Primate Origins: Implications of a Cretaceous Ancestry

Sequences, phylogeny and evolution of mitochondrial delta-1-pyrroline-5-carboxylate dehydrogenases (ALDH4A1). Evidence for a second locus (ALDH4A2) in Drosophila

ALDH4A1 genes encode mitochondrial enzymes of delta-1-pyrroline-5-carboxylate metabolism, generating glutamate from either proline or ornithine. Analyses were undertaken of several vertebrate and invertebrate genomes using reported human and mouse ALDH4A1 amino acid sequences. ALDH4A1 sequences and structures were highly conserved, including residues involved in catalysis, coenzyme binding and enzyme structure, previously reported for mouse and human ALDH4A1. The human ALDH4A1 gene contained 15 coding exons and was more highly expressed in human liver and kidney cortex. Vertebrate ALDH4A1 mitochondrial leader sequences exhibited diverse sequences. Phylogeny studies supported the appearance of the ALDH4A1 gene in invertebrate evolution which has been conserved and retained throughout subsequent vertebrate evolution as a single ALDH4A1 gene. Exceptions included polyploidy observed for the Atlantic salmon (Salmo salar) and African toad (Xenopus laevis) genes. An examination of ALDH4A1 sequences from related Drosophila species supported the appearance of a second ALDH4A gene (ALDH4A2) and time dependent evolutionary changes over the past 50 million years for both genes.

Polarized, Amelogenin Expressing Ameloblast-Like Cells from Cervical Loop/Dental Pulp Cocultures in Bioreactors

The growth of long and polarized ameloblast-like cells has long been heralded as a major prerequisite for enamel tissue engineering. In this study, we have designed three-dimensional bioreactor/scaffold microenvironments to propagate and assess the ability of cervical loop derivatives to become long and polarized ameloblast-like cells. Our studies demonstrated that cervical loop/periodontal progenitor coculture in a growth-factor-enriched medium resulted in the formation of ameloblast-like cells expressing high levels of amelogenin and ameloblastin. Coculture of cervical loop cells with dental pulp cells on tailored collagen scaffolds enriched with leucine-rich amelogenin peptide (LRAP) and early enamel matrix resulted in singular, elongated, and polarized ameloblast-like cells that expressed and secreted ameloblastin and amelogenin enamel proteins. Bioreactor microenvironments enriched with enamel matrix and LRAP also proved advantageous for the propagation of HAT-7 cells, resulting in a ∼20-fold higher expression of amelogenin and ameloblastin enamel proteins compared with controls growing on plain scaffolds. Together, studies presented here highlight the benefits of microgravity culture systems combined with ameloblast-specific microenvironments and tailored scaffolds for the growth of ameloblast-like cells.

Macroevolutionary effects on primate trophic evolution and their implications for reconstructing primate origins

The visual-predation hypothesis proposes that certain derived features shared by crown primates reflect an insectivorous ancestry. Critics of this idea have argued that because insectivory is uncommon among extant primates it is unlikely to have been a major influence on early primate evolution. According to this perspective, the low frequency of insectivory indicates that it is an apomorphic deviation from the mostly conserved primate ecological pattern of herbivory. The present study tests two alternative hypotheses that are compatible with an insectivorous ancestor: (1) that trophic evolution was biased, such that herbivory evolved repeatedly with few shifts back to insectivory, and (2) that insectivorous lineages have diversified at a lower rate than herbivorous lineages owing to differential trophic effects on speciation and extinction probabilities. Model-based analysis conducted using trait data for 307 extant primate species indicates that rates of transition into and out of insectivory are similar, rejecting the hypothesis of biased trophic evolution. On the other hand, the hypothesis of asymmetric diversification is supported, with insectivorous lineages having a lower rate of diversification than herbivorous lineages. This correlation is mediated by activity pattern: insectivory occurs mostly in nocturnal lineages, which have a lower diversification rate than diurnal lineages. The frequency of insectivory also appears to have been shaped by repeated transitions into ecological contexts in which insectivory is absent (large body size) or rare (diurnality). These findings suggest that the current distribution of trophic strategies among extant primates is the result of macroevolutionary processes that have favored the proliferation and persistence of herbivory relative to insectivory. This conclusion implies that the low frequency of insectivory is not necessarily evidence against the visual-predation hypothesis.

Wearable Nail Deformation Sensing for Behavioral and Biomechanical Monitoring and Human-Computer Interaction

The dynamics of the human fingertip enable haptic sensing and the ability to manipulate objects in the environment. Here we describe a wearable strain sensor, associated electronics, and software to detect and interpret the kinematics of deformation in human fingernails. Differential forces exerted by fingertip pulp, rugged connections to the musculoskeletal system and physical contact with the free edge of the nail plate itself cause fingernail deformation. We quantify nail warpage on the order of microns in the longitudinal and lateral axes with a set of strain gauges attached to the nail. The wearable device transmits raw deformation data to an off-finger device for interpretation. Simple motions, gestures, finger-writing, grip strength, and activation time, as well as more complex idioms consisting of multiple grips, are identified and quantified. We demonstrate the use of this technology as a human-computer interface, clinical feature generator, and means to characterize workplace tasks.

The role of dietary competition in the origination and early diversification of North American euprimates

The conditions under which early euprimates (adapids and omomyids) originated and evolved is an area of longstanding debate. The leading hypotheses of euprimate origins promulgate diet as a core component of the early evolution of this group, despite the role of dietary competition in euprimate originations never being tested directly. This study compared three competition models (non-competition, competitive displacement, competitive coexistence) with observed patterns of dietary niche overlap, reconstructed from three-dimensional molar morphology, at the time of the euprimate radiation in North America (at the Paleocene-Eocene boundary). Overlap of reconstructed multidimensional dietary niches between euprimates and members of their guild were analysed using a modified MANOVA to establish the nature of the competitive environment surrounding euprimate origins in North America (an immigration event). Results indicated that adapids entered the mammalian guild in the absence of competition, suggesting dietary adaptations that were unique within the community. Conversely, omomyids experienced strong, but transitory, competition with nyctitheriids, suggesting that omomyids possessed the ability to out-compete this group. These results show that adapids and omomyids experienced different competitive scenarios upon their arrival (origination) in North America and confirm the significance of diet (and dietary adaptations) in euprimate origination and early diversification in mammalian communities.

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.

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.

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.

Forest structure drives global diversity of primates

Geographic gradients in the species richness of non-human primates have traditionally been attributed to the variation in forest productivity (related to precipitation levels), although an all-inclusive, global-scale analysis has never been conducted. We perform a more comprehensive test on the role of precipitation and biomass production and propose an alternative hypothesis - the variation in vertical structure of forest habitats as measured by forest canopy height - in determining primate species richness on a global scale. Considering the potential causal relationships among precipitation, productivity and forest structure, we arranged these variables within a path framework to assess their direct and indirect associations with the pattern of primate species richness using structural equation modelling. The analysis also accounted for the influence of spatial autocorrelation in the relationships and assessed possible historical differences among biogeographical regions. The path coefficients indicate that forest canopy height (used as a proxy for vertical forest structure) is a better predictor of primate species richness than either precipitation or productivity on both global and continental scales. The only exception was Asia, where precipitation prevailed, albeit independently from productivity or forest structure. The influence of spatially structured processes varied markedly among biogeographical regions. Our results challenge the traditional rainfall-based viewpoint in favour of forest distribution and structure as primary drivers of primate species richness, which aggregate potential effects from both climatic factors and habitat complexity. These findings may support predictions of the impact of forest removal on primate species richness.

Modeling the origins of mammalian sociality: moderate evidence for matrilineal signatures in mouse lemur vocalizations

INTRODUCTION

Maternal kin selection is a driving force in the evolution of mammalian social complexity and it requires that kin are distinctive from nonkin. The transition from the ancestral state of asociality to the derived state of complex social groups is thought to have occurred via solitary foraging, in which individuals forage alone, but, unlike the asocial ancestors, maintain dispersed social networks via scent-marks and vocalizations. We hypothesize that matrilineal signatures in vocalizations were an important part of these networks. We used the solitary foraging gray mouse lemur (Microcebus murinus) as a model for ancestral solitary foragers and tested for matrilineal signatures in their calls, thus investigating whether such signatures are already present in solitary foragers and could have facilitated the kin selection thought to have driven the evolution of increased social complexity in mammals. Because agonism can be very costly, selection for matrilineal signatures in agonistic calls should help reduce agonism between unfamiliar matrilineal kin. We conducted this study on a well-studied population of wild mouse lemurs at Ankarafantsika National Park, Madagascar. We determined pairwise relatedness using seven microsatellite loci, matrilineal relatedness by sequencing the mitrochondrial D-loop, and sleeping group associations using radio-telemetry. We recorded agonistic calls during controlled social encounters and conducted a multi-parametric acoustic analysis to determine the spectral and temporal structure of the agonistic calls. We measured 10 calls for each of 16 females from six different matrilineal kin groups.

RESULTS

Calls were assigned to their matriline at a rate significantly higher than chance (pDFA: correct = 47.1%, chance = 26.7%, p = 0.03). There was a statistical trend for a negative correlation between acoustic distance and relatedness (Mantel Test: g = -1.61, Z = 4.61, r = -0.13, p = 0.058).

CONCLUSIONS

Mouse lemur agonistic calls are moderately distinctive by matriline. Because sleeping groups consisted of close maternal kin, both genetics and social learning may have generated these acoustic signatures. As mouse lemurs are models for solitary foragers, we recommend further studies testing whether the lemurs use these calls to recognize kin. This would enable further modeling of how kin recognition in ancestral species could have shaped the evolution of complex sociality.

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.

Parallel episodes of phyletic dwarfism in callitrichid and cheirogaleid primates

The Callitrichidae are the smallest anthropoids, whereas the Cheirogaleidae include the smallest of all primates. Using species-level analyses, we show that these are derived conditions; both neonatal and adult body mass decreased in a gradual, phyletic manner in parallel across callitrichids, and across cheirogaleids. We identify lineages with particularly rapid decreases and highlight the pygmy marmoset, Callithrix pygmaea, as a phenotypic outlier. The life-history traits associated with body-mass reduction in each clade suggest that the convergent evolution of small body size was achieved by changes in different ontogenetic stages. Body-size reduction in callitrichids appears to be almost exclusively due to alterations in prenatal growth rate, whereas body-size reduction in cheirogaleids may have been largely due to reduced duration of growth phases. Finally, we use these results to discuss some of the debates surrounding the evolution of Homo floresiensis and suggest potential parallels between the evolution of H. floresiensis and callitrichids.

Dating primate divergences through an integrated analysis of palaeontological and molecular data

Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth-death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.

New perspectives on anthropoid origins

Adaptive shifts associated with human origins are brought to light as we examine the human fossil record and study our own genome and that of our closest ape relatives. However, the more ancient roots of many human characteristics are revealed through the study of a broader array of living anthropoids and the increasingly dense fossil record of the earliest anthropoid radiations. Genomic data and fossils of early primates in Asia and Africa clarify relationships among the major clades of primates. Progress in comparative anatomy, genomics, and molecular biology point to key changes in sensory ecology and brain organization that ultimately set the stage for the emergence of the human lineage.

Genetics of primary cerebral gyrification: Heritability of length, depth and area of primary sulci in an extended pedigree of Papio baboons

Genetic control over morphological variability of primary sulci and gyri is of great interest in the evolutionary, developmental and clinical neurosciences. Primary structures emerge early in development and their morphology is thought to be related to neuronal differentiation, development of functional connections and cortical lateralization. We measured the proportional contributions of genetics and environment to regional variability, testing two theories regarding regional modulation of genetic influences by ontogenic and phenotypic factors. Our measures were surface area, and average length and depth of eleven primary cortical sulci from high-resolution MR images in 180 pedigreed baboons. Average heritability values for sulcal area, depth and length (h(2)(Area)=.38+/-.22; h(2)(Depth)=.42+/-.23; h(2)(Length)=.34+/-.22) indicated that regional cortical anatomy is under genetic control. The regional pattern of genetic contributions was complex and, contrary to previously proposed theories, did not depend upon sulcal depth, or upon the sequence in which structures appear during development. Our results imply that heritability of sulcal phenotypes may be regionally modulated by arcuate U-fiber systems. However, further research is necessary to unravel the complexity of genetic contributions to cortical morphology.

Primate color vision: a comparative perspective

Thirty years ago virtually everything known about primate color vision derived from psychophysical studies of normal and color-defective humans and from physiological investigations of the visual system of the macaque monkey, the most popular of human surrogates for this purpose. The years since have witnessed much progress toward the goal of understanding this remarkable feature of primate vision. Among many advances, investigations focused on naturally occurring variations in color vision in a wide range of nonhuman primate species have proven to be particularly valuable. Results from such studies have been central to our expanding understanding of the interrelationships between opsin genes, cone photopigments, neural organization, and color vision. This work is also yielding valuable insights into the evolution of color vision.

The oldest Asian record of Anthropoidea

Undisputed anthropoids appear in the fossil record of Africa and Asia by the middle Eocene, about 45 Ma. Here, we report the discovery of an early Eocene eosimiid anthropoid primate from India, named Anthrasimias, that extends the Asian fossil record of anthropoids by 9-10 million years. A phylogenetic analysis of 75 taxa and 343 characters of the skull, postcranium, and dentition of Anthrasimias and living and fossil primates indicates the basal placement of Anthrasimias among eosimiids, confirms the anthropoid status of Eosimiidae, and suggests that crown haplorhines (tarsiers and monkeys) are the sister clade of Omomyoidea of the Eocene, not nested within an omomyoid clade. Co-occurence of Anthropoidea, Omomyoidea, and Adapoidea makes it evident that peninsular India was an important center for the diversification of primates of modern aspect (euprimates) in the early Eocene. Adaptive reconstructions indicate that early anthropoids were mouse-lemur-sized ( approximately 75 grams) and consumed a mixed diet of fruit and insects. Eosimiids bear little adaptive resemblance to later Eocene-early Oligocene African Anthropoidea.

Primate chromosome evolution: ancestral karyotypes, marker order and neocentromeres

In 1992 the Japanese macaque was the first species for which the homology of the entire karyotype was established by cross-species chromosome painting. Today, there are chromosome painting data on more than 50 species of primates. Although chromosome painting is a rapid and economical method for tracking translocations, it has limited utility for revealing intrachromosomal rearrangements. Fortunately, the use of BAC-FISH in the last few years has allowed remarkable progress in determining marker order along primate chromosomes and there are now marker order data on an array of primate species for a good number of chromosomes. These data reveal inversions, but also show that centromeres of many orthologous chromosomes are embedded in different genomic contexts. Even if the mechanisms of neocentromere formation and progression are just beginning to be understood, it is clear that these phenomena had a significant impact on shaping the primate genome and are fundamental to our understanding of genome evolution. In this report we complete and integrate the dataset of BAC-FISH marker order for human syntenies 1, 2, 4, 5, 8, 12, 17, 18, 19, 21, 22 and the X. These results allowed us to develop hypotheses about the content, marker order and centromere position in ancestral karyotypes at five major branching points on the primate evolutionary tree: ancestral primate, ancestral anthropoid, ancestral platyrrhine, ancestral catarrhine and ancestral hominoid. Current models suggest that between-species structural rearrangements are often intimately related to speciation. Comparative primate cytogenetics has become an important tool for elucidating the phylogeny and the taxonomy of primates. It has become increasingly apparent that molecular cytogenetic data in the future can be fruitfully combined with whole-genome assemblies to advance our understanding of primate genome evolution as well as the mechanisms and processes that have led to the origin of the human genome.