Artificial neural networks reconstruct missing perikymata in worn teeth

Dental evolutionary studies in hominins are key to understanding how our ancestors and close fossil relatives grew from the early stages of embryogenesis into adults. In a sense, teeth are like an airplane's 'black box' as they record important variables for assessing developmental timing, enabling comparisons within and between populations, species, and genera. The ability to discern this type of nuanced information is embedded in the nature of how tooth enamel and dentin form: incrementally and over years. This incremental growth leaves chronological indicators in the histological structure of enamel, visible on the crown surface as perikymata. These structures are used in the process of reconstructing the rate and timing of tooth formation. Unfortunately, the developmentally earliest growth lines in lateral enamel are quickly lost to wear once the tooth crown erupts. We developed a method to reconstruct these earliest, missing perilymata from worn teeth through knowledge of the later-developed, visible perikymata for all tooth types (incisors, canines, premolars, and molars) using a modern human dataset. Building on our previous research using polynomial regressions, here we describe an artificial neural networks (ANN) method. This new ANN method mostly predicts within 2 counts the number of perikymata present in each of the first three deciles of the crown height for all tooth types. Our ANN method for estimating perikymata lost through wear has two immediate benefits: more accurate values can be produced and worn teeth can be included in dental research. This tool is available on the open-source platform R within the package teethR released under GPL v3.0 license, enabling other researchers the opportunity to expand their datasets for studies of periodicity in histological growth, dental development, and evolution.

Uncovering the mosaic evolution of the carnivoran skeletal system

The diversity of vertebrate skeletons is often attributed to adaptations to distinct ecological factors such as diet, locomotion, and sensory environment. Although the adaptive evolution of skull, appendicular skeleton, and vertebral column is well studied in vertebrates, comprehensive investigations of all skeletal components simultaneously are rarely performed. Consequently, we know little of how modes of evolution differ among skeletal components. Here, we tested if ecological and phylogenetic effects led to distinct modes of evolution among the cranial, appendicular and vertebral regions in extant carnivoran skeletons. Using multivariate evolutionary models, we found mosaic evolution in which only the mandible, hindlimb and posterior (i.e. last thoracic and lumbar) vertebrae showed evidence of adaptation towards ecological regimes whereas the remaining skeletal components reflect clade-specific evolutionary shifts. We hypothesize that the decoupled evolution of individual skeletal components may have led to the origination of distinct adaptive zones and morphologies among extant carnivoran families that reflect phylogenetic hierarchies. Overall, our work highlights the importance of examining multiple skeletal components simultaneously in ecomorphological analyses. Ongoing work integrating the fossil and palaeoenvironmental record will further clarify deep-time drivers that govern the carnivoran diversity we see today and reveal the complexity of evolutionary processes in multicomponent systems.

Peopling of the Americas: A new approach to assessing dental morphological variation in Asian and Native American populations

OBJECTIVES

Through biodistance analyses, anthropologists have used dental morphology to elucidate how people moved into and throughout the Americas. Here, we apply a method that focuses on individuals rather than sample frequencies through the application rASUDAS2, based on a naïve Bayes' algorithm.

MATERIALS AND METHODS

Using the database of C.G. Turner II, we calculated the probability that an individual could be assigned to one of seven biogeographic groups (American Arctic, North & South America, East Asia, Southeast Asia & Polynesia, Australo-Melanesia, Western Eurasia, & Sub-Saharan Africa) through rASUDAS2. The frequency of classifications for each biogeographic group was determined for 1418 individuals from six regions across Asia and the Americas.

RESULTS

Southeast Asians show mixed assignments but rarely to American Arctic or "American Indian." East Asians are assigned to East Asia half the time while 30% are assigned as Native American. People from the American Arctic and North & South America are assigned to Arctic America or non-Arctic America 75%-80% of the time, with 10%-15% classified as East Asian.

DISCUSSION

All Native American groups have a similar degree of morphological affinity to East Asia, as 10%-15% are classified as East Asian. East Asians are classified as Native American in 30% of cases. Individuals in the Western Hemisphere are decreasingly classified as Arctic the farther south they are located. Equivalent levels of classification as East Asian across all Native American groups suggests one divergence between East Asians and the population ancestral to all Native Americans. Non-arctic Native American groups are derived from the Arctic population, which represents the Native American founder group.

Beringia and the peopling of the Western Hemisphere

Did Beringian environments represent an ecological barrier to humans until less than 15 000 years ago or was access to the Americas controlled by the spatial-temporal distribution of North American ice sheets? Beringian environments varied with respect to climate and biota, especially in the two major areas of exposed continental shelf. The East Siberian Arctic Shelf ('Great Arctic Plain' (GAP)) supported a dry steppe-tundra biome inhabited by a diverse large-mammal community, while the southern Bering-Chukchi Platform ('Bering Land Bridge' (BLB)) supported mesic tundra and probably a lower large-mammal biomass. A human population with west Eurasian roots occupied the GAP before the Last Glacial Maximum (LGM) and may have accessed mid-latitude North America via an interior ice-free corridor. Re-opening of the corridor less than 14 000 years ago indicates that the primary ancestors of living First Peoples, who already had spread widely in the Americas at this time, probably dispersed from the NW Pacific coast. A genetic 'arctic signal' in non-arctic First Peoples suggests that their parent population inhabited the GAP during the LGM, before their split from the former. We infer a shift from GAP terrestrial to a subarctic maritime economy on the southern BLB coast before dispersal in the Americas from the NW Pacific coast.

A Pleistocene assemblage of near-modern Papio hamadryas from the Middle Awash study area, Afar Rift, Ethiopia

OBJECTIVES

The aim of this study is to assess a new assemblage of papionin fossils (n = 143) recovered from later Pleistocene sediments in the Middle Awash study area in the Afar Rift of Ethiopia.

MATERIALS AND METHODS

We collected metric and qualitative data to compare the craniodental and postcranial anatomy of the papionin fossils with subspecies of modern Papio hamadryas and with Plio-Pleistocene African papionins. We also estimated sex and ontogenetic age.

RESULTS

The new fossils fit well within the range of morphological variation observed for extant P. hamadryas, overlapping most closely in dental size and proportions with the P. h. cynocephalus individuals in our extant samples, and well within the ranges of P. h. anubis and P. h. hamadryas. The considerable overlap in craniodental anatomy with multiple subspecies precludes subspecific diagnosis. We therefore referred 143 individuals to P. hamadryas ssp. The majority of the individuals assessed for ontogenetic age fell into middle- and old-adult age categories based on the degree of dental wear. Males (26%) were better represented than females (12%) among individuals preserving the canine-premolar honing complex.

DISCUSSION

These new near-modern P. hamadryas fossils provide a window into population-level variation in the later Pleistocene. Our findings echo previous suggestions from genomic studies that the papionin family tree may have included a ghost population and provide a basis for future testing of hypotheses regarding hybridization in the recent evolutionary history of this taxon.

Keeping 21st Century Paleontology Grounded: Quantitative Genetic Analyses and Ancestral State Reconstruction Re-Emphasize the Essentiality of Fossils

Simple Summary

Over the last two decades of biological research, our understanding of how genes determine dental development and variation has expanded greatly. Here, we explore how this new knowledge can be applied to the fossil record of cercopithecid monkeys. We compare a traditional paleontological method for assessing dental size variation with measurement approaches derived from quantitative genetics and developmental biology. We find that these new methods for assessing dental variation provide novel insight to the evolution of the cercopithecid monkey dentition, different from the insight provided by traditional size measurements. When we explore the variation of these traits in the cercopithecid fossil record, we find that the variation is outside the range predicted based on extant variation alone. Our 21st century biological approach to paleontology reveals that we have even more to learn from fossils than previously recognized.

Abstract

Advances in genetics and developmental biology are revealing the relationship between genotype and dental phenotype (G:P), providing new approaches for how paleontologists assess dental variation in the fossil record. Our aim was to understand how the method of trait definition influences the ability to reconstruct phylogenetic relationships and evolutionary history in the Cercopithecidae, the Linnaean Family of monkeys currently living in Africa and Asia. We compared the two-dimensional assessment of molar size (calculated as the mesiodistal length of the crown multiplied by the buccolingual breadth) to a trait that reflects developmental influences on molar development (the inhibitory cascade, IC) and two traits that reflect the genetic architecture of postcanine tooth size variation (defined through quantitative genetic analyses: MMC and PMM). All traits were significantly influenced by the additive effects of genes and had similarly high heritability estimates. The proportion of covariate effects was greater for two-dimensional size compared to the G:P-defined traits. IC and MMC both showed evidence of selection, suggesting that they result from the same genetic architecture. When compared to the fossil record, Ancestral State Reconstruction using extant taxa consistently underestimated MMC and PMM values, highlighting the necessity of fossil data for understanding evolutionary patterns in these traits. Given that G:P-defined dental traits may provide insight to biological mechanisms that reach far beyond the dentition, this new approach to fossil morphology has the potential to open an entirely new window onto extinct paleobiologies. Without the fossil record, we would not be able to grasp the full range of variation in those biological mechanisms that have existed throughout evolution.

Evolutionary adaptation highlights the interconnection of fatty acids, sunlight, inflammation and epithelial adhesion

Gene variants that influence human biology today reflect thousands of years of evolution. Genetic effects on infant health are a major point of selective pressure, given that childhood survival is essential to evolutionary success. Knowledge of this evolutionary history can have implications for paediatric research. CONCLUSION: An episode of human adaptation to the extremely low ultraviolet radiation environment of the Arctic 20,000 years ago implicates the Ectodysplasin A Receptor (EDAR) and the Fatty Acid Desaturases (FADS) in human lactation and epithelial inflammation.

Evidence of selection in the ectodysplasin pathway among endangered aquatic mammals

Synopsis

The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical Wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least 4 orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD, and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in 3 endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation.

Spanish

La vía de la ectodisplasina ha sido objeto de la evolución repetidamente. La variación genética en los principales genes de esta vía (EDA, EDAR y EDARADD) da como resultado una gran diversidad de efectos pleiotrópicos en las estructuras derivadas del ectodermo, incluidos los dientes, el cabello, las glándulas sudoríparas y las glándulas mamarias. Además, una vía wnt no canónica tiene un papel funcional muy similar, por lo que la variación en el gen WNT10A también tiene importancia evolutiva. La adaptación de los mamíferos a los entornes acuáticos se ha producido de forma independiente en al menos cuatro órdenes, cuyas especies ocupan un amplio rango geográfico (desde regiones ecuatoriales a polares) y presentan una gran variación fenotípica en las estructuras derivadas del ectodermo, incluyendo la presencia o ausencia de pelaje y estrategias de lactancia muy diferentes. El papel de la vía de la ectodisplasina en la adaptación a entornos acuáticos no se ha explorado nunca en especies de mamíferos. En este estudio, analizamos la variación genética en las secuencias codificantes ortólogas de los genes EDA, EDAR, EDARADD y WNT10A junto con la variación fenotípica derivada del ectodermo de 34 especies de mamíferos acuáticos y no acuáticos para evaluar señales de selección positiva, coevolución gen-rasgo y convergencia genética. Nuestro estudio revela señales de selección positiva en regiones de las secuencias codificantes de los genes EDA y EDAR en tres mamíferos acuáticos en peligro de extinción (la foca monje de Hawái, la marsopa lisa y la nutria marina). Estas señales podrían tener implicaciones funcionales potencialmente relacionadas con la adaptación al entorno acuático de baja latitud en la foca monje de Hawái y el agua dulce en la marsopa lisa. La señal en la nutria marina es probablemente el resultado de una mayor deriva genética tras un intenso un cuello de botella y una reducción de la diversidad genética. A parte de selección positiva, no hemos detectado señales sólidas de coevolución gen-rasgo o cambios convergentes de aminoácidos en la vía de la ectodisplasina asociados a rasgos fenotípicos compartidos entre mamíferos acuáticos. Este estudio proporciona nuevas evidencias del papel evolutivo de la vía de la ectodisplasina y quiere promover futuras investigaciones con estudios funcionales para acabar de resolver la relación de esta vía con la adaptación acuática de los mamíferos.

Conserved and Taxon-Specific Patterns of Phenotypic Modularity in the Mammalian Dentition

Previous genotype:phenotype mapping of the mouse and primate dentition revealed the presence of pre- and post-canine modules in mice and anthropoid primates, as well as molar and premolar submodules in anthropoid primates. We estimated phenotypic correlation matrices for species that sample broadly across Mammalia to test the hypothesis that these modules exist across a broader range of taxa and thereby represent a conserved mammalian trait. We calculated phenotypic correlation matrices from linear dental measurements of 419 individual specimens representing 5 species from 4 mammalian orders: Artiodactyla (Odocoileus hemionus), Carnivora (Canis latrans and Ursus americanus), Didelphimorphia (Didelphis virginiana), and Primates (Colobus guereza). Our results based on hierarchical clustering indicate a generally higher correlation within incisors and among post-canine teeth. However, the post-canine phenotypic correlation matrices do not consistently exhibit the premolar and molar submodularity observed in anthropoid primates. Additionally, we find evidence of sex differences in the Odocoileus phenotypic correlation matrices: Males of this species exhibit overall higher inter-trait correlations compared to females. Our overall findings support the interpretation that incisors and post-canine dentition represent different phenotypic modules, and that this architecture may be a conserved trait for mammals.

Association of EDARV370A with breast density and metabolic syndrome in Latinos

The ectodysplasin receptor (EDAR) is a tumor necrosis factor receptor (TNF) superfamily member. A substitution in an exon of EDAR at position 370 (EDARV370A) creates a gain of function mutant present at high frequencies in Asian and Indigenous American populations but absent in others. Its frequency is intermediate in populations of Mexican ancestry. EDAR regulates the development of ectodermal tissues, including mammary ducts. Obesity and type 2 diabetes mellitus are prevalent in people with Indigenous and Latino ancestry. Latino patients also have altered prevalence and presentation of breast cancer. It is unknown whether EDARV370A might connect these phenomena. The goals of this study were to determine 1) whether EDARV370A is associated with metabolic phenotypes and 2) if there is altered breast anatomy in women carrying EDARV370A. Participants were from two Latino cohorts, the Arizona Insulin Resistance (AIR) registry and Sangre por Salud (SPS) biobank. The frequency of EDARV370A was 47% in the Latino cohorts. In the AIR registry, carriers of EDARV370A (GG homozygous) had significantly (p < 0.05) higher plasma triglycerides, VLDL, ALT, 2-hour post-challenge glucose, and a higher prevalence of prediabetes/diabetes. In a subset of the AIR registry, serum levels of ectodysplasin A2 (EDA-A2) also were associated with HbA1c and prediabetes (p < 0.05). For the SPS biobank, participants that were carriers of EDARV370A had lower breast density and higher HbA1c (both p < 0.05). The significant associations with measures of glycemia remained when the cohorts were combined. We conclude that EDARV370A is associated with characteristics of the metabolic syndrome and breast density in Latinos.

Effects of hybridization on pelvic morphology: A macaque model

Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.

Evidence of strong stabilizing effects on the evolution of boreoeutherian (Mammalia) dental proportions

The dentition is an extremely important organ in mammals with variation in timing and sequence of eruption, crown morphology, and tooth size enabling a range of behavioral, dietary, and functional adaptations across the class. Within this suite of variable mammalian dental phenotypes, relative sizes of teeth reflect variation in the underlying genetic and developmental mechanisms. Two ratios of postcanine tooth lengths capture the relative size of premolars to molars (premolar-molar module, PMM), and among the three molars (molar module component, MMC), and are known to be heritable, independent of body size, and to vary significantly across primates. Here, we explore how these dental traits vary across mammals more broadly, focusing on terrestrial taxa in the clade of Boreoeutheria (Euarchontoglires and Laurasiatheria). We measured the postcanine teeth of N = 1,523 boreoeutherian mammals spanning six orders, 14 families, 36 genera, and 49 species to test hypotheses about associations between dental proportions and phylogenetic relatedness, diet, and life history in mammals. Boreoeutherian postcanine dental proportions sampled in this study carry conserved phylogenetic signal and are not associated with variation in diet. The incorporation of paleontological data provides further evidence that dental proportions may be slower to change than is dietary specialization. These results have implications for our understanding of dental variation and dietary adaptation in mammals.

Craniodental Allometry, Prenatal Growth Rates, and the Evolutionary Loss of the Third Molars in New World Monkeys

A growing body of literature demonstrates that genetic patterning mechanisms underlie the relative proportions of the mammalian postcanine dentition with the third molar being key to understanding variation within the molar row. With this relatively recent insight, there has been renewed interest in mammalian taxa that have lost the third molars. Within platyrrhines, the marmosets and tamarins (Callitrichidae family) are characterized by small body size, claw-like nails, twinning, and reduced molar number. Small body size is hypothesized to have resulted in the third molar being crowded out of the jaws leading to its evolutionary loss in this family. To further explore this hypothesis, we measured the cranium and dentition of 142 individuals spanning all five platyrrhine families. These data reveal that callitrichids have a significantly smaller proportion of mandibular postcanine tooth row length relative to other platyrrhines, refuting the "crowding out" hypothesis. However, postcanine tooth row length is significantly correlated with mandibular length and cranial length (P < 0.01) across all platyrrhines providing evidence for a strong allometric association between postcanine tooth row length and body size more generally. The small body size that characterizes callitrichids results in part from slower prenatal growth rates. Given the allometric relationship between postcanine tooth row length and body size, reported here and in previous studies, we hypothesize that the evolutionary loss of the third molars in callitrichids results from the inhibition of third molar development as a consequence of the slower prenatal growth rates associated with small body size in this family. Anat Rec, 302:1419-1433, 2019. © 2018 Wiley Periodicals, Inc.

Recent insights into the evolution of quantitative traits in non-human primates

The past few years of genetic research on primate quantitative trait variation have been notable in the diversity of phenotypes explored, ranging from classic skeletal measurements to behavior, through to levels of gene expression, and with observations from both captive and wild populations. These studies demonstrate the importance of captive pedigreed breeding colonies, populations that can be matched to their wild counterparts to enable comparison of genetic architectures. Non-human primate genotype:phenotype maps are essential for placing human variation within an evolutionary framework as well as for gaining insight to human biology. While the demographic history of most primates has been fairly stable since the Late Pleistocene, humans experienced a dramatic population expansion that increased the number of rare, mildly deleterious mutations. These rare genetic variants complicate the genotype:phenotype association because they account for a disproportionate amount of the genetic variance and are harder to detect. The similar physiologies of our closest living relatives may prove to be key for overcoming the hurdles posed by humans' peculiar demographic explosion.

OH 83: A new early modern human fossil cranium from the Ndutu beds of Olduvai Gorge, Tanzania

OBJECTIVE

Herein we introduce a newly recovered partial calvaria, OH 83, from the upper Ndutu Beds of Olduvai Gorge, Tanzania. We present the geological context of its discovery and a comparative analysis of its morphology, placing OH 83 within the context of our current understanding of the origins and evolution of Homo sapiens.

MATERIALS AND METHODS

We comparatively assessed the morphology of OH 83 using quantitative and qualitative data from penecontemporaneous fossils and the W.W. Howells modern human craniometric dataset.

RESULTS

OH 83 is geologically dated to ca. 60-32 ka. Its morphology is indicative of an early modern human, falling at the low end of the range of variation for post-orbital cranial breadth, the high end of the range for bifrontal breadth, and near average in frontal length.

DISCUSSION

There have been numerous attempts to use cranial anatomy to define the species Homo sapiens and identify it in the fossil record. These efforts have not met wide agreement by the scientific community due, in part, to the mosaic patterns of cranial variation represented by the fossils. The variable, mosaic pattern of trait expression in the crania of Middle and Late Pleistocene fossils implies that morphological modernity did not occur at once. However, OH 83 demonstrates that by ca. 60-32 ka modern humans in Africa included individuals that are at the fairly small and gracile range of modern human cranial variation.

A one-million-year-old hominid distal ulna from Olduvai Gorge, Tanzania

OBJECTIVE

Our aim was to recover new evidence of the evolution of the hominid lineage.

METHODS

We undertook paleontological fieldwork at Olduvai Gorge, Tanzania, in one of the richest paleoanthropological sites in the world, documenting the evolution of our lineage and its environmental contexts over the last 2 million years.

RESULTS

During field work in 2012, the Olduvai Vertebrate Paleontology Project discovered the distal end of a hominid ulna (OH 82) on the north side of Olduvai Gorge a few meters west of the Third Fault, eroding from Bed III sediments that are ∼1 million years in age.

DISCUSSION

The size and morphology of this distal ulna falls within the normal range of variation seen in humans, although at the larger end of the distribution.

A comparative examination of odontogenic gene expression in both toothed and toothless amniotes

A well-known tenet of murine tooth development is that BMP4 and FGF8 antagonistically initiate odontogenesis, but whether this tenet is conserved across amniotes is largely unexplored. Moreover, changes in BMP4-signaling have previously been implicated in evolutionary tooth loss in Aves. Here we demonstrate that Bmp4, Msx1, and Msx2 expression is limited proximally in the red-eared slider turtle (Trachemys scripta) mandible at stages equivalent to those at which odontogenesis is initiated in mice, a similar finding to previously reported results in chicks. To address whether the limited domains in the turtle and the chicken indicate an evolutionary molecular parallelism, or whether the domains simply constitute an ancestral phenotype, we assessed gene expression in a toothed reptile (the American alligator, Alligator mississippiensis) and a toothed non-placental mammal (the gray short-tailed opossum, Monodelphis domestica). We demonstrate that the Bmp4 domain is limited proximally in M. domestica and that the Fgf8 domain is limited distally in A. mississippiensis just preceding odontogenesis. Additionally, we show that Msx1 and Msx2 expression patterns in these species differ from those found in mice. Our data suggest that a limited Bmp4 domain does not necessarily correlate with edentulism, and reveal that the initiation of odontogenesis in non-murine amniotes is more complex than previously imagined. Our data also suggest a partially conserved odontogenic program in T. scripta, as indicated by conserved Pitx2, Pax9, and Barx1 expression patterns and by the presence of a Shh-expressing palatal epithelium, which we hypothesize may represent potential dental rudiments based on the Testudinata fossil record.

Identification of a derived dental trait in the papionini relative to other old world monkeys

Variation in the shape of teeth provides an immense amount of information about the evolutionary history and adaptive strategy of a mammalian lineage. Here, we explore variation in the expression of a purported molar lingual remnant (the interconulus) across the Old World Monkeys (Primates: Cercopithecidae) with the aim of elucidating a component of the adaptive radiation of this family. This radiation is characterized by a wide geographic range (Asia and Africa) as well as diverse dietary niches. While all of the cercopithecids are distinguished by their derived bilophodont molars, the colobines have evolved taller and more pointed cusps compared with the cercopithecines. We investigate whether the interconulus also correlates with phylogenetic affinity and/or dietary adaptation. We assess the frequency and range of interconulus expression in 522 specimens representing seven species of Old World Monkeys (Cercopithecus mitis, n = 78; Macaca fascicularis, n = 85; Macaca mulatta, n = 70; Papio hamadryas, n = 55; Colobus guereza, n = 76; Presbytis melalophos, n = 82; Presbytis rubicunda, n = 76). Results show that the interconulus has a significantly higher frequency and degree of expression in Tribe Papionini and exhibits ordered metameric variation with greatest expression in the third molars. Given the rarity of the interconulus in other closely related taxa, and its morphological distinction from the purportedly homologous features in other primates, we interpret the high degree of expression of the interconulus to be a trait derived in papionins that originated in the Miocene baboon/macaque ancestor.

Impact of maternal prenatal stress on growth of the offspring

Unperturbed fetal development is essential for future health of an individual. Previous studies have linked diseases of aging to harmful alterations that happen during fetal development. Given the significant long-term impact that intrauterine environment has on an individual's life, it was hypothesized that maternal stress during pregnancy will have negative effects on the offspring's prenatal and postnatal growth. To test this, twenty-eight female and seven male Wistar rats (Rattus norvegicus) were purchased and bred to produce 176 offspring. During pregnancy, dams were randomly divided into four groups (n=7, per group) and immobilization stress induced as follows; Group 1 (GW1): immobilization stress on days 1-7 of pregnancy, Group 2 (GW2): on days 8-14, Group 3 (GW3): on days 15-21, Group 4 (Controls): left undisturbed. Maternal cortisol hormone, food intake, and weight gain were monitored during pregnancy. Pups were raised under normal laboratory conditions and sacrificed at ages: 4, 8, 12, and 16 weeks to determine the effect of prenatal stress. At necropsy, the tibia was removed and processed for histology. Differences among groups were determined by T-test or analysis of variance (ANOVA). Linear regression analysis was performed to establish the relationship between stress in utero and indicators of bone development in offspring. P values ≤ 0.05 were considered significant. Cortisol hormone levels in controls were lower than those of stressed animals. Stressed dams consumed 12.5% less food per day compared to controls. Animals in GW1 and GW2 gained less weight during pregnancy but had larger litters than did GW3 or the control group. Offspring born to GW3 were heavier compared to all other groups. GW3 offspring had a higher rate of bone formation. In conclusion, stress during pregnancy resulted in increased cortisol and reduced food intake in mothers, but faster growth and higher weight gain in offspring compared to controls.

Modularity in the mammalian dentition: mice and monkeys share a common dental genetic architecture

The concept of modularity provides a useful tool for exploring the relationship between genotype and phenotype. Here, we use quantitative genetics to identify modularity within the mammalian dentition, connecting the genetics of organogenesis to the genetics of population-level variation for a phenotype well represented in the fossil record. We estimated the correlations between dental traits owing to the shared additive effects of genes (pleiotropy) and compared the pleiotropic relationships among homologous traits in two evolutionary distant taxa-mice and baboons. We find that in both mice and baboons, who shared a common ancestor >65 Ma, incisor size variation is genetically independent of molar size variation. Furthermore, baboon premolars show independent genetic variation from incisors, suggesting that a modular genetic architecture separates incisors from these posterior teeth as well. Such genetic independence between modules provides an explanation for the extensive diversity of incisor size variation seen throughout mammalian evolution-variation uncorrelated with equivalent levels of postcanine tooth size variation. The modularity identified here is supported by the odontogenic homeobox code proposed for the patterning of the rodent dentition. The baboon postcanine pattern of incomplete pleiotropy is also consistent with predictions from the morphogenetic field model.

Genetic integration of molar cusp size variation in baboons

Many studies of primate diversity and evolution rely on dental morphology for insight into diet, behavior, and phylogenetic relationships. Consequently, variation in molar cusp size has increasingly become a phenotype of interest. In 2007 we published a quantitative genetic analysis of mandibular molar cusp size variation in baboons. Those results provided more questions than answers, as the pattern of genetic integration did not fit predictions from odontogenesis. To follow up, we expanded our study to include data from the maxillary molar cusps. Here we report on these later analyses, as well as inter-arch comparisons with the mandibular data. We analyzed variation in two-dimensional maxillary molar cusp size using data collected from a captive pedigreed breeding colony of baboons, Papio hamadryas, housed at the Southwest National Primate Research Center. These analyses show that variation in maxillary molar cusp size is heritable and sexually dimorphic. We also estimated additive genetic correlations between cusps on the same crown, homologous cusps along the tooth row, and maxillary and mandibular cusps. The pattern for maxillary molars yields genetic correlations of one between the paracone-metacone and protocone-hypocone. Bivariate analyses of cuspal homologues on adjacent teeth yield correlations that are high or not significantly different from one. Between dental arcades, the nonoccluding cusps consistently yield high genetic correlations, especially the metaconid-paracone and metaconid-metacone. This pattern of genetic correlation does not immediately accord with the pattern of development and/or calcification, however these results do follow predictions that can be made from the evolutionary history of the tribosphenic molar.

Taphonomic, avian, and small-vertebrate indicators of Ardipithecus ramidus habitat

Thousands of vertebrate specimens were systematically collected from the stratigraphic interval containing Ardipithecus ramidus. The carcasses of larger mammals were heavily ravaged by carnivores. Nearly 10,000 small-mammal remains appear to be derived primarily from decomposed owl pellets. The rich avifauna includes at least 29 species, mostly nonaquatic forms. Modern analogs of the most abundant birds and of a variety of rodents are associated with mesic woodland environments distant from large water bodies. These findings support inferences from associated geological, isotopic, invertebrate, and large-vertebrate assemblages. The combined results suggest that Ar. ramidus occupied a wooded Pliocene habitat.

Genetic correlations between mandibular molar cusp areas in baboons

Primate evolutionary studies rely significantly on dental variation given the large role that teeth play in how an organism interacts with its environment (animal and plant) and conspecifics. Variation in cusp size has been shown to vary among primate taxa, although most studies to date focused on extant and extinct hominoids. Here we test the assumed hypothesis that a significant proportion of this variation in baboons is due to the additive effects of genes. We perform quantitative genetic analyses on variation in two-dimensional (2-D) mandibular molar cusp size in a captive pedigreed breeding population of baboons (Papio hamadryas) from the Southwest National Primate Research Center. These analyses show that variation in cusp size is heritable and sexually dimorphic. Additionally, we tested for genetic correlations between cusps on the same crown, between morphological homologues along the tooth row, and between cusp area and crown buccolingual width. We find that four of the six cusp pairs on the first molar have a genetic correlation of one, save for the metaconid-hypoconid and entoconid-hypoconid, which are not statistically different from zero. The second and third molars have lower genetic correlations, although the metaconid-hypoconid correlation is similarly estimated at zero and the entoconid-protoconid correlation is estimated to be one. This cross pattern of genetic and no genetic correlation does not immediately accord with the known pattern of development and/or calcification. We propose two explanative hypotheses.

A multivariate comparison of dental variation in wild and captive populations of baboons (Papio hamadryas)

Phenotypic variation is critical to many aspects of biological research. Use of a captive population to address questions concerning the genetics and evolution of dental variation raises the question of how the pattern of phenotypic variation under study compares with that in a wild population of the same species. Differences in the pattern of variation within wild and captive populations may indicate different genetic and non-genetic factors, and also may have implications for how well the captive group can serve as a model for its wild type relatives. We compared dental size measures from two Papio hamadryas populations, one captive and one wild. Lengths and widths of maxillary and mandibular second molars (M2s) were collected from 630 baboons from a captive pedigreed breeding colony housed at the Southwest National Primate Research Center in San Antonio, Texas, and 125 baboons from a wild population culled from a sisal plantation in Kibweze, Kenya. Although the two populations consistently differed with respect to lengths and widths of the M2s, principal components analyses show that the basic pattern to variation in these molar crown traits is remarkably similar in both populations; and linear functions based on these measures cannot reliably discriminate between the two groups. This similarity in the pattern of variation among these dental crown measures in these two groups suggests that analyses to dissect their genetic architecture in captive populations is likely to be highly relevant to dental variation in wild baboons as well.

Evolution of genetically correlated traits: tooth size and body size in baboons

Within a population, only phenotypic variation that is influenced by genes will respond to selection. Genes with pleiotropic effects are known to influence numerous traits, complicating our understanding of their evolution through time. Here we use quantitative genetic analyses to identify and estimate the shared genetic effects between molar size and trunk length in a pedigreed, breeding population of baboons housed at the Southwest National Primate Research Center. While crown area has a genetic correlation with trunk length, specific linear measurements yield different results. We find that variation in molar buccolingual width and trunk length is influenced by overlapping additive genetic effects. In contrast, mesiodistal molar length appears to be genetically independent of body size. This is the first study to demonstrate a significant genetic correlation between tooth size and body size in primates. The evolutionary implications are discussed.

Asa Issie, Aramis and the origin of Australopithecus

The origin of Australopithecus, the genus widely interpreted as ancestral to Homo, is a central problem in human evolutionary studies. Australopithecus species differ markedly from extant African apes and candidate ancestral hominids such as Ardipithecus, Orrorin and Sahelanthropus. The earliest described Australopithecus species is Au. anamensis, the probable chronospecies ancestor of Au. afarensis. Here we describe newly discovered fossils from the Middle Awash study area that extend the known Au. anamensis range into northeastern Ethiopia. The new fossils are from chronometrically controlled stratigraphic sequences and date to about 4.1-4.2 million years ago. They include diagnostic craniodental remains, the largest hominid canine yet recovered, and the earliest Australopithecus femur. These new fossils are sampled from a woodland context. Temporal and anatomical intermediacy between Ar. ramidus and Au. afarensis suggest a relatively rapid shift from Ardipithecus to Australopithecus in this region of Africa, involving either replacement or accelerated phyletic evolution.

Mandibular Symphysis of Large-Bodied Hominoids

The hominoid mandibular symphysis has received a great deal of attention from anatomists, human biologists, and paleontologists. Much of this research has focused on functional interpretations of symphyseal shape variation. Here, we examine the two-dimensional cross-sectional shape of the adult mandibular symphysis for 45 humans, 42 chimpanzees, 37 gorillas, and 51 orangutans using eigenshape analysis, an outline-based morphometric approach. Our results demonstrate that a large proportion of the variation described by the first eigenshape correlates with proposed functional adaptations to counteract stresses at the mandibular midline during mastication. Subsequent eigenshapes describe subtle aspects of shape variation in the mandibular symphysis. The morphology associated with these eigenshapes does not conform with functional predictions, nor does it show a relationship with sexual dimorphism. However, eigenshapes provide for considerable taxonomic discrimination between the four taxa studied and may consequently prove useful in the analysis of fossil material. Comparison with elliptical Fourier analysis of the mandibular symphysis identifies eigenshape analysis as providing superior taxonomic discrimination. The results presented here demonstrate that the cross-sectional shape of the mandibular symphysis results from a complex interplay of functional and nonfunctional influences and for the first time identifies and quantifies the specific aspects of variation attributable to these factors.

Statistical genetics of molar cusp patterning in pedigreed baboons: implications for primate dental development and evolution

Gene expression and knock-out studies provide considerable information about the genetic mechanisms required for tooth organogenesis. Quantitative genetic studies of normal phenotypic variation are complementary to these developmental studies and may help elucidate the genes and mechanisms that contribute to the normal population-level phenotypic variation upon which selection acts. Here we present the first quantitative genetic analysis of molar cusp positioning in mammals. We analyzed quantitative measures of molar cusp position in a captive pedigreed baboon breeding colony housed at the Southwest National Primate Research Center in San Antonio, Texas. Our results reveal complete pleiotropy between antimeric pairs of traits--i.e., they are influenced by the same gene or suite of genes. Mandibular morphological homologues in the molar series also exhibit complete pleiotropy. In contrast, morphological homologues in maxillary molar series appear to be influenced by partial, incomplete pleiotropic effects. Variation in the mandibular mesial and distal molar loph orientation on the same molar crown is estimated to be genetically independent, whereas the maxillary molar mesial and distal loph orientation is estimated to have partially overlapping genetic affects. The differences between the maxillary and mandibular molar patterning, and the degree of genetic independence found between lophs on the same molar crown, may be indicative of previously unrecognized levels of modularity in the primate dentition.

Protostylid variation in Australopithecus

Recent advances in computed tomography (CT) and genetics provide new insights into the morphology and biology of anatomical traits, particularly in the dentition. As we move towards a fuller understanding of the genetic and developmental bases for dental traits, we need to reassess the taxonomic and evolutionary variation of established characters. Quantitative genetic analyses indicate that the degree of expression of upper and lower primate cingular remnants are genetically interdependent. This has serious evolutionary implications that need to be explored for fossil hominids. Studies of Carabelli's cusp, a cingular remnant on hominid upper molars, have been advanced through both genetic and CT analyses setting the stage for such an investigation. But its mandibular morphological homologue, the protostylid has not been similarly studied. This paper represents the first step towards a quantitative understanding of the variation and evolution of this trait in early hominids. Since the first discoveries of Australopithecus specimens in South Africa more than sixty years ago, cingular features on lower molars have played a significant role in the description and comparison of hominid taxa. This largely qualitative history is reviewed. Because the modern human classification system for protostylid variation does not adequately describe the variation seen in Australopithecus samples, a quantification scheme with six expression states is established. Using this new protocol, protostylid variation in six species of Australopithecus is assessed. Results from these analyses show that the distribution of the degree of protostylid expression in these species is highly varied. When first, second, and third molar samples are considered separately, the distribution of expression states is found to differ considerably within the same species. These results provide a foundation for further genetic and developmental research on the evolutionary history of the hominid dentition.

Integrating the genotype and phenotype in hominid paleontology

Competing interpretations of human origins and evolution have recently proliferated despite the accelerated pace of fossil discovery. These controversies parallel those involving other vertebrate families and result from the difficulty of studying evolution among closely related species. Recent advances in developmental and quantitative genetics show that some conventions routinely used by hominid and other mammalian paleontologists are unwarranted. These same advances provide ways to integrate knowledge of the genotype into the study of the phenotype. The result is an approach that promises to yield a fuller understanding of evolution below the family level.

Genetics and the evolution of primate enamel thickness: A baboon model

The thickness of mammalian tooth enamel plays a prominent role in paleontology because it correlates with diet, and thicker enamel protects against tooth breakage and wear. Hominid evolutionary studies have stressed the importance of this character for over 30 years, from the identification of "Ramapithecus" as an early Miocene hominid, to the recent discovery that the earliest hominids display molar enamel intermediate in thickness between extant chimpanzees and Australopithecus. Enamel thickness remains largely unexplored for nonhominoid primate fossils, though there is significant variation across modern species. Despite the importance of enamel thickness variation to primate evolution, the mechanisms underlying variation in this trait have not yet been elucidated. We report here on the first quantitative genetic analysis of primate enamel thickness, an analysis based on 506 pedigreed baboons from a captive breeding colony. Computed tomography analysis of 44 Papio mandibular molars shows a zone of sufficiently uniform enamel thickness on the lateral surface of the protoconid. With this knowledge, we developed a caliper metric measurement protocol for use on baboon molars worn to within this zone, enabling the collection of a data set large enough for genetic analyses. Quantitative genetic analyses show that a significant portion of the phenotypic variance in enamel thickness is due to the additive effects of genes and is independent of sex and tooth size. Our models predict that enamel thickness could rapidly track dietary adaptive shifts through geological time, thus increasing the potential for homoplasy in this character. These results have implications for analyses of hominoid enamel thickness variation, and provide a foundation from which to explore the evolution of this phenotype in the papionin fossil record.

Genetic contributions to expression of the baboon cingular remnant

Primitive mammalian molar morphology is characterised in part by a ridge of enamel that encircles the entire base of the molar crown, the cingulum. Many higher primates have reduced the cingulum, but often retain remnant features on the lingual surface of maxillary molars and the labial surface of mandibular molars. Two of these remnants in cercopithecoid primates, the interconulus and interconulid, are morphologically similar though the interconulus is found on maxillary molars and the interconulid is located on mandibular molars. Here we present results from a quantitative genetic analysis of expression of these two traits in a sample of 479 modern savannah baboons from the Southwest Foundation for Biomedical Research (SFBR). We found that both traits are significantly heritable with little variance attributable to other factors, such as sex, age, and molar crown size. Bivariate analyses yielded point estimates for genetic correlations between left and right side expression that are either equal to or not significantly different from 1.0; meaning that 100% of their additive genetic variance is due to the effects of the same gene or suite of genes. By contrast, our estimates of the genetic correlations between maxillary and mandibular expression of this trait range from 0.52 to 0.72, suggesting that 28-52% of the additive genetic variance in the interconulus and interconulid is due to the effects of shared genes. These results demonstrate that intra-arch expression is characterised by complete pleiotropy whereas inter-arch expression is caused by incomplete pleiotropy. These results are relevant to dental developmental studies as well as paleontological analyses of the evolution of the primate dentition.

Identifying metameric variation in extant hominoid and fossil hominid mandibular molars

Landmark data were collected from cross sections and occlusal images of mandibular molar crowns, and Euclidean distance matrix analysis (EDMA) was used to identify metameric morphological variation between the first and second mandibular molars of living taxa: Gorilla gorilla (n = 30), Pan troglodytes (n = 34), and Homo sapiens (n = 26). Two patterns of metameric variation were identified, one unique to humans and the other shared by chimpanzees and gorillas. In order to assess the utility of this type of analysis for the interpretation of the hominid fossil record, 19 mandibular molars from Sterkfontein Member 4, South Africa, were examined. The pattern of metameric variation of the Sterkfontein molars resembled that of the African great apes, and differed from the modern human pattern. These results demonstrate that data on metameric variation may provide information regarding function or developmental processes previously indiscernible from fossil material.

Statistical genetic comparison of two techniques for assessing molar crown size in pedigreed baboons

Dental anthropologists and paleoanthropologists commonly use an estimated molar crown area (mesiodistal length multiplied by buccolingual width) to describe and compare individuals, populations, and species. Advances in digital imaging now allow researchers to measure the actual crown area of a molar in an occlusal two-dimensional plane. Because error is reduced by this more accurate measurement, actual crown area is thought to be a better representation of the mechanisms that determine tooth crown size, meriting the additional time required to collect it. We tested this assumption by estimating the heritability of both these measurements for the second left mandibular molar from a sample of individuals (n = 332) from a captive breeding colony of baboons. Heritability estimates of both the actual and estimated crown areas of molars are approximately 0.83. Therefore, both measurements are informative as population descriptors, with no significant difference between the accuracy of either to reflect additive genetic contributions to molar crown size. This is fortunate, because genetic studies and inference can be based on estimated areas rather than actual crown area. The heritability estimates for mesiodistal length and buccolingual width are both substantial but lower: approximately 0.67 and approximately 0.73, respectively. The best fitting models in these analyses show that sex, body size, and subspecific affinity differentially affect molar length and width. We interpret these results to suggest that potentially some of the genetics underlying these covariates also underlie tooth size. As such, measurements designed to describe molar crown size are useful for general descriptive purposes, but do not conform to the assumption of independence inherent in phylogenetic analyses, such as cladistics (Hennig [1966] Phylogenetic Systematics. Urbana: University of Illinois Press). Therefore, if variables like actual crown area and estimated crown area are to be used in phylogenetic parsimony analyses, we suggest that researchers account for the effects of covariates such as sex and body size in their analyses.