Bovid postcranial ecomorphological survey of the Laetoli paleoenvironment

A 3D geometric morphometric analysis of the bovid distal humerus, with special reference to Rusingoryx atopocranion (Pleistocene, Eastern Africa)

The family Bovidae [Mammalia: Artiodactyla] is speciose and has extant representatives on every continent, forming key components of mammal communities. For these reasons, bovids are ideal candidates for studies of ecomorphology. In particular, the morphology of the bovid humerus has been identified as highly related to functional variables such as body mass and habitat. This study investigates the functional morphology of the bovid distal humerus in isolation due to its increased likelihood of preservation in the fossil record, and the resulting opportunity for a better understanding of the ecomorphology of extinct bovids. A landmark scheme of 30 landmarks was used to capture the 3D distal humerus morphology in 111 extant bovid specimens. We find that the distal humerus has identifiable morphologies associated with body mass, habitat preference and tribe affiliation and that some characteristics are shared between high body mass bovids and those living on hard, flat terrain which is likely due to the high stress on the bone in both cases. We directly apply our findings regarding extant bovids to the extinct alcelaphine bovid, Rusingoryx atopocranion from the mid to late Pleistocene (>33-45 ka) Lake Victoria region of Kenya. This species is known for some peculiar morphologies including a domed cranium with hollow nasal crests, and having small hooves for a bovid of its size. Another interesting aspect of Rusingoryx's skeletal morphology which has not been addressed is an unusual protrusion on the lateral epicondyle of the distal humerus. Despite considerable individual variation in the Rusingoryx specimens, we find evidence to support its historical assignment to the tribe Alcelaphini, and that it likely preferred open grassland habitats, which is consistent with independent reconstructions of the palaeoenvironment. We also provide the most accurate body mass estimate for Rusingoryx to date, based on distal humerus centroid size. Overall, we are able to conclude that the distal humerus in extant bovids is highly informative regarding body mass, habitat preference and tribe, and that this can be applied directly to a fossil taxon with promising results.

Three-dimensional geometric morphometric analyses of humerus ecomorphology: New perspectives for paleohabitat reconstruction in carnivorans and ungulates

Long bone ecomorphology has proven effective for paleohabitat reconstructions across a wide range of mammalian clades. Still, there is no comprehensive framework to allow interpretation of long bone morphological variation within and between different monophyletic groups. Here, we investigated the use of humerus morphometry to classify living members of the orders Carnivora and ungulates based on their preferred habitats. Using geometric morphometrics, we extracted three different kinds of humerus shape data describing interspecific variation with and without accounting for evolutionary allometry and phylogenetic signal. The traditional a priori categorization of species in open, mixed, and closed habitats was employed in combination with selected subsets of shape variables to identify the best-predictive models for habitat adaptation. These were identified based on the statistical performance of phylogenetic and non-phylogenetic discriminant analyses and then applied to predict habitats on a subsample of fossil species. Size-free shape data combined with phylogenetic discriminant analyses showed the highest rate of accuracy in habitat classification for a combined sample of carnivorans and ungulates. Conversely, when the two groups were investigated separately, traditional shape data analyzed with phylogenetic discriminant function analyses provided models with the greatest predictive power. By combining carnivorans and ungulates within the same methodological framework we identified common adaptive features in closed habitat-adapted species that show compressed epiphyses, while open habitat-adapted species have expanded epiphyses. These morphologies evolved to allow significant degree of direction switches during locomotion in closed habitats compared to open habitat-adapted species whose forelimb joints evolved to stabilize articulations for increasing speed.

Hominin turnover at Laetoli is associated with vegetation change: Multiproxy evidence from the large herbivore community

Vegetation change in eastern Africa during the Pliocene would have had an important impact on hominin adaptation and ecology, and it may have been a key driver of hominin macroevolution, including the extinction of Australopithecus and the emergence of Paranthropus and Homo. The Pliocene paleoanthropological site of Laetoli in Tanzania provides an opportunity to investigate the relationship between vegetation change and hominin turnover because it encompasses the time period when grass cover was spreading across eastern Africa and because hominin species turnover occurred locally at Laetoli, with Paranthropus aethiopicus in the Upper Ndolanya Beds (UNB) replacing Australopithecus afarensis in the Upper Laetolil Beds (ULB). However, it remains unresolved how the vegetation of the UNB and the ULB differed from each other. To examine differences between the two stratigraphic units, multiple proxies-hypsodonty, mesowear, and stable carbon isotopes of tooth enamel (δ13Cenamel)-are used to infer the diets of large herbivores and compare the dietary guild structure of the large herbivore communities. All three proxies indicate an increase in the abrasiveness and C4-content in the diets of the large herbivores in the UNB relative to those in the ULB. After inferring the diets of species based on all three proxies, the large herbivore community of the UNB had a greater proportion of grazers and a smaller proportion of mixed feeders than in the ULB but maintained a similar proportion of browsers and frugivores. The ULB community has few modern-day analogs, whereas the UNB community is most closely analogous to those in modern African grasslands. Thus, hominin turnover at Laetoli is associated with an increase in grass cover within a woodland-grassland mosaic and is part of a broader transformation of the herbivore community structure.

Reconstructing past migratory behaviour of reindeer (Rangifer tarandus): Insights from geometric morphometric analysis of proximal phalanx morphology from extant caribou populations

Reindeer mobility patterns vary widely in modern ecosystems, notably between more open or more wooded environments. This renders the reconstruction of past reindeer mobility patterns challenging, while being at the same time key if archaeologists want to better understand the role that reindeer herds played in the subsistence and territorial organisation of Prehistoric hunter-gatherer societies. Studying the morphology associated with different habitats and mobility patterns can be a useful method for understanding past reindeer behaviour. To access paleoecological information, the relationship between locomotor anatomy and substrate type can be explored in modern animals and transposed to the past, as previous studies have proven that an animal´s environment affects bone morphology. In this study, 3D Geometric Morphometrics are used to explore the impact of extant reindeer habitat type and mobility pattern on phalanx morphology. Results obtained reflects on the potential archaeological application of such an approach for paleoecological reconstructions. Size and shape of phalanx vary significantly, yet complex to interpret in light of interplaying factors such as subspecies, sexual dimorphism and the influence of migration costs, snow cover and substrate type. If direct application to the archaeological record remains preliminary, this first study permits to highlight promising avenues for future research.

Ecomorphology of the cervid intermediate phalanx and its implications for palaeoenvironmental reconstruction

This paper reports on newly developed ecomorphological models for the cervid intermediate phalanx. Using a geometric morphometric approach, we quantitatively assess the overall gracility of the bone, the depth and concavity of the proximal articulation and the roundness and symmetry of the distal articulation in the intermediate phalanx, to establish relationships between morphology, locomotor behavior and environment. The morphology of the phalanx was found to vary along a gradient from gracile phalanges with shallow proximal articulations in forms adapted to yielding substrate, to robust phalanges with deeper proximal articulations in taxa adapted to firm substrate. Phylogeny and allometry are accounted for using regressions and phylogenetic comparative methods. Although the results indicate phylogeny explains part of the morphological variation, overall the shape of the intermediate phalanx appears mainly driven by differences in function. Consequently, this element promises to be a useful palaeoenvironmental proxy that can be applied on fossil assemblages with cervid remains.

Mutated lncRNA increase the risk of type 2 diabetes by promoting β cell dysfunction and insulin resistance

Islet β cell dysfunction and insulin resistance are the main pathogenesis of type 2 diabetes (T2D), but the mechanism remains unclear. Here we identify a rs3819316 C > T mutation in lncRNA Reg1cp mainly expressed in islets associated with an increased risk of T2D. Analyses in 16,113 Chinese adults reveal that Mut-Reg1cp individuals had higher incidence of T2D and presented impaired insulin secretion as well as increased insulin resistance. Mice with islet β cell specific Mut-Reg1cp knock-in have more severe β cell dysfunction and insulin resistance. Mass spectrometry assay of proteins after RNA pulldown demonstrate that Mut-Reg1cp directly binds to polypyrimidine tract binding protein 1 (PTBP1), further immunofluorescence staining, western blot analysis, qPCR analysis and glucose stimulated insulin secretion test reveal that Mut-Reg1cp disrupts the stabilization of insulin mRNA by inhibiting the phosphorylation of PTBP1 in β cells. Furthermore, islet derived exosomes transfer Mut-Reg1cp into peripheral tissue, which then promote insulin resistance by inhibiting AdipoR1 translation and adiponectin signaling. Our findings identify a novel mutation in lncRNA involved in the pathogenesis of T2D, and reveal a new mechanism for the development of T2D.

Geometric morphometrics of mandibles for dietary differentiation of Bovidae (Mammalia: Artiodactyla)

The mammalian family Bovidae has been widely studied in ecomorphological research, with important applications to paleoecological and paleohabitat reconstructions. Most studies of bovid craniomandibular features in relation to diet have used linear measurements. In this study, we conduct landmark-based geometric-morphometric analyses to evaluate whether different dietary groups can be distinguished by mandibular morphology. Our analysis includes data for 100 species of extant bovids, covering all bovid tribes and 2 dietary classifications. For the first classification with 3 feeding categories, we found that browsers (including frugivores), mixed feeders, and grazers are moderately well separated using mandibular shape. A finer dietary classification (frugivore, browser, browser-grazer intermediate, generalist, variable grazer, and obligate grazer) proved to be more useful for differentiating dietary extremes (frugivores and obligate grazers) but performed equally or less well for other groups. Notably, frugivorous bovids, which belong in tribe Cephalophini, have a distinct mandibular shape that is readily distinguished from all other dietary groups, yielding a 100% correct classification rate from jackknife cross-validation. The main differences in mandibular shape found among dietary groups are related to the functional needs of species during forage prehension and mastication. Compared with browsers, both frugivores and grazers have mandibles that are adapted for higher biomechanical demand of chewing. Additionally, frugivore mandibles are adapted for selective cropping. Our results call for more work on the feeding ecology and functional morphology of frugivores and offer an approach for reconstructing the diet of extinct bovids.

Ecomorphology of the cervid calcaneus as a proxy for paleoenvironmental reconstruction

This study presents new ecomorphological models for the cervid calcaneus that can be used to make predictions about the nature of ancient environments. Using geometric morphometrics to quantitatively assess the length of the articular surface supporting the malleolus, the length and orientation of the tuber calcanei, and the position of the articular facets, we aimed to establish correlations between morphological traits, locomotor behavior, and environmental parameters in extant cervids. The morphology of the calcaneus was found to primarily vary with locomotor strategy and habitat, along a continuum from habitats with an open vegetation structure to habitats with a closed vegetation structure. Confounding factors, including sexual dimorphism, allometry, and phylogeny were accounted for using Principal Component Analysis, regressions and phylogenetic comparative methods. The results of our analyses suggested that these factors did not substantially obscure habitat predictions. As such, the calcaneus provides a valuable proxy for paleoenvironmental reconstruction that is broadly applicable to Quaternary fossil assemblages with a sufficiently large sample of cervids.

Cretaceous origins of the vibrotactile bill-tip organ in birds

Some probe-foraging birds locate their buried prey by detecting mechanical vibrations in the substrate using a specialized tactile bill-tip organ comprising mechanoreceptors embedded in densely clustered pits in the bone at the tip of their beak. This remarkable sensory modality is known as 'remote touch', and the associated bill-tip organ is found in probe-foraging taxa belonging to both the palaeognathous (in kiwi) and neognathous (in ibises and shorebirds) clades of modern birds. Intriguingly, a structurally similar bill-tip organ is also present in the beaks of extant, non-probing palaeognathous birds (e.g. emu and ostriches) that do not use remote touch. By comparison with our comprehensive sample representing all orders of extant modern birds (Neornithes), we provide evidence that the lithornithids (the most basal known palaeognathous birds which evolved in the Cretaceous period) had the ability to use remote touch. This finding suggests that the occurrence of the vestigial bony bill-tip organ in all modern non-probing palaeognathous birds represents a plesiomorphic condition. Furthermore, our results show that remote-touch probe foraging evolved very early among the Neornithes and it may even have predated the palaeognathous-neognathous divergence. We postulate that the tactile bony bill-tip organ in Neornithes may have originated from other snout tactile specializations of their non-avian theropod ancestors.

Ecomorphological variation in artiodactyl calcanei using 3D geometric morphometrics

Artiodactyl postcrania are commonly used as paleoecological indicators but these studies are usually limited to artiodactyls within a single family. Here, we use 3D geometric morphometrics to analyze the morphology of calcanei from five artiodactyl families (Antilocapridae, Bovidae, Cervidae, Giraffidae, and Tragulidae) and identify common ecological trends among these families using principal component analysis. Our results indicate that antilocaprid and some bovid calcanei show convergent evolution of cursorial morphology and that other bovids have independently evolved less cursorial morphology that is more similar to cervids. This study shows that parallel ecomorphological trends can be identified in multiple families of artiodactyls, as well as within artiodactyl groups. This further suggests that the calcaneus may be a good indicator of ecology and function in fossil groups that are taxonomically ambiguous or not closely related to living taxa.

Phenotypic Plasticity of Staphylococcus aureus in Liquid Medium Containing Vancomycin

Phenotypic plasticity enables individuals to develop different phenotypes in a changing environment and promotes adaptive evolution. Genome-wide association study (GWAS) facilitates the study of the genetic basis of bacterial phenotypes, and provides a new opportunity for bacterial phenotypic plasticity research. To investigate the relationship between growth plasticity and genotype in bacteria, 41 Staphylococcus aureus strains, including 29 vancomycin-intermediate S. aureus (VISA) strains, were inoculated in the absence or presence of vancomycin for 48 h. Growth curves and maximum growth rates revealed that strains with the same minimum inhibitory concentration (MIC) showed different levels of plasticity in response to vancomycin. A bivariate GWAS was performed to map single-nucleotide polymorphisms (SNPs) associated with growth plasticity. In total, 227 SNPs were identified from 14 time points, while 15 high-frequency SNPs were mapped to different annotated genes. The P-values and growth variations between the two cultures suggest that non-coding region (SNP 738836), ebh (SNP 1394043), drug transporter (SNP 264897), and pepV (SNP 1775112) play important roles in the growth plasticity of S. aureus. Our study provides an alternative strategy for dissecting the adaptive growth of S. aureus in vancomycin and highlights the feasibility of bivariate GWAS in bacterial phenotypic plasticity research.

The ecomorphology of southern African rodent incisors: Potential applications to the hominin fossil record

The taxonomic identification of mammalian fauna within fossil assemblages is a well-established component of paleoenvironmental reconstructions. However, many fragmentary specimens recovered from fossil sites are often disregarded as they can be difficult to identify with the precision required for taxonomic methods. For this reason, the large numbers of isolated rodent incisors that are often recovered from hominin fossil bearing sites are generally regarded as offering little interpretive value. Ecomorphological analysis, often referred to as a “taxon-free” method, can potentially circumvent this problem by focusing on the adaptive, rather than the taxonomic significance of rodent incisor morphology. Here, we determine if the morphology of the upper incisors of modern southern African rodents reflects dietary behavior using discriminant function analysis. Our model suggests that a strong ecomorphological signal exists in our modern sample and we apply these results to two samples of isolated incisors from the hominin fossil bearing sites, Sterkfontein and Swartkrans.

How scientists perceive the evolutionary origin of human traits: Results of a survey study

Various hypotheses have been proposed for why the traits distinguishing humans from other primates originally evolved, and any given trait may have been explained both as an adaptation to different environments and as a result of demands from social organization or sexual selection. To find out how popular the different explanations are among scientists, we carried out an online survey among authors of recent scientific papers in journals covering relevant fields of science (paleoanthropology, paleontology, ecology, evolution, human biology). Some of the hypotheses were clearly more popular among the 1,266 respondents than others, but none was universally accepted or rejected. Even the most popular of the hypotheses were assessed "very likely" by <50% of the respondents, but many traits had 1-3 hypotheses that were found at least moderately likely by >70% of the respondents. An ordination of the hypotheses identified two strong gradients. Along one gradient, the hypotheses were sorted by their popularity, measured by the average credibility score given by the respondents. The second gradient separated all hypotheses postulating adaptation to swimming or diving into their own group. The average credibility scores given for different subgroups of the hypotheses were not related to respondent's age or number of publications authored. However, (paleo)anthropologists were more critical of all hypotheses, and much more critical of the water-related ones, than were respondents representing other fields of expertise. Although most respondents did not find the water-related hypotheses likely, only a small minority found them unscientific. The most popular hypotheses were based on inherent drivers; that is, they assumed the evolution of a trait to have been triggered by the prior emergence of another human-specific behavioral or morphological trait, but opinions differed as to which of the traits came first.

A new fossil cercopithecid tibia from Laetoli and its implications for positional behavior and paleoecology

Detailed analyses and comparisons of postcranial specimens of Plio-Pleistocene cercopithecids provide an opportunity to examine the recent evolutionary history and locomotor diversity in Old World monkeys. Studies examining the positional behavior and substrate preferences of fossil cercopithecids are also important for reconstructing the paleoenvironments of Plio-Pleistocene hominin sites. Here we describe a new fossil cercopithecid tibia (EP 1100/12) from the Australopithecus afarensis-bearing Upper Laetolil Beds (∼3.7 Ma) of Laetoli in northern Tanzania. The fossil tibia is attributed to cf. Rhinocolobus sp., which is the most common colobine at Laetoli. In addition to qualitative comparisons, the tibial shape of EP 1100/12 was compared to that of 190 extant cercopithecids using three-dimensional landmarks. Discriminant function analyses of the shape data were used to assess taxonomic affinity and shape variation relating to positional behavior. EP 1100/12 clustered with extant colobines, particularly the large-bodied genera Nasalis and Rhinopithecus. Comparisons reveal that EP 1100/12 belongs to a large-bodied monkey that engaged in arboreal pronograde quadrupedalism. These findings add further support to previous inferences that woodland and forest environments dominated the paleoenvironment of the Upper Laetolil Beds, which supported the diverse community of cercopithecids at Laetoli. The inferred paleoecology and the presence of large-bodied arboreally-adapted monkeys at Laetoli show that A. afarensis had access to a range of diverse habitats, including woodlands and forests. This supports the possibility that A. afarensis, with its potential range of positional capabilities, was able to utilize arboreal settings for food acquisition and refuge from predators.

Contextualising primate origins--an ecomorphological framework

Ecomorphology - the characterisation of the adaptive relationship between an organism's morphology and its ecological role - has long been central to theories of the origin and early evolution of the primate order. This is exemplified by two of the most influential theories of primate origins: Matt Cartmill's Visual Predation Hypothesis, and Bob Sussman's Angiosperm Co-Evolution Hypothesis. However, the study of primate origins is constrained by the absence of data directly documenting the events under investigation, and has to rely instead on a fragmentary fossil record and the methodological assumptions inherent in phylogenetic comparative analyses of extant species. These constraints introduce particular challenges for inferring the ecomorphology of primate origins, as morphology and environmental context must first be inferred before the relationship between the two can be considered. Fossils can be integrated in comparative analyses and observations of extant model species and laboratory experiments of form-function relationships are critical for the functional interpretation of the morphology of extinct species. Recent developments have led to important advancements, including phylogenetic comparative methods based on more realistic models of evolution, and improved methods for the inference of clade divergence times, as well as an improved fossil record. This contribution will review current perspectives on the origin and early evolution of primates, paying particular attention to their phylogenetic (including cladistic relationships and character evolution) and environmental (including chronology, geography, and physical environments) contextualisation, before attempting an up-to-date ecomorphological synthesis of primate origins.

Exploring morphological generality in the Old World monkey postcranium using an ecomorphological framework

Nearly all primates are ecologically dependent on trees, but they are nonetheless found in an enormous range of habitats, from highly xeric environments to dense rainforest. Most primates have a relatively 'generalised' skeleton, enabling locomotor flexibility and facilitating other crucial functions, such as manual foraging and grooming. This paper explores the associations between habitat, locomotion and morphology in the forelimbs of cercopithecids (Old World monkeys), contextualising their skeletal ecomorphological patterns with those of other mammals, and complementing functional morphological analyses with phylogenetic comparative techniques. The ecomorphological signals present in the generalised primate postcranium, and how an ancestral arboreal 'bauplan' might be modified to incorporate terrestriality or exploit distinct arboreal substrates, are investigated. Analysis of ecomorphological variation in guenons indicates that terrestrial Chlorocebus species retain core elements of a general guenon form, with modifications for terrestriality that vary by species. Adaptation to different modes of arboreality has also occurred in Cercopithecus. The considerable morphological similarity in the guenons sampled emphasises the importance of generality in the primate postcranium - much forelimb variation appears to have emerged stochastically, with a smaller number of traits having a strong functional signal. Analysis of a broader sample of cercopithecids and comparison with felids, suids and bovids indicates that although the cercopithecid humerus has functional morphological signals that enable specimens to be assigned with a reasonable degree of certainty to habitat groups, there is considerable overlap in the specimens assigned to each habitat group. This probably reflects ecological dependence on trees, even in predominantly terrestrial species, as well as the multiple functions of the forelimb and, in some cases, wide geographic distributions that promote intraspecific variation. The use of phylogenetic correction reduced the discriminatory power of the models, indicating that, like allometry, phylogeny contains important ecomorphological information, and should not necessarily be factored out of analyses.

On Mesopithecus habitat: Insights from late Miocene fossil vertebrate localities of Bulgaria

The aim of this study is to describe the environments where the cercopithecid Mesopithecus was found during latest Miocene in Europe. For this purpose, we investigate the paleoecology of the herbivorous ungulate mesofauna of three very rich late Miocene fossil localities from southwestern Bulgaria: Hadjidimovo, Kalimantsi and Strumyani. While Mesopithecus has been found in the two first localities, no primate remains have yet been identified in Strumyani. Comparison between localities with and without primates using the herbivore mesofauna allows the cross-corroboration of paleoenvironmental conditions where this primate did and did not live. A multi-parameter statistical approach involving 117 equid and 345 bovid fossil dental and postcranial (phalanges, metapodia, astragali) remains from these three localities provides species to generic-level diet and locomotor habit information in order to characterize the environment in which Mesopithecus evolved. The analysis of dental mesowear indicates that the bovids were mainly mixed feeders, while coeval equids were more engaged in grazing. Meanwhile, postcranial remains show that the ungulate species from Hadjidimovo and Kalimantsi evolved in dry environments with a continuum of habitats ranging from slightly wooded areas to relatively open landscapes, whereas the Mesopithecus-free Strumyani locality was in comparison reflecting a rather contrasted mosaic of environments with predominant open and some more closed and wet areas. Environments in which Mesopithecus is known during the late Miocene were not contrasted landscapes combining open grassy areas and dense forested patches, but instead rather restricted to slightly wooded and homogeneous landscapes including a developed grassy herbaceous layer.

Locomotion and posture from the common hominoid ancestor to fully modern hominins, with special reference to the last common panin/hominin ancestor

Based on our knowledge of locomotor biomechanics and ecology we predict the locomotion and posture of the last common ancestors of (a) great and lesser apes and their close fossil relatives (hominoids); (b) chimpanzees, bonobos and modern humans (hominines); and (c) modern humans and their fossil relatives (hominins). We evaluate our propositions against the fossil record in the context of a broader review of evolution of the locomotor system from the earliest hominoids of modern aspect (crown hominoids) to early modern Homo sapiens. While some early East African stem hominoids were pronograde, it appears that the adaptations which best characterize the crown hominoids are orthogrady and an ability to abduct the arm above the shoulder - rather than, as is often thought, manual suspension sensu stricto. At 7-9 Ma (not much earlier than the likely 4-8 Ma divergence date for panins and hominins, see Bradley, 2008) there were crown hominoids in southern Europe which were adapted to moving in an orthograde posture, supported primarily on the hindlimb, in an arboreal, and possibly for Oreopithecus, a terrestrial context. By 7 Ma, Sahelanthropus provides evidence of a Central African hominin, panin or possibly gorilline adapted to orthogrady, and both orthogrady and habitually highly extended postures of the hip are evident in the arboreal East African protohominin Orrorin at 6 Ma. If the traditional idea that hominins passed through a terrestrial 'knuckle-walking' phase is correct, not only does it have to be explained how a quadrupedal gait typified by flexed postures of the hindlimb could have preadapted the body for the hominin acquisition of straight-legged erect bipedality, but we would have to accept a transition from stem-hominoid pronogrady to crown hominoid orthogrady, back again to pronogrady in the African apes and then back to orthogrady in hominins. Hand-assisted arboreal bipedality, which is part of a continuum of orthograde behaviours, is used by modern orangutans to forage among the small branches at the periphery of trees where the core hominoid dietary resource, ripe fruit, is most often to be found. Derivation of habitual terrestrial bipedality from arboreal hand-assisted bipedality requires fewer transitions, and is also kinematically and kinetically more parsimonious.