Cranial and postcranial morphological data in ruminant phylogenetics

While the identity and validity of the extant families of ruminants are undoubted, there are significant problems with the determination of the interrelationships among the families, notably within the families of the Pecora, or horned ruminants. The morphological features used to construct ruminant phylogeny have been a source of controversy: many features used over the past century have been shown to be highly homoplastic and related to functional similarities. Ruminants evolved in the context of the later Cenozoic climatic changes, and many lineages adopted functional morphological adaptations related to feeding on more abrasive diets (resulting in the parallel evolution of a greater extent of loph development in the molars and, in some lineages, hypsodonty) and locomotion in open habitats (resulting in the parallel evolution of fused metapodials and reduction and/or loss of lateral digits). The fact that the molecular phylogeny shows a very different pattern from the currently accepted morphological one is of particular cause for concern, especially as molecular data are of no use for understanding the relationships of extinct lineages. Here we review the morphological data used in ruminant phylogenetics, and show even many of the less obviously functional features (e.g., number and position of the lacrimal orifices) are subject to homoplasy and variation, especially when fossil taxa are included. In addition, many morphological features treated as independent traits in phylogenetics are correlated (e.g., cranial morphology associated with hypsodonty). Some potentially reliable features are identified, but these do not help to sort out relationships within the Pecora. We advocate for the investigation into better morphological features, possibly derived from basicranial and ear region characters (although these features are not without their own issues of homoplasy), and for caution in character consideration in performing phylogenetic analyses

Jurassic Pork: What Could a Jewish Time Traveler Eat?

Paleontologists use multiple methods to reconstruct the anatomy and behavior of extinct animals, including direct observations from well-preserved fossils and inferences from the phylogeny of modern and extinct relatives. We illustrate these techniques by reference to the biblical definitions of kosher and non-kosher animals; that is, how can we apply these approaches to the hypothetical question of whether an extinct form would have been kosher. The biblical categories do not readily map to modern understandings of systematics, but are heavily based on life mode. When given, distinguishing characteristics, such as the presence of fins and scales in aquatic animals, can be readily seen directly in fossils. In other cases, such as cud chewing, they need to be inferred from the phylogenetic relationships of the fossil forms. Dinosaurs (other than birds), unfortunately, are not kosher. A kosher “paleo diet” would be increasingly difficult further in the past. The use of biblical content as a way of introducing concepts from paleontology and evolutionary biology, such as crown groups and stem groups, should be of broad interest.https://doi.org/10.1186/s12052-015-0047-

Sharpening the mesowear tool: geometric morphometric analysis of cusp shape and diet in ruminants

Mesowear is a dietary proxy that relates attritive wear and abrasive wear to the shape of worn tooth cusps of ungulates. Traditional mesowear methods categorize cusps according to relief and sharpness. A geometric morphometric approach has the potential to measure shape with higher precision and to discover unrecognized aspects of cusp shape, possibly improving the efficacy of mesowear. We quantified mesowear in extant Ruminantia, using a 2-D semilandmark outline technique on upper second molar metacones generated from photographs. Among the 91 species sampled, 65 were preassigned to dietary categories, browser, grazer, mixed feeder, and frugivore based on substantiated documentation of diet in the wildlife literature. Metacone cusp shape and metacone mesowear score were found to be independent of size. Principal component and discriminant function analyses of Procrustes transformed semilandmark coordinates revealed two diet-related components of cusp shape. The primary component is related to the traditional mesowear variables of cusp height and side steepness. The secondary shape component reveals variation in the mesiodistal symmetry of the metacone and may relate to a proal vector during the power stroke phase or the relative orientation of the cusps with respect to the chewing stroke vector. Discriminant function analysis of semilandmark data accurately classified the diets of species more frequently (67.2%) than the traditional mesowear method (56.1%). The semilandmark data successfully recognized the diets of grazing and browsing species with correct classification rates ranging from 69% to 95%. The diets of frugivorous and mixed feeding species were less frequently correctly recognized (33%–53%). Mixed feeding diets may be more difficult to recognize due to more heterogeneous diets when compared to browsers and grazers. Frugivores are more difficult to recognize because their rounded cusp apices resemble those of mixed feeders and grazers. We conclude that quantitative shape analysis improves the potential of mesowear. When used as a dietary proxy, we anticipate that mesowear analysis will correctly categorize the diets of most species. When misclassifications are made, they may most often be misclassifications of generalist mixed feeders and frugivores as either browsers or grazers

The Drosophila Mitochondrial Translation Elongation Factor G1 Contains a Nuclear Localization Signal and Inhibits Growth and DPP Signaling

Mutations in the human mitochondrial elongation factor G1 (EF-G1) are recessive lethal and cause death shortly after birth. We have isolated mutations in iconoclast (ico), which encodes the highly conserved Drosophila orthologue of EF-G1. We find that EF-G1 is essential during fly development, but its function is not required in every tissue. In contrast to null mutations, missense mutations exhibit stronger, possibly neomorphic phenotypes that lead to premature death during embryogenesis. Our experiments show that EF-G1 contains a secondary C-terminal nuclear localization signal. Expression of missense mutant forms of EF-G1 can accumulate in the nucleus and cause growth and patterning defects and animal lethality. We find that transgenes that encode mutant human EF-G1 proteins can rescue ico mutants, indicating that the underlying problem of the human disease is not just the loss of enzymatic activity. Our results are consistent with a model where EF-G1 acts as a retrograde signal from mitochondria to the nucleus to slow down cell proliferation if mitochondrial energy output is low

Common Functional Correlates of Head-Strike Behavior in the Pachycephalosaur Stegoceras validum (Ornithischia, Dinosauria) and Combative Artiodactyls

BACKGROUND: Pachycephalosaurs were bipedal herbivorous dinosaurs with bony domes on their heads, suggestive of head-butting as seen in bighorn sheep and musk oxen. Previous biomechanical studies indicate potential for pachycephalosaur head-butting, but bone histology appears to contradict the behavior in young and old individuals. Comparing pachycephalosaurs with fighting artiodactyls tests for common correlates of head-butting in their cranial structure and mechanics. METHODS/PRINCIPAL FINDINGS: Computed tomographic (CT) scans and physical sectioning revealed internal cranial structure of ten artiodactyls and pachycephalosaurs Stegoceras validum and Prenocephale prenes. Finite element analyses (FEA), incorporating bone and keratin tissue types, determined cranial stress and strain from simulated head impacts. Recursive partition analysis quantified strengths of correlation between functional morphology and actual or hypothesized behavior. Strong head-strike correlates include a dome-like cephalic morphology, neurovascular canals exiting onto the cranium surface, large neck muscle attachments, and dense cortical bone above a sparse cancellous layer in line with the force of impact. The head-butting duiker Cephalophus leucogaster is the closest morphological analog to Stegoceras, with a smaller yet similarly rounded dome. Crania of the duiker, pachycephalosaurs, and bighorn sheep Ovis canadensis share stratification of thick cortical and cancellous layers. Stegoceras, Cephalophus, and musk ox crania experience lower stress and higher safety factors for a given impact force than giraffe, pronghorn, or the non-combative llama. CONCLUSIONS/SIGNIFICANCE: Anatomy, biomechanics, and statistical correlation suggest that some pachycephalosaurs were as competent at head-to-head impacts as extant analogs displaying such combat. Large-scale comparisons and recursive partitioning can greatly refine inference of behavioral capability for fossil animals

Best practices for justifying fossil calibrations.

Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule, with replacement rates established (calibrated) using paleontological age estimates from textbooks (e.g., Dodson 1960). Since that time, the amount of molecular sequence data has increased dramatically, affording ever-greater opportunities to apply molecular divergence approaches to fundamental problems in evolutionary biology

Cheek Tooth Morphology and Ancient Mitochondrial DNA of Late Pleistocene Horses from the Western Interior of North America: Implications for the Taxonomy of North American Late Pleistocene Equus

Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus) and a non-caballine (E. conversidens) species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis) was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study

Combined searches for the production of supersymmetric top quark partners in proton-proton collisions at root s=13 TeV

A combination of searches for top squark pair production using proton-proton collision data at a center-of-mass energy of 13 TeV at the CERN LHC, corresponding to an integrated luminosity of 137 fb(-1) collected by the CMS experiment, is presented. Signatures with at least 2 jets and large missing transverse momentum are categorized into events with 0, 1, or 2 leptons. New results for regions of parameter space where the kinematical properties of top squark pair production and top quark pair production are very similar are presented. Depending on themodel, the combined result excludes a top squarkmass up to 1325 GeV for amassless neutralino, and a neutralinomass up to 700 GeV for a top squarkmass of 1150 GeV. Top squarks with masses from 145 to 295 GeV, for neutralino masses from 0 to 100 GeV, with a mass difference between the top squark and the neutralino in a window of 30 GeV around the mass of the top quark, are excluded for the first time with CMS data. The results of theses searches are also interpreted in an alternative signal model of dark matter production via a spin-0 mediator in association with a top quark pair. Upper limits are set on the cross section for mediator particle masses of up to 420 GeV