Development and Assessment of Fully Automated and Globally Transitive Geometric Morphometric Methods, With Application to a Biological Comparative Dataset With High Interspecific Variation

Applications of Microct Imaging to Archaeobotanical Research

The potential applications of microCT scanning in the field of archaeobotany are only just beginning to be explored. The imaging technique can extract new archaeobotanical information from existing archaeobotanical collections as well as create new archaeobotanical assemblages within ancient ceramics and other artefact types. The technique could aid in answering archaeobotanical questions about the early histories of some of the world's most important food crops from geographical regions with amongst the poorest rates of archaeobotanical preservation and where ancient plant exploitation remains poorly understood. This paper reviews current uses of microCT imaging in the investigation of archaeobotanical questions, as well as in cognate fields of geosciences, geoarchaeology, botany and palaeobotany. The technique has to date been used in a small number of novel methodological studies to extract internal anatomical morphologies and three-dimensional quantitative data from a range of food crops, which includes sexually-propagated cereals and legumes, and asexually-propagated underground storage organs (USOs). The large three-dimensional, digital datasets produced by microCT scanning have been shown to aid in taxonomic identification of archaeobotanical specimens, as well as robustly assess domestication status. In the future, as scanning technology, computer processing power and data storage capacities continue to improve, the possible applications of microCT scanning to archaeobotanical studies will only increase with the development of machine and deep learning networks enabling the automation of analyses of large archaeobotanical assemblages.

A Comparison of Semilandmarking Approaches in the Analysis of Size and Shape

Often, few landmarks can be reliably identified in analyses of form variation and covariation. Thus, ‘semilandmarking’ algorithms have increasingly been applied to surfaces and curves. However, the locations of semilandmarks depend on the investigator’s choice of algorithm and their density. In consequence, to the extent that different semilandmarking approaches and densities result in different locations of semilandmarks, they can be expected to yield different results concerning patterns of variation and co-variation. The extent of such differences due to methodology is, as yet, unclear and often ignored. In this study, the performance of three landmark-driven semilandmarking approaches is assessed, using two different surface mesh datasets (ape crania and human heads) with different degrees of variation and complexity, by comparing the results of morphometric analyses. These approaches produce different semilandmark locations, which, in turn, lead to differences in statistical results, although the non-rigid semilandmarking approaches are consistent. Morphometric analyses using semilandmarks must be interpreted with due caution, recognising that error is inevitable and that results are approximations. Further work is needed to investigate the effects of using different landmark and semilandmark templates and to understand the limitations and advantages of different semilandmarking approaches.

First evidence of the link between internal and external structure of the human inner ear otolith system using 3D morphometric modeling

Our sense of balance is among the most central of our sensory systems, particularly in the evolution of human positional behavior. The peripheral vestibular system (PVS) comprises the organs responsible for this sense; the semicircular canals (detecting angular acceleration) and otolith organs (utricle and saccule; detecting linear acceleration, vibration, and head tilt). Reconstructing vestibular evolution in the human lineage, however, is problematic. In contrast to considerable study of the canals, relationships between external bone and internal membranous otolith organs (otolith system) remain largely unexplored. This limits our understanding of vestibular functional morphology. This study combines spherical harmonic modeling and landmark-based shape analyses to model the configuration of the human otolith system. Our approach serves two aims: (1) test the hypothesis that bony form covaries with internal membranous anatomy; and (2) create a 3D morphometric model visualizing bony and membranous structure. Results demonstrate significant associations between bony and membranous tissues of the otolith system. These data provide the first evidence that external structure of the human otolith system is directly related to internal anatomy, suggesting a basic biological relationship. Our results visualize this structural relationship, offering new avenues into vestibular biomechanical modeling and assessing the evolution of the human balance system.

Endostructural and periosteal growth of the human humerus

The growth and development of long bones are of considerable interests in the fields of comparative anatomy and palaeoanthropology, as evolutionary changes and adaptations to specific physical activity patterns are expected to be revealed during bone ontogeny. Traditionally, the cross-sectional geometry of long bones has been examined at discrete locations usually placed at set intervals or fixed percentage distances along the midline axis of the bone shaft. More recently, the technique of morphometric mapping has enabled the continuous analysis of shape variation along the shaft. Here we extend this technique to the full sequence of late fetal and postnatal development of the humeral shaft in a modern human population sample, with the aim of establishing the shape changes during growth and their relationship with the development of the arm musculature and activity patterns. A sample of modern human humeri from individuals of age ranging from 24 weeks in utero to 18 years was imaged using microtomography at multiple resolutions and custom Matlab scripts. Standard biomechanical properties, cortical thickness, surface curvature, and pseudo-landmarks were extracted along radial vectors spaced at intervals of 1° at each 0.5% longitudinal increment measured along the shaft axis. Heat maps were also generated for cortical thickness and surface curvature. The results demonstrate that a whole bone approach to analysis of cross-sectional geometry is more desirable where possible, as there is a continuous pattern of variation along the shaft. It is also possible to discriminate very young individuals and adolescents from other groups by relative cortical thickness, and also by periosteal surface curvature.

Microevolutionary variation in molar morphology of Onychomys leucogaster decoupled from genetic structure

In neutral models of quantitative trait evolution, both genetic and phenotypic divergence scale as random walks, producing a correlation between the two measures. However, complexity in the genotype-phenotype map may alter the correlation between genotypic and phenotypic divergence, even when both are evolving neutrally or nearly so. Understanding this correlation between phenotypic and genetic variation is critical for accurately interpreting the fossil record. This study compares the geographic structure and scaling of morphological variation of the shape of the first lower molar of 77 individuals of the northern grasshopper mouse Onychomys leucogaster to genome-wide SNP variation in the same sample. We found strong genetic structure but weak or absent morphological structure indicating that the scaling of each type of variation is decoupled from one another. Low P_ST values relative to F_ST values are consistent with a lack of morphological divergence in contrast to genetic divergence between groups. This lack of phenotypic structure and the presence of notable within-sample phenotypic variance are consistent with uniform selection or constraints on molar shape across a wide geographic and environmental range. Over time, this kind of decoupling may result in patterns of phenotypic stasis masking underlying genetic patterns.

Unveiling the third dimension in morphometry with automated quantitative volumetric computations

As computed tomography and related technologies have become mainstream tools across a broad range of scientific applications, each new generation of instrumentation produces larger volumes of more-complex 3D data. Lagging behind are step-wise improvements in computational methods to rapidly analyze these new large, complex datasets. Here we describe novel computational methods to capture and quantify volumetric information, and to efficiently characterize and compare shape volumes. It is based on innovative theoretical and computational reformulation of volumetric computing. It consists of two theoretical constructs and their numerical implementation: the spherical wave decomposition (SWD), that provides fast, accurate automated characterization of shapes embedded within complex 3D datasets; and symplectomorphic registration with phase space regularization by entropy spectrum pathways (SYMREG), that is a non-linear volumetric registration method that allows homologous structures to be correctly warped to each other or a common template for comparison. Together, these constitute the Shape Analysis for Phenomics from Imaging Data (SAPID) method. We demonstrate its ability to automatically provide rapid quantitative segmentation and characterization of single unique datasets, and both inter-and intra-specific comparative analyses. We go beyond pairwise comparisons and analyze collections of samples from 3D data repositories, highlighting the magnified potential our method has when applied to data collections. We discuss the potential of SAPID in the broader context of generating normative morphologies required for meaningfully quantifying and comparing variations in complex 3D anatomical structures and systems.

Insights from macroevolutionary modelling and ancestral state reconstruction into the radiation and historical dietary ecology of Lemuriformes (Primates, Mammalia)

Background

Lemurs once rivalled the diversity of rest of the primate order despite thier confinement to the island of Madagascar. We test the adaptive radiation model of Malagasy lemur diversity using a novel combination of phylogenetic comparative methods and geometric methods for quantifying tooth shape.

Results

We apply macroevolutionary model fitting approaches and disparity through time analysis to dental topography metrics associated with dietary adaptation, an aspect of mammalian ecology which appears to be closely related to diversification in many clades. Metrics were also reconstructed at internal nodes of the lemur tree and these reconstructions were combined to generate dietary classification probabilities at internal nodes using discriminant function analysis. We used these reconstructions to calculate rates of transition toward folivory per million-year intervals. Finally, lower second molar shape was reconstructed at internal nodes by modelling the change in shape of 3D meshes using squared change parsimony along the branches of the lemur tree. Our analyses of dental topography metrics do not recover an early burst in rates of change or a pattern of early partitioning of subclade disparity. However, rates of change in adaptations for folivory were highest during the Oligocene, an interval of possible forest expansion on the island.

Conclusions

There was no clear phylogenetic signal of bursts of morphological evolution early in lemur history. Reconstruction of the molar morphologies corresponding to the ancestral nodes of the lemur tree suggest that this may have been driven by a shift toward defended plant resources, however. This suggests a response to the ecological opportunity offered by expanding forests, but not necessarily a classic adaptive radiation initiated by dispersal to Madagascar.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01793-x.

Skull diversity and evolution in miniaturized amphibians, genus Brachycephalus (Anura: Brachycephalidae)

Miniaturized amphibians of the genus Brachycephalus are phenotypically diverse. The species of Brachycephalus have bufoniform or leptodactyliform Baupläne and any of three skeletal states: nonhyperossified, hyperossified without dorsal shield, and hyperossified with dorsal shield. We integrate high-resolution microcomputed tomography, geometric morphometrics, and an estimate of molecular phylogenetic relationships to investigate skull diversity in shape and size-shape space in selected species of Brachycephalus. Skull diversity amongst species of Brachycephalus can be partitioned into shape and size-shape space according to the four conditions of skeletal states-Baupläne, namely, nonhyperossified leptodactyliform, nonhyperossified bufoniform, hyperossified bufoniform without dorsal shield, and hyperossified bufoniform with dorsal shield. Skull diversity in shape and size-shape space in nonhyperossified leptodactyliform species of Brachycephalus is markedly larger, when compared to skull diversity in species of the three other conditions of skeletal states-Baupläne. Variation in skull shape scales with size across Brachycephalus and, therefore, can be explained by allometry. Skull diversity, Baupläne, and skeletal states covary to a large extent with monophyletic lineages of Brachycephalus, as revealed by a mitochondrial DNA species tree. Nonhyperossified bufoniform species and hyperossified bufoniform species with or without dorsal shield are monophyletic lineages, as inferred from a mitochondrial DNA species tree. Nonhyperossified leptodactyliform species of Brachycephalus do not share, however, a most recent common ancestor. The nonhyperossified leptodactyliform species of Brachycephalus, due to their marked skull diversity and lack of monophyly, emerge as evolutionarily complex. Therefore, further sampling of the nonhyperossified leptodactyliform condition of skeletal states-Baupläne will be necessary to further understand the evolutionary history of Brachycephalus.

A Practical Guide to Sliding and Surface Semilandmarks in Morphometric Analyses

Advances in imaging technologies, such as computed tomography (CT) and surface scanning, have facilitated the rapid generation of large datasets of high-resolution three-dimensional (3D) specimen reconstructions in recent years. The wealth of phenotypic information available from these datasets has the potential to inform our understanding of morphological variation and evolution. However, the ever-increasing ease of compiling 3D datasets has created an urgent need for sophisticated methods of capturing high-density shape data that reflect the biological complexity in form. Landmarks often do not take full advantage of the rich shape information available from high-resolution 3D specimen reconstructions, as they are typically restricted to sutures or processes that can be reliably identified across specimens and exclude most of the surface morphology. The development of sliding and surface semilandmark techniques has greatly enhanced the quantification of shape, but their application to diverse datasets can be challenging, especially when dealing with the variable absence of some regions within a structure. Using comprehensive 3D datasets of crania that span the entire clades of birds, squamates and caecilians, we demonstrate methods for capturing morphology across incredibly diverse shapes. We detail many of the difficulties associated with applying semilandmarks to comparable regions across highly disparate structures, and provide solutions to some of these challenges, while considering the consequences of decisions one makes in applying these approaches. Finally, we analyze the benefits of high-density sliding semilandmark approaches over landmark-only studies for capturing shape across diverse organisms and discuss the promise of these approaches for the study of organismal form.

Efficacy of diffeomorphic surface matching and 3D geometric morphometrics for taxonomic discrimination of Early Pleistocene hominin mandibular molars

Morphometric assessments of the dentition have played significant roles in hypotheses relating to taxonomic diversity among extinct hominins. In this regard, emphasis has been placed on the statistical appraisal of intraspecific variation to identify morphological criteria that convey maximum discriminatory power. Three-dimensional geometric morphometric (3D GM) approaches that utilize landmarks and semi-landmarks to quantify shape variation have enjoyed increasingly popular use over the past twenty-five years in assessments of the outer enamel surface (OES) and enamel-dentine junction (EDJ) of fossil molars. Recently developed diffeomorphic surface matching (DSM) methods that model the deformation between shapes have drastically reduced if not altogether eliminated potential methodological inconsistencies associated with the a priori identification of landmarks and delineation of semi-landmarks. As such, DSM has the potential to better capture the geometric details that describe tooth shape by accounting for both homologous and non-homologous (i.e., discrete) features, and permitting the statistical determination of geometric correspondence. We compare the discriminatory power of 3D GM and DSM in the evaluation of the OES and EDJ of mandibular permanent molars attributed to Australopithecus africanus, Paranthropus robustus and early Homo sp. from the sites of Sterkfontein and Swartkrans. For all three molars, classification and clustering scores demonstrate that DSM performs better at separating the A. africanus and P. robustus samples than does 3D GM. The EDJ provided the best results. P. robustus evinces greater morphological variability than A. africanus. The DSM assessment of the early Homo molar from Swartkrans reveals its distinctiveness from either australopith sample, and the "unknown" specimen from Sterkfontein (Stw 151) is notably more similar to Homo than to A. africanus.

A fly in a tube: Macroevolutionary expectations for integrated phenotypes

Phenotypic integration and modularity are ubiquitous features of complex organisms, describing the magnitude and pattern of relationships among biological traits. A key prediction is that these relationships, reflecting genetic, developmental, and functional interactions, shape evolutionary processes by governing evolvability and constraint. Over the last 60 years, a rich literature of research has quantified patterns of integration and modularity across a variety of clades and systems. Only recently has it become possible to contextualize these findings in a phylogenetic framework to understand how trait integration interacts with evolutionary tempo and mode. Here, we review the state of macroevolutionary studies of integration and modularity, synthesizing empirical and theoretical work into a conceptual framework for predicting the effects of integration on evolutionary rate and disparity: a fly in a tube. While magnitude of integration is expected to influence the potential for phenotypic variation to be produced and maintained, thus defining the shape and size of a tube in morphospace, evolutionary rate, or the speed at which a fly moves around the tube, is not necessarily controlled by trait interactions. Finally, we demonstrate this reduced disparity relative to the Brownian expectation for a given rate of evolution with an empirical example: the avian cranium.

Semi-supervised determination of pseudocryptic morphotypes using observer-free characterizations of anatomical alignment and shape

Accurate, quantitative characterization of complex shapes is recognized as a key methodological challenge in biology. Recent development of automated three‐dimensional geometric morphometric protocols (auto3dgm) provides a promising set of tools to help address this challenge. While auto3dgm has been shown to be useful in characterizing variation across clades of morphologically very distinct mammals, it has not been adequately tested in more problematic cases where pseudolandmark placement error potentially confounds interpretation of true shape variation. Here, we tested the sensitivity of auto3dgm to the degree of variation and various parameterization settings using a simulation and three microCT datasets that characterize mammal tooth crown morphology as biological examples. The microCT datasets vary in degree of apparent morphological differentiation, with two that include grossly similar morphospecies and one that includes two laboratory strains of a single species. Resulting alignments are highly sensitive to the number of pseudolandmarks used to quantify shapes. The degree to which the surfaces were downsampled and the apparent degree of morphological differentiation across the dataset also influenced alignment repeatability. We show that previous critiques of auto3dgm were based on poorly parameterized alignments and suggest that sample‐specific sensitivity analyses should be added to any research protocol including auto3dgm. Auto3dgm is a useful tool for studying samples when pseudolandmark placement error is small relative to the true differences between specimens. This method therefore represents a promising avenue forward in morphometric studies at a wide range of scales, from samples that differ by a single genetic locus to samples that represent multiple phylogenetically diverse clades.