Sauropod dinosaurs evolved moderately sized genomes unrelated to body size

The coevolution of rostral keratin and tooth distribution in dinosaurs

Teeth evolved early in vertebrate evolution, and their morphology reflects important specializations in diet and ecology among species. The toothless jaws (edentulism) in extant birds likely coevolved with beak keratin, which functionally replaced teeth. However, extinct dinosaurs lost teeth multiple times independently and exhibited great variation in toothrow distribution and rhamphotheca-like keratin structures. Here, we use rostral jawbone surface texture as a proxy for rostral keratin covering and phylogenetic comparative models to test for the influence of rostral keratin on toothrow distribution in Mesozoic dinosaurs. We find that the evolution of rostral keratin covering explains partial toothrow reduction but not jaw toothlessness. Toothrow reduction preceded the evolution of rostral keratin cover in theropods. Non-theropod dinosaurs evolved continuous toothrows despite evolving rostral keratin covers (e.g. some ornithischians and sauropodomorphs). We also show that rostral keratin covers did not significantly increase the evolutionary rate of tooth loss, which further delineates the antagonistic relationship between these structures. Our results suggest that the evolution of rostral keratin had a limited effect on suppressing tooth development. Independent changes in jaw development may have facilitated further tooth loss. Furthermore, the evolution of strong chemical digestion, a gizzard, and a dietary shift to omnivory or herbivory likely alleviated selective pressures for tooth development.

Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem

The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.

Quantifying intracortical bone microstructure: A critical appraisal of 2D and 3D approaches for assessing vascular canals and osteocyte lacunae

Describing and quantifying vascular canal orientation and volume of osteocyte lacunae in bone is important in studies of bone growth, mechanics, health and disease. It is also an important element in analysing fossil bone in palaeohistology, key to understanding the growth, life and death of extinct animals. Often, bone microstructure is studied using two-dimensional (2D) sections, and three-dimensional (3D) shape and orientation of structures are estimated by modelling the structures using idealised geometries based on information from their cross sections. However, these methods rely on structures meeting strict geometric assumptions. Recently, 3D methods have been proposed which could provide a more accurate and robust approach to bone histology, but these have not been tested in direct comparison with their 2D counterparts in terms of accuracy and sensitivity to deviations from model assumptions. We compared 2D and 3D methodologies for estimating key microstructural traits using a combination of experimental and idealised test data sets. We generated populations of cylinders (canals) and ellipsoids (osteocyte lacunae), varying the cross-sectional aspect ratios of cylinders and orientation of ellipsoids to test sensitivity to deviations from cylindricality and longitudinal orientation, respectively. Using published methods, based on 2D sections and 3D data sets, we estimated cylinder orientation and ellipsoid volume. We applied the same methods to six CT data sets of duck cortical bone, using the full volumes for 3D measurements and single CT slices to represent 2D sections. Using in silico test data sets that did deviate from ideal cylinders and ellipsoids resulted in inaccurate estimates of cylinder or canal orientation, and reduced accuracy in estimates of ellipsoid and lacunar volume. These results highlight the importance of using appropriate 3D imaging and quantitative methods for quantifying volume and orientation of 3D structures and offer approaches to significantly enhance our understanding of bone physiology based on accurate measures for bone microstructures.

Three-dimensional characterization of osteocyte volumes at multiple scales, and its relationship with bone biology and genome evolution in ray-finned fishes

Osteocytes, cells embedded within the bone mineral matrix, inform on key aspects of vertebrate biology. In particular, a relationship between volumes of the osteocytes and bone growth and/or genome size has been proposed for several tetrapod lineages. However, the variation in osteocyte volume across different scales is poorly characterized and mostly relies on incomplete, two-dimensional information. In this study, we characterize the variation of osteocyte volumes in ray-finned fishes (Actinopterygii), a clade including more than half of modern vertebrate species in which osteocyte biology is poorly known. We use X-ray synchrotron micro-computed tomography (SRµCT) to achieve a three-dimensional visualization of osteocyte lacunae and direct measurement of their size (volumes). Our specimen sample is designed to characterize variation in osteocyte lacuna morphology at three scales: within a bone, among the bones of one individual and among species. At the intra-bone scale, we find that osteocyte lacunae vary noticeably in size between zones of organized and woven bone (being up to six times larger in woven bone), and across cyclical bone deposition. This is probably explained by differences in bone deposition rate, with larger osteocyte lacunae contained in bone that deposits faster. Osteocyte lacuna volumes vary 3.5-fold among the bones of an individual, and this cannot readily be explained by variation in bone growth rate or other currently observable factors. Finally, we find that genome size provides the best explanation of variation in osteocyte lacuna volume among species: actinopterygian taxa with larger genomes (polyploid taxa in particular) have larger osteocyte lacunae (with a ninefold variation in median osteocyte volume being measured). Our findings corroborate previous two-dimensional studies in tetrapods that also observed similar patterns of intra-individual variation and found a correlation with genome size. This opens new perspectives for further studies on bone evolution, physiology and palaeogenomics in actinopterygians, and vertebrates as a whole.

The relationship between genome size and metabolic rate in extant vertebrates

Genome size has long been hypothesized to affect the metabolic rate in various groups of animals. The mechanism behind this proposed association is the nucleotypic effect, in which large nucleus and cell sizes influence cellular metabolism through surface area-to-volume ratios. Here, we provide a review of the recent literature on the relationship between genome size and metabolic rate. We also conduct an analysis using phylogenetic comparative methods and a large sample of extant vertebrates. We find no evidence that the effect of genome size improves upon models in explaining metabolic rate variation. Not surprisingly, our results show a strong positive relationship between metabolic rate and body mass, as well as a substantial difference in metabolic rate between endothermic and ectothermic vertebrates, controlling for body mass. The presence of endothermy can also explain elevated rate shifts in metabolic rate whereas genome size cannot. We further find no evidence for a punctuated model of evolution for metabolic rate. Our results do not rule out the possibility that genome size affects cellular physiology in some tissues, but they are consistent with previous research suggesting little support for a direct functional connection between genome size and basal metabolic rate in extant vertebrates. This article is part of the theme issue 'Vertebrate palaeophysiology'.

Scaling of statically derived osteocyte lacunae in extant birds: implications for palaeophysiological reconstruction

Osteocytes are mature versions of osteoblasts, bone-forming cells that develop in two ways: via 'static' osteogenesis, differentiating and ossifying tissue in situ to form a scaffold upon which other bone can form, or 'dynamic' osteogenesis, migrating to infill or lay down bone around neurovasculature. A previous study regressed the volume of osteocyte lacunae derived from dynamic osteogenesis (DO) of a broad sample of extant bird species against body mass, the growth rate constant ( k), mass-specific metabolic rate, genome size, and erythrocyte size. There were significant relationships with body mass, growth rate, metabolic rate, and genome size, with the latter being the strongest. Using the same avian histological dataset, we measured over 3800 osteocyte lacunar axes derived from static osteogenesis (SO) in order to look for differences in the strength of form-function relationships inferred for DO-derived lacunae at the cellular and tissue levels. The relationship between osteocyte lacunar volume and body mass was stronger when measuring SO lacunae, whereas relationships between osteocyte lacunar volume versus growth rate and basal metabolic rate disappeared. The relationship between osteocyte lacuna volume and genome size remained significant and moderately strong when measuring SO lacunae, whereas osteocyte lacuna volume was still unrelated to erythrocyte size. Our results indicate that growth and metabolic rate signals are contained in avian DO but not SO osteocyte lacunae, suggesting that the former should be used in estimating these parameters in extinct animals.

Quantitative histological models suggest endothermy in plesiosaurs

Background

Plesiosaurs are marine reptiles that arose in the Late Triassic and survived to the Late Cretaceous. They have a unique and uniform bauplan and are known for their very long neck and hydrofoil-like flippers. Plesiosaurs are among the most successful vertebrate clades in Earth’s history. Based on bone mass decrease and cosmopolitan distribution, both of which affect lifestyle, indications of parental care, and oxygen isotope analyses, evidence for endothermy in plesiosaurs has accumulated. Recent bone histological investigations also provide evidence of fast growth and elevated metabolic rates. However, quantitative estimations of metabolic rates and bone growth rates in plesiosaurs have not been attempted before.

Methods

Phylogenetic eigenvector maps is a method for estimating trait values from a predictor variable while taking into account phylogenetic relationships. As predictor variable, this study employs vascular density, measured in bone histological sections of fossil eosauropterygians and extant comparative taxa. We quantified vascular density as primary osteon density, thus, the proportion of vascular area (including lamellar infillings of primary osteons) to total bone area. Our response variables are bone growth rate (expressed as local bone apposition rate) and resting metabolic rate (RMR).

Results

Our models reveal bone growth rates and RMRs for plesiosaurs that are in the range of birds, suggesting that plesiosaurs were endotherm. Even for basal eosauropterygians we estimate values in the range of mammals or higher.

Discussion

Our models are influenced by the availability of comparative data, which are lacking for large marine amniotes, potentially skewing our results. However, our statistically robust inference of fast growth and fast metabolism is in accordance with other evidence for plesiosaurian endothermy. Endothermy may explain the success of plesiosaurs consisting in their survival of the end-Triassic extinction event and their global radiation and dispersal.

Long bone histology of the stem salamander Kokartus honorarius (Amphibia: Caudata) from the Middle Jurassic of Kyrgyzstan

Kokartus honorarius from the Middle Jurassic (Bathonian) of Kyrgyzstan is one of the oldest salamanders in the fossil record, characterized by a mixture of plesiomorphic morphological features and characters shared with crown-group salamanders. Here we present a detailed histological analysis of its long bones. The analysis of a growth series demonstrates a significant histological maturation during ontogeny, expressed by the progressive appearance of longitudinally oriented primary vascular canals, primary osteons, growth marks, remodelling features in primary bone tissues, as well as progressive resorption of the calcified cartilage, formation of endochondral bone and development of cartilaginous to bony trabeculae in the epiphyses. Apart from the presence of secondary osteons, the long bone histology of Kokartus is very similar to that of miniaturized temnospondyls, other Jurassic stem salamanders, miniaturized seymouriamorphs and modern crown-group salamanders. We propose that the presence of secondary osteons in Kokartus honorarius is a plesiomorphic feature, and the loss of secondary osteons in the long bones of crown-group salamanders as well as in those of miniaturized temnospondyls is the result of miniaturization processes. Hitherto, all stem salamander long bong histology (Kokartus, Marmorerpeton and 'salamander A') has been generally described as having paedomorphic features (i.e. the presence of Katschenko's Line and a layer of calcified cartilage), these taxa were thus most likely neotenic forms. The absence of clear lines of arrested growth and annuli in long bones of Kokartus honorarius suggests that the animals lived in an environment with stable local conditions.

Measurement, variation, and scaling of osteocyte lacunae: a case study in birds

Basic issues surrounding osteocyte biology are still poorly understood, including the variability of osteocyte morphology within and among bones, individuals, and species. Several studies have suggested that the volume or shape of osteocytes (or their lacunae) is related to bone and/or organismal growth rate or metabolism, but the nature of this relationship, if any, is unclear. Furthermore, several studies have linked osteocyte lacuna volume with genome size or growth rate and suggested that osteocyte lacuna volume is unrelated to body size. Herein the scaling of osteocyte lacuna volume with body mass, growth and basal metabolic rates, genome size, and red blood cell size is examined using a broad sample of extant birds within a phylogenetic framework. Over 12,000 osteocyte lacuna axes were measured in a variety of bones from 34 avian and four non-avian dinosaur species. Osteocyte lacunae in parallel-fibered bone are scalene ellipsoids; their morphology and volume cannot be reliably estimated from any single thin section, and using a prolate ellipsoid model to estimate osteocyte lacuna volume results in a substantial (ca. 2-7 times) underestimate relative to true lacunar volume. Orthogonal thin sections reveal that in birds, even when only observing parallel-fibered, primary, cortical bone, intra-skeletal variation in osteocyte lacuna volume and shape is very high (volumes vary by a factor of 5.4 among different bones), whereas variation among homologous bones of the same species is low (1.2-44%; mean=12%). Ordinary and phylogenetically informed bivariate and multiple regressions demonstrate that in birds, osteocyte volume scales significantly but weakly with body mass and mass-specific basal metabolic rate and moderately with genome size, but not with erythrocyte size. Avian whole-body growth rate and osteocyte lacuna volume are weakly and inversely related. Finally, we present the first three-dimensionally calculated osteocyte volumes for several non-avian dinosaurs, which are much larger than previously reported values and smaller than those of large extant avians. Osteocyte volumes estimated from a single transverse section and assuming prolate morphology, as done in previous studies, are relative underestimates in theropod dinosaurs compared to sauropod dinosaurs, raising the possibility that no major change in osteocyte volumes (and genome size) occurred within Theropoda on the lineage leading to birds. Osteocyte volume is intertwined with several organismal attributes whose relative importance varies at a number of hierarchical levels.

Variation in osteocytes morphology vs bone type in turtle shell and their exceptional preservation from the Jurassic to the present

Here we describe variations in osteocytes derived from each of the three bone layers that comprise the turtle shell. We examine osteocytes in bone from four extant turtle species to form a morphological 'baseline', and then compare these with morphologies of osteocytes preserved in Cenozoic and Mesozoic fossils. Two different morphotypes of osteocytes are recognized: flattened-oblate osteocytes (FO osteocytes), which are particularly abundant in the internal cortex and lamellae of secondary osteons in cancellous bone, and stellate osteocytes (SO osteocytes), principally present in the interstitial lamellae between secondary osteons and external cortex. We show that the morphology of osteocytes in each of the three bone layers is conserved through ontogeny. We also demonstrate that these morphological variations are phylogenetically independent, as well as independent of the bone origin (intramembranous or endochondral). Preservation of microstructures consistent with osteocytes in the morphology in Cenozoic and Mesozoic fossil turtle bones appears to be common, and occurs in diverse diagenetic environments including marine, freshwater, and terrestrial deposits. These data have potential to illuminate aspects of turtle biology and evolution previously unapproachable, such as estimates of genome size of extinct species, differences in metabolic rates among different bones from a single individual, and potential function of osteocytes as capsules for preservation of ancient biomolecules.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

Variation of osteocyte lacunae size within the tetrapod skeleton: implications for palaeogenomics

Recent studies have emphasized the ability to reconstruct genome sizes (C-values) of extinct organisms such as dinosaurs, using correlations between known genome sizes and bone cell (osteocyte lacunae) volumes. Because of the established positive relationship between cell size and genome size in extant vertebrates, osteocyte lacunae volume is a viable proxy for reconstructing C-values in the absence of any viable genetic material. However, intra-skeletal osteocyte lacunae size variation, which could cause error in genome size estimation, has remained unexplored. Here, 11 skeletal elements of one individual from each of four major clades (Mammalia, Amphibia, Aves, Reptilia) were examined histologically. Skeletal elements in all four clades exhibit significant differences in the average sizes of their lacunae. This variation, however, generally does not cause a significant difference in the estimated genome size when common phylogenetic estimation methods are employed. On the other hand, the spread of the estimations illustrates that this method may not be precise. High variance in genome size estimations remains an outstanding problem. Additionally, a suite of new methods is introduced to further automate the measurement of bone cells and other microstructural features on histological thin sections.

Genome evolution in Reptilia, the sister group of mammals

The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.