Laser-stimulated fluorescence in paleontology.

Fluorescence using ultraviolet (UV) light has seen increased use as a tool in paleontology over the last decade. Laser-stimulated fluorescence (LSF) is a next generation technique that is emerging as a way to fluoresce paleontological specimens that remain dark under typical UV. A laser's ability to concentrate very high flux rates both at the macroscopic and microscopic levels results in specimens fluorescing in ways a standard UV bulb cannot induce. Presented here are five paleontological case histories that illustrate the technique across a broad range of specimens and scales. Novel uses such as back-lighting opaque specimens to reveal detail and detection of specimens completely obscured by matrix are highlighted in these examples. The recent cost reductions in medium-power short wavelength lasers and use of standard photographic filters has now made this technique widely accessible to researchers. This technology has the potential to automate multiple aspects of paleontology, including preparation and sorting of microfossils. This represents a highly cost-effective way to address paleontology's preparatory bottleneck.

Raman spectroscopic documentation of Oligocene bladder stone.

Discovery of a fossil (30-35 million-year-old) urolith from Early Oligocene deposits in northeastern Colorado provides the earliest evidence for the antiquity of bladder stones. These are spherical objects with a layered phosphatic structure and a hollow center. Each layer is composed of parallel crystals oriented perpendicular to the surface. Macroscopic and microscopic examination and X-ray diffraction analysis, along with comparison with 1,000 contemporary uroliths, were used as evidence in the confirmation of this diagnosis. Raman microspectroscopy verified the presence of organic material between layers, confirming its biologic origin.

Physical evidence of predatory behavior in Tyrannosaurus rex.

Feeding strategies of the large theropod, Tyrannosaurus rex, either as a predator or a scavenger, have been a topic of debate previously compromised by lack of definitive physical evidence. Tooth drag and bone puncture marks have been documented on suggested prey items, but are often difficult to attribute to a specific theropod. Further, postmortem damage cannot be distinguished from intravital occurrences, unless evidence of healing is present. Here we report definitive evidence of predation by T. rex: a tooth crown embedded in a hadrosaurid caudal centrum, surrounded by healed bone growth. This indicates that the prey escaped and lived for some time after the injury, providing direct evidence of predatory behavior by T. rex. The two traumatically fused hadrosaur vertebrae partially enclosing a T. rex tooth were discovered in the Hell Creek Formation of South Dakota.

Mycobacterium tuberculosis complex lipid virulence factors preserved in the 17,000-year-old skeleton of an extinct bison, Bison antiquus.

Tracing the evolution of ancient diseases depends on the availability and accessibility of suitable biomarkers in archaeological specimens. DNA is potentially information-rich but it depends on a favourable environment for preservation. In the case of the major mycobacterial pathogens, Mycobacterium tuberculosis and Mycobacterium leprae, robust lipid biomarkers are established as alternatives or complements to DNA analyses. A DNA report, a decade ago, suggested that a 17,000-year-old skeleton of extinct Bison antiquus, from Natural Trap Cave, Wyoming, was the oldest known case of tuberculosis. In the current study, key mycobacterial lipid virulence factor biomarkers were detected in the same two samples from this bison. Fluorescence high-performance liquid chromatography (HPLC) indicated the presence of mycolic acids of the mycobacterial type, but they were degraded and could not be precisely correlated with tuberculosis. However, pristine profiles of C(29), C(30) and C(32) mycocerosates and C(27) mycolipenates, typical of the Mycobacterium tuberculosis complex, were recorded by negative ion chemical ionization gas chromatography mass spectrometry of pentafluorobenzyl ester derivatives. These findings were supported by the detection of C(34) and C(36) phthiocerols, which are usually esterified to the mycocerosates. The existence of Pleistocene tuberculosis in the Americas is confirmed and there are many even older animal bones with well-characterised tuberculous lesions similar to those on the analysed sample. In the absence of any evidence of tuberculosis in human skeletons older than 9,000 years BP, the hypothesis that this disease evolved as a zoonosis, before transfer to humans, is given detailed consideration and discussion.

Species-specific responses of Late Quaternary megafauna to climate and humans.

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.

Fossil evidence of avian crops from the Early Cretaceous of China.

The crop is characteristic of seed-eating birds today, yet little is known about its early history despite remarkable discoveries of many Mesozoic seed-eating birds in the past decade. Here we report the discovery of some early fossil evidence for the presence of a crop in birds. Two Early Cretaceous birds, the basal ornithurine Hongshanornis and a basal avian Sapeornis, demonstrate that an essentially modern avian digestive system formed early in avian evolution. The discovery of a crop in two phylogenetically remote lineages of Early Cretaceous birds and its absence in most intervening forms indicates that it was independently acquired as a specialized seed-eating adaptation. Finally, the reduction or loss of teeth in the forms showing seed-filled crops suggests that granivory was possibly one of the factors that resulted in the reduction of teeth in early birds.

Model tests of gliding with different hindwing configurations in the four-winged dromaeosaurid Microraptor gui.

Fossils of the remarkable dromaeosaurid Microraptor gui and relatives clearly show well-developed flight feathers on the hind limbs as well as the front limbs. No modern vertebrate has hind limbs functioning as independent, fully developed wings; so, lacking a living example, little agreement exists on the functional morphology or likely flight configuration of the hindwing. Using a detailed reconstruction based on the actual skeleton of one individual, cast in the round, we developed light-weight, three-dimensional physical models and performed glide tests with anatomically reasonable hindwing configurations. Models were tested with hindwings abducted and extended laterally, as well as with a previously described biplane configuration. Although the hip joint requires the hindwing to have at least 20 degrees of negative dihedral (anhedral), all configurations were quite stable gliders. Glide angles ranged from 3 degrees to 21 degrees with a mean estimated equilibrium angle of 13.7 degrees, giving a lift to drag ratio of 4.1:1 and a lift coefficient of 0.64. The abducted hindwing model's equilibrium glide speed corresponds to a glide speed in the living animal of 10.6 m x s(-1). Although the biplane model glided almost as well as the other models, it was structurally deficient and required an unlikely weight distribution (very heavy head) for stable gliding. Our model with laterally abducted hindwings represents a biologically and aerodynamically reasonable configuration for this four-winged gliding animal. M. gui's feathered hindwings, although effective for gliding, would have seriously hampered terrestrial locomotion.

100-million-year dynasty of giant planktivorous bony fishes in the Mesozoic seas.

Large-bodied suspension feeders (planktivores), which include the most massive animals to have ever lived, are conspicuously absent from Mesozoic marine environments. The only clear representatives of this trophic guild in the Mesozoic have been an enigmatic and apparently short-lived Jurassic group of extinct pachycormid fishes. Here, we report several new examples of these giant bony fishes from Asia, Europe, and North America. These fossils provide the first detailed anatomical information on this poorly understood clade and extend its range from the lower Middle Jurassic to the end of the Cretaceous, showing that this group persisted for more than 100 million years. Modern large-bodied, planktivorous vertebrates diversified after the extinction of pachycormids at the Cretaceous-Paleogene boundary, which is consistent with an opportunistic refilling of vacated ecospace.

The birdlike raptor Sinornithosaurus was venomous.

We suggest that some of the most avian dromaeosaurs, such as Sinornithosaurus, were venomous, and propose an ecological model for that taxon based on its unusual dentition and other cranial features including grooved teeth, a possible pocket for venom glands, and a groove leading from that pocket to the exposed bases of the teeth. These features are all analogous to the venomous morphology of lizards. Sinornithosaurus and related dromaeosaurs probably fed on the abundant birds of the Jehol forests during the Early Cretaceous in northeastern China.

Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity.

Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions.

Density-based load estimation using two-dimensional finite element models: a parametric study.

A parametric investigation was conducted to determine the effects on the load estimation method of varying: (1) the thickness of back-plates used in the two-dimensional finite element models of long bones, (2) the number of columns of nodes in the outer medial and lateral sections of the diaphysis to which the back-plate multipoint constraints are applied and (3) the region of bone used in the optimization procedure of the density-based load estimation technique. The study is performed using two-dimensional finite element models of the proximal femora of a chimpanzee, gorilla, lion and grizzly bear. It is shown that the density-based load estimation can be made more efficient and accurate by restricting the stimulus optimization region to the metaphysis/epiphysis. In addition, a simple method, based on the variation of diaphyseal cortical thickness, is developed for assigning the thickness to the back-plate. It is also shown that the number of columns of nodes used as multipoint constraints does not have a significant effect on the method.

Did ice-age bovids spread tuberculosis?

Pathognomonic metacarpal undermining is a skeletal pathology that has been associated with Mycobacterium tuberculosis in bovids. Postcranial artiodactyl, perissodactyl, and carnivore skeletons were examined in major university and museum collections of North America and Europe for evidence of this and other pathology potentially attributable to tuberculosis. Among nonproboscidean mammals from pre-Holocene North America, bone lesions indicative of tuberculosis were restricted to immigrant bovids from Eurasia. No bone lesions compatible with diagnosis of tuberculosis were found in large samples of other pre-Holocene (164 Oligocene, 397 Miocene, and 1,041 Plio-Pleistocene) North American mammals, including 114 antilocaprids. Given the unchanged frequency of bovid tubercular disease during the Pleistocene, it appears that most did not die from the disease but actually reached an accommodation with it (as did the mastodon) (Rothschild and Laub 2006). Thus, they were sufficiently long-lived to assure greater spread of the disease. The relationships of the proboscidean examples need further study, but present evidence suggests a Holarctic spread of tuberculosis during the Pleistocene, with bovids acting as vectors. While the role of other animals in the transmission of tuberculosis could be considered, the unique accommodation achieved by bovids and mastodons makes them the likely "culprits" in its spread.

A contact algorithm for density-based load estimation.

An algorithm, which includes contact interactions within a joint, has been developed to estimate the dominant loading patterns in joints based on the density distribution of bone. The algorithm is applied to the proximal femur of a chimpanzee, gorilla and grizzly bear and is compared to the results obtained in a companion paper that uses a non-contact (linear) version of the density-based load estimation method. Results from the contact algorithm are consistent with those from the linear method. While the contact algorithm is substantially more complex than the linear method, it has some added benefits. First, since contact between the two interacting surfaces is incorporated into the load estimation method, the pressure distributions selected by the method are more likely indicative of those found in vivo. Thus, the pressure distributions predicted by the algorithm are more consistent with the in vivo loads that were responsible for producing the given distribution of bone density. Additionally, the relative positions of the interacting bones are known for each pressure distribution selected by the algorithm. This should allow the pressure distributions to be related to specific types of activities. The ultimate goal is to develop a technique that can predict dominant joint loading patterns and relate these loading patterns to specific types of locomotion and/or activities.

Rise and fall of the Beringian steppe bison.

The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.