New Paleocene skeletons and the relationship of plesiadapiforms to crown-clade primates

Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification

The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary. Phillips (2016) proposed a soft explosive model that allows for the emergence of a few lineages (Xenarthra, Afrotheria, Euarchontoglires, Laurasiatheria) in the Cretaceous, but otherwise agrees with the explosive model in positing the majority of interordinal diversification after the KPg mass extinction. Phillips (2016) argues that rate transference errors associated with large body size and long lifespan have inflated previous estimates of interordinal divergence times, and further suggests that most interordinal divergences are positioned after the KPg boundary when rate transference errors are avoided through the elimination of calibrations in large-bodied and/or long lifespan clades. Here, we show that rate transference errors can also occur in the opposite direction and drag forward estimated divergence dates when calibrations in large-bodied/long lifespan clades are omitted. This dragging forward effect results in the occurrence of more than half a billion years of 'zombie lineages' on Phillips' preferred timetree. By contrast with ghost lineages, which are a logical byproduct of an incomplete fossil record, zombie lineages occur when estimated divergence dates are younger than the minimum age of the oldest crown fossils. We also present the results of new timetree analyses that address the rate transference problem highlighted by Phillips (2016) by deleting taxa that exceed thresholds for body size and lifespan. These analyses recover all interordinal divergence times in the Cretaceous and are consistent with the long fuse model of placental diversification. Finally, we outline potential problems with morphological cladistic analyses of higher-level relationships among placental mammals that may account for the perceived discrepancies between molecular and paleontological estimates of placental divergence times.

Effects of support diameter and compliance on common marmoset (Callithrix jacchus) gait kinematics

Locomotion is precarious in an arboreal habitat, where supports can vary in both diameter and level of compliance. Several previous studies have evaluated the influence of substrate diameter on the locomotor performance of arboreal quadrupeds. The influence of substrate compliance, however, has been mostly unexamined. Here, we used a multifactorial experimental design to investigate how perturbations in both diameter and compliance affect the gait kinematics of marmosets (Callithrix jacchus; N=2) moving over simulated arboreal substrates. We used 3D-calibrated video to quantify marmoset locomotion over a horizontal trackway consisting of variably sized poles (5, 2.5 and 1.25 cm in diameter), analyzing a total of 120 strides. The central portion of the trackway was either immobile or mounted on compliant foam blocks, depending on condition. We found that narrowing diameter and increasing compliance were both associated with relatively longer substrate contact durations, though adjustments to diameter were often inconsistent relative to compliance-related adjustments. Marmosets also responded to narrowing diameter by reducing speed, flattening center of mass (CoM) movements and dampening support displacement on the compliant substrate. For the subset of strides on the compliant support, we found that speed, contact duration and CoM amplitude explained >60% of the variation in substrate displacement over a stride, suggesting a direct performance advantage to these kinematic adjustments. Overall, our results show that compliant substrates can exert a significant influence on gait kinematics. Substrate compliance, and not just support diameter, should be considered a critical environmental variable when evaluating locomotor performance in arboreal quadrupeds.

Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculoskeletal-related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140 kb of orthologous sequence data from colugo museum specimens sampled across their range and identified large genetic differences between many geographically isolated populations that may result in a >300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.

Euarchontan Opsin Variation Brings New Focus to Primate Origins

Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, that is, the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here, we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) visual sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in the color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination.

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.

Sampling diverse characters improves phylogenies: Craniodental and postcranial characters of vertebrates often imply different trees

Morphological cladograms of vertebrates are often inferred from greater numbers of characters describing the skull and teeth than from postcranial characters. This is either because the skull is believed to yield characters with a stronger phylogenetic signal (i.e., contain less homoplasy), because morphological variation therein is more readily atomized, or because craniodental material is more widely available (particularly in the palaeontological case). An analysis of 85 vertebrate datasets published between 2000 and 2013 confirms that craniodental characters are significantly more numerous than postcranial characters, but finds no evidence that levels of homoplasy differ in the two partitions. However, a new partition test, based on tree-to-tree distances (as measured by the Robinson Foulds metric) rather than tree length, reveals that relationships inferred from the partitions are significantly different about one time in three, much more often than expected. Such differences may reflect divergent selective pressures in different body regions, resulting in different localized patterns of homoplasy. Most systematists attempt to sample characters broadly across body regions, but this is not always possible. We conclude that trees inferred largely from either craniodental or postcranial characters in isolation may differ significantly from those that would result from a more holistic approach. We urge the latter.

Astragalar and calcaneal morphology of the middle Eocene primate Anchomomys frontanyensis (Anchomomyini): Implications for early primate evolution

Astragali and calcanei of Anchomomys frontanyensis, a small adapiform from the middle Eocene of Sant Jaume de Frontanyà (Southern Pyrenean basins, northeastern Spain) are described in detail. Though these bones have been known for some time, they have never been carefully analyzed in a context that is comprehensively comparative, quantitative, considers sample variation (astragalus n = 4; calcaneus n = 16), and assesses the phylogenetic significance of the material in an explicit cladistic context, as we do here. Though these bones are isolated, regression analyses provide the first formal statistical support for attribution to A. frontanyensis. The astragalus presents features similar to those of the small stem strepsirrhine Djebelemur from the middle Eocene of Tunisia, while the calcaneus more closely resembles those of the basal omomyiform Teilhardina. The new phylogenetic analyses that include Anchomomys' postcranial and dental data recover anchomomyins outside of the adapiform clade, and closer to djebelemurids, azibiids, and crown strepsirrhines. The small size of A. frontanyensis allows comparison of similarly small adapiforms and omomyiforms (haplorhines) such that observed variation has more straightforward implications for function. Previous studies have demonstrated that distal calcaneal elongation is reflective of leaping proclivity when effects of body mass are appropriately accounted for; in this context, A. frontanyensis has calcaneal elongation suggesting a higher degree of leaping specialization than other adapiforms and even some early omomyiforms. Moreover, comparison to a similarly-sized early adapiform from India, Marcgodinotius (which shows no calcaneal elongation) confirms that high distal calcaneal elongation in A. frontanyensis cannot be simply explained by allometric effects of small size compared to larger adapiform taxa. This pattern is consistent with the idea that significant distal calcaneal elongation evolved at least twice in early euprimates, and that early primate niche space frequently included demands for increased leaping specialization.

Virtual endocasts of Eocene Paramys (Paramyinae): oldest endocranial record for Rodentia and early brain evolution in Euarchontoglires

Understanding the pattern of brain evolution in early rodents is central to reconstructing the ancestral condition for Glires, and for other members of Euarchontoglires including Primates. We describe the oldest virtual endocasts known for fossil rodents, which pertain to Paramys copei (Early Eocene) and Paramys delicatus (Middle Eocene). Both specimens of Paramys have larger olfactory bulbs and smaller paraflocculi relative to total endocranial volume than later occurring rodents, which may be primitive traits for Rodentia. The encephalization quotients (EQs) of Pa. copei and Pa. delicatus are higher than that of later occurring (Oligocene) Ischyromys typus, which contradicts the hypothesis that EQ increases through time in all mammalian orders. However, both species of Paramys have a lower relative neocortical surface area than later rodents, suggesting neocorticalization occurred through time in this Order, although to a lesser degree than in Primates. Paramys has a higher EQ but a lower neocortical ratio than any stem primate. This result contrasts with the idea that primates were always exceptional in their degree of overall encephalization and shows that relative brain size and neocortical surface area do not necessarily covary through time. As such, these data contradict assumptions made about the pattern of brain evolution in Euarchontoglires.

An early Oligocene fossil demonstrates treeshrews are slowly evolving "living fossils"

Treeshrews are widely considered a “living model” of an ancestral primate, and have long been called “living fossils”. Actual fossils of treeshrews, however, are extremely rare. We report a new fossil species of Ptilocercus treeshrew recovered from the early Oligocene (~34 Ma) of China that represents the oldest definitive fossil record of the crown group of treeshrews and nearly doubles the temporal length of their fossil record. The fossil species is strikingly similar to the living Ptilocercus lowii, a species generally recognized as the most plesiomorphic extant treeshrew. It demonstrates that Ptilocercus treeshrews have undergone little evolutionary change in their morphology since the early Oligocene. Morphological comparisons and phylogenetic analysis support the long-standing idea that Ptilocercus treeshrews are morphologically conservative and have probably retained many characters present in the common stock that gave rise to archontans, which include primates, flying lemurs, plesiadapiforms and treeshrews. This discovery provides an exceptional example of slow morphological evolution in a mammalian group over a period of 34 million years. The persistent and stable tropical environment in Southeast Asia through the Cenozoic likely played a critical role in the survival of such a morphologically conservative lineage.

The first major primate extinction: An evaluation of paleoecological dynamics of North American stem primates using a homology free measure of tooth shape

OBJECTIVES

The disappearance of the North American plesiadapoids (stem primates, or plesiadapiforms) in the latest Paleocene has been attributed to competition with rodents over dietary resources. This study compares molar morphology of plesiadapoids and early rodents to assess whether all taxa were adapted to consuming foods of the same structural properties with similar mechanical efficacy.

MATERIALS AND METHODS

Micro-CT scans of second mandibular molars (M2 s) of plesiadapoids (n = 181) and ischyromyid (early fossil) rodents (n = 13) were evaluated using Dirichlet normal energy (DNE), a dental topographic metric that quantifies the curvature of a tooth's occlusal surface, independent of the orientation of the occlusal plane; this metric can be used to infer diet.

RESULTS

Comparisons of DNE values for plesiadapoids and rodents show that rodents shared functionally similar dental morphology with at least some plesiadapid plesiadapoids and thus were likely adapted to processing foods with similar physical properties. However, the DNE values for rodents contrast markedly with those for the other two plesiadapoid families, the Carpolestidae and Saxonellidae.

CONCLUSIONS

It is unlikely that direct competition over food resources with rodents played a major role in the extinction of carpolestids and saxonellids, as members of these families were capable of consuming a range of foods that were not accessible to rodents. Although several plesiadapid species overlap with rodents in their range of DNE values, only three overlap in time. One of these (Plesiadapis cookei) may have been too large to be in direct competition with rodents, another (Plesiadapis dubius) has DNE values substantially different (higher) than those of rodents, whereas the third, Chiromyoides, has teeth of both a similar size and DNE value to those of Clarkforkian rodents. If dietary niche overlap with rodents played a direct role in the decline of plesiadapiforms, it can only have potentially done so for Chiromyoides.

What limits the morphological disparity of clades?

The morphological disparity of species within major clades shows a variety of trajectory patterns through evolutionary time. However, there is a significant tendency for groups to reach their maximum disparity relatively early in their histories, even while their species richness or diversity is comparatively low. This pattern of early high-disparity suggests that there are internal constraints (e.g. developmental pleiotropy) or external restrictions (e.g. ecological competition) upon the variety of morphologies that can subsequently evolve. It has also been demonstrated that the rate of evolution of new character states decreases in most clades through time (character saturation), as does the rate of origination of novel bodyplans and higher taxa. Here, we tested whether there was a simple relationship between the level or rate of character state exhaustion and the shape of a clade's disparity profile: specifically, its centre of gravity (CG). In a sample of 93 extinct major clades, most showed some degree of exhaustion, but all continued to evolve new states up until their extinction. Projection of states/steps curves suggested that clades realized an average of 60% of their inferred maximum numbers of states. Despite a weak but significant correlation between overall levels of homoplasy and the CG of clade disparity profiles, there were no significant relationships between any of our indices of exhaustion curve shape and the clade disparity CG. Clades showing early high-disparity were no more likely to have early character saturation than those with maximum disparity late in their evolution.

New partial skeletons of Palaeocene Nyctitheriidae and evaluation of proposed euarchontan affinities

Small-bodied, insectivorous Nyctitheriidae are known in the Palaeogene fossil record almost exclusively from teeth and fragmentary jaws and have been referred to Eulipotyphla (shrews, moles and hedgehogs) based on dental similarities. By contrast, isolated postcrania attributed to the group suggest arboreality and a relationship to Euarchonta (primates, treeshrews and colugos). Cretaceous-Palaeocene adapisoriculid insectivores have also been proposed as early euarchontans based on postcranial similarities. We describe the first known dentally associated nyctitheriid auditory regions and postcrania, and use them to test the proposed relationship to Euarchonta with cladistic analyses of 415 dental, cranial and postcranial characteristics scored for 92 fossil and extant mammalian taxa. Although nyctitheriid postcrania share similarities with euarchontans likely related to arboreality, results of cladistic analyses suggest that nyctitheriids are closely related to Eulipotyphla. Adapisoriculidae is found to be outside of crown Placentalia. These results suggest that similarities in postcranial morphology among nyctitheriids, adapisoriculids and euarchontans represent separate instances of convergence or primitive retention of climbing capabilities.

Life history of the most complete fossil primate skeleton: exploring growth models for Darwinius

Darwinius is an adapoid primate from the Eocene of Germany, and its only known specimen represents the most complete fossil primate ever found. Its describers hypothesized a close relationship to Anthropoidea, and using a Saimiri model estimated its age at death. This study reconstructs the ancestral permanent dental eruption sequences for basal Euprimates, Haplorhini, Anthropoidea, and stem and crown Strepsirrhini. The results show that the ancestral sequences for the basal euprimate, haplorhine and stem strepsirrhine are identical, and similar to that of Darwinius. However, Darwinius differs from anthropoids by exhibiting early development of the lower third molars relative to the lower third and fourth premolars. The eruption of the lower second premolar marks the point of interruption of the sequence in Darwinius. The anthropoid Saimiri as a model is therefore problematic because it exhibits a delayed eruption of P2. Here, an alternative strepsirrhine model based on Eulemur and Varecia is presented. Our proposed model shows an older age at death than previously suggested (1.05-1.14 years), while the range for adult weight is entirely below the range proposed previously. This alternative model is more consistent with hypotheses supporting a stronger relationship between adapoids and strepsirrhines.

The position of tree shrews in the mammalian tree: Comparing multi-gene analyses with phylogenomic results leaves monophyly of Euarchonta doubtful

The well-accepted Euarchonta grandorder is a pruned version of Archonta nested within the Euarchontoglires (or Supraprimates) clade. At present, it includes tree shrews (Scandentia), flying lemurs (Dermoptera) and primates (Primates). Here, a phylogenomic dataset containing 1912 exons from 22 representative mammals was compiled to investigate the phylogenetic relationships within this group. Phylogenetic analyses and hypothesis testing suggested that tree shrews can be classified as a sister group to Primates or to Glires or even as a basal clade within Euarchontoglires. Further analyses of both modified and original previously published datasets found that the phylogenetic position of tree shrews is unstable. We also found that two of three exonic indels reported as synapomorphies of Euarchonta in a previous study do not unambiguously support the monophyly of such a clade. Therefore, the monophyly of both Euarchonta and Sundatheria (Dermoptera + Scandentia) are suspect. Molecular dating and divergence rate analyses suggested that the ancestor of Euarchontoglires experienced a rapid divergence, which may cause the unresolved position of tree shrews even using the whole genomic data.

Quantification of neocortical ratios in stem primates

Extant euprimates (=crown primates) have a characteristically expanded neocortical region of the brain relative to that of other mammals, but the timing of that expansion in their evolutionary history is poorly resolved. Examination of anatomical landmarks on fossil endocasts of Eocene euprimates suggests that significant neocortical expansion relative to contemporaneous mammals was already underway. Here, we provide quantitative estimates of neocorticalization in stem primates (plesiadapiforms) relevant to the question of whether relative neocortical expansion was uniquely characteristic of the crown primate radiation. Ratios of neocortex to endocast surface areas were calculated for plesiadapiforms using measurements from virtual endocasts of the paromomyid Ignacius graybullianus (early Eocene, Wyoming) and the microsyopid Microsyops annectens (middle Eocene, Wyoming). These data are similar to a published estimate for the plesiadapid, Plesiadapis tricuspidens, but contrast with those calculated for early Tertiary euprimates in being within the 95% confidence intervals for archaic mammals generally. Interpretation of these values is complicated by the paucity of sampled endocasts for older stem primates and euarchontogliran outgroups, as well as by a combination of effects related to temporal trends, allometry, and taxon-unique specializations. Regardless, these results are consistent with the hypothesis that a shift in brain organization occurred in the first euprimates, likely in association with elaborations to the visual system.

Oldest known euarchontan tarsals and affinities of Paleocene Purgatorius to Primates

Earliest Paleocene Purgatorius often is regarded as the geologically oldest primate, but it has been known only from fossilized dentitions since it was first described half a century ago. The dentition of Purgatorius is more primitive than those of all known living and fossil primates, leading some researchers to suggest that it lies near the ancestry of all other primates; however, others have questioned its affinities to primates or even to placental mammals. Here we report the first (to our knowledge) nondental remains (tarsal bones) attributed to Purgatorius from the same earliest Paleocene deposits that have yielded numerous fossil dentitions of this poorly known mammal. Three independent phylogenetic analyses that incorporate new data from these fossils support primate affinities of Purgatorius among euarchontan mammals (primates, treeshrews, and colugos). Astragali and calcanei attributed to Purgatorius indicate a mobile ankle typical of arboreal euarchontan mammals generally and of Paleocene and Eocene plesiadapiforms specifically and provide the earliest fossil evidence of arboreality in primates and other euarchontan mammals. Postcranial specializations for arboreality in the earliest primates likely played a key role in the evolutionary success of this mammalian radiation in the Paleocene.

Modeling olfactory bulb evolution through primate phylogeny

Adaptive characterizations of primates have usually included a reduction in olfactory sensitivity. However, this inference of derivation and directionality assumes an ancestral state of olfaction, usually by comparison to a group of extant non-primate mammals. Thus, the accuracy of the inference depends on the assumed ancestral state. Here I present a phylogenetic model of continuous trait evolution that reconstructs olfactory bulb volumes for ancestral nodes of primates and mammal outgroups. Parent-daughter comparisons suggest that, relative to the ancestral euarchontan, the crown-primate node is plesiomorphic and that derived reduction in olfactory sensitivity is an attribute of the haplorhine lineage. The model also suggests a derived increase in olfactory sensitivity at the strepsirrhine node. This oppositional diversification of the strepsirrhine and haplorhine lineages from an intermediate and non-derived ancestor is inconsistent with a characterization of graded reduction through primate evolution.

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.

The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis

The development and evolution of organisms is heavily influenced by their environment. Thus, understanding the historical biogeography of taxa can provide insights into their evolutionary history, adaptations and trade-offs realized throughout time. In the present study we have taken a phylogenomic approach to infer New World monkey phylogeny, upon which we have reconstructed the biogeographic history of extant platyrrhines. In order to generate sufficient phylogenetic signal within the New World monkey clade, we carried out a large-scale phylogenetic analysis of approximately 40 kb of non-genic genomic DNA sequence in a 36 species subset of extant New World monkeys. Maximum parsimony, maximum likelihood and Bayesian inference analysis all converged on a single optimal tree topology. Divergence dating and biogeographic analysis reconstruct the timing and geographic location of divergence events. The ancestral area reconstruction describes the geographic locations of the last common ancestor of extant platyrrhines and provides insight into key biogeographic events occurring during platyrrhine diversification. Through these analyses we conclude that the diversification of the platyrrhines took place concurrently with the establishment and diversification of the Amazon rainforest. This suggests that an expanding rainforest environment rather than geographic isolation drove platyrrhine diversification.

Endocranial morphology of Palaeocene Plesiadapis tricuspidens and evolution of the early primate brain

Expansion of the brain is a key feature of primate evolution. The fossil record, although incomplete, allows a partial reconstruction of changes in primate brain size and morphology through time. Palaeogene plesiadapoids, closest relatives of Euprimates (or crown-group primates), are crucial for understanding early evolution of the primate brain. However, brain morphology of this group remains poorly documented, and major questions remain regarding the initial phase of euprimate brain evolution. Micro-CT investigation of the endocranial morphology of Plesiadapis tricuspidens from the Late Palaeocene of Europe--the most complete plesiadapoid cranium known--shows that plesiadapoids retained a very small and simple brain. Plesiadapis has midbrain exposure, and minimal encephalization and neocorticalization, making it comparable with that of stem rodents and lagomorphs. However, Plesiadapis shares a domed neocortex and downwardly shifted olfactory-bulb axis with Euprimates. If accepted phylogenetic relationships are correct, then this implies that the euprimate brain underwent drastic reorganization during the Palaeocene, and some changes in brain structure preceded brain size increase and neocortex expansion during evolution of the primate brain.

Functional and evolutionary aspects of axial stability in euarchontans and other mammals

The presence of a stable thoracolumbar region, found in many arboreal mammals, is considered advantageous for bridging and cantilevering between discontinuous branches. However, no study has directly explored the link between osteological features cited as enhancing axial stability and the frequency of cantilevering and bridging behaviors in a terminal branch environment. To fill this gap, we collected metric data on costal and vertebral morphology of primate and nonprimate mammals known to cantilever and bridge frequently and those that do not. We also quantified the frequency and duration of cantilevering and bridging behaviors using experimental setups for species that have been reported to show differences in use of small branches and back anatomy (Caluromys philander, Loris tardigradus, Monodelphis domestica, and Cheirogaleus medius). Phylogenetically corrected principal component analysis reveals that taxa employing frequent bridging and cantilevering (C. philander and lorises) also exhibit reduced intervertebral and intercostal spaces, which can serve to increase thoracolumbar stability, when compared to closely related species (M. domestica and C. medius). We observed C. philander cantilevering and bridging significantly more often than M. domestica, which never cantilevered or crossed any arboreal gaps. Although no difference in the frequency of cantilevering was observed between L. tardigradus and C. medius, the duration of cantilevering bouts was significantly greater in L. tardigradus. These data suggest that osteological features promoting axial rigidity may be part of a morpho-behavioral complex that increases stability in mammals moving and foraging in a terminal branch environment.

Interspecific scaling patterns of talar articular surfaces within primates and their closest living relatives

The articular facets of interosseous joints must transmit forces while maintaining relatively low stresses. To prevent overloading, joints that transmit higher forces should therefore have larger facet areas. The relative contributions of body mass and muscle-induced forces to joint stress are unclear, but generate opposing hypotheses. If mass-induced forces dominate, facet area should scale with positive allometry to body mass. Alternatively, muscle-induced forces should cause facets to scale isometrically with body mass. Within primates, both scaling patterns have been reported for articular surfaces of the femoral and humeral heads, but more distal elements are less well studied. Additionally, examination of complex articular surfaces has largely been limited to linear measurements, so that 'true area' remains poorly assessed. To re-assess these scaling relationships, we examine the relationship between body size and articular surface areas of the talus. Area measurements were taken from microCT scan-generated surfaces of all talar facets from a comprehensive sample of extant euarchontan taxa (primates, treeshrews, and colugos). Log-transformed data were regressed on literature-derived log-body mass using reduced major axis and phylogenetic least squares regressions. We examine the scaling patterns of muscle mass and physiological cross-sectional area (PCSA) to body mass, as these relationships may complicate each model. Finally, we examine the scaling pattern of hindlimb muscle PCSA to talar articular surface area, a direct test of the effect of mass-induced forces on joint surfaces. Among most groups, there is an overall trend toward positive allometry for articular surfaces. The ectal (= posterior calcaneal) facet scales with positive allometry among all groups except 'sundatherians', strepsirrhines, galagids, and lorisids. The medial tibial facet scales isometrically among all groups except lemuroids. Scaling coefficients are not correlated with sample size, clade inclusivity or behavioral diversity of the sample. Muscle mass scales with slight positive allometry to body mass, and PCSA scales at isometry to body mass. PCSA generally scales with negative allometry to articular surface area, which indicates joint surfaces increase faster than muscles' ability to generate force. We suggest a synthetic model to explain the complex patterns observed for talar articular surface area scaling: whether 'muscles or mass' drive articular facet scaling is probably dependent on the body size range of the sample and the biological role of the facet. The relationship between 'muscle vs. mass' dominance is likely bone- and facet-specific, meaning that some facets should respond primarily to stresses induced by larger body mass, whereas others primarily reflect muscle forces.

Comparative study of notoungulate (Placentalia, Mammalia) bony labyrinths and new phylogenetically informative inner ear characters

The phylogenetic relationships of notoungulates, an extinct group of predominantly South American herbivores, remain poorly resolved with respect to both other placental mammals and among one another. Most previous phylogenetic analyses of notoungulates have not included characters of the internal cranium, not least because few such features, including the bony labyrinth, have been described for members of the group. Here we describe the inner ears of the notoungulates Altitypotherium chucalensis (Mesotheriidae), Pachyrukhos moyani (Hegetotheriidae) and Cochilius sp. (Interatheriidae) based on reconstructions of bony labyrinths obtained from computed tomography imagery. Comparisons of the bony labyrinths of these taxa with the basally diverging notoungulate Notostylops murinus (Notostylopidae), an isolated petrosal from Itaboraí, Brazil, referred to Notoungulata, and six therian outgroups, yielded an inner ear character matrix of 25 potentially phylogenetically informative characters, 14 of them novel to this study. Two equivocally optimized character states potentially support a pairing of Mesotheriidae and Hegetotheriidae, whereas four others may be diagnostic of Notoungulata. Three additional characters are potentially informative for diagnosing more inclusive clades: one for crown Placentalia; another for a clade containing Kulbeckia, Zalambdalestes, and Placentalia; and a third for Eutheria (crown Placentalia plus stem taxa). Several other characters are apomorphic for at least one notoungulate in our study and are of potential interest for broader taxonomic sampling within Notoungulata to clarify currently enigmatic interrelationships. Measures of the semicircular canals were used to infer agility (e.g. capable of quick movements vs. lethargic movements) of these taxa. Agility scores calculated from these data generally corroborate interpretations based on postcranial remains of these or closely related species. We provide estimates of the low-frequency hearing limits in notoungulates based on the ratio of radii of the apical and basal turns of the cochlea. These limits range from 15 Hz in Notostylops to 149 Hz in Pachyrukhos, values comparable to the Asian elephant (Elephas maximus) and the California sea lion (Zalophus californianus) when hearing in air, respectively.

New insights into the ear region anatomy and cranial blood supply of advanced stem Strepsirhini: evidence from three primate petrosals from the Eocene of Chambi, Tunisia

We report the discovery of three isolated primate petrosal fragments from the fossiliferous locality of Chambi (Tunisia), a primate-bearing locality dating from the late early to the early middle Eocene. These fossils display a suite of anatomical characteristics otherwise found only in strepsirhines, and as such might be attributed either to Djebelemur or/and cf. Algeripithecus, the two diminutive stem strepsirhine primates recorded from this locality. Although damaged, the petrosals provide substantial information regarding the ear anatomy of these advanced stem strepsirhines (or pre-tooth-combed primates), notably the patterns of the pathway of the arterial blood supply. Using μCT-scanning techniques and digital segmentation of the structures, we show that the transpromontorial and stapedial branches of the internal carotid artery (ICA) were present (presence of bony tubes), but seemingly too small to supply enough blood to the cranium alone. This suggests that the ICA was not the main cranial blood supply in stem strepsirhines, but that the pharyngeal or vertebral artery primitively ensured a great part of this role instead, an arterial pattern that is reminiscent of modern cheirogaleid, lepilemurid lemuriforms and lorisiforms. This could explain parallel loss of the ICA functionality among these families. Specific measurements made on the cochlea indicate that the small strepsirhine primate(s) from Chambi was (were) highly sensitive to high frequencies and poorly sensitive to low frequencies. Finally, variance from orthogonality of the plane of the semicircular canals (SCs) calculated on one petrosal (CBI-1-569) suggests that Djebelemur or cf. Algeripithecus likely moved (at least its head) in a way similar to that of modern mouse lemurs.

First record of the genus Microchoerus (Omomyidae, Primates) in the western Iberian Peninsula and its palaeobiogeographic implications

In this paper we describe new material of Microchoerus (Microchoerinae, Omomyidae, Primates) from Zambrana (Miranda-Trebiño Basin, northern Iberian Peninsula, Spain), a locality assigned to Reference Level MP18 (middle Headonian, Late Eocene). The specimens studied consist of two mandibular fragments, bearing p3-m3 and p4-m3. The teeth resemble in size and morphology those of Microchoerus erinaceus from Hordle Cliff, England, although some differences prevent us from making a definitive ascription to this species. We therefore refer the material from Zambrana to Microchoerus aff. erinaceus. Some traits, such as the development of the mesoconid and hypoconulid in the m1 and m2, and the shape of the hypoconulid lobe in the m3, are intermediate between those of M. erinaceus and Microchoerus edwardsi. Thus, the material from Zambrana is very similar to other species of Microchoerus present in Europe, representing a transitional form between M. erinaceus and M. edwardsi. The described material represents the first discovery of a primate from the Miranda-Trebiño Basin, and also the westernmost record of the genus Microchoerus in the Iberian Peninsula. Moreover, the identification of this microchoerine, with clear similarities to the representatives of this genus described from other European sites, reinforces the idea of the existence of connections between western Iberia and the rest of Europe in the Late Eocene, previously hypothesized after the discovery of typical European artiodactyls in the site of Zambrana.

Systematics of Paleogene Micromomyidae (euarchonta, primates) from North America

New specimens of micromomyid plesiadapiforms recovered from the late Paleocene and early Eocene of the Clarks Fork and Powder River Basins, Wyoming, include previously unknown tooth positions of Chalicomomys antelucanus, the earliest record and first substantial Paleocene sample of Tinimomys graybulliensis, and additional specimens of early Eocene T. graybulliensis, forming the largest known sample (n = 84, MNI = 14) of a micromomyid species from a single fossil locality. These specimens and newly documented intraspecific variability, coupled with the first detailed descriptions of the dentition of Dryomomys szalayi, allow for a systematic revision of the family. Cladistic analysis of the 11 known micromomyid species using 28 morphological characters produced three most-parsimonious cladograms. Results suggest that several Tiffanian taxa previously classified in the genus Micromomys (excluding the type species Micromomys silvercouleei) are more primitive and are referred to a new genus Foxomomys (Foxomomys fremdi, Foxomomys vossae, and Foxomomys gunnelli). Two other Paleocene and early Eocene species previously classified in Micromomys are instead found to share a special relationship with Dryomomys (Dryomomys millennius and Dryomomys willwoodensis) based primarily on the relative size and shape of the premolars. Results further suggest that early Eocene Chalicomomys (monotypic: Chalicomomys antelucanus) is the sister taxon to a clade that includes Dryomomys and Tinimomys, which diverged from each other by the late Tiffanian. The shape of P4 and the relative size of P(3) have distinct patterns of change through the evolution of the group. Additionally, there is a gradual reduction of P2, with Foxomomys having a double-rooted P2, Micromomys, Chalicomomys, and Dryomomys having a single-rooted P2, and Tinimomys lacking a P2. Body size increases from more primitive micromomyids (Foxomomys and Chalicomomys) to more derived genera (Dryomomys and Tinimomys), and size also increases from the older and/or more primitive species within the Dryomomys and Tinimomys lineages.

Evolution and allometry of calcaneal elongation in living and extinct primates

Specialized acrobatic leaping has been recognized as a key adaptive trait tied to the origin and subsequent radiation of euprimates based on its observed frequency in extant primates and inferred frequency in extinct early euprimates. Hypothesized skeletal correlates include elongated tarsal elements, which would be expected to aid leaping by allowing for increased rates and durations of propulsive acceleration at takeoff. Alternatively, authors of a recent study argued that pronounced distal calcaneal elongation of euprimates (compared to other mammalian taxa) was related primarily to specialized pedal grasping. Testing for correlations between calcaneal elongation and leaping versus grasping is complicated by body size differences and associated allometric affects. We re-assess allometric constraints on, and the functional significance of, calcaneal elongation using phylogenetic comparative methods, and present an evolutionary hypothesis for the evolution of calcaneal elongation in primates using a Bayesian approach to ancestral state reconstruction (ASR). Results show that among all primates, logged ratios of distal calcaneal length to total calcaneal length are inversely correlated with logged body mass proxies derived from the area of the calcaneal facet for the cuboid. Results from phylogenetic ANOVA on residuals from this allometric line suggest that deviations are explained by degree of leaping specialization in prosimians, but not anthropoids. Results from ASR suggest that non-allometric increases in calcaneal elongation began in the primate stem lineage and continued independently in haplorhines and strepsirrhines. Anthropoid and lorisid lineages show stasis and decreasing elongation, respectively. Initial increases in calcaneal elongation in primate evolution may be related to either development of hallucal-grasping or a combination of grasping and more specialized leaping behaviors. As has been previously suggested, subsequent increases in calcaneal elongation are likely adaptations for more effective acrobatic leaping, highlighting the importance of this behavior in early euprimate evolution.

Expression and Evolution of Short Wavelength Sensitive Opsins in Colugos: A Nocturnal Lineage That Informs Debate on Primate Origins

A nocturnal activity pattern is central to almost all hypotheses on the adaptive origins of primates. This enduring view has been challenged in recent years on the basis of variation in the opsin genes of nocturnal primates. A correspondence between the opsin genes and activity patterns of species in Euarchonta-the superordinal group that includes the orders Primates, Dermoptera (colugos), and Scandentia (treeshrews)-could prove instructive, yet the basic biology of the dermopteran visual system is practically unknown. Here we show that the eye of the Sunda colugo (Galeopterus variegatus) lacks a tapetum lucidum and has an avascular retina, and we report on the expression and spectral sensitivity of cone photopigments. We found that Sunda colugos have intact short wavelength sensitive (S-) and long wavelength sensitive (L-) opsin genes, and that both opsins are expressed in cone photoreceptors of the retina. The inferred peak spectral sensitivities are 451 and 562 nm, respectively. In line with adaptation to nocturnal vision, cone densities are low. Surprisingly, a majority of S-cones coexpress some L-opsin. We also show that the ratio of rates of nonsynonymous to synonymous substitutions of exon 1 of the S-opsin gene is indicative of purifying selection. Taken together, our results suggest that natural selection has favored a functional S-opsin in a nocturnal lineage for at least 45 million years. Accordingly, a nocturnal activity pattern remains the most likely ancestral character state of euprimates.

Testing the inhibitory cascade model in Mesozoic and Cenozoic mammaliaforms

Background

Much of the current research in the growing field of evolutionary development concerns relating developmental pathways to large-scale patterns of morphological evolution, with developmental constraints on variation, and hence diversity, a field of particular interest. Tooth morphology offers an excellent model system for such ‘evo-devo’ studies, because teeth are well preserved in the fossil record, and are commonly used in phylogenetic analyses and as ecological proxies. Moreover, tooth development is relatively well studied, and has provided several testable hypotheses of developmental influences on macroevolutionary patterns. The recently-described Inhibitory Cascade (IC) Model provides just such a hypothesis for mammalian lower molar evolution. Derived from experimental data, the IC Model suggests that a balance between mesenchymal activators and molar-derived inhibitors determines the size of the immediately posterior molar, predicting firstly that molars either decrease in size along the tooth row, or increase in size, or are all of equal size, and secondly that the second lower molar should occupy one third of lower molar area. Here, we tested the IC Model in a large selection of taxa from diverse extant and fossil mammalian groups, ranging from the Middle Jurassic (~176 to 161 Ma) to the Recent.

Results

Results show that most taxa (~65%) fell within the predicted areas of the Inhibitory Cascade Model. However, members of several extinct groups fell into the regions where m2 was largest, or rarely, smallest, including the majority of the polyphyletic “condylarths”. Most Mesozoic mammals fell near the centre of the space with equality of size in all three molars. The distribution of taxa was significantly clustered by diet and by phylogenetic group.

Conclusions

Overall, the IC Model was supported as a plesiomorphic developmental system for Mammalia, suggesting that mammal tooth size has been subjected to this developmental constraint at least since the divergence of australosphenidans and boreosphenidans approximately 180 Ma. Although exceptions exist, including many ‘condylarths’, these are most likely to be secondarily derived states, rather than alternative ancestral developmental models for Mammalia.

Primate origins, human origins, and the end of higher taxa

When people learn that I study human evolution and we start talking about it, they sometimes ask me, "How long ago did the first humans live?" My answer is usually another question: "What do you mean by 'humans'?" That response seems as baffling and wrong-headed to them as their question seems to me, and it usually takes us a while to straighten things out. © 2012 Wiley Periodicals, Inc.

The placental mammal ancestor and the post-K-Pg radiation of placentals

To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria.