Finite element analysis of crenulated and non-crenulated hominid molars : A functional hypothesis explaining the adaptive significance of molar crenulation

Objectives The occlusal surface of many mammalian teeth has grooves that have been collectively called crenulations. The evolutionary significance of this trait is unknown, but it has been associated with a hard diet. It has not been explained, however, why crenulated molars may present an increased mechanical resistance. The objective of this study was to determine whether a crenulated surface dissipate mechanical stress more efficiently than a smooth one. Materials and methods Using mu CT scans we built 3D models of lower second molars from Homo, Pan, Gorilla, and Pongo. The crenulated models from Homo and Pongo were modified to remove crenulations. Finite element analysis was used to determine the distribution of mechanical stress in all the models when a vertical force was applied. Results The results show that crenulated molars have a distinctive pattern of mechanical stress, namely the stress is higher in the valleys than in the crests of the crenulations. In non-crenulated molars, mechanical stress is more homogeneously distributed. Highly crenulated molars of orangutans show the smallest values of mean stress among the compared species. Artificially removing crenulations results in more homogeneous distribution of stresses and increased mean stress values. Conclusions Molar crenulations may increase molar resistance by canalizing mechanical stress from the tip to the base of the cusps. The overall cusp shape also influences the distribution of stress. This mechanism may be a functional hypothesis to explain the association between crenulated molars and mechanically demanding diets.Peer reviewe

Mapping molar shapes on signaling pathways

A major challenge in evolutionary developmental biology is to understand how genetic mutations underlie phenotypic changes. In principle, selective pressures on the phenotype screen the gene pool of the population. Teeth are an excellent model for understanding evolutionary changes in the genotype-phenotype relationship since they exist throughout vertebrates. Genetically modified mice (mutants) with abnormalities in teeth have been used to explore tooth development. The relationship between signaling pathways and molar shape, however, remains elusive due to the high intrinsic complexity of tooth crowns. This hampers our understanding of the extent to which developmental factors explored in mutants explain developmental and phenotypic variation in natural species that represent the consequence of natural selection. Here we combine a novel morphometric method with two kinds of data mining techniques to extract data sets from the three-dimensional surface models of lower first molars: i) machine learning to maximize classification accuracy of 22 mutants, and ii) phylogenetic signal for 31 Murinae species. Major shape variation among mutants is explained by the number of cusps and cusp distribution on a tooth crown. The distribution of mutant mice in morphospace suggests a nonlinear relationship between the signaling pathways and molar shape variation. Comparative analysis of mutants and wild murines reveals that mutant variation overlaps naturally occurring diversity, including more ancestral and derived morphologies. However, taxa with transverse lophs are not fully covered by mutant variation, suggesting experimentally unexplored developmental factors in the evolutionary radiation of Murines. Author summary Teeth are found in almost all vertebrates, and they show many different morphologies. In mammals, especially the cheek teeth or molars are highly diverse in shape, reflecting a vast range of dietary habits and efficiency of occlusion. As teeth are the most durable part of the body, they preserve well in the fossil record. The diversity of molar fossils has been useful in reconstructing the diet and phylogeny of extinct mammals. Genetically modified mice (mutants) show diverse modifications of their molar morphology, but we lack computational tools to test to what extent mutant morphologies account for the natural diversity found in the wild. We developed data mining using machine learning and phylogeny-based methods to analyze three-dimensional molar shapes in mouse mutants and natural species. Although many mutants and species have comparable features, most of the mutant molar variation covers the more evolutionarily ancestral than the more evolutionary derived shapes. Yet to be explored developmental factors may underly the more extreme shapes.Peer reviewe

A microCT Study of Three-Dimensional Patterns of Biomineralization in Pig Molars

Domestic pig molars provide an interesting system to study the biomineralization process. The large size, thick enamel and complex crown morphology make pig molars relatively similar to human molars. However, compared to human molars, pig molars develop considerably faster. Here we use microCT to image the developing pig molars and to decipher spatial patterns of biomineralization. We used mineral grains to calibrate individual microCT-scans, which allowed an accurate measure of the electron density of the developing molars. The microCT results show that unerupted molars that are morphologically at the same stage of development, can be at markedly different stage of enamel biomineralization. Erupted molars show increased electron density, suggesting that mineralization continues in oral cavity. Yet, our comparisons show that human enamel has slightly higher electron density than pig enamel. These results support the relatively low hardness values and calcium level values that have been reported earlier in literature for pig teeth. The mineral calibration was an efficient method for the microCT-absorption models, allowing a relatively robust way to detect scanning artifacts. In conclusions, whereas thin sections remain the preferred way to analyze enamel features, such as incremental lines and crystal orientation, the microCT allows efficient and non-destructive comparisons between different teeth and species.Domestic pig molars provide an interesting system to study the biomineralization process. The large size, thick enamel and complex crown morphology make pig molars relatively similar to human molars. However, compared to human molars, pig molars develop considerably faster. Here we use microCT to image the developing pig molars and to decipher spatial patterns of biomineralization. We used mineral grains to calibrate individual microCT-scans, which allowed an accurate measure of the electron density of the developing molars. The microCT results show that unerupted molars that are morphologically at the same stage of development, can be at markedly different stage of enamel biomineralization. Erupted molars show increased electron density, suggesting that mineralization continues in oral cavity. Yet, our comparisons show that human enamel has slightly higher electron density than pig enamel. These results support the relatively low hardness values and calcium level values that have been reported earlier in literature for pig teeth. The mineral calibration was an efficient method for the microCT-absorption models, allowing a relatively robust way to detect scanning artifacts. In conclusions, whereas thin sections remain the preferred way to analyze enamel features, such as incremental lines and crystal orientation, the microCT allows efficient and non-destructive comparisons between different teeth and species.Peer reviewe

Population- and individual-level dynamics of the intestinal microbiota of a small primate

Longitudinal sampling for intestinal microbiota in wild animals is difficult, leading to a lack of information on bacterial dynamics occurring in nature. We studied how the composition of microbiota communities changed temporally in free-ranging small primates, rufous mouse lemurs (Microcebus rufus). We marked and recaptured mouse lemurs during their mating season in Ranomafana National Park in southeastern mountainous rainforests of Madagascar for 2 years and determined the fecal microbiota compositions of these mouse lemurs with MiSeq sequencing. We collected 160 fecal samples from 71 animals and had two or more samples from 39 individuals. We found small, but statistically significant, effects of site and age on microbiota richness and diversity and effects of sex, year, and site on microbiota composition, while the within-year temporal trends were less clear. Within-host microbiota showed pervasive variation in intestinal bacterial community composition, especially during the second study year. We hypothesize that the biological properties of mouse lemurs, including their small body size and fast metabolism, may contribute to the temporal intraindividual-level variation, something that should be testable with more-extensive sampling regimes.Peer reviewe

Chromosomal neighbourhoods allow identification of organ specific changes in gene expression

Author summary Development of organs is typically associated with small and hard to detect changes in gene expression. Here we examined how often genes regulating specific organs are neighbours to each other in the genome, and whether this gene neighbourhood helps in the detection of changes in gene expression. We found that genes regulating individual organ development are very rarely close to each other in the mouse and human genomes. We built an algorithm, called DELocal, to detect changes in gene expression that incorporates information about neighbouring genes. Using transcriptomes of developing mouse molar teeth containing gene expression profiles of thousands of genes, we show how genes regulating tooth development are ranked high by DELocal even if their expression level changes are subtle. We propose that developmental biology studies can benefit from gene neighbourhood analyses in the detection of differential expression and identification of organ specific genes. Although most genes share their chromosomal neighbourhood with other genes, distribution of genes has not been explored in the context of individual organ development; the common focus of developmental biology studies. Because developmental processes are often associated with initially subtle changes in gene expression, here we explored whether neighbouring genes are informative in the identification of differentially expressed genes. First, we quantified the chromosomal neighbourhood patterns of genes having related functional roles in the mammalian genome. Although the majority of protein coding genes have at least five neighbours within 1 Mb window around each gene, very few of these neighbours regulate development of the same organ. Analyses of transcriptomes of developing mouse molar teeth revealed that whereas expression of genes regulating tooth development changes, their neighbouring genes show no marked changes, irrespective of their level of expression. Finally, we test whether inclusion of gene neighbourhood in the analyses of differential expression could provide additional benefits. For the analyses, we developed an algorithm, called DELocal that identifies differentially expressed genes by comparing their expression changes to changes in adjacent genes in their chromosomal regions. Our results show that DELocal removes detection bias towards large changes in expression, thereby allowing identification of even subtle changes in development. Future studies, including the detection of differential expression, may benefit from, and further characterize the significance of gene-gene neighbour relationships.Peer reviewe

Contemporary temperature-driven divergence in a Nordic freshwater fish under conditions commonly thought to hinder adaptation

BACKGROUND: Evaluating the limits of adaptation to temperature is important given the IPCC-predicted rise in global temperatures. The rate and scope of evolutionary adaptation can be limited by low genetic diversity, gene flow, and costs associated with adaptive change. Freshwater organisms are physically confined to lakes and rivers, and must therefore deal directly with climate variation and change. In this study, we take advantage of a system characterised by low genetic variation, small population size, gene flow and between-trait trade-offs to study how such conditions affect the ability of a freshwater fish to adapt to climate change. We test for genetically-based differences in developmental traits indicating local adaptation, by conducting a common-garden experiment using embryos and larvae from replicate pairs of sympatric grayling demes that spawn and develop in natural cold and warm water, respectively. These demes have common ancestors from a colonization event 22 generations ago. Consequently, we explore if diversification may occur under severely constraining conditions. RESULTS: We found evidence for divergence in ontogenetic rates. The divergence pattern followed adaptation predictions as cold-deme individuals displayed higher growth rates and yolk conversion efficiency than warm-deme individuals at the same temperature. The cold-deme embryos had a higher rate of muscle mass development. Most of the growth- and development differences occurred prior to hatch. The divergence was probably not caused by genetic drift as there was a strong degree of parallelism in the divergence pattern and because phenotypic differentiation (Q(ST)) was larger than estimated genetic drift levels (microsatellite F(ST)) between demes from different temperature groups. We also document that these particular grayling populations cannot develop successfully at temperatures above 12°C, whereas other European populations can, and that increasing the muscle mass development rate comes at the cost of some skeletal trait development rates. CONCLUSIONS: This study shows that genetically based phenotypic divergence can prevail even under conditions of low genetic variation and ongoing gene flow. Furthermore, population-specific maximum development temperatures along with musculoskeletal developmental trade-offs may constrain adaptation

Metabarcoding gastrointestinal nematodes in sympatric endemic and non-endemic species in Ranomafana National Park, Madagascar

Sympatric species are known to host the same parasites species. Nevertheless, surveys examining parasite assemblages in sympatric species are rare. To understand how parasite assemblages in sympatric host species differ in a given locality, we used a noninvasive identification method based on high-throughput sequencing. We collected fecal samples from sympatric species in Ranomafana National Park, Madagascar, from September to December in 2010, 2011, and 2012 and identified their parasites by metabarcoding, sequencing a region of the small ribosomal subunit (18S) gene. Our survey included 11 host species, including endemic primates, rodents, frogs, gastropods, and nonendemic rats and dogs. We collected 872 samples, of which 571 contained nematodes and 249 were successfully sequenced. We identified nine putative species of parasites, although their correspondence to actual parasite species is not clear as the resolution of the marker gene differs between nematode clades. For the host species that we successfully sampled with 10 or more positive occurrences of nematodes, i.e., mouse lemurs (Microcebus rufus), black rats (Rattus rattus), and frogs (Anura), the parasite assemblage compositions differed significantly among host species, sampling sites, and sampling years. Our metabarcoding method shows promise in interrogating parasite assemblages in sympatric host species and our results emphasize the importance of choosing marker regions for parasite identification accuracy.Peer reviewe

Modeling enamel matrix secretion in mammalian teeth

The most mineralized tissue of the mammalian body is tooth enamel. Especially in species with thick enamel, three-dimensional (3D) tomography data has shown that the distribution of enamel varies across the occlusal surface of the tooth crown. Differences in enamel thickness among species and within the tooth crown have been used to examine taxonomic affiliations, life history, and functional properties of teeth. Before becoming fully mineralized, enamel matrix is secreted on the top of a dentine template, and it remains to be explored how matrix thickness is spatially regulated. To provide a predictive framework to examine enamel distribution, we introduce a computational model of enamel matrix secretion that maps the dentine topography to the enamel surface topography. Starting from empirical enamel-dentine junctions, enamel matrix deposition is modeled as a diffusion-limited free boundary problem. Using laboratory microCT and synchrotron tomographic data of pig molars that have markedly different dentine and enamel surface topographies, we show how diffusion-limited matrix deposition accounts for both the process of matrix secretion and the final enamel distribution. Simulations reveal how concave and convex dentine features have distinct effects on enamel surface, thereby explaining why the enamel surface is not a straightforward extrapolation of the dentine template. Human and orangutan molar simulations show that even subtle variation in dentine topography can be mapped to the enamel surface features. Mechanistic models of extracellular matrix deposition can be used to predict occlusal morphologies of teeth. Author summary Teeth of most mammals are covered by a layer of highly mineralized enamel that cannot be replaced or repaired. The enamel layer is not uniform over the underlying dentine, and spatial regulation of enamel formation is critical for making a functional tooth. To explore which kind of mechanisms could underlie the complex patterns of enamel distribution, we present a computational model. Starting from tomography-imaged teeth from which enamel has been digitally removed, enamel is restored on dentine surfaces by simulating diffusion-limited secretion of enamel matrix. Our simulations show how the combination of subtle features of dentine and diffusion-limited secretion of the enamel matrix can substantially increase the complexity of the enamel surface. We propose that the strength of the diffusion-limited process is a key factor in determining enamel distribution among mammalian species.Peer reviewe

Automated 3D phenotype analysis using data mining

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Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population

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