evolved there and not in South America. Several bacterial species are located in gut tissues or abdominal organs of the evolutionarily derived, but not the basal attine ants. The composition of abdominal microbiomes appears to be affected by the presence/absence of defensive antibiotic‐producing actinobacterial biofilms on the worker ants' cuticle, but the significance of this association remains unclear. The patterns of diversity, abundance and sensitivity of the abdominal microbiomes that we obtained explore novel territory in the comparative analysis of attine fungus farming symbioses and raise new questions for further in‐depth research., see also the Perspective by Pringle

BackgroundChondrichthyans represent a monophyletic group of crown group gnathostomes and are central to our understanding of vertebrate evolution. Like all vertebrates, cartilaginous fishes evolved concretions of material within their inner ears to aid with equilibrium and balance detection. Up to now, these materials have been identified as calcium carbonate-bearing otoconia, which are small bio-crystals consisting of an inorganic mineral and a protein, or otoconial masses (aggregations of otoconia bound by an organic matrix), being significantly different in morphology compared to the singular, polycrystalline otolith structures of bony fishes, which are solidified bio-crystals forming stony masses. Reinvestigation of the morphological and chemical properties of these chondrichthyan otoconia revises our understanding of otolith composition and has implications on the evolution of these characters in both the gnathostome crown group, and cartilaginous fishes in particular.ResultsDissections ofAmblyraja radiata,Potamotrygon leopoldi, andScyliorhinus canicularevealed three pairs of singular polycrystalline otolith structures with a well-defined morphology within their inner ears, as observed in bony fishes. IR spectroscopy identified the material to be composed of carbonate/collagen-bearing apatite in all taxa. These findings contradict previous hypotheses suggesting these otoconial structures were composed of calcium carbonate in chondrichthyans. A phylogenetic mapping using 37 chondrichthyan taxa further showed that the acquisition of phosphatic otolith structures might be widespread within cartilaginous fishes.ConclusionsDifferences in the size and shape of otoliths between taxa indicate a taxonomic signal within elasmobranchs. Otoliths made of carbonate/collagen-bearing apatite are reported for the first time in chondrichthyans. The intrinsic pathways to form singular, polycrystalline otoliths may represent the plesiomorphic condition for vertebrates but needs further testing. Likewise, the phosphatic composition of otoliths in early vertebrates such as cyclostomes and elasmobranchs is probably closely related to the lack of bony tissue in these groups, supporting a close relationship between skeletal tissue mineralization patterns and chemical otolith composition, underlined by physiological constraints.

Scorpions (Arachnida: Scorpiones Koch, 1837) are an ancient chelicerate arthropod lineage characterised by distinctive subdivision of the opisthosoma and venomous toxicity. The crown group is represented by over 2400 extant species, and unambiguous fossil representatives are known at least from the Cretaceous Period. However, a number of extinct scorpion lineages existed in the Palaeozoic Era, many of which are of a contentious marine (or at least semi-aquatic) lifestyle, and have long caused confusion regarding the nature of arachnid terrestrialization and arachnid phylogeny more broadly. To clarify the process of terrestrialization, there is a need to marry fossil and extant scorpions in a common evolutionary framework utilising modern advances in phylogenetics. Here, we review phylogenetic hypotheses of arachnid and scorpion interrelationships, relevant advances in phylogenetic divergence time estimation and the scorpion fossil record—especially with reference to terrestrialization. In addition, we provide a list of scorpion fossil calibrations for use in molecular dating and demonstrate their utility in deriving a novel scorpion time tree using Bayesian relaxed-clock methods. Our results reveal a window of divergence from 335 to 266 Mya for the scorpion crown group, consistent with a Pangean origin of crown scorpions inferred from the biogeographical distribution of the extant fauna, R. J. Howard was supported by NERC GW4+ doctoral training partnership, D. A. Legg was supported by a Dame Kathleen Ollerenshaw Fellowship from the University of Manchester, and J. L-F was supported by a Marie Skłodowska-Curie fellowship (655814).

Background In comparative neurobiology, major transitions in behavior are thought to be associated with proportional size changes in brain regions. Bird-line theropod dinosaurs underwent a drastic locomotory shift from terrestrial to volant forms, accompanied by a suite of well-documented postcranial adaptations. To elucidate the potential impact of this locomotor shift on neuroanatomy, we first tested for a correlation between loss of flight in extant birds and whether the brain morphology of these birds resembles that of their flightless, non-avian dinosaurian ancestors. We constructed virtual endocasts of the braincase for 80 individuals of non-avian and avian theropods, including 25 flying and 19 flightless species of crown group birds. The endocasts were analyzed using a three-dimensional (3-D) geometric morphometric approach to assess changes in brain shape along the dinosaur-bird transition and secondary losses of flight in crown-group birds (Aves). Results While non-avian dinosaurs and crown-group birds are clearly distinct in endocranial shape, volant and flightless birds overlap considerably in brain morphology. Phylogenetically informed analyses show that locomotory mode does not significantly account for neuroanatomical variation in crown-group birds. Linear discriminant analysis (LDA) also indicates poor predictive power of neuroanatomical shape for inferring locomotory mode. Given current sampling, Archaeopteryx, typically considered the oldest known bird, is inferred to be terrestrial based on its endocranial morphology. Conclusion The results demonstrate that loss of flight does not correlate with an appreciable amount of neuroanatomical changes across Aves, but rather is partially constrained due to phylogenetic inertia, evident from sister taxa having similarly shaped endocasts. Although the present study does not explicitly test whether endocranial changes along the dinosaur-bird transition are due to the acquisition of powered flight, the prominent relative expansion of the cerebrum, in areas associated with flight-related cognitive capacity, suggests that the acquisition of flight may have been an important initial driver of brain shape evolution in theropods. Electronic supplementary material The online version of this article (10.1186/s12862-018-1312-0) contains supplementary material, which is available to authorized users.

Ottelia Pers. is the second largest genus of the family Hydrocharitaceae, including approximately 23 extant species. The genus exhibits a diversity of both bisexual and unisexual flowers, and complex reproductive system comprising cross-pollinated to cleistogamous flowers. Ottelia has been regarded as a pivotal group to study the evolution of Hydrocharitaceae, but the phylogenic relationships and evolutionary history of the genus remain unresolved. Here, we reconstructed a robust phylogenetic framework for Ottelia using 40 newly assembled complete plastomes. Our results resolved Ottelia as a monophyletic genus consisting of two major clades, which correspond to the main two centers of diversity in Asia and Africa. According to the divergence time estimation analysis, the crown group Ottelia began to diversify around 13.09 Ma during the middle Miocene. The biogeographical analysis indicated the existence of the most recent common ancestor somewhere in Africa/Australasia/Asia. Basing on further insights from the morphological evolution of Ottelia, we hypothesized that the ancestral center of origin was in Africa, from where the range expanded by transoceanic dispersal to South America and Australasia, and further from Australasia to Asia. We suggested that the climatic change and global cooling since the mid-Miocene, such as the development of East Asian monsoon climate and tectonic movement of the Yunnan-Guizhou Plateau (YGP), might have played a crucial role in the evolution of Ottelia in China.

Actualistic observations form the basis of many taphonomic studies in paleontology. However, surveys limited by environment or taxon may not be applicable far beyond the bounds of the initial observations. Even when multiple studies exploring the potential variety within a taphonomic process exist, quantitative methods for comparing these datasets in order to identify larger scale patterns have been understudied. This research uses modern bite marks collected from 21 of the 23 generally recognized species of extant Crocodylia to explore statistical and phylogenetic methods of synthesizing taphonomic datasets. Bite marks were identified, and specimens were then coded for presence or absence of different mark morphotypes. Attempts to find statistical correlation between trace types, marking animal vital statistics, and sample collection protocol were unsuccessful. Mapping bite mark character states on a eusuchian phylogeny successfully predicted the presence of known diagnostic, bisected marks in extinct taxa. Predictions for clades that may have created multiple subscores, striated marks, and extensive crushing were also generated. Inclusion of fossil bite marks which have been positively associated with extinct species allow this method to be projected beyond the crown group. The results of this study indicate that phylogenies can and should be further explored for use as predictive tools in a taphonomic framework.