Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network.

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

Jumping performance in tree squirrels: Insights into primate evolution.

Morphological traits suggesting powerful jumping abilities are characteristic of early crown primate fossils. Because tree squirrels lack certain 'primatelike' grasping features but frequently travel on the narrow terminal branches of trees, they make a viable extant model for an early stage of primate evolution. Here, we explore biomechanical determinants of jumping performance in the arboreal Eastern gray squirrel (Sciurus carolinensis, n = 3) as a greater understanding of the biomechanical strategies that squirrels use to modulate jumping performance could inform theories of selection for increased jumping ability during early primate evolution. We assessed vertical jumping performance by using instrumented force platforms upon which were mounted launching supports of various sizes, allowing us to test the influence of substrate diameter on jumping kinetics and performance. We used standard ergometric methods to quantify jumping parameters (e.g., takeoff velocity, total displacement, peak mechanical power) from force platform data during push-off. We found that tree squirrels display divergent mechanical strategies according to the type of substrate, prioritizing force production on flat ground versus center of mass displacement on narrower poles. As jumping represents a significant part of the locomotor behavior of most primates, we suggest that jumping from small arboreal substrates may have acted as a potential driver of the selection for elongated hindlimb segments in primates, allowing the center of mass to be accelerated over a longer distance-and thereby reducing the need for high substrate reaction forces.

Unveiling the third dimension in morphometry with automated quantitative volumetric computations.

As computed tomography and related technologies have become mainstream tools across a broad range of scientific applications, each new generation of instrumentation produces larger volumes of more-complex 3D data. Lagging behind are step-wise improvements in computational methods to rapidly analyze these new large, complex datasets. Here we describe novel computational methods to capture and quantify volumetric information, and to efficiently characterize and compare shape volumes. It is based on innovative theoretical and computational reformulation of volumetric computing. It consists of two theoretical constructs and their numerical implementation: the spherical wave decomposition (SWD), that provides fast, accurate automated characterization of shapes embedded within complex 3D datasets; and symplectomorphic registration with phase space regularization by entropy spectrum pathways (SYMREG), that is a non-linear volumetric registration method that allows homologous structures to be correctly warped to each other or a common template for comparison. Together, these constitute the Shape Analysis for Phenomics from Imaging Data (SAPID) method. We demonstrate its ability to automatically provide rapid quantitative segmentation and characterization of single unique datasets, and both inter-and intra-specific comparative analyses. We go beyond pairwise comparisons and analyze collections of samples from 3D data repositories, highlighting the magnified potential our method has when applied to data collections. We discuss the potential of SAPID in the broader context of generating normative morphologies required for meaningfully quantifying and comparing variations in complex 3D anatomical structures and systems.

Insights from macroevolutionary modelling and ancestral state reconstruction into the radiation and historical dietary ecology of Lemuriformes (Primates, Mammalia).

BACKGROUND: Lemurs once rivalled the diversity of rest of the primate order despite thier confinement to the island of Madagascar. We test the adaptive radiation model of Malagasy lemur diversity using a novel combination of phylogenetic comparative methods and geometric methods for quantifying tooth shape. RESULTS: We apply macroevolutionary model fitting approaches and disparity through time analysis to dental topography metrics associated with dietary adaptation, an aspect of mammalian ecology which appears to be closely related to diversification in many clades. Metrics were also reconstructed at internal nodes of the lemur tree and these reconstructions were combined to generate dietary classification probabilities at internal nodes using discriminant function analysis. We used these reconstructions to calculate rates of transition toward folivory per million-year intervals. Finally, lower second molar shape was reconstructed at internal nodes by modelling the change in shape of 3D meshes using squared change parsimony along the branches of the lemur tree. Our analyses of dental topography metrics do not recover an early burst in rates of change or a pattern of early partitioning of subclade disparity. However, rates of change in adaptations for folivory were highest during the Oligocene, an interval of possible forest expansion on the island. CONCLUSIONS: There was no clear phylogenetic signal of bursts of morphological evolution early in lemur history. Reconstruction of the molar morphologies corresponding to the ancestral nodes of the lemur tree suggest that this may have been driven by a shift toward defended plant resources, however. This suggests a response to the ecological opportunity offered by expanding forests, but not necessarily a classic adaptive radiation initiated by dispersal to Madagascar.

First navicular remains of a European adapiform (Anchomomys frontanyensis) from the Middle Eocene of the Eastern Pyrenees (Catalonia, Spain): implications for early primate locomotor behavior and navicular evolution.

We describe the first known navicular bones for an Eocene euprimate from Europe and assess their implications for early patterns of locomotor evolution in primates. Recovered from the fossil site of Sant Jaume de Frontanyà-3C (Barcelona, Spain), the naviculars are attributed to Anchomomys frontanyensis. The small size of A. frontanyensis allows us to consider behavioral implications of comparisons with omomyiforms, regardless of allometric sources of navicular variation. Researchers usually consider omomyiforms to be more prone to leaping than contemporaneous adapiforms partly because of the more pronounced elongation of omomyiform tarsal elements. However, A. frontanyensis differs from other adapiforms and is similar to some omomyiforms in its more elongated navicular proportions. Although this might raise questions about attribution of these naviculars to A. frontanyensis, the elements exhibit clear strepsirrhine affinities leaving little doubt about the attribution: the bones' mesocuneiform facets contact their cuboid facets. We further propose that this strepsirrhine-specific feature in A. frontanyensis and other adapiforms reflects use of more inverted foot postures and potentially smaller substrates than sympatric omomyiforms that lack it. Thus substrate differences may have influenced niche partitioning in Eocene euprimate communities along with differences in locomotor agility. As previous studies on the astragalus and the calcaneus have suggested, this study on the navicular is consistent with the hypothesis that the locomotor mode of A. frontanyensis was similar to that of extant cheirogaleids, especially species of Microcebus and Mirza.

A digital collection of rare and endangered lemurs and other primates from the Duke Lemur Center.

Scientific study of lemurs, a group of primates found only on Madagascar, is crucial for understanding primate evolution. Unfortunately, lemurs are among the most endangered animals in the world, so there is a strong impetus to maximize as much scientific data as possible from available physical specimens. MicroCT scanning efforts at Duke University have resulted in scans of more than 100 strepsirrhine cadavers representing 18 species from the Duke Lemur Center. An error study of the microCT scanner recovered less than 0.3% error at multiple resolution levels. Scans include specimen overviews and focused, high-resolution selections of complex anatomical regions (e.g., cranium, hands, feet). Scans have been uploaded to MorphoSource, an online digital repository for 3D data. As captive (but free ranging) individuals, these specimens have a wealth of associated information that is largely unavailable for wild populations, including detailed life history data. This digital collection maximizes the information obtained from rare and endangered animals with minimal degradation of the original specimens.

Vertical support use and primate origins.

Adaptive scenarios of crown primate origins remain contentious due to uncertain order of acquisition and functional significance of the clade's diagnostic traits. A feature of the talus bone in the ankle, known as the posterior trochlear shelf (PTS), is well-regarded as a derived crown primate trait, but its adaptive significance has been obscured by poorly understood function. Here we propose a novel biomechanical function for the PTS and model the talus as a cam mechanism. By surveying a large sample of primates and their closest relatives, we demonstrate that the PTS is most strongly developed in extant taxa that habitually grasp vertical supports with strongly dorsiflexed feet. Tali of the earliest fossils likely to represent crown primates exhibit more strongly developed PTS cam mechanisms than extant primates. As a cam, the PTS may increase grasping efficiency in dorsiflexed foot postures by increasing the path length of the flexor fibularis tendon, and thus improve the muscle's ability to maintain flexed digits without increasing energetic demands. Comparisons are made to other passive digital flexion mechanisms suggested to exist in other vertebrates. These results provide robust anatomical evidence that the habitual vertical support use exerted a strong selective pressure during crown primate origins.

My branch is your branch: Talar morphology correlates with relative substrate size in platyrrhines at Tiputini Biodiversity Station, Ecuador.

Given that most species of primates are predominantly arboreal, maintaining the ability to move among branches of varying sizes has presumably been a common selective force in primate evolution. However, empirical evaluations of the relationships between morphological variation and characteristics of substrate geometry, such as substrate diameter relative to an animal's body mass, have been limited by the lack of quantified substrate usage in the wild. Here we use recently published quantitative data to assess the relationships between relative substrate size and talar morphology in nine New World monkey species at the Tiputini Biodiversity Station, Ecuador. Within this sample, both fibular facet angle (the angle between the fibular facet and the trochlear rims) and body-mass-standardized area of the medial tibial facet decrease as average and maximum relative substrate size increases. Correlations between medial tibial facet area and relative substrate size are driven by the inclusion of callitrichids in this sample. Nevertheless, these findings strengthen the hypothesis that variation in fibular facet orientation and medial tibial facet area are functionally correlated with habitual degrees of pedal inversion. They also strengthen the notion that evolutionarily changing body mass could impact habitat geometry experienced by a lineage and thereby substantially impact major trends in primate morphological evolution. This study highlights the importance of empirical data on substrate use in living primates for inferring functional and evolutionary implications of morphological variation.

Carotid foramen size in the human skull tracks developmental changes in cerebral blood flow and brain metabolism.

OBJECTIVES: In humans, neuronal processes related to brain development elevate the metabolic rate of brain tissue relative to the body during early childhood. This phenomenon has been hypothesized to contribute to slow somatic growth in preadolescent Homo sapiens. The uncoupling of the brain's metabolic rate from brain size during development complicates the study of the evolutionary emergence of these traits in the fossil record. Here, we extend a method previously developed to predict interspecific differences in cerebral blood flow (a correlate of cerebral glucose use) to predict ontogenetic changes in human brain metabolism. MATERIALS AND METHODS: Radii of the carotid foramen from an ontogenetic series of modern human crania were used to predict blood flow rates through the internal carotid arteries (ICA), which were compared to empirically measured ICA flow and brain metabolism values. RESULTS: Predictions of both absolute ICA blood flow rates and perfusion (ICA blood flow rates relative to brain size) generally match measured values in infancy and childhood. Maximum predicted ICA blood flow rates and perfusion were found to occur between ages 5 and 8, which roughly correspond to the age of maximum measured ICA blood flow rate and absolute and brain mass-specific rate of whole brain glucose uptake. DISCUSSION: These findings suggest that, during human growth and development, the size of the carotid foramen corresponds well to blood flow requirements through the ICA, and the method tested here may provide new opportunities for studying developmental changes in brain metabolism using osteological samples, including fossil hominins.

New fossils, systematics, and biogeography of the oldest known crown primate Teilhardina from the earliest Eocene of Asia, Europe, and North America.

Omomyiform primates are among the most basal fossil haplorhines, with the oldest classified in the genus Teilhardina and known contemporaneously from Asia, Europe, and North America during the Paleocene-Eocene Thermal Maximum (PETM) ∼56 mya. Characterization of morphology in this genus has been limited by small sample sizes and fragmentary fossils. A new dental sample (n = 163) of the North American species Teilhardina brandti from PETM strata of the Bighorn Basin, Wyoming, documents previously unknown morphology and variation, prompting the need for a systematic revision of the genus. The P4 of T. brandti expresses a range of variation that encompasses that of the recently named, slightly younger North American species 'Teilhardina gingerichi,' which is here synonymized with T. brandti. A new partial dentary preserving the alveoli for P1-2 demonstrates that T. brandti variably expresses an unreduced, centrally-located P1, and in this regard is similar to that of T. asiatica from China. This observation, coupled with further documentation of variability in P1 alveolar size, position, and presence in the European type species T. belgica, indicates that the original diagnosis of T. asiatica is insufficient at distinguishing this species from either T. belgica or T. brandti. Likewise, the basal omomyiform 'Archicebus achilles' requires revision to be distinguished from Teilhardina. Results from a phylogenetic analysis of 1890 characters scored for omomyiforms, adapiforms, and other euarchontan mammals produces a novel clade including T. magnoliana, T. brandti, T. asiatica, and T. belgica to the exclusion of two species previously referred to Teilhardina, which are here classified in a new genus (Bownomomys americanus and Bownomomys crassidens). While hypotheses of relationships and inferred biogeographic patterns among species of Teilhardina could change with the discovery of more complete fossils, the results of these analyses indicate a similar probability that the genus originated in either Asia or North America.

Group-wise Shape Correspondence of Variable and Complex Objects.

We present a group-wise shape correspondence method for analyzing variable and complex objects in a population study. The proposed method begins with the standard spherical harmonics (SPHARM) point distribution models (PDM) with their spherical mappings. In case of complex and variable objects, the equal area spherical mapping based SPHARM correspondence is imperfect. For such objects, we present here a novel group-wise correspondence. As an example dataset, we use 12 second mandibular molars representing 6 living or fossil euarchontan species. To improve initial correspondence of the SPHARM-PDM representation, we first apply a rigid transformation on each subject using five well-known landmarks (molar cusps). We further enhance the correspondence by optimizing landmarks (local) and multidimensional geometric property (global) over each subject with spherical harmonic representation. The resulting average shape model better captures sharp landmark representation in quantitative evaluation as well as a nice separation of different species compared with that of the SPHARM-PDM method.

Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar's aye-aye.

In 1967 G.G. Simpson described three partial mandibles from early Miocene deposits in Kenya that he interpreted as belonging to a new strepsirrhine primate, Propotto. This interpretation was quickly challenged, with the assertion that Propotto was not a primate, but rather a pteropodid fruit bat. The latter interpretation has not been questioned for almost half a century. Here we re-evaluate the affinities of Propotto, drawing upon diverse lines of evidence to establish that this strange mammal is a strepsirrhine primate as originally suggested by Simpson. Moreover, our phylogenetic analyses support the recognition of Propotto, together with late Eocene Plesiopithecus from Egypt, as African stem chiromyiform lemurs that are exclusively related to the extant aye-aye (Daubentonia) from Madagascar. Our results challenge the long-held view that all lemurs are descended from a single ancient colonization of Madagascar, and present an intriguing alternative scenario in which two lemur lineages dispersed from Africa to Madagascar independently, possibly during the later Cenozoic.

Oldest evidence for grooming claws in euprimates.

Euprimates are unusual among mammals in having fingers and toes with flat nails. While it seems clear that the ancestral stock from which euprimates evolved had claw-bearing digits, the available fossil record has not yet contributed a detailed understanding of the transition from claws to nails. This study helps clarify the evolutionary history of the second pedal digit with fossils representing the distal phalanx of digit two (dpII), and has broader implications for other digits. Among extant primates, the keratinized structure on the pedal dpII widely varies in form. Extant strepsirrhines and tarsiers have narrow, distally tapering, dorsally inclined nails (termed a 'grooming claws' for their use in autogrooming), while extant anthropoids have more typical nails that are wider and lack distal tapering or dorsal inclination. At least two fossil primate species thought to be stem members of the Strepsirrhini appear to have had grooming claws, yet reconstructions of the ancestral euprimate condition based on direct evidence from the fossil record are ambiguous due to inadequate fossil evidence for the earliest haplorhines. Seven recently discovered, isolated distal phalanges from four early Eocene localities in Wyoming (USA) closely resemble those of the pedal dpII in extant prosimians. On the basis of faunal associations, size, and morphology, these specimens are recognized as the grooming phalanges of five genera of haplorhine primates, including one of the oldest known euprimates (∼56 Ma), Teilhardina brandti. Both the phylogenetic distribution and antiquity of primate grooming phalanges now strongly suggest that ancestral euprimates had grooming claws, that these structures were modified from a primitive claw rather than a flat nail, and that the evolutionary loss of 'grooming claws' represents an apomorphy for crown anthropoids.

Scaling of bony canals for encephalic vessels in euarchontans: Implications for the role of the vertebral artery and brain metabolism.

Supplying the central nervous system with oxygen and glucose for metabolic activities is a critical function for all animals at physiologic, anatomical, and behavioral levels. A relatively proximate challenge to nourishing the brain is maintaining adequate blood flow. Euarchontans (primates, dermopterans and treeshrews) display a diversity of solutions to this challenge. Although the vertebral artery is a major encephalic vessel, previous research has questioned its importance for irrigating the cerebrum. This presents a puzzling scenario for certain strepsirrhine primates (non-cheirogaleid lemuriforms) that have reduced promontorial branches of the internal carotid artery and no apparent alternative encephalic vascular route except for the vertebral artery. Here, we present results of phylogenetic comparative analyses of data on the cross-sectional area of bony canals that transmit the vertebral artery (transverse foramina). These results show that, across primates (and within major primate subgroups), variation in the transverse foramina helps significantly to explain variation in forebrain mass even when variation in promontorial canal cross-sectional areas are also considered. Furthermore, non-cheirogaleid lemuriforms have larger transverse foramina for their endocranial volume than other euarchontans, suggesting that the vertebral arteries compensate for reduced promontorial artery size. We also find that, among internal carotid-reliant euarchontans, species that are more encephalized tend to have a promontorial canal that is larger relative to the transverse foramina. Tentatively, we consider the correlation between arterial canal diameters (as a proxy for blood flow) and brain metabolic demands. The results of this analysis imply that human investment in brain metabolism (∼27% of basal metabolic rate) may not be exceptional among euarchontans.

Development and Assessment of Fully Automated and Globally Transitive Geometric Morphometric Methods, With Application to a Biological Comparative Dataset With High Interspecific Variation.

Automated geometric morphometric methods are promising tools for shape analysis in comparative biology, improving researchers' abilities to quantify variation extensively (by permitting more specimens to be analyzed) and intensively (by characterizing shapes with greater fidelity). Although use of these methods has increased, published automated methods have some notable limitations: pairwise correspondences are frequently inaccurate and pairwise mappings are not globally consistent (i.e., they lack transitivity across the full sample). Here, we reassess the accuracy of published automated methods-cPDist (Boyer et al. Proc Nat Acad Sci 108 () 18221-18226) and auto3Dgm (Boyer et al.: Anat Rec 298 () 249-276)-and evaluate several modifications to these methods. We show that a substantial percentage of alignments and pairwise maps between specimens of dissimilar geometries were inaccurate in the study of Boyer et al. (Proc Nat Acad Sci 108 () 18221-18226), despite a taxonomically partitioned variance structure of continuous Procrustes distances. We show these inaccuracies are remedied using a globally informed methodology within a collection of shapes, rather than relying on pairwise comparisons (c.f. Boyer et al.: Anat Rec 298 () 249-276). Unfortunately, while global information generally enhances maps between dissimilar objects, it can degrade the quality of correspondences between similar objects due to the accumulation of numerical error. We explore a number of approaches to mitigate this degradation, quantify their performance, and compare the generated pairwise maps (and the shape space characterized by these maps) to a "ground truth" obtained from landmarks manually collected by geometric morphometricians. Novel methods both improve the quality of the pairwise correspondences relative to cPDist and achieve a taxonomic distinctiveness comparable to auto3Dgm. Anat Rec, 301:636-658, 2018. © 2017 Wiley Periodicals, Inc.

Postcrania of the most primitive euprimate and implications for primate origins.

The fossil record of early primates is largely comprised of dentitions. While teeth can indicate phylogenetic relationships and dietary preferences, they say little about hypotheses pertaining to the positional behavior or substrate preference of the ancestral crown primate. Here we report the discovery of a talus bone of the dentally primitive fossil euprimate Donrussellia provincialis. Our comparisons and analyses indicate that this talus is more primitive than that of other euprimates. It lacks features exclusive to strepsirrhines, like a large medial tibial facet and a sloping fibular facet. It also lacks the medially positioned flexor-fibularis groove of extant haplorhines. In these respects, the talus of D. provincialis comes surprisingly close to that of the pen-tailed treeshrew, Ptilocercus lowii, and extinct plesiadapiforms for which tali are known. However, it differs from P. lowii and is more like other early euprimates in exhibiting an expanded posterior trochlear shelf and deep talar body. In overall form, the bone approximates more leaping reliant euprimates. The phylogenetically basal signal from the new fossil is confirmed with cladistic analyses of two different character matrices, which place D. provincialis as the most basal strepsirrhine when the new tarsal data are included. Interpreting our results in the context of other recent discoveries, we conclude that the lineage leading to the ancestral euprimate had already become somewhat leaping specialized, while certain specializations for the small branch niche came after crown primates began to radiate.

Semi-supervised determination of pseudocryptic morphotypes using observer-free characterizations of anatomical alignment and shape.

Accurate, quantitative characterization of complex shapes is recognized as a key methodological challenge in biology. Recent development of automated three-dimensional geometric morphometric protocols (auto3dgm) provides a promising set of tools to help address this challenge. While auto3dgm has been shown to be useful in characterizing variation across clades of morphologically very distinct mammals, it has not been adequately tested in more problematic cases where pseudolandmark placement error potentially confounds interpretation of true shape variation. Here, we tested the sensitivity of auto3dgm to the degree of variation and various parameterization settings using a simulation and three microCT datasets that characterize mammal tooth crown morphology as biological examples. The microCT datasets vary in degree of apparent morphological differentiation, with two that include grossly similar morphospecies and one that includes two laboratory strains of a single species. Resulting alignments are highly sensitive to the number of pseudolandmarks used to quantify shapes. The degree to which the surfaces were downsampled and the apparent degree of morphological differentiation across the dataset also influenced alignment repeatability. We show that previous critiques of auto3dgm were based on poorly parameterized alignments and suggest that sample-specific sensitivity analyses should be added to any research protocol including auto3dgm. Auto3dgm is a useful tool for studying samples when pseudolandmark placement error is small relative to the true differences between specimens. This method therefore represents a promising avenue forward in morphometric studies at a wide range of scales, from samples that differ by a single genetic locus to samples that represent multiple phylogenetically diverse clades.

Physical activity alters limb bone structure but not entheseal morphology.

Studies of ancient human skeletal remains frequently proceed from the assumption that individuals with robust limb bones and/or rugose, hypertrophic entheses can be inferred to have been highly physically active during life. Here, we experimentally test this assumption by measuring the effects of exercise on limb bone structure and entheseal morphology in turkeys. Growing females were either treated with a treadmill-running regimen for 10 weeks or served as controls. After the experiment, femoral cortical and trabecular bone structure were quantified with µCT in the mid-diaphysis and distal epiphysis, respectively, and entheseal morphology was quantified in the lateral epicondyle. The results indicate that elevated levels of physical activity affect limb bone structure but not entheseal morphology. Specifically, animals subjected to exercise displayed enhanced diaphyseal and trabecular bone architecture relative to controls, but no significant difference was detected between experimental groups in entheseal surface topography. These findings suggest that diaphyseal and trabecular structure are more reliable proxies than entheseal morphology for inferring ancient human physical activity levels from skeletal remains.