Morphometry and allometry of the primate humerus

The primate distal humerus has been used both in phylogenetic reconstruction and in assessing locomotor and postural adaptations. This study uses an allometric approach to predict locomotor patterns of extant primates regardless of phylogenetic position. By showing the relationship between form and function in living primate taxa it will be possible to use this data set to predict locomotor behavior of extinct primates. Several linear measurements were taken from the distal humerus of 71 extant primate species (anthropoids and prosimians). Allometric regressions of each measurement were performed with mandibular M₂ area as a surrogate for body size. These measurements were used to determine if significant differences in distal humerus morphology exist among locomotor groups. The results were then used to test several hypotheses about the relationship between humeral form and function. For example, the hypothesis that suspensory primates have a large medial epicondyle is confirmed; the hypothesis that terrestrial quadrupeds have a deep olecranon fossa could not be confirmed with quantitative data. In addition to this hypothesis testing, the residuals from the allometric regressions of the humeral measurements were used in a discriminant functions analysis to estimate locomotor behavior from distal humerus morphology. The discriminant functions analysis correctly reclassified 64/71 (90%) species.     

Locomotion,posture, and the foramen magnum in primates: Reliability of indices and insights into hominin bipedalism

The position (FMP) and orientation (FMO) of the foramen magnum have been used as proxies for locomotion and posture in extant and extinct primates. Several indices have been designed to quantify FMP and FMO but their application has led to conflicting results. Here, we test six widely used indices and two approaches (univariate and multivariate) for their capability to discriminate between postural and locomotor types in extant primates and fossil hominins. We then look at the locomotion of australopithecines and Homo on the base of these new findings. The following measurements are used: the opisthocranion–prosthion (OP–PR) and the opisthocranion–glabella (OP–GL) indices, the basion–biporion (BA–BP) and basion–bicarotid chords, the foramen magnum angle (FMA), and the basion–sphenoccipital ratio. After exploring the indices variability using principal component analysis, pairwise comparisons are performed to test for the association between each index and the locomotor and postural habits. Cranial size and phylogeny are taken into account. Our analysis indicates that none of the indices or approaches provides complete discrimination across locomotor and postural categories, although some differences are highlighted. FMA and BA–BP distinguish respectively obligate and facultative bipeds from all other groups. For what concerns posture, orthogrades and pronogrades differ with respects to OP–PR, OP–GL, and FMA. Although the multivariate approach seems to have some discrimination power, the results are most likely driven by facial and neurocranial variability embedded in some of the indices. These results demonstrate that indices relying on the anteroposterior positioning of the foramen may not be appropriate proxies for locomotion among primates. The assumptions about locomotor and postural habits in fossil hominins based on foramen magnum indices should be revised in light of these new findings.     

Future directions for the analysis of musculoskeletal design and locomotor performance

New techniques and conceptual frameworks offer new challenges and exciting opportunities for research on the biomechanics and physiology of vertebrate musculoskeletal design and locomotor performance. Past research based on electromyography and two-dimensional kinematics has greatly advanced the field of vertebrate functional morphology. Studies using these approaches have revealed much about vertebrate structure and function and have emphasized the importance of incorporating historical and developmental constraint and ecological context. Continued use of these experimental tools, but with greater emphasis on three-dimensional analysis of body movement, in combination with 3D kinetics and flow visualization of fluid movement past moving organisms, can now take advantage of the considerable advances in computing power and digital video technology. Indeed, surprisingly few detailed 3D analyses of movement for many locomotor modes and differing organisms are presently available. A challenge of 3D analyses will be to reduce the complexity of the data obtained in order to identify general principles of movement and biomechanics. New techniques and approaches for measuring muscle forces and length changes, together with activation patterns and movement, under dynamic conditions of more varied motor behavior are now also available. These provide the opportunity to study the mechanics and physiology of muscle function at greater depth and under more realistic conditions than has been previously possible. The importance of studying intact, behaving organisms under a broader range of locomotor conditions (other than steady state) and in the context of their natural environment remains a critical need for vertebrate biologists. This provides the much-needed opportunity for placing advances at more cellular and molecular levels into the context of whole organism function. Hence, studies at the organismal level remain paramount.     

New Frontiers for Machine Learning in Protein Science

Protein function is fundamentally reliant on inter-molecular interactions that underpin the ability of proteins to form complexes driving biological processes in living cells. Increasingly, such interactions are recognised as being formed between proteins that exist on a broad spectrum of dynamic conformational states and levels of intrinsic disorder. Additionally, the sizes of the structures formed can range from simple binary complexes to large dynamic biomolecular condensates measuring 100 nm or more. Understanding the parameters that govern such interactions, how they form, how they lead to function and what happens when they take place in unintended manners and lead to disease, represent some of the core questions for molecular biosciences. In light of recent advances made in solving the protein folding problem by machine learning methods, we discuss here the challenges and opportunities brought by these new data-driven approaches for the next frontiers of biomolecular science.     

Reconciling the convergence of supraspinous fossa shape among hominoids in light of locomotor differences

Differences in scapular morphology between modern humans and the African and lesser apes are associated with the distinct locomotor habits of these groups. However, several traits, particularly aspects of the supraspinous fossa, are convergent between Homo and Pongo—an unexpected result given their divergent locomotor habits. Many morphological assessments of the scapula rely on the limited number of static landmarks available, and traditional approaches like these tend to oversimplify scapular shape. Here, we present the results of two geometric morphometric (GM) analyses of hominoid supraspinous fossa shape—one employing five homologous landmarks and another with 83 sliding semilandmarks—alongside those of traditional methods to evaluate if three-dimensional considerations of fossa shape afford more comprehensive insights into scapular shape and functional morphology. Traditional measures aligned Pongo and Homo with narrow and transversely oriented supraspinous fossae, whereas African ape and Hylobates fossae are broader and more obliquely situated. However, our GM results highlight that much of the convergence between Homo and Pongo is reflective of their more medially positioned superior angles. These approaches offered a more complete assessment of supraspinous shape and revealed that the Homo fossa, with an intermediate superior angle position and moderate superoinferior expansion, is actually reminiscent of the African ape shape. Additionally, both Pongo and Hylobates were shown to have more compressed fossae, something that has not previously been identified through traditional analyses. Thus, the total morphological pattern of the Pongo supraspinous fossa is unique among hominoids, and possibly indicative of its distinctive locomotor habits. Am J Phys Anthropol 156:498–510, 2015. © 2015 Wiley Periodicals, Inc.     

Allometric scaling and locomotor function in the primate pelvis

Identification of positional behavior adaptation in the pelvis of primates is complicated by possible confounding effects of body size and phylogeny. Previous work on primate pelvic allometry has focused primarily on sexual dimorphism and its relationship to obstetric constraints in species with large fetal size relative to maternal size. This study investigates patterns of pelvic scaling with a specific aim to understand how pelvic scaling relates to locomotor function. Patterns of scaling of nine pelvic dimensions were examined in a broad comparative sample of 40 species of primates, covering both haplorhines and strepsirrhines, while accounting for phylogenetic nonindependence. Phylogenetic reduced major axis regressions on pelvic scaling patterns suggest that primate-wide patterns are reflected in haplorhine- and strepsirrhine-specific analyses. Many measures scale isometrically with pelvis size, but notably, features of the ilium tend to scale allometrically. As predicted, ilium width and lower ilium cross-sectional area scale with positive allometry, while lower iliac height scales with negative allometry. Further regression analyses by locomotor group suggest that these ilium measures, as well as pubic symphysis and ischium lengths, differ in their scaling patterns according to locomotor mode. These results suggest that scaling differences within primates, when present, are related to functional differences in locomotor behavior and mechanics. This study supports recent work that identifies adaptations to locomotor loading in the ilium and highlights the need for a better understanding of the relationship between pelvic structural mechanics and the mechanical requirements of primate locomotion. Am J Phys Anthropol 156:511–530, 2015. © 2015 Wiley Periodicals, Inc.     

Functional morphology of the hallucal metatarsal with implications for inferring grasping ability in extinct primates

Primate evolutionary morphologists have argued that selection for life in a fine branch niche resulted in grasping specializations that are reflected in the hallucal metatarsal (Mt1) morphology of extant “prosimians”, while a transition to use of relatively larger, horizontal substrates explains the apparent loss of such characters in anthropoids. Accordingly, these morphological characters—Mt1 torsion, peroneal process length and thickness, and physiological abduction angle—have been used to reconstruct grasping ability and locomotor mode in the earliest fossil primates. Although these characters are prominently featured in debates on the origin and subsequent radiation of Primates, questions remain about their functional significance. This study examines the relationship between these morphological characters of the Mt1 and a novel metric of pedal grasping ability for a large number of extant taxa in a phylogenetic framework. Results indicate greater Mt1 torsion in taxa that engage in hallucal grasping and in those that utilize relatively small substrates more frequently. This study provides evidence that Carpolestes simpsoni has a torsion value more similar to grasping primates than to any scandentian. The results also show that taxa that habitually grasp vertical substrates are distinguished from other taxa in having relatively longer peroneal processes. Furthermore, a longer peroneal process is also correlated with calcaneal elongation, a metric previously found to reflect leaping proclivity. A more refined understanding of the functional associations between Mt1 morphology and behavior in extant primates enhances the potential for using these morphological characters to comprehend primate (locomotor) evolution. Am J Phys Anthropol 156:327–348, 2015. © 2014 Wiley Periodicals, Inc.     

New characters for the functional interpretation of primate scapulae and proximal humeri

The study of muscle function in nonhuman primates through the technique of electromyography (EMG) has facilitated the identification of specific functional roles for muscles in particular behaviors. This has led to a more complete understanding of the biomechanics of certain regions of the musculoskeletal system, and should facilitate our ability to identify morphological features useful in the functional interpretation of fossil material. The current paper represents one such investigation of a new set of morphometric characters of the scapula and proximal humerus suggested by EMG analyses of shoulder muscle function. A set of new metric variables were examined on the scapulae and proximal humeri of 25 species of extant anthropoid primates, as well as on casts of scapulae and humeri of three fossil primate taxa. The variables are primarily related to the line of action and attachments of the rotator cuff muscles. The position of the scapular spine, the degree of lateral expansion of the subscapular fossa, the size and shape of the subscapularis insertion facet on the lesser tubercle, and the orientation of the infraspinatus insertion facet on the greater tubercle all appear to successfully sort the extant taxa into locomotor groups. Their appearance on the fossil specimens generally supports previous functional interpretations of each taxon's locomotor abilities based on a variety of other characters, suggesting that these traits are equally applicable to fossil material. © Wiley-Liss, Inc.     

Ontogeny of the hominoid scapula: The influence of locomotion on morphology

Primate shoulder morphology has been linked with locomotor habits, oftentimes irrespective of phylogenetic heritage. Among hominoids, juvenile African apes are known to climb more frequently than adults, while orangutans and gibbons maintain an arboreal lifestyle throughout ontogeny. This study examined if these ontogenetic locomotor differences carry a morphological signal, which should be evident in the scapulae of chimpanzees and gorillas but absent in taxa that do not display ontogenetic behavioral shifts. The scapular morphology of five hominoid primates and one catarrhine outgroup was examined throughout ontogeny to evaluate if scapular traits linked with arboreal activities are modified in response to ontogenetic behavioral shifts away from climbing. Specifically, the following questions were addressed: 1) which scapular characteristics distinguish taxa with different locomotor habits; and 2) do these traits show associated changes during development in taxa known to modify their behavioral patterns? Several traits characterized suspensory taxa from nonsuspensory forms, such as cranially oriented glenohumeral joints, obliquely oriented scapular spines, relatively narrow infraspinous fossae, and inferolaterally expanded subscapularis fossae. The relative shape of the dorsal scapular fossae changed in Pan, Gorilla, and also Macaca in line with predictions based on reported ontogenetic changes in locomotor behavior. These morphological changes were mostly distinct from those seen in Pongo, Hylobates, and Homo and imply a unique developmental pattern, possibly related to ontogenetic locomotor shifts. Accordingly, features that sorted taxa by locomotor habits and changed in concert with ontogenetic behavioral patterns should be particularly useful for reconstructing the locomotor habits of fossil forms. Am J Phys Anthropol 152:239–260, 2013. © 2013 Wiley Periodicals, Inc.     

Expression of Myosin Heavy Chain Isoforms in the Supraspinatus Muscle of Different Primate Species: Implications for the Study of the Adaptation of Primate Shoulder Muscles to Different Locomotor Modes

The supraspinatus muscle is a key component of the soft tissues of the shoulder. In pronograde primates, its main function, in combination with the other rotator cuff muscles (subscapularis, infraspinatus, and teres minor), is to stabilize the glenohumeral joint, whereas in orthograde primates it functions together with the deltoid, to elevate the upper extremity in the scapular plane. To determine whether these functional differences are also reflected in the molecular biochemistry of the supraspinatus muscles involved in these different locomotor modes, we used real-time polymerase chain reaction (RT-PCR) to analyze the expression of the myosin heavy chain (MHC) isoforms in supraspinatus muscles from modern humans and 12 species of pronograde and orthograde primates. The MHC expression pattern in the supraspinatus muscle of pronograde primates was consistent with its function as a tonic and postural muscle, whereas the MHC expression pattern observed in the supraspinatus muscle of nonhuman orthograde primates was that of a muscle that emphasizes speed, strength, and less resistance to fatigue. These findings are consistent with the role of the supraspinatus in the posture and locomotor modes of these groups of nonhuman primates. The humans included in the study had an expression pattern similar to that of the nonhuman orthograde primates. In conclusion, molecular analysis of skeletal muscles via RT-PCR can contribute to a better understanding of the morphological and functional characteristics of the primate musculoskeletal system.     

Locomotion in ornithischian dinosaurs: an assessment using three‐dimensional computational modelling

Ornithischian dinosaurs were primitively bipedal with forelimbs modified for grasping, but quadrupedalism evolved in the clade on at least three occasions independently. Outside of Ornithischia, quadrupedality from bipedal ancestors has only evolved on two other occasions, making this one of the rarest locomotory transitions in tetrapod evolutionary history. The osteological and myological changes associated with these transitions have only recently been documented, and the biomechanical consequences of these changes remain to be examined. Here, we review previous approaches to understanding locomotion in extinct animals, which can be broadly split into form–function approaches using analogy based on extant animals, limb‐bone scaling, and computational approaches. We then carry out the first systematic attempt to quantify changes in locomotor muscle function in bipedal and quadrupedal ornithischian dinosaurs. Using three‐dimensional computational modelling of the major pelvic locomotor muscle moment arms, we examine similarities and differences among individual taxa, between quadrupedal and bipedal taxa, and among taxa representing the three major ornithischian lineages (Thyreophora, Ornithopoda, Marginocephalia). Our results suggest that the ceratopsid Chasmosaurus and the ornithopod Hypsilophodon have relatively low moment arms for most muscles and most functions, perhaps suggesting poor locomotor performance in these taxa. Quadrupeds have higher abductor moment arms than bipeds, which we suggest is due to the overall wider bodies of the quadrupeds modelled. A peak in extensor moment arms at more extended hip angles and lower medial rotator moment arms in quadrupeds than in bipeds may be due to a more columnar hindlimb and loss of medial rotation as a form of lateral limb support in quadrupeds. We are not able to identify trends in moment arm evolution across Ornithischia as a whole, suggesting that the bipedal ancestry of ornithischians did not constrain the development of quadrupedal locomotion via a limited number of functional pathways. Functional anatomy appears to have had a greater effect on moment arms than phylogeny, and the differences identified between individual taxa and individual clades may relate to differences in locomotor performance required for living in different environments or for clade‐specific behaviours.     

Acoustic sequences in non‐human animals: a tutorial review and prospectus

Animal acoustic communication often takes the form of complex sequences, made up of multiple distinct acoustic units. Apart from the well‐known example of birdsong, other animals such as insects, amphibians, and mammals (including bats, rodents, primates, and cetaceans) also generate complex acoustic sequences. Occasionally, such as with birdsong, the adaptive role of these sequences seems clear (e.g. mate attraction and territorial defence). More often however, researchers have only begun to characterise – let alone understand – the significance and meaning of acoustic sequences. Hypotheses abound, but there is little agreement as to how sequences should be defined and analysed. Our review aims to outline suitable methods for testing these hypotheses, and to describe the major limitations to our current and near‐future knowledge on questions of acoustic sequences. This review and prospectus is the result of a collaborative effort between 43 scientists from the fields of animal behaviour, ecology and evolution, signal processing, machine learning, quantitative linguistics, and information theory, who gathered for a 2013 workshop entitled, ‘Analysing vocal sequences in animals’. Our goal is to present not just a review of the state of the art, but to propose a methodological framework that summarises what we suggest are the best practices for research in this field, across taxa and across disciplines. We also provide a tutorial‐style introduction to some of the most promising algorithmic approaches for analysing sequences. We divide our review into three sections: identifying the distinct units of an acoustic sequence, describing the different ways that information can be contained within a sequence, and analysing the structure of that sequence. Each of these sections is further subdivided to address the key questions and approaches in that area. We propose a uniform, systematic, and comprehensive approach to studying sequences, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies. Allowing greater interdisciplinary collaboration will facilitate the investigation of many important questions in the evolution of communication and sociality.     

Enigmatic ear stones: what we know about the functional role and evolution of fish otoliths

Otoliths in bony fishes play an important role in the senses of balance and hearing. Otolith mass and shape are, among others, likely to be decisive factors influencing otolith motion and thus ear functioning. Yet our knowledge of how exactly these factors influence otolith motion is incomplete. In addition, experimental studies directly investigating the function of otoliths in the inner ear are scarce and yield partly conflicting results. Herein, we discuss questions and hypotheses on how otolith mass and shape, and the relationship between the sensory epithelium and overlying otolith, influence otolith motion. We discuss (i) the state‐of‐the‐art knowledge regarding otolith function, (ii) gaps in knowledge that remain to be filled, and (iii) future approaches that may improve our understanding of the role of otoliths in ear functioning. We further link these functional questions to the evolution of solid teleost otoliths instead of numerous tiny otoconia as found in most other vertebrates. Until now, the selective forces and/or constraints driving the evolution of solid calcareous otoliths and their diversity in shape in teleosts are largely unknown. Based on a data set on the structure of otoliths and otoconia in more than 160 species covering the main vertebrate groups, we present a hypothetical framework for teleost otolith evolution. We suggest that the advent of solid otoliths may have initially been a selectively neutral ‘by‐product’ of other key innovations during teleost evolution. The teleost‐specific genome duplication event may have paved the way for diversification in otolith shape. Otolith shapes may have evolved along with the considerable diversity of, and improvements in, auditory abilities in teleost fishes. However, phenotypic plasticity may also play an important role in the creation of different otolith types, and different portions of the otolith may show different degrees of phenotypic plasticity. Future studies should thus adopt a phylogenetic perspective and apply comparative and methodologically integrative approaches, including fossil otoliths, when investigating otoconia/otolith evolution and their function in the inner ear.     

The bony labyrinth of the early platyrrhine primate Chilecebus

We document the morphology of the bony labyrinth of Chilecebus carrascoensis, one of the best preserved early platyrrhines known, based on high resolution CT scanning and 3D digital reconstruction. The cochlea is low and conical in form, as in other anthropoids, but has only 2.5 spiral turns. When the allometric relationship with body mass is considered, cochlear size is similar to that in extant primates. The relative size of the semicircular canals, which is well within the range of other primates, indicates that Chilecebus carrascoensis was probably not as agile in its locomotion as other small-bodied platyrrhines such as Leontopithecus rosalia, Saguinus oedipus, and Callithrix jacchus, but it probably was not a suspensory acrobat or a slow climber. The proportion, shape, and orientation of the semicircular canals in Chilecebus carrascoensis also mirror that typically seen in extant primates. However, no single variable can be used for predicting the locomotor pattern in Chilecebus carrascoensis. Based on Principle Component Analysis (PCA) scores we calculated rescaled Euclidean distances for various taxa; primates with similar locomotor patterns tend to share shorter distances. Results for Chilecebus carrascoensis underscore its general resemblance to living quadrupedal primate taxa, but it is not positioned especially near any single living taxon.     

The effects of substratum on locomotor performance in lacertid lizards

Locomotion is important to animals because it has direct implications for fitness through its role in predator escape, prey capture, and territory defence. Despite significant advances in our understanding of animal locomotion, studies exploring how substrate properties affect locomotor performance remain scant. In the present study, we explore how variation in substrate (sand, slate, cork) affects locomotor performance in lacertid lizards that differ in morphology. Moreover, we explore whether substrate effects are the same for different types of locomotor performance (speed, acceleration, and stamina). Our results show that the substrate affected most types of locomotor performance studied but not always in the same way. Although substrate effects were species‐dependent for the maximal speed over 50 cm and the distance run to exhaustion, this was not the case for acceleration capacity. These results suggest that substrate texture differentially affects burst performance vs. longer duration measures of locomotor performance. Finally, straightforward relationships between habitat use and the substrate on which performance was maximized were not observed. This suggests that the evolution of locomotor capacity is complex and that animals may show compromise phenotypes allowing them to deal with a variety of substrates in their natural environment. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.     

Dynamic roles for G4 DNA in the biology of eukaryotic cells

Recent advances have made a persuasive case for the existence of G4 DNA in living cells, but what--if any--are its functions? Experiments have established how G4 DNA may contribute to the biology of eukaryotic cells, and genomic analysis has identified new ways in which the potential to form G4 DNA may influence gene regulation and genomic stability. This Perspective highlights those advances and identifies some key open questions.     

Scale-dependence in species-area relationships

Species-area relationships (SARs) are among the most studied phenomena in ecology, and are important both to our basic understanding of biodiversity and to improving our ability to conserve it. But despite many advances to date, our knowledge of how various factors contribute to SARs is limited, searches for single causal factors are often inconclusive, and true predictive power remains elusive. We believe that progress in these areas has been impeded by 1) an emphasis on single-factor approaches and thinking of factors underlying SARs as mutually exclusive hypotheses rather than potentially interacting processes, and 2) failure to place SAR-generating factors in a scale-dependent framework. We here review mathematical, ecological, and evolutionary factors contributing to species-area relationships, synthesizing major hypotheses from the literature in a scale-dependent context. We then highlight new research directions and unanswered questions raised by this scale-dependent synthesis.