The integration of quantitative genetics, paleontology, and neontology reveals genetic underpinnings of primate dental evolution

Significance Experimental research on mice has yielded tremendous biological insight. However, the ∼140 million y of evolution that separate mice from humans pose a hurdle to direct application of this knowledge to humans. We report here that considerable progress for identifying genetically patterned skeletal phenotypes beyond the mouse model is possible through transdisciplinary approaches that include the anatomical sciences. Indeed, anatomy and paleontology offer unique opportunities through which to develop and test hypotheses about the underlying genetic mechanisms of the skeleton for taxa that are not well suited to experimental manipulation, such as ourselves. Abstract Developmental genetics research on mice provides a relatively sound understanding of the genes necessary and sufficient to make mammalian teeth. However, mouse dentitions are highly derived compared with human dentitions, complicating the application of these insights to human biology. We used quantitative genetic analyses of data from living nonhuman primates and extensive osteological and paleontological collections to refine our assessment of dental phenotypes so that they better represent how the underlying genetic mechanisms actually influence anatomical variation. We identify ratios that better characterize the output of two dental genetic patterning mechanisms for primate dentitions. These two newly defined phenotypes are heritable with no measurable pleiotropic effects. When we consider how these two phenotypes vary across neontological and paleontological datasets, we find that the major Middle Miocene taxonomic shift in primate diversity is characterized by a shift in these two genetic outputs. Our results build on the mouse model by combining quantitative genetics and paleontology, and thereby elucidate how genetic mechanisms likely underlie major events in primate evolution

Quantitative Genetics, Pleiotropy, and Morphological Integration in the Dentition of Papio hamadryas

Variation in the mammalian dentition is highly informative of adaptations and evolutionary relationships, and consequently has been the focus of considerable research. Much of the current research exploring the genetic underpinnings of dental variation can trace its roots to Olson and Miller's 1958 book Morphological Integration. These authors explored patterns of correlation in the post-canine dentitions of the owl monkey and Hyopsodus, an extinct condylarth from the Eocene. Their results were difficult to interpret, as was even noted by the authors, due to a lack of genetic information through which to view the patterns of correlation. Following in the spirit of Olson and Miller's research, we present a quantitative genetic analysis of dental variation in a pedigreed population of baboons. We identify patterns of genetic correlations that provide insight to the genetic architecture of the baboon dentition. This genetic architecture indicates the presence of at least three modules: an incisor module that is genetically independent of the post-canine dentition, and a premolar module that demonstrates incomplete pleiotropy with the molar module. We then compare this matrix of genetic correlations to matrices of phenotypic correlations between the same measurements made on museum specimens of another baboon subspecies and the Southeast Asian colobine Presbytis. We observe moderate significant correlations between the matrices from these three primate taxa. From these observations we infer similarity in modularity and hypothesize a common pattern of genetic integration across the dental arcade in the Cercopithecoidea

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

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. View Full-Tex

Using Machine Learning to Classify Extant Apes and Interpret the Dental Morphology of the Chimpanzee-human Last Common Ancestor

Machine learning is a formidable tool for pattern recognition in large datasets. We developed and expanded on these methods, applying machine learning pattern recognition to a problem in paleoanthropology and evolution. For decades, paleontologists have used the chimpanzee as a model for the chimpanzee-human last common ancestor (LCA) because they are our closest living primate relative. Using a large sample of extant and extinct primates, we tested the hypothesis that machine learning methods can accurately classify extant apes based on dental data. We then used this classification tool to observe the affinities between extant apes and Miocene hominoids. We assessed the discrimination accuracy of supervised learning algorithms when tasked with the classification of extant apes (n=175), using three types of data from the postcanine dentition: linear, 2-dimensional, and the morphological output of two genetic patterning mechanisms that are independent of body size: molar module component (MMC) and premolar-molar module (PMM) ratios. We next used the trained algorithms to classify a sample of fossil hominoids (n=95), treated as unknowns. Machine learning classifies extant apes with greater than 92% accuracy with linear and 2-dimensional dental measurements, and greater than 60% accuracy with the MMC and PMM ratios. Miocene hominoids are morphologically most similar in dental size and shape to extant chimpanzees. However, relative dental proportions of Miocene hominoids are more similar to extant gorillas and follow a strong trajectory through evolutionary time. Machine learning is a powerful tool that can discriminate between the dentitions of extant apes with high accuracy and quantitatively compare fossil and extant morphology. Beyond detailing applications of machine learning to vertebrate paleontology, our study highlights the impact of phenotypes of interest and the importance of comparative samples in paleontological studies

Allometric Variation in Modern Humans and the Relationship Between Body Proportions and Elite Athletic Success

In many sports, greater height and arm span are purportedly linked to athletic success. While variation in body proportions has been explored across an array of scientific disciplines, studies focusing on humans of tall stature outside of clinical cases are limited. We investigated body size proportions in a sample of elite athletes, employing data on recruits for the National Basketball Association (NBA, n=2,990), mixed martial arts (MMA) fighters (mixed-sex, n=1,284), as well as a control sample of healthy young adults who are not professional athletes, represented here by male (n=4,082) and female (n=1,986) recruits for the United States Army, to test two hypotheses: 1) There is a significant difference in arm span to height ratios between elite professional athletes and the control population, and 2) There is a significant relationship between arm span to height ratio and athletic success within the NBA and MMA. We find that NBA players are significantly taller, with absolutely and relatively wider arm spans than MMA fighters and the control population. Additionally, we find that basketball players are significantly more likely to be drafted earlier in the NBA, and MMA fighters are significantly more likely to have a better loss to win ratio, if their arm span to height ratio falls above the regression line. However, we note that arm span and height, as well as athletic success, are impacted by a myriad of factors, and some of the most successful professional athletes do not have particularly long arms relative to their height

Hominin diversity and occlusal pattern variations: New insights from Early Pleistocene discoveries in the Shungura Formation (Ethiopia)

Field missions conducted in the Shungura formation (Ethiopia) by the International Omo Research Expedition (IORE, 1967-1974) and the Omo Group Research Expedition (OGRE, 2006 to present) have yielded numerous fossil remains, including hundreds of hominin teeth. The most recent members, from H to L (1.89 to 1.09 Ma), deposited during the Early Pleistocene, have been little surveyed by the IORE. This time interval, documents the appearance of more derived species of Homo, such as H. ergaster/e..

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

Paleoecology of the Serengeti during the Oldowan-Acheulean transition at Olduvai Gorge, Tanzania : The mammal and fish evidence

Eight years of excavation work by the Olduvai Geochronology and Archaeology Project (OGAP) has produced a rich vertebrate fauna from several sites within Bed II, Olduvai Gorge, Tanzania. Study of these as well as recently re-organized collections from Mary Leakey's 1972 HWK EE excavations here provides a synthetic view of the faunal community of Olduvai during Middle Bed II at similar to 1.7-1.4 Ma, an interval that captures the local transition from Oldowan to Acheulean technology. We expand the faunal list for this interval, name a new bovid species, clarify the evolution of several mammalian lineages, and record new local first and last appearances. Compositions of the fish and large mammal assemblages support previous indications for the dominance of open and seasonal grassland habitats at the margins of an alkaline lake. Fish diversity is low and dominated by cichlids, which indicates strongly saline conditions. The taphonomy of the fish assemblages supports reconstructions of fluctuating lake levels with mass die-offs in evaporating pools. The mammals are dominated by grazing bovids and equids. Habitats remained consistently dry and open throughout the entire Bed II sequence, with no major turnover or paleoecological changes taking place. Rather, wooded and wet habitats had already given way to drier and more open habitats by the top of Bed I, at 1.85-1.80 Ma. This ecological change is close to the age of the Oldowan-Acheulean transition in Kenya and Ethiopia, but precedes the local transition in Middle Bed II. The Middle Bed II large mammal community is much richer in species and includes a much larger number of large-bodied species (>300 kg) than the modern Serengeti. This reflects the severity of Pleistocene extinctions on African large mammals, with the loss of large species fitting a pattern typical of defaunation or 'downsizing' by human disturbance. However, trophic network (food web) analyses show that the Middle Bed II community was robust, and comparisons with the Serengeti community indicate that the fundamental structure of food webs remained intact despite Pleistocene extinctions. The presence of a generalized meateating hominin in the Middle Bed II community would have increased competition among carnivores and vulnerability among herbivores, but the high generality and interconnectedness of the Middle Bed II food web suggests this community was buffered against extinctions caused by trophic interactions. (C) 2017 Published by Elsevier Ltd.Peer reviewe