Methods for studying allometry in geometric morphometrics: a comparison of performance

Allometry and phylogenetic divergence: Correspondence or incongruence?

The potential connection between trends of within species variation, such as those of allometric change in morphology, and phylogenetic divergence has been a central topic in evolutionary biology for more than a century, including in the context of human evolution. In this study, I focus on size-related shape change in craniofacial proportions using a sample of more than 3200 adult Old World monkeys belonging to 78 species, of which 2942 specimens of 51 species are selected for the analysis. Using geometric morphometrics, I assess whether the divergence in the direction of static allometries increases in relation to phyletic differences. Because both small samples and taxonomic sampling may bias the results, I explore the sensitivity of the main analyses to the inclusion of more or less taxa depending on the choice of a threshold for the minimum sample size of a species. To better understand the impact of sampling error, I also use randomized subsampling experiments in the largest species samples. The study shows that static allometries vary broadly in directions without any evident phylogenetic signal. This variation is much larger than previously found in ontogenetic trajectories of Old World monkeys, but the conclusion of no congruence with phylogenetic divergence is the same. Yet, the effect of sampling error clearly contributes to inaccuracies and tends to magnify the differences in allometric change. Thus, morphometric research at the boundary between micro- and macro-evolution in primates, and more generally in mammals, critically needs very large and representative samples. Besides sampling error, I suggest other non-mutually exclusive explanations for the lack of correspondence between allometric and phylogenetic divergence in Old World monkeys, and also discuss why directions might be more variable in static compared to ontogenetic trajectories. Even if allometric variation may be a poor source of information in relation to phylogeny, the evolution of allometry is a fascinating subject and the study of size-related shape changes remains a fundamental piece of the puzzle to understand morphological variation within and between species in primates and other animals.

Three-Dimensional Geometric Morphometric Characterization of Facial Sexual Dimorphism in Juveniles

Background: The characterization of facial sexual dimorphic patterns in healthy populations serves as valuable normative data to tailor functionally effective surgical treatments and predict their aesthetic outcomes and to identify dysmorphic facial traits related to hormonal disorders and genetic syndromes. Although the analysis of facial sexual differences in juveniles of different ages has already been investigated, few studies have approached this topic with three-dimensional (3D) geometric morphometric (GMM) analysis, whose interpretation may add important clinical insight to the current understanding. This study aims to investigate the location and extent of facial sexual variations in juveniles through a spatially dense GMM analysis. Methods: We investigated 3D stereophotogrammetric facial scans of 304 healthy Italians aged 3 to 18 years old (149 males, 155 females) and categorized into four different age groups: early childhood (3-6 years), late childhood (7-12 years), puberty (13-15 years), and adolescence (16-18 years). Geometric morphometric analyses of facial shape (allometry, general Procrustes analysis, Principal Component Analysis, Procrustes distance, and Partial Least Square Regression) were conducted to detail sexually dimorphic traits in each age group. Results: The findings confirmed that males have larger faces than females of the same age, and significant differences in facial shape between the two sexes exist in all age groups. Juveniles start to express sexual dimorphism from 3 years, even though biological sex becomes a predictor of facial soft tissue morphology from the 7th year of life, with males displaying more protrusive medial facial features and females showing more outwardly placed cheeks and eyes. Conclusions: We provided a detailed characterization of facial change trajectories in the two sexes along four age classes, and the provided data can be valuable for several clinical disciplines dealing with the craniofacial region. Our results may serve as comparative data in the early diagnosis of craniofacial abnormalities and alterations, as a reference in the planning of personalized surgical and orthodontic treatments and their outcomes evaluation, as well as in several forensic applications such as the prediction of the face of missing juveniles.

Convergent evolution in shape in European lineages of gobies

During their radiation, certain groups of animals evolved significant phenotypic disparity (morphological diversity), enabling them to thrive in diverse environments. Adaptations to the same type of environment can lead to convergent evolution in function and morphology. However, well-documented examples in repeated adaptations of teleost fishes to different habitats, which are not primarily related to trophic specialization, are still scarce. Gobies are a remarkable fish group, exhibiting a great species diversity, morphological variability, and extraordinary ability to colonize very different environments. A variety of lifestyles and body forms evolved also in European lineages of gobies. We conducted two-dimensional geometric morphometric and phylomorphospace analyses in European lineages of gobies and evaluated the extent of convergent evolution in shape associated with adaptation to various habitats. Our analyses revealed the change in shape along the nektonic-cryptobenthic axis, from very slender head and body to stout body and wide head. We showed convergent evolution related to mode of locomotion in the given habitat in four ecological groups: nektonic, hyperbenthic, cryptobenthic, and freshwater gobies. Gobies, therefore, emerge as a highly diversified lineage with unique lifestyle variations, offering invaluable insights into filling of ecomorphological space and mechanisms of adaptation to various aquatic environments with distinct locomotion requirements.

Geometric morphometric analysis of red fox (Vulpes vulpes) skulls using radiometric techniques at three and six months of development

BACKGROUND

Morphological growth naturally progresses with age; however, the rate of growth varies across different parts of an organism, with certain structures developing more rapidly than others. This study aimed to analyze and compare the skull development of red foxes (Vulpes vulpes) during two specific developmental stages: the 3rd and 6th months, which represent distinct growth phases in their early ontogeny.

METHODS

In this study, we aimed to analyze and compare skull development in red foxes (Vulpes vulpes) during two specific post-natal time points: the 3rd and 6th months. Shape analysis was performed using radiographic images of nine red foxes at both the third and sixth months.

RESULTS

Shape differences were observed in the skulls of red foxes (Vulpes vulpes) at these two ages. Our findings confirmed the hypothesis that skull shape changes over time, reflecting distinct morphological adaptations associated with age-related growth. In the measurements at the 3rd month, the neurocranial region exhibited a more distinct and developed structure compared to the facial bones. Toward the 6th month, the skull displayed a thinner and more elongated structure with the further development of the facial bones.

CONCLUSIONS

This difference indicates a period of rapid growth and development in the neurocranial area, suggesting that red foxes experience significant neurological and sensory development early in life. Future studies on skull shape variation across different developmental stages in red foxes can expand on these findings. Age-related morphological studies, such as this one, provide essential baseline data on the natural growth and development of wild species like red foxes. This knowledge is essential for identifying deviations from normal development, which could result from environmental stressors, habitat changes, or malnutrition.

Techno-structural and 3-D geometric morphometric analysis applied for investigating the variability of Holocene unifacial tools in tropical Central Brazil

During the transition from the Pleistocene to the Holocene and in the early Holocene period, hunter-gatherer communities across tropical South America deployed a range of technological strategies to adapt to diverse environmental conditions. This period witnessed a rich tapestry of technological practices, from enduring, widely disseminated tools to local and sporadically utilized technologies, shaping a multifaceted landscape of technological traditions. Lithic technology during this period was mainly marked by localized sourcing of raw materials, the use of multifunctional tools, a variety of projectile point designs, and the frequently utilization of unifacial shaping technology. In tropical Central Brazil, the Itaparica technocomplex, with unique unifacial lithic tools like limaces, is a pivotal innovation from the Late Pleistocene through the Holocene. However, the factors influencing their morphological and structural variability remain largely unexplored, obscuring our understanding of their ergonomics and their role as mediators between humans and tropical environments. This study hypothesizes that the variability observed within and among unifacial tools from the GO-Ni sites in Central Brazil is a result of a combination of factors, including raw material availability and functional and ergonomic requirements. To test this hypothesis, a study of 67 unifacial tools from this region was conducted, employing techno-structural analysis and 3D geometric morphometrics. This approach was designed to precisely quantify tool geometry and uncover their functional potentials. The analysis revealed significant variability within the techno-structural groups, often intersecting with typological classifications. These results indicate that despite their production attributes, unifacially shaped artifacts demonstrate considerable morpho-structural diversity. The study delineated nine distinct techno-structural groups, each suggesting potentially different functional organizations and deviating from conventional typologies. These results indicate that unifacially shaped artifacts, while embodying a novel technological paradigm of production, exhibit a broader spectrum of variation mainly due to different tool functions. The combined approach adopted in this research highlights on the cultural significance of unifacial tools within Paleoamerican technological systems. It suggests probable unique tool concepts specific to the study area, challenges existing classifications, and enriches our comprehension of early lithic technology in South America.

Two methods for geometric morphometric analysis of trichodinids from killifishes

In this study, we compared the efficacy of geometric morphometric techniques, including outlines and landmark-based approaches, to support the differentiation of Trichodina bellottii from three co-occurring killifish species. Both methods were able to differentiate trichodinids from different host species. However, discriminat analyses and MANOVA results based on landmarks had greater accuracy possibly because these analyses only provide information on certain points defined by the researcher, while the analyses based on outlines take into account points with less taxonomic information.

Exploring motion using geometric morphometrics in microscopic aquatic invertebrates: 'modes' and movement patterns during feeding in a bdelloid rotifer model species

BACKGROUND

Movement is a defining aspect of animals, but it is rarely studied using quantitative methods in microscopic invertebrates. Bdelloid rotifers are a cosmopolitan class of aquatic invertebrates of great scientific interest because of their ability to survive in very harsh environment and also because they represent a rare example of an ancient lineage that only includes asexually reproducing species. In this class, Adineta ricciae has become a model species as it is unusually easy to culture. Yet, relatively little is known of its ethology and almost nothing on how it behaves during feeding.

METHODS

To explore feeding behaviour in A. ricciae, as well as to provide an example of application of computational ethology in a microscopic invertebrate, we apply Procrustes motion analysis in combination with ordination and clustering methods to a laboratory bred sample of individuals recorded during feeding.

RESULTS

We demonstrate that movement during feeding can be accurately described in a simple two-dimensional shape space with three main 'modes' of motion. Foot telescoping, with the body kept straight, is the most frequent 'mode', but it is accompanied by periodic rotations of the foot together with bending while the foot is mostly retracted.

CONCLUSIONS

Procrustes motion analysis is a relatively simple but effective tool for describing motion during feeding in A. ricciae. The application of this method generates quantitative data that could be analysed in relation to genetic and ecological differences in a variety of experimental settings. The study provides an example that is easy to replicate in other invertebrates, including other microscopic animals whose behavioural ecology is often poorly known.

Utilizing geometric morphometrics to investigate gene function during organ growth: Insights through the study of beetle horn shape allometry

Static allometry is a major component of morphological variation. Much of the literature on the development of allometry investigates how functional perturbations of diverse pathways affect the relationship between trait size and body size. Often, this is done with the explicit objective to identify developmental mechanisms that enable the sensing of organ size and the regulation of relative growth. However, changes in relative trait size can also be brought about by a range of other distinctly different developmental processes, such as changes in patterning or tissue folding, yet standard univariate biometric approaches are usually unable to distinguish among alternative explanations. Here, we utilize geometric morphometrics to investigate the degree to which functional genetic manipulations known to affect the size of dung beetle horns also recapitulate the effect of horn shape allometry. We reasoned that the knockdown phenotypes of pathways governing relative growth should closely resemble shape variation induced by natural allometric variation. In contrast, we predicted that if genes primarily affect alternative developmental processes, knockdown effects should align poorly with shape allometry. We find that the knockdown effects of several genes (e.g., doublesex, Foxo) indeed closely aligned with shape allometry, indicating that their corresponding pathways may indeed function primarily in the regulation of relative trait growth. In contrast, other knockdown effects (e.g., Distal-less, dachs) failed to align with allometry, implicating these pathways in potentially scaling-independent processes. Our findings moderate the interpretation of studies focusing on trait length and highlight the usefulness of multivariate approaches to study allometry and phenotypic plasticity.

Integrative species delimitation in the common ophiuroid Ophiothrix angulata (Echinodermata: Ophiuroidea): insights from COI, ITS2, arm coloration, and geometric morphometrics

Ophiothrix angulata (Say, 1825) is one of the most common and well-known ophiuroids in the Western Atlantic, with a wide geographic and bathymetric range. The taxonomy of this species has been controversial for a century because of its high morphological variability. Here we integrate information from DNA sequence data, color patterns, and geometric morphometrics to assess species delimitation and geographic differentiation in O. angulata. We found three deeply divergent mtDNA-COI clades (K2P 17.0-27.9%). ITS2 nuclear gene and geometric morphometrics of dorsal and ventral arm plates differentiate one of these lineages, as do integrative species delineation analyses, making this a confirmed candidate species.

Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild-caught populations of Drosophila melanogaster

Identifying the genetic architecture of complex traits is important to many geneticists, including those interested in human disease, plant and animal breeding, and evolutionary genetics. Advances in sequencing technology and statistical methods for genome-wide association studies have allowed for the identification of more variants with smaller effect sizes, however, many of these identified polymorphisms fail to be replicated in subsequent studies. In addition to sampling variation, this failure to replicate reflects the complexities introduced by factors including environmental variation, genetic background, and differences in allele frequencies among populations. Using Drosophila melanogaster wing shape, we ask if we can replicate allelic effects of polymorphisms first identified in a genome-wide association studies in three genes: dachsous, extra-macrochaete, and neuralized, using artificial selection in the lab, and bulk segregant mapping in natural populations. We demonstrate that multivariate wing shape changes associated with these genes are aligned with major axes of phenotypic and genetic variation in natural populations. Following seven generations of artificial selection along the dachsous shape change vector, we observe genetic differentiation of variants in dachsous and genomic regions containing other genes in the hippo signaling pathway. This suggests a shared direction of effects within a developmental network. We also performed artificial selection with the extra-macrochaete shape change vector, which is not a part of the hippo signaling network, but showed a largely shared direction of effects. The response to selection along the emc vector was similar to that of dachsous, suggesting that the available genetic diversity of a population, summarized by the genetic (co)variance matrix (G), influenced alleles captured by selection. Despite the success with artificial selection, bulk segregant analysis using natural populations did not detect these same variants, likely due to the contribution of environmental variation and low minor allele frequencies, coupled with small effect sizes of the contributing variants.

Dimensions of Morphological Integration

Over several generations of evolutionary and developmental biologists, ever since Olson and Miller’s pioneering work of the 1950’s, the concept of “morphological integration” as applied to Gaussian representations $$N(\mu ,\Sigma )$$ N ( μ , Σ ) of morphometric data has been a focus equally of methodological innovation and methodological perplexity. Reanalysis of a century-old example from Sewall Wright shows how some fallacies of distance analysis by correlations can be avoided by careful matching of the distance rosters involved to a different multivariate approach, factor analysis. I reinterpret his example by restoring the information (means and variances) ignored by the correlation matrix, while confirming what Wright called “special size factors” by a different technique, inspection of the concentration matrix $$\Sigma ^{-1}.$$ Σ - 1 . In geometric morphometrics (GMM), data accrue instead as Cartesian coordinates of labelled points; nevertheless, just as in the Wright example, statistical manipulations do better when they reconsider the normalizations that went into the generation of those coordinates. Here information about both $$\mu $$ μ and $$\Sigma ,$$ Σ , the means and the variances/covariances, can be preserved via the Boas coordinates (Procrustes shape coordinates without the size adjustment) that protect the role of size per se as an essential explanatory factor while permitting the analyst to acknowledge the realities of animal anatomy and its trajectories over time or size in the course of an analysis. A descriptive quantity for this purpose is suggested, the correlation of vectorized $$\mu $$ μ against the first eigenvector of $$\Sigma $$ Σ for the Boas coordinates. The paper reanalyzes two GMM data sets from this point of view. In one, the classic Vilmann rodent neurocranial growth data, a description of integration can be aligned with the purposes of evolutionary and developmental biology by a graphical exegesis based mainly in the loadings of the first Boas principal component. There results a multiplicity of morphometric patterns, some homogeneous and others characterized by gradients. In the other, a Vienna data set comprising human midsagittal skull sections mostly sampled along curves, a further integrated feature emerges, thickening of the calvaria, that requires a reparametrization and a modified thin plate spline graphic distinct from the digitized configurations per se. This new GMM protocol fulfills the original thrust of Olson & Miller’s (Evolution 5:325–338, 1951) “$$\rho $$ ρ F-groups,” the alignment of statistical and biological explanatory guidance, while respecting the enormously greater range of morphological descriptors afforded by well-designed landmark/semilandmark configurations.