Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

BACKGROUND

Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.

RESULTS

Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued.

CONCLUSIONS

The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/

Normal genetic variation of the human foot: part 1: the paradox of normal anatomical alignment in an evolutionary epigenetic context

Molecular genetics is changing our understanding of the developmental translation of genotype to phenotype between and within different phylogenetic groups. Together with a growing understanding of our own evolutionary relationships to common ancestors, the epigenetic processes involved enforce a reexamination of what is regarded as a normal foot structure. A revised populationist approach is proposed and supported by paleoanthropologic evidence that reflects a picture of emerging suitability for bipedalism that is driven by natural genetic divergence.

The role of modularity in the evolution of primate postcanine dental formula: integrating jaw space with patterns of dentition

The assembly of a phenotype into modules or developmental fields, which are semiautonomous units in development and function, seems to be one of the strategies to increase the capacity to produce phenotypic variation. In mammals the upper dentition is formed on two distinct developmental units, wherein incisors are formed on the primary palate, which is derived from the embryonic frontonasal process, and the other teeth (canine, premolar, and molar) are formed on the alveolar bone, which is derived from the maxillary process (termed herein as PALATE2). The aim of the present work was to analyze the variations in size and number of premolar and molar teeth in primate dentition and to correlate these morphometrical parameters with the relative size of these tooth classes with respect to PALATE2. Furthermore, we seek to understand to what extent the changes in the relative size of premolar and molar fields can influence the size of each tooth within its respective field, and how these parameters connect with the variations in the dental formula that occurred during primate evolution. The data presented here not only indicate that premolar and molar fields can be seen as submodules of a larger and hierarchically superior module (i.e., PALATE2) but also present quantitative parameters that allow us to understand how variations in the relative size of premolar and molar teeth connect with the variations in the dental formula that occurred during primate evolution.

Functional significance of genetic variation underlying limb bone diaphyseal structure

Limb bone diaphyseal structure is frequently used to infer hominin activity levels from skeletal remains, an approach based on the well-documented ability of bone to adjust to its loading environment during life. However, diaphyseal structure is also determined in part by genetic factors. This study investigates the possibility that genetic variation underlying diaphyseal structure is influenced by the activity levels of ancestral populations and might also have functional significance in an evolutionary context. We adopted an experimental evolution approach and tested for differences in femoral diaphyseal structure in 1-week-old mice from a line that had been artificially selected (45 generations) for high voluntary wheel running and non-selected controls. As adults, selected mice are significantly more active on wheels and in home cages, and have thicker diaphyses. Structural differences at 1 week can be assumed to primarily reflect the effects of selective breeding rather than direct mechanical stimuli, given that the onset of locomotion in mice is shortly after Day 7. We hypothesized that if genetically determined diaphyseal structure reflects the activity patterns of members of a lineage, then selected animals will have relatively larger diaphyseal dimensions at 1 week compared to controls. The results provide strong support for this hypothesis and suggest that limb bone cross sections may not always only reflect the activity levels of particular fossil individuals, but also convey an evolutionary signal providing information about hominin activity in the past.

Brief communication: Methods of sequence heterochrony for describing modular developmental changes in human evolution

Interest in the developmental changes leading to apomorphic features of human anatomy is longstanding. Although most research has focused on quantitative measures of size and shape, additional information may be available in the sequence of events in development, including aspects of phenotypic integration. I apply two recently proposed techniques for analyzing developmental sequences to literature data on human and chimpanzee age of limb element ossification center appearance in radiographs. The event-pair cracking method of Jeffery et al. (Syst Biol 51 [2002] 478-491) offers little additional insight on sequence differences in this data set than a simpler difference of ranks. Both reveal shifts in timing that are likely related to locomotor differences between the two species. Poe's (Evolution 58 [2004] 1852-1855) test for modularity in a sequence identifies the ankle, wrist, and hind limb as developmental modules, which may correspond to localized combinations of developmental genes. Ossification patterns of the rays of the hand and foot show little modularity. Integrating these and other methods of sequence analysis with traditional metrics of size and shape remains an underdeveloped area of inquiry.

Developmental basis of limb length in rodents: evidence for multiple divisions of labor in mechanisms of endochondral bone growth

Mammals are remarkably diverse in limb lengths and proportions, but the number and kind of developmental mechanisms that contribute to length differences between limb bones remain largely unknown. Intra- and interspecific differences in bone length could result from variations in the cellular processes of endochondral bone growth, creating differences in rates of chondrocyte proliferation or hypertrophy, variation in the shape and size of chondrocytes, differences in the number of chondrocytes in precursor populations and throughout growth, or a combination of these mechanisms. To address these questions, this study compared cellular mechanisms of endochondral bone growth in cross-sectional ontogenetic series of the appendicular skeleton of two rodent species: the mouse (Mus musculus) and Mongolian gerbil (Meriones unguiculatus). Results indicate that multiple cellular processes of endochondral bone growth contribute to phenotypic differences in limb bone length. The data also suggest that separate developmental processes contribute to intraspecific length differences in proximal versus distal limb bones, and that these proximo-distal mechanisms are distinct from mechanisms that contribute to interspecific differences in limb bone length related to body size. These developmental "divisions of labor" are hypothesized to be important features of vertebrate limb development that allow (1) morphology in the autopods to evolve independently of the proximal limb skeleton, and (2) adaptive changes in limb proportions related to locomotion to evolve independently of evolutionary changes in body size.

Who's afraid of the big bad Wolff?: "Wolff's law" and bone functional adaptation

"Wolff's law" is a concept that has sometimes been misrepresented, and frequently misunderstood, in the anthropological literature. Although it was originally formulated in a strict mathematical sense that has since been discredited, the more general concept of "bone functional adaptation" to mechanical loading (a designation that should probably replace "Wolff's law") is supported by much experimental and observational data. Objections raised to earlier studies of bone functional adaptation have largely been addressed by more recent and better-controlled studies. While the bone morphological response to mechanical strains is reduced in adults relative to juveniles, claims that adult morphology reflects only juvenile loadings are greatly exaggerated. Similarly, while there are important genetic influences on bone development and on the nature of bone's response to mechanical loading, variations in loadings themselves are equally if not more important in determining variations in morphology, especially in comparisons between closely related individuals or species. The correspondence between bone strain patterns and bone structure is variable, depending on skeletal location and the general mechanical environment (e.g., distal vs. proximal limb elements, cursorial vs. noncursorial animals), so that mechanical/behavioral inferences based on structure alone should be limited to corresponding skeletal regions and animals with similar basic mechanical designs. Within such comparisons, traditional geometric parameters (such as second moments of area and section moduli) still give the best available estimates of in vivo mechanical competence. Thus, when employed with appropriate caution, these features may be used to reconstruct mechanical loadings and behavioral differences within and between past populations.

Forelimb segment length proportions in extant hominoids and Australopithecus afarensis

Forelimb proportions have been used to infer locomotor adaptation in Australopithecus afarensis. However, little is known about proportions among individual forelimb segments in extant or fossil hominoids. The partial A. afarensis skeleton A.L. 438-1 and the more complete skeleton A.L. 288-1 provide the opportunity to assess relative length of the arm, forearm, wrist, and palm. We compare scaling relationships between pairs of forelimb bones of extant hominoids and A. afarensis, and length of individual forelimb elements to a body size surrogate. Hylobatids, and to a lesser extent orangutans, have the longest forelimb bones relative to size, although the carpus varies little among taxa, perhaps due to functional constraints of the wrist. Pan species are unique in having long metacarpals relative to ulnar length, demonstrating that they probably differ from the common chimp-human ancestor, and also that developmental mechanisms can be altered to results in differential growth of individual forelimb segments. A. afarensis has no forelimb bones that are significantly longer than those of humans for its size. It falls within the range of variation seen in modern humans for all comparisons relative to size, but appears to differ from the typical human brachial index due to a slightly shorter humerus and/or slightly longer ulna. It has short metacarpals like humans only among hominoids. Thus, while Pan may have elongated its metacarpus relative to ulnar length, A. afarensis may have reduced the length of its metacarpals and possibly its humerus relative to body size from the primitive condition.

Molar scaling in strepsirrhine primates

We examined how maxillary molar dimensions change with body and skull size estimates among 54 species of living and subfossil strepsirrhine primates. Strepsirrhine maxillary molar areas tend to scale with negative allometry, or possibly isometry, relative to body mass. This observation supports several previous scaling analyses showing that primate molar areas scale at or slightly below geometric similarity relative to body mass. Strepsirrhine molar areas do not change relative to body mass(0.75), as predicted by the metabolic scaling hypothesis. Relative to basicranial length, maxillary molar areas tend to scale with positive allometry. Previous claims that primate molar areas scale with positive allometry relative to body mass appear to rest on the incorrect assumption that skull dimensions scale isometrically with body mass. We identified specific factors that help us to better understand these observed scaling patterns. Lorisiform and lemuriform maxillary molar scaling patterns did not differ significantly, suggesting that the two infraorders had little independent influence on strepsirrhine scaling patterns. Contrary to many previous studies of primate dental allometry, we found little evidence for significant differences in molar area scaling patterns among frugivorous, folivorous, and insectivorous groups. We were able to distinguish folivorous species from frugivorous and insectivorous taxa by comparing M1 lengths and widths. Folivores tend to have a mesiodistally elongated M1 for a given buccolingual M1 width when compared to the other two dietary groups. It has recently been shown that brain mass has a strong influence on primate dental eruption rates. We extended this comparison to relative maxillary molar sizes, but found that brain mass appears to have little influence on the size of strepsirrhine molars. Alternatively, we observed a strong correlation between the relative size of the facial skull and relative molar areas among strepsirrhines. We hypothesize that this association may be underlain by a partial sharing of the patterning of development between molar and facial skull elements.

Thomas Henry Huxley (1825-1895) puts us in our place

Thomas Huxley was one of the 19th century's most active defenders of Darwin's idea that life has evolved through natural processes. An anatomist and paleontologist, he extended his energies to science and education policy, the democratization of science, and the broad societal implications of evolution. Since his time the fossil record has greatly improved and the genetic 'revolution' has occurred, deepening our understanding of primate and human evolution in ways that would please Huxley: improved systematics relies heavily on genetic data, and molecular technologies are opening our understanding of the genetic basis of complex traits of traditional anthropological interest-but in ways that are thoroughly dependent on the fact of evolution. A more unified biological synthesis is forming that unites genes, developmental process, structure, and inheritance. But the tempo and mode of evolution remain unresolved. Huxley was one of many who have had trouble accepting Darwin's gradual natural selection as the central evolutionary mechanism, and views spanning the antipodes of gradualism and saltation find advocates even in our genetic era.

Modularity and integration in the hominoid scapula

In this paper, several hypotheses of morphological integration within the hominoid (ape) scapula are tested. In particular, whether the scapula represents a set of developmental tissues sharing tight correlations between constituent parts (i.e., highly integrated) or is more modularly organized (i.e., covariation is greater within regions than between) is tested. Whether the patterns of integration in the scapula have changed over phylogenetic time or in response to selective forces is also examined. Results from two different analyses (matrix correlations and edge deviance) indicate traits comprising the blade and acromion, and to a weaker degree the glenoid, correlate highly with each other. The coracoid exhibits more independence from other parts of the scapula, perhaps reflecting its distinct evolutionary developmental history. Overall, similarity in species-specific patterns of correlation was high between all taxa. Correlation matrix similarity was significantly correlated with functional similarity and morphological distance, but not with phylogenetic distance. These results are congruent with other studies of integration that suggest correlation patterns remain stable over evolutionary time. There are changes associated with phylogeny, but the tight link between functional similarity and phylogenetic distance at this level of comparison presents possible challenges to interpretation. Overall similarities in the pattern of integration in all taxa might be better interpreted as relative strengthening or weakening of trait correlations rather than broadscale changes in the pattern of relationship between developmental regions. Larger sample sizes with greater taxonomic/functional breadth, and finer scale analyses of patterns of correlation are needed to test these hypotheses further.

The aging of Wolff's ?law?: Ontogeny and responses to mechanical loading in cortical bone

The premise that bones grow and remodel throughout life to adapt to their mechanical environment is often called Wolff's law. Wolff's law, however, is not always true, and in fact comprises a variety of different processes that are best considered separately. Here we review the molecular and physiological mechanisms by which bone senses, transduces, and responds to mechanical loads, and the effects of aging processes on the relationship (if any) between cortical bone form and mechanical function. Experimental and comparative evidence suggests that cortical bone is primarily responsive to strain prior to sexual maturity, both in terms of the rate of new bone growth (modeling) as well as rates of turnover (Haversian remodeling). Rates of modeling and Haversian remodeling, however, vary greatly at different skeletal sites. In addition, there is no simple relationship between the orientation of loads in long bone diaphyses and their cross-sectional geometry. In combination, these data caution against assuming without testing adaptationist views about form-function relationships in order to infer adult activity patterns from skeletal features such as cross-sectional geometry, cortical bones density, and musculo-skeletal stress markers. Efforts to infer function from shape in the human skeleton should be based on biomechanical and developmental models that are experimentally tested and validated.

The anthropoid postcranial axial skeleton: Comments on development, variation, and evolution

Within-species phenotypic variation is the raw material on which natural selection acts to shape evolutionary change, and understanding more about the developmental genetics of intraspecific as well as interspecific phenotypic variation is an important component of the Evo-Devo agenda. The axial skeleton is a useful system to analyze from such a perspective. Its development is increasingly well understood, and between-species differences in functionally important developmental parameters are well documented. I present data on intraspecific variation in the axial postcranial skeleton of some Primates, including hominoids (apes and humans). Hominoid species are particularly valuable, because counts of total numbers of vertebrae, and hence original somite numbers, are available for large samples. Evolutionary changes in the axial skeleton of various primate lineages, including bipedal humans, are reviewed, and hypotheses presented to explain the changes in terms of developmental genetics. Further relevant experiments on model organisms are suggested in order to explore more fully the differences in developmental processes between primate species, and hence to test these hypotheses.

Developmental Biology and Human Evolution

▪ Abstract  Our understanding of developmental biology burgeoned during the last decade. This review summarizes recent advances, provides definitions and explanations of some basic principles, and does so in a way that will aid anthropologists in understanding their profound implications. Crucial concepts, such as developmental fields, selector and realizator genes, cell signaling mechanisms, and gene regulatory elements are briefly described and then integrated with the emergence of skeletal morphology. For the postcranium, a summary of events from limb bud formation, the appearance of anlagen, the expression of Hox genes, and the fundamentals of growth plate dynamics are briefly summarized. Of particular importance are revelations that bony morphology is largely determined by pattern formation, that growth foci such as physes and synovial joints appear to be regulated principally by positional information, and that variation in these fields is most likely determined by cis-regulatory elements acting on restricted numbers of anabolic genes downstream of selectors (such as Hox). The implications of these discoveries for the interpretation of both contemporary and ancient human skeletal morphology are profound. One of the most salient is that strain transduction now appears to play a much reduced role in shaping the human skeleton. Indeed, the entirety of “Wolff's Law” must now be reassessed in light of new knowledge about pattern formation. The review concludes with a brief discussion of some implications of these findings, including their impact on cladistics and homology, as well as on biomechanical and morphometric analyses of both ancient and modern human skeletal material.

Evolution and development of mammalian limb integumentary structures

The adaptive radiation of mammalian clades has involved marked changes in limb morphology that have affected not only the skeleton but also the integumentary structures. For example, didelphid marsupials show distinct differences in nail and claw morphology that are functionally related to the evolution of arboreal, terrestrial, and aquatic foraging behaviors. Vespertilionoid bats have evolved different volar pad structures such as adhesive discs, scales, and skin folds, whereas didelphid marsupials have apical pads covered either with scales, ridges, or small cones. Comparative analysis of pad and claw development reveals subtle differences in mesenchymal and ectodermal patterning underlying interspecific variation in morphology. Analysis of gene expression during pad and claw development reveals that signaling molecules such as Msx1 and Hoxc13 play important roles in the morphogenesis of these integumentary structures. These findings suggest that evolutionary change in the expression of these molecules, and in the response of mesenchymal and ectodermal cells to these signaling factors, may underlie interspecific differences in nail, claw, and volar pad morphology. Evidence from comparative morphology, development, and functional genomics therefore sheds new light on both the patterns and mechanisms of evolutionary change in mammalian limb integumentary structures.

Interpreting the posture and locomotion of Australopithecus afarensis: where do we stand?

Reconstructing the transition to bipedality is key to understanding early hominin evolution. Because it is the best-known early hominin species, Australopithecus afarensis forms a baseline for interpreting locomotion in all early hominins. While most researchers agree that A. afarensis individuals were habitual bipeds, they disagree over the importance of arboreality for them. There are two main reasons for the disagreement. First, there are divergent perspectives on how to interpret primitive characters. Primitive traits may be retained by stabilizing selection, pleiotropy, or other ontogenetic mechanisms. Alternately, they could be in the process of being reduced, or they simply could be selectively neutral. Second, researchers are asking fundamentally different questions about the fossils. Some are interested in reconstructing the history of selection that shaped A. afarensis, while others are interested in reconstructing A. afarensis behavior. By explicitly outlining whether we are interested in reconstructing selective history or behavior, we can develop testable hypotheses to govern our investigations of the fossils. To infer the selective history that shaped a taxon, we must first consider character polarity. Derived traits that enhance a particular function, are found to be associated with that function in extant homologs, and that epigenetically sensitive data indicate were actually being used for that function, can be interpreted as adaptations. The null hypothesis to explain the retention of primitive traits is that of selective neutrality, or nonaptation. Disproving this requires demonstration of active stabilizing or negative selection (disaptation). Stabilizing selection can be inferred when primitive traits compromise a derived function clearly of adaptive value. Prolonged stasis, continued use of the trait for a particular function, or no change in variability in the trait are evidence that can support a hypothesis of adaptation for primitive traits, but still do not falsify the null hypothesis. Disaptation, or negative selection, should result in a trait being reduced or lost. To infer the behaviors of a fossil species, we must first determine its adaptations, use this to make hypotheses about its behavior, and test these hypotheses using epigenetically sensitive traits that are modified by an individual's activity pattern. When the A. afarensis data are evaluated using this framework, it is clear that these hominins had undergone selection for habitual bipedality, but the null hypothesis of nonaptation to explain the retention of primitive, ape-like characters cannot be falsified at present. The apparent stasis in Australopithecus postcranial form is currently the strongest evidence for stabilizing selection maintaining its primitive features. Evidence from features affected by individual behaviors during ontogeny shows that A. afarensis individuals were habitually traveling bipedally, but evidence presented for arboreal behavior so far is not conclusive. By clearly identifying the questions we are asking about early hominin fossils, refining our knowledge about character polarities, and elucidating the factors influencing morphology, we will be able to progress in our understanding of the posture and locomotion of A. afarensis and all early hominins.

Canalization, developmental stability, and morphological integration in primate limbs

Canalization and developmental stability refer to the tendency of developmental processes to follow particular trajectories, despite external or internal perturbation. Canalization is the tendency for development of a specific genotype to follow the same trajectory under different conditions (different environments or different genetic backgrounds), while developmental stability is the tendency for the development of a specific genotype to follow the same trajectory under the same conditions. Morphological integration refers to the tendency for structures to show correlated variation because they develop in response to shared developmental processes or function in concert with other structures. All three phenomena are emergent properties of developmental systems that can affect the interaction of development and evolution. In this paper, we review the topics of canalization, developmental stability, and morphological integration and their relevance to primate and human evolution. We then test three developmentally motivated hypotheses about the patterning of variability components in the mammalian limb. We find that environmental variances and fluctuating asymmetries (FA) increase distally along the limb in adult macaques but not in fetal mice. We infer that the greater variability of more distal segments in macaques is due to postnatal mechanical effects. We also find that heritability and FA are significantly correlated when different limb measurements are compared in fetal mice. This supports the idea that the mechanisms underlying canalization and developmental stability are related. Finally, we report that the covariation structure of fore- and hindlimb skeletal elements shows evidence for morphological integration between serially homologous structures between the limbs. This is evidence for the existence of developmental modules that link structures between the limbs. Such modules would produce covariation that would need to be overcome by selection for divergence in hind- and forelimb morphology.