ariaDNE: A robustly implemented algorithm for Dirichlet energy of the normal

Dental topography of prosimian premolars predicts diet: A comparison in premolar and molar dietary classification accuracies

OBJECTIVES

This study tests whether (1) premolar topography of extant "prosimians" (strepsirrhines and tarsiers) successfully predicts diet and (2) whether the combination of molar and premolar topography yields higher classification accuracy than using either tooth position in isolation.

MATERIALS AND METHODS

Dental topographic metrics (ariaDNE, relief index, and orientation patch count rotated) were calculated for 118 individual matched-pairs of mandibular fourth premolars (P4) and second molars (M2). The sample represents 7 families and 22 genera. Tooth variables were analyzed in isolation (P4 only; M2 only), together (P4 and M2), and combined (PC1 scores of bivariate principal component analyses of P4 and M2 for each metric). Discriminant function analyses were conducted with and without a measure of size (two-dimensional surface area).

RESULTS

When using topography only, "prosimian" P4 shape predicts diet with a success rate that is slightly higher than that of M2 shape. When absolute size is included, premolars and molars perform comparably well. Including both premolar and molar topography (separately or combined) improves classification accuracy for every analysis beyond considering either in isolation. Classification accuracy is highest when premolar and molar topography and size are included.

DISCUSSION

Our findings indicate that molar teeth incompletely summarize the functional requirements of oral food breakdown for a given diet, and that the mechanism selecting for premolar form is more varied than what is expressed by molar teeth. Finally, our findings suggest that fossil P4s (in isolation or with the M2) can be used for meaningful dietary reconstruction of extinct primates.

Bayesian Prediction of Multivariate Ecology from Phenotypic Data Yields New Insights into the Diets of Extant and Extinct Taxa

AbstractMorphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations, such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Furthermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa but yields new insights into the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet but serves as a general framework for predicting multivariate ecology from phenotypic traits.

Baculum shape complexity correlates to metrics of post-copulatory sexual selection in Musteloidea

The penis bone, or baculum, is present in many orders of mammals, although its function is still relatively unknown, mainly due to the challenges with studying the baculum in vivo. Suggested functions include increasing vaginal friction, prolonging intromission and inducing ovulation. Since it is difficult to study baculum function directly, functional morphology can give important insights. Shape complexity techniques, in particular, are likely to offer a useful metric of baculum morphology, especially since finding homologous landmarks on such a structure is challenging. This study focuses on measuring baculum shape complexity in the Musteloidea-a large superfamily spanning a range of body sizes with well-developed, qualitatively diverse bacula. We compared two shape complexity metrics-alpha shapes and ariaDNE and conducted analyses over a range of six different coefficients, or bandwidths, in 32 species of Musteloidea. Overall, we found that shape complexity, especially at the baculum distal tip, is associated with intromission duration using both metrics. These complexities can include hooks, bifurcations and other additional projections. In addition, alpha shapes complexity was also associated with relative testes mass. These results suggest that post-copulatory mechanisms of sexual selection are probably driving the evolution of more complex-shaped bacula tips in Musteloidea and are likely to be especially involved in increasing intromission duration during copulation.

Basal Primatomorpha colonized Ellesmere Island (Arctic Canada) during the hyperthermal conditions of the early Eocene climatic optimum

Anthropogenically induced warming is transforming Arctic ecosystems across a geologically short timescale, but earlier episodes of Earth history provide insights on the nature and limitations of biotic change in a rapidly warming Arctic. Late early Eocene strata (~52 Ma) of the Margaret Formation on Ellesmere Island, Nunavut, Canada sample a warm temperate ecosystem with a polar light regime situated at ~77°N paleolatitude. This extinct boreal ecosystem hosted a diversity of early Cenozoic vertebrates, including thermophilic taxa such as crocodilians and tapiroid perissodactyls. Here we describe two new species of the early primatomorphan Ignacius from Ellesmere, which are by far the northernmost known records for Paleogene Primatomorpha. Ellesmere species of Ignacius are sister taxa, indicating a single colonization of Ellesmere from farther south in North America coincident with the onset of the hyperthermal Early Eocene Climatic Optimum (EECO). The Ellesmere Ignacius clade differs from closely related taxa inhabiting mid-latitudes in being larger (thereby conforming to Bergmann's rule) and having modified dentition and muscles of mastication for a dietary regime emphasizing hard objects, possibly reflecting an increased reliance on fallback foods during long polar winters. The late early Eocene mammalian fauna of Ellesmere indicates that its unique paleoenvironment rendered it uninhabitable to some clades, including euprimates, while selected taxa were able to adapt to its challenging conditions and diversify.

The computational age-at-death estimation from 3D surface models of the adult pubic symphysis using data mining methods

Age-at-death estimation of adult skeletal remains is a key part of biological profile estimation, yet it remains problematic for several reasons. One of them may be the subjective nature of the evaluation of age-related changes, or the fact that the human eye is unable to detect all the relevant surface changes. We have several aims: (1) to validate already existing computer models for age estimation; (2) to propose our own expert system based on computational approaches to eliminate the factor of subjectivity and to use the full potential of surface changes on an articulation area; and (3) to determine what age range the pubic symphysis is useful for age estimation. A sample of 483 3D representations of the pubic symphyseal surfaces from the ossa coxae of adult individuals coming from four European (two from Portugal, one from Switzerland and Greece) and one Asian (Thailand) identified skeletal collections was used. A validation of published algorithms showed very high error in our dataset-the Mean Absolute Error (MAE) ranged from 16.2 and 25.1 years. Two completely new approaches were proposed in this paper: SASS (Simple Automated Symphyseal Surface-based) and AANNESS (Advanced Automated Neural Network-grounded Extended Symphyseal Surface-based), whose MAE values are 11.7 and 10.6 years, respectively. Lastly, it was demonstrated that our models could estimate the age-at-death using the pubic symphysis over the entire adult age range. The proposed models offer objective age estimates with low estimation error (compared to traditional visual methods) and are able to estimate age using the pubic symphysis across the entire adult age range.

Feeding ecology of the last European colobine monkey, Dolichopithecus ruscinensis

Currently, very little is known about the ecology of extinct Eurasian cercopithecids. Dietary information is crucial in understanding the ecological adaptations and diversity of extinct cercopithecids and the evolution of this family. For example, the colobine genus Dolichopithecus is represented by multiple large-bodied species that inhabited Eurasia during the Pliocene-Early Pleistocene. The available evidence, though limited, suggests semiterrestrial locomotion, which contrasts with most extant African and Asian colobines that exhibit morphological and physiological adaptations for arboreality and folivory. These differences raise questions regarding the dietary specialization of early colobine taxa and how/if that influenced their dispersion out of Africa and into Eurasia. To further our understanding of the ecology of Plio-Pleistocene cercopithecids, we characterized the dental capabilities and potential dietary adaptations of Dolichopithecus ruscinensis through dental topographic and enamel thickness analyses on an M¹ from the locality of Serrat d'en Vacquer, Perpignan (France). We also assessed the feeding behavior of D. ruscinensis through dental microwear texture analysis on a broad sample of fossil molars from fossil sites in France, Greece, Bulgaria, and Romania. Dental topographic and enamel thickness analyses suggest that D. ruscinensis could efficiently process a wide range of foods. Results of the dental microwear texture analysis suggest that its diet ranged from folivory to the consumption of more mechanically challenging foods. Collectively, this suggests a more opportunistic feeding behavior for Dolichopithecus than characteristic of most extant colobines.

Dental topographic and three-dimensional geometric morphometric analysis of carnassialization in different clades of carnivorous mammals (Dasyuromorphia, Carnivora, Hyaenodonta)

The evolution of carnassial teeth in mammals, especially in the Carnivora, has been subject of many morphometric and some dental topographic studies. Here, we use a combination of dental topographic analysis (Dirichlet normal energy) and 3D geometric morphometrics of less and high carnassialized lower teeth of carnivoran, dasyuromorph and hyaenodont taxa. Carnassial crown curvature, as indicated by Dirichlet normal energy, is high in lesser carnassialized teeth and low in higher carnassialized teeth, where it is influenced by the reduction of crown features such as cusps and crests. PC1 of the geometric morphometric analysis is linked to enlargement of the carnassial blade, reduction of the talonid crushing basin and an increasingly asymmetric cervix line with an enlarged mesial flexure in more carnassialized teeth. Distribution of PC1 values further indicates that along the tooth row of dasyuromorphs (m2-m4) and hyaenodonts (m1-m3) the most distal carnassial is the most carnassialized (principal carnassial), and in most taxa with overall higher carnassialized teeth, carnassialization successively increases from the anterior to the posterior tooth position along the tooth row. PC2 indicates that a longitudinal elongated carnassial is present in caniforms and in unspecialized feliforms, which separates these taxa in morphospace from all dasyuromorphs, hyaenodonts and specialized feliforms. An ancestral state reconstruction shows that this longitudinal elongation may be a plesiomorphic ancestral state for the Carnivora, which is different from the Dasyuromorphia and the Hyaenodonta. This elongation, enabling the presence of a longitudinally aligned carnassial blade as well as a complete talonid basin, might have provided the Carnivora with an advantage in terms of adaptive versatility.

Widespread loss of mammalian lineage and dietary diversity in the early Oligocene of Afro-Arabia

Diverse lines of geological and geochemical evidence indicate that the Eocene-Oligocene transition (EOT) marked the onset of a global cooling phase, rapid growth of the Antarctic ice sheet, and a worldwide drop in sea level. Paleontologists have established that shifts in mammalian community structure in Europe and Asia were broadly coincident with these events, but the potential impact of early Oligocene climate change on the mammalian communities of Afro-Arabia has long been unclear. Here we employ dated phylogenies of multiple endemic Afro-Arabian mammal clades (anomaluroid and hystricognath rodents, anthropoid and strepsirrhine primates, and carnivorous hyaenodonts) to investigate lineage diversification and loss since the early Eocene. These analyses provide evidence for widespread mammalian extinction in the early Oligocene of Afro-Arabia, with almost two-thirds of peak late Eocene diversity lost in these clades by ~30 Ma. Using homology-free dental topographic metrics, we further demonstrate that the loss of Afro-Arabian rodent and primate lineages was associated with a major reduction in molar occlusal topographic disparity, suggesting a correlated loss of dietary diversity. These results raise new questions about the relative importance of global versus local influences in shaping the evolutionary trajectories of Afro-Arabia's endemic mammals during the Oligocene.

The effects of femoral metaphyseal morphology on growth plate biomechanics in juvenile chimpanzees and humans

The distal femoral metaphyseal surface presents dramatically different morphologies in juvenile extant hominoids-humans have relatively flat metaphyseal surfaces when compared with the more complex metaphyseal surfaces of apes. It has long been speculated that these different morphologies reflect different biomechanical demands placed on the growth plate during locomotor behaviour, with the more complex metaphyseal surfaces of apes acting to protect the growth plate during flexed-knee behaviours like squatting and climbing. To test this hypothesis, we built subject-specific parametric finite-element models from the surface scans of the femora of five Pan and six Homo juveniles. We then simulated the loading conditions of either a straight-leg or flexed-knee gait and measured the resulting stresses at the growth plate. When subjected to the simulated flexed-knee loading conditions, both the maximum and mean von Mises stresses were significantly lower in the Pan models than in the Homo models. Further, during these loading conditions, von Mises stresses were strongly negatively correlated with ariaDNE, a measure of complexity of the metaphyseal surface. These results indicate that metaphyseal surface morphology has a robust effect on growth plate mechanics.

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01793-x.

The landscape of tooth shape: Over 20 years of dental topography in primates

Diet plays an incontrovertible role in primate evolution, affecting anatomy, growth and development, behavior, and social structure. It should come as no surprise that a myriad of methods for reconstructing diet have developed, mostly utilizing the element that is not only most common in the fossil record but also most pertinent to diet: teeth. Twenty years ago, the union of traditional, anatomical analyses with emerging scanning and imaging technologies led to the development of a new method for quantifying tooth shape and reconstructing the diets of extinct primates. This method became known as dental topography.

Ontogeny of the distal femoral metaphyseal surface and its relationship to locomotor behavior in hominoids

OBJECTIVE

Distal femoral metaphyseal surface morphology is highly variable in extant mammals. This variation has previously been linked to differences in locomotor behavior. We perform the first systematic survey and description of the development of this morphology in extant hominoids.

MATERIALS AND METHODS

We collected 3D surface laser scans of the femora of 179 human and great ape individuals throughout all subadult stages of development. We qualitatively and quantitatively describe metaphyseal surface morphology.

RESULTS

We find that the metaphysis is topographically simple in all hominoids during the fetal and infant periods relative to later developmental periods, and in apes it develops significant complexity throughout development. Humans, by contrast, retain relatively flat metaphyseal surfaces throughout ontogeny.

DISCUSSION

Major shifts in morphology appear to coincide with major shifts in locomotor behavior, suggesting that metaphyseal morphology is developmentally plastic and highly dependent on the biomechanical loadings at the knee joint. This is consistent with a large body of biomedical research, which demonstrates the primacy of mechanical forces in determining growth plate ossification patterns. Additionally, specific metaphyseal morphology appears highly correlated with specific locomotor modes, suggesting that metaphyseal surface morphology will be useful for reconstructing the locomotor behavior of fossil primate taxa.

Ecometric modelling of tooth shape and precipitation gradients among lemurs on Madagascar

Ecometric modelling relates spatial environmental variables to phenotypic characters to better understand morphological adaptation and help reconstruct past environments. Here, the community means of the dental topography metrics Dirichlet normal energy (DNE) and orientation patch count (OPC) are tested against annual precipitation and precipitation seasonality among lemurs across Madagascar. Dry, seasonal environments are expected to be associated with high DNE and OPC, as lemurs living in these environments are more likely to rely on tougher foods. Ecometric models are also used to calculate ecometric loads for lemur taxa hypothesized to be experiencing evolutionary disequilibria and to reconstruct annual precipitation and precipitation seasonality at the ~500 years BP subfossil cave site of Ankilitelo. DNE was highest in highly seasonal but wet environments. Seasonal exploitation of fallback foods and the availability of new leaves during wet periods may be most important in driving community DNE. OPC was weakly predicted by annual precipitation and seasonality but its distribution appeared to be driven by a stepwise increase in its community values in rainforest environments. The lemur fauna from Ankilitelo appears to resemble communities from moister environments than occur in the spiny desert zone in which the site is situated today.