Measurement error in geometric morphometrics

Unexpectedly uneven distribution of functional trade-offs explains cranial morphological diversity in carnivores

Functional trade-offs can affect patterns of morphological and ecological evolution as well as the magnitude of morphological changes through evolutionary time. Using morpho-functional landscape modelling on the cranium of 132 carnivore species, we focused on the macroevolutionary effects of the trade-off between bite force and bite velocity. Here, we show that rates of evolution in form (morphology) are decoupled from rates of evolution in function. Further, we found theoretical morphologies optimising for velocity to be more diverse, while a much smaller phenotypic space was occupied by shapes optimising force. This pattern of differential representation of different functions in theoretical morphological space was highly correlated with patterns of actual morphological disparity. We hypothesise that many-to-one mapping of cranium shape on function may prevent the detection of direct relationships between form and function. As comparatively only few morphologies optimise bite force, species optimising this function may be less abundant because they are less likely to evolve. This, in turn, may explain why certain clades are less variable than others. Given the ubiquity of functional trade-offs in biological systems, these patterns may be general and may help to explain the unevenness of morphological and functional diversity across the tree of life.

Shape variation and sex differences of the adult human mandible evaluated by geometric morphometrics

In cases of osseous defects, knowledge of the anatomy, and its age and sex-related variations, is essential for reconstruction of normal morphology. Here, we aimed at creating a 3D atlas of the human mandible in an adult sample using dense landmarking and geometric morphometrics. We segmented 50 male and 50 female mandibular surfaces from CBCT images (age range: 18.9-73.7 years). Nine fixed landmarks and 510 sliding semilandmarks were digitized on the mandibular surface, and then slid by minimizing bending energy against the average shape. Principal component analysis extracted the main patterns of shape variation. Sexes were compared with permutation tests and allometry was assessed by regressing on the log of the centroid size. Almost 49 percent of shape variation was described by the first three principal components. Shape variation was related to width, height and length proportions, variation of the angle between ramus and corpus, height of the coronoid process and inclination of the symphysis. Significant sex differences were detected, both in size and shape. Males were larger than females, had a higher ramus, more pronounced gonial angle, larger inter-gonial width, and more distinct antegonial notch. Accuracy of sexing based on the first two principal components in form space was 91 percent. The degree of edentulism was weakly related to mandibular shape. Age effects were not significant. The resulting atlas provides a dense description of mandibular form that can be used clinically as a guide for planning surgical reconstruction.

Investigating temporal bone variation of colonial populations from St-Lawrence Valley, Quebec: A 3D geometric morphometric approach

OBJECTIVES

In Quebec, genetic and genealogical research are used to document migratory events and family structures since colonial times, because bioarchaeological analysis is limited by poor skeletal preservation. This article aims to fill this gap by exploring past population structure in the St-Lawrence Valley from the French (1683-1760) and British (1760-1867) regimes using morphological variation of well-preserved temporal bones.

MATERIALS AND METHODS

3D geometric morphometrics shape data from seven populations (five Catholics of French descent and two Protestants of British descent; n = 214) were collected from temporal bones. Using Procrustes distances and both MANOVA and Discriminant Function Analysis, morphological differences were measured to calculate affinities patterns among populations. Shape variations were explored with between-group analysis, Mahalanobis distances and quantified by means of Fst estimates using Relethford-Blangero analysis.

RESULTS

Despite strong affinities between all Catholic cemeteries, all show divergent morphological regional diversity -especially Montreal and the fortified villages dedicated to its defense. Montreal exhibits low increase in morphological variance over three centuries. As our results show no morphological differences between the Catholic and the Protestant cemeteries in Montreal, this fact may highlight the potential presence of Irish or admixed individuals in Montreal cemeteries after the British takeover.

DISCUSSION

Patterns of morphological diversity highlighted that French colonists did not equally contribute to the descendant populations as reflected by significant interregional variation. Although historical records show that French and English-speaking populations did not tend to admix, morphological affinities between Protestants and Catholics in the beginning of the industrial era in Montreal could reflect the genetic contribution of Catholic Irish migrants.

RESEARCH HIGHLIGHTS

All Catholic cemeteries display distinct morphologies, highlighting differential contributions from French colonists and founder effects, which have increased regional differences. Montreal Catholic (French descent) and Protestant (English colonists) cemeteries show significant morphological affinities at the beginning of the industrial era. The Irish migration following the British conquest may explain morphological similarities observed between Catholic and Protestant cemeteries.

Breaking the Law: Is It Correct to Use the Converse Bergmann Rule in Ceroglossus chilensis? An Overview Using Geometric Morphometrics

The converse Bergmann's rule is a pattern of body size variation observed in many ectothermic organisms that contradicts the classic Bergmann's rule and suggests that individuals inhabiting warmer climates tend to exhibit larger body sizes compared to those inhabiting colder environments. Due to the thermoregulatory nature of Bergmann's rule, its application among ectotherms might prove to be more complicated, given that these organisms obtain heat by absorbing it from their habitat. The existence of this inverse pattern therefore challenges the prevailing notion that larger body size is universally advantageous in colder climates. Ceroglossus chilensis is a native Chilean beetle that has the largest latitudinal range of any species in the genus, from 34.3° S to 47.8° S. Within Chile, it continuously inhabits regions extending from Maule to Aysen, thriving on both native and non-native forest species. Beyond their remarkable color variation, populations of C. chilensis show minimal morphological disparity, noticeable only through advanced morphological techniques (geometric morphometrics). Based on both (1) the "temperature-size rule", which suggests that body size decreases with increasing temperature, and (2) the reduced resource availability in high-latitude environments that may lead to smaller body sizes, we predict that C. chilensis populations will follow the converse Bergmann's rule. Our results show a clear converse pattern to the normal Bergmann rule, where smaller centroid sizes were found to be measured in the specimens inhabiting the southern areas of Chile. Understanding the prevalence of the converse Bergmann's rule for ectotherm animals and how often this rule is broken is of utmost importance to understand the underlying mechanisms allowing organisms to adapt to different environments and the selective pressures they face.

Fine Structure of the Mouthparts of Three Tomicus Beetles Co-Infecting Pinus yunnanensis in Southwestern China with Some Functional Comments

Tomicus yunnanensis, T. brevipilosus, and T. minor are the most economically significant pests of Pinus yunnanensis in Southwestern China. Chemical and physical factors play critical roles in diverse biological activities. Here, we describe the fine structure of the adult mouthparts of these three Tomicus species using scanning and transmission electron microscopy. We identified three types of mandibular shapes, which determine their biomechanical properties, their ability to process food, and their preferred foraging locations on tree trunks. Eleven types of sensilla were discernible, including sensilla basiconica (Sb.1-2), sensilla twig basiconica (Stb.1-3), sensilla coeloconica (Sco), sensilla chaetica (Sch.1-2), sensilla trichoidea (Str.1-2), and sensilla digitiformia (Sdi). Each basiconic sensillum occurs on the palpal tips and is innervated by 2-6 dendrites. Sb.1 are gustatory receptors, Sb.2 are olfactory receptors, and the three other sensilla have dual taste and mechanical functions. Sco, Sch, and Str are mechanoreceptors. Sdi are mechanical vibration receptions, given that they are innervated by one dendrite with numerous dendritic branches into the nonporous cuticle. No significant differences among the sexes or species were identified; however, intraspecific variability in the number of Stb.3 and Sdi sensilla was evident. These results will aid future studies of Tomicus beetle behaviors.

Mapping sexual dimorphism signal in the human cranium

The study of sexual dimorphism in human crania has important applications in the fields of human evolution and human osteology. Current, the identification of sex from cranial morphology relies on manual visual inspection of identifiable anatomical features, which can lead to bias due to user's expertise. We developed a landmark-based approach to automatically map the sexual dimorphism signal on the human cranium. We used a sex-known sample of 228 individuals from different geographical locations to identify which cranial regions are most sexually dimorphic taking into account shape, form and size. Our results, which align with standard protocols, show that glabellar and supraciliary regions, the mastoid process and the nasal region are the most sexually dimorphic traits (with an accuracy of 73%). The accuracy increased to 77% if they were considered together. Surprisingly the occipital external protuberance resulted to be not sexually dimorphic but mainly related to variations in size. Our approach here applied could be expanded to map other variable signals on skeletal morphology.

A geometric morphometric analysis of variation in Australian frog ilia and taxonomic interpretations

Anurans including frogs and toads exhibit an ilium that is often regarded as taxonomically diagnostic. The ilium, one of the three paired bones that make up the pelvic girdle, has been important in the fossil record for identifying anuran morphotypes. Osteological collections for Australian frogs are rare in herpetological museums, and skeletonizing whole-bodied specimens requires destroying soft tissue morphology which is valuable to anuran specialists working on living species. Computed tomography scans provide the opportunity to study anuran osteology without the loss of soft tissues. Our study, based on microcomputed tomography scans of extant Australian frogs from the public repository Morphosource and from museum collections focuses on the morphological differences between Australian frogs at the familial and generic levels using geometric morphometrics to compare the diagnostic shape of the ilium. Principal component analysis (PCA) and canonical variate analysis (CVA) were conducted to assess differences in the ilium between supraspecific groups of Australian frogs. The canonical variates analysis accurately predicted group membership (i.e., the correct family) with up to 76.2% success for cross-validated predictions and 100% of original group predictions. While the sample was limited to familial and generic level analyses, our research shows that ilial morphology in Australian frogs is taxonomically informative. This research provides a guide for identifying Australian anurans, including fossils, as well as new information relevant to considerations about their phylogenetic relationships, and the potential use of the fossil record to enhance efforts to conserve threatened living frog species.

Is shape in the eye of the beholder? Assessing landmarking error in geometric morphometric analyses on live fish

Geometric morphometrics is widely used to quantify morphological variation between biological specimens, but the fundamental influence of operator bias on data reproducibility is rarely considered, particularly in studies using photographs of live animals taken under field conditions. We examined this using four independent operators that applied an identical landmarking scheme to replicate photographs of 291 live Atlantic salmon (Salmo salar L.) from two rivers. Using repeated measures tests, we found significant inter-operator differences in mean body shape, suggesting that the operators introduced a systematic error despite following the same landmarking scheme. No significant differences were detected when the landmarking process was repeated by the same operator on a random subset of photographs. Importantly, in spite of significant operator bias, small but statistically significant morphological differences between fish from the two rivers were found consistently by all operators. Pairwise tests of angles of vectors of shape change showed that these between-river differences in body shape were analogous across operator datasets, suggesting a general reproducibility of findings obtained by geometric morphometric studies. In contrast, merging landmark data when fish from each river are digitised by different operators had a significant impact on downstream analyses, highlighting an intrinsic risk of bias. Overall, we show that, even when significant inter-operator error is introduced during digitisation, following an identical landmarking scheme can identify morphological differences between populations. This study indicates that operators digitising at least a sub-set of all data groups of interest may be an effective way of mitigating inter-operator error and potentially enabling data sharing.

Molecular and morphometric analyses reveal host-specific cryptic speciation in a mite species, Tetranychus neocaledonicus (Andre, 1933) (Acari: Tetranychidae)

Host- and habitat-induced morphological shape and size variations are common in phytophagous and parasitic taxa. Several integrated morphological and molecular techniques have been commonly used to understand host-induced morpho-cryptic species forms. Compared to other arthropods, cryptic speciation was more common in Acari. This study focused on the host-specific morphological cryptic shape and size variations of Tetranychus neocaledonicus, collected from moringa and cassava hosts. We used geometric morphometric analysis to uncover the shape and size of inter-and intra-spider mite populations, and discovered that host-specific shape and size variations existed in spider mites regardless of sex. Interestingly, there was no phylogenetic signal in spider mites, implying that the morpho-cryptic speciation of T. neocaledonicus is solely based on the host-induced selection. The molecular clock hypothesis was accepted in our CO1 and 18s rRNA phylogeny analyses, and spider mites collected from both hosts were genetically less diverse. We conclude that T. neocaledonicus exhibited morphologically detectable cryptic population diversity in each host but that these populations are evolutionarily young form. Apart from these host-induced variations, we also monitored the impact of the clearing agent (lactic acid) on the shape and size of T. neocaledonicus; from this study, we proved that the clearing agent significantly alters the taxonomically important morphological traits of spider mites irrespective of the mites' sex, as confirmed by multivariate statistical analysis. This is the first study report to investigated the host-induced morphological variations of spider mites and the impact of a clearing agent.

Community-scale relationships between body shape and trophic ecology in tropical demersal marine fish of northeast Brazil

Functional morphology investigates the relationships between morphological characters and external factors, such as environmental, physical and ecological features. Here, we evaluate the functional relationships between body shape and trophic ecology of a tropical demersal marine fish community using geometric morphometrics techniques and modelling, hypothesizing that shape variables could partially explain fish trophic level. Fish were collected over the continental shelf of northeast Brazil (4-9°S). Analysed fish were distributed into 14 orders, 34 families and 72 species. Each individual was photographed in lateral view, and 18 landmarks were distributed along the body. A principal component analysis (PCA) applied on morphometric indices revealed that fish body elongation and fin base shape were the main axes of variation explaining the morphology. Low trophic levels (herbivore and omnivore) are characterized by deep bodies and longer dorsal and anal fin bases, while predators present elongated bodies and narrow fin bases. Fin position (dorsal and anal fins) on the fish body is another important factor contributing to (i) body stability at high velocity (top predators) or (ii) manoeuvrability (low trophic levels). Using multiple linear regression, we verified that 46% of trophic level variability could be explained by morphometric variables, with trophic level increasing with body elongation and size. Interestingly, intermediate trophic categories (e.g., low predators) presented morphological divergence for a given trophic level. Our results, which can likely be expanded to other tropical and nontropical systems, show that morphometric approaches can provide important insights into fish functional characteristics, especially in trophic ecology.

Vitamin D and adolescent idiopathic scoliosis, should we stop the hype? A cross-sectional observational prospective study based on a geometric morphometrics approach

PURPOSE

There is strong evidence supporting the presence of fluctuating asymmetry (FA) in Adolescents with Idiopathic Scoliosis (AIS). Additionally, recent research investigating the relationship between vitamin D and AIS found a relation between them. We hypothesize a negative correlation between FA and vitamin D.

METHODS

We performed a surface scan of the torso of 53 AIS patients, a blood test to measure vitamin D and the radiographic Cobb angle. A correlation analysis between vitamin D and FA was carried out to test our hypothesis, and a regression of vitamin D on 3D shape was performed to observe shape differences between the vitamin D deficiency and insufficiency groups.

RESULTS

There was no correlation between vitamin D and FA. We found a strong negative correlation between vitamin D and the Cobb angle only in the premenarche group (n = 7; r = - 0.92). Differences in shape were observed between the deficiency and insufficiency groups, and that differences were related to the width of the torso, but not the rotation or lateral flexion.

CONCLUSIONS

Our results do not support the massive screening of vitamin D in AIS. Shape analysis revealed differences between the shape of the deficiency and insufficiency groups related to robustness. However, this finding had no relation with the scoliosis characteristics, it just reflected different body composition, and its importance should be explored in future.

Implementation of a personal identification system using alveolar bone images

OBJECTIVE

In recent years, personal identification has been performed using antemortem panoramic X-ray images and postmortem-CT images. Using these, we have developed a personal identification method that focuses on the alveolar bone. This study examined the effectiveness of this method and aimed to implement a reproducible system.

MATERIALS AND METHODS

For personal identification, a total of 633 CT images and panoramic X-ray images belonging to three groups with different conditions were used.　These images were 160 sets in the same person group and 96,820 in the other groups. The similarity of alveolar bone images was calculated using the landmark method of Procrustes analysis. The processes were system implemented and the methodology was validated.

RESULTS

The ability to identify between the same person group and other person groups showed 0.9769 as the area under the curve (AUC: ROC curve). At the cutoff value of 4.978, there was no false rejection rate, but false acceptance rate was slightly higher.

CONCLUSION

This method was useful as a screening method for personal identification. In addition, system implementation was efficient and reduced human error. In the future, we aim to realize a more efficient personal identification method using distortion-corrected images and including auto-detective landmarks using deep learning.

Ecomorphology of toothed whales (Cetacea, Odontoceti) as revealed by 3D skull geometry

Extant odontocetes (toothed whales) exhibit differences in body size and brain mass, biosonar mode, feeding strategies, and diving and habitat adaptations. Strong selective pressures associated with these factors have likely contributed to the morphological diversification of their skull. Here, we used 3D landmark geometric morphometric data from the skulls of 60 out of ~ 72 extant odontocete species and a well-supported phylogenetic tree to test whether size and shape variation are associated with ecological adaptations at an interspecific scale. Odontocete skull morphology exhibited a significant phylogenetic signal, with skull size showing stronger signal than shape. After accounting for phylogeny, significant associations were detected between skull size and biosonar mode, body length, brain and body mass, maximum and minimum prey size, and maximum peak frequency. Brain mass was also strongly correlated with skull shape together with surface temperature and average and minimum prey size. When asymmetric and symmetric components of shape were analysed separately, a significant correlation was detected between sea surface temperature and both symmetric and asymmetric components of skull shape, and between diving ecology and the asymmetric component. Skull shape variation of odontocetes was strongly influenced by evolutionary allometry but most of the associations with ecological variables were not supported after phylogenetic correction. This suggests that ecomorphological feeding adaptations vary more between, rather than within, odontocete families, and functional anatomical patterns across odontocete clades are canalised by size constraints.

Species morphospace boundary revisited through wing phenotypic variations of Antodynerus species (Hymenoptera: Vespidae: Eumeninae) from the Indian subcontinent

The main objective of this study was to investigate the taxonomic significance of wing phenotypic variations (size and shape) for classifying potter wasps. This is the first study investigating the wing size and shape variations, as well as wing asymmetry, sexual dimorphism, wing integration, and phylogenetic signal analysis of all known Antodynerus species from the Indian subcontinent: A. flavescens, A. limbatus, and A. punctatipennis. We used forewings and hindwings for geometric morphometric analysis, and we proved that each species’ wing had unique size and shape variations, as well as significant right–left wing asymmetry and sexual dimorphism across the Antodynerus species, as verified by discriminant function analysis. Wings of Vespidae are longitudinally folded; based on that, we tested two alternative wing modular hypotheses for evaluating the wing integration, using two subsets organization, such as anterior–posterior (AP) and proximal-distal (PD) wing modular organization. We proved that Antodynerus species wings are highly integrated units (RV > 0.5), and we rejected our hypothesis at p < 0.05. The morphospace distribution analysis revealed that each species has its unique morphospace boundary, although they share some level of homoplasy, which suggests to us that we can use wing morphometric traits for Antodynerus species delimitation. In addition, we revealed the phylogenetic signal of Antodynerus species. Surprisingly, we found a shape-related phylogenetic signal in the forewing, and there is no significant (p > 0.05) phylogenetic signal in forewing size, hindwing shape, and size. We observed that the Antodynerus species’ forewing shape is evolutionarily more highly constrained than the hindwing. We found that A. limbatus and A. flavescens with distinct geographical distribution share a similar evolutionary history, while A. punctatipennis evolved independently.

Description of Bothriurus mistral n. sp., the highest-dwelling Bothriurus from the western Andes (Scorpiones, Bothriuridae), using multiple morphometric approaches

We describe Bothriurus mistral n. sp. (Scorpiones, Bothriuridae) from the Chilean north-central Andes of the Coquimbo Region. This is the highest elevational discovery for Bothriurus in the western slopes of the Andes. This species was collected in the Estero Derecho Private Protected Area and Natural Sanctuary as part of the First National Biodiversity Inventory of Chile of the Integrated System for Monitoring and Evaluation of Native Forest Ecosystems (SIMEF). Bothriurus mistral n. sp. is closely related to Bothriurus coriaceus Pocock, 1893, from the lowlands of central Chile. This integrative research includes a combination of traditional morphometrics and geometric morphometric analyses to support the taxonomic delimitation of the species.

Ecomorphology and Morphological Disparity of Caquetaia Kraussii (Perciformes: Cichlidae) in Colombia

Understanding the interspecific morphological variability of Caquetaia kraussii (Perciformes: Cichlidae) between different localities in its distribution range is becoming essential, as this species constitutes a valuable resource for the economy and subsistence of the local human communities where it is endemic in Colombia and Venezuela. In order to develop efficient farming and handling plans for this species, a deep understanding of the factors and mechanisms generating morphological variability is crucial. This study analyzes the morphological variability of C. kraussii by using geometric morphometrics in four localities distributed between the Dique and North channels, which are part of the Bolívar department in Colombia. Likewise, the effect of environmental variables such as temperature (T°), dissolved oxygen (OD) and pH on morphological variability was analyzed using a partial least squares approach. The results show that environmental stress has an influence on ~10% of the body shape of C. kraussii, whereas ~90% of the body shape is not directly influenced by environmental parameters, suggesting an effect from stress related to sexual dimorphism. Similarly, the analyses show shape variation among localities, mainly between populations of lotic environments and those of lentic environments. This morphological disparity seems to be subject to environmental and sexual stresses in the different localities.

Automated landmarking via multiple templates

Manually collecting landmarks for quantifying complex morphological phenotypes can be laborious and subject to intra and interobserver errors. However, most automated landmarking methods for efficiency and consistency fall short of landmarking highly variable samples due to the bias introduced by the use of a single template. We introduce a fast and open source automated landmarking pipeline (MALPACA) that utilizes multiple templates for accommodating large-scale variations. We also introduce a K-means method of choosing the templates that can be used in conjunction with MALPACA, when no prior information for selecting templates is available. Our results confirm that MALPACA significantly outperforms single-template methods in landmarking both single and multi-species samples. K-means based template selection can also avoid choosing the worst set of templates when compared to random template selection. We further offer an example of post-hoc quality check for each individual template for further refinement. In summary, MALPACA is an efficient and reproducible method that can accommodate large morphological variability, such as those commonly found in evolutionary studies. To support the research community, we have developed open-source and user-friendly software tools for performing K-means multi-templates selection and MALPACA.

Testing inter-observer error under a collaborative research framework for studying lithic shape variability

Evaluating error that arises through the aggregation of data recorded by multiple observers is a key consideration in many metric and geometric morphometric analyses of stone tool shape. One of the most common approaches involves the convergence of observers for repeat trails on the same set of artefacts: however, this is logistically and financially challenging when collaborating internationally and/or at a large scale. We present and evaluate a unique alternative for testing inter-observer error, involving the development of 3D printed copies of a lithic reference collection for distribution among observers. With the aim of reducing error, clear protocols were developed for photographing and measuring the replicas, and inter-observer variability was assessed on the replicas in comparison with a corresponding data set recorded by a single observer. Our results demonstrate that, when the photography procedure is standardized and dimensions are clearly defined, the resulting metric and geometric morphometric data are minimally affected by inter-observer error, supporting this method as an effective solution for assessing error under collaborative research frameworks. Collaboration is becoming increasingly important within archaeological and anthropological sciences in order to increase the accessibility of samples, encourage dual-project development between foreign and local researchers and reduce the carbon footprint of collection-based research. This study offers a promising validation of a collaborative research design whereby researchers remotely work together to produce comparable data capturing lithic shape variability.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12520-022-01676-2.

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.

Thirty years of geometric morphometrics: Achievements, challenges, and the ongoing quest for biological meaningfulness

The foundations of geometric morphometrics were worked out about 30 years ago and have continually been refined and extended. What has remained as a central thrust and source of debate in the morphometrics community is the shared goal of meaningful biological inference through a tight connection between biological theory, measurement, multivariate biostatistics, and geometry. Here we review the building blocks of modern geometric morphometrics: the representation of organismal geometry by landmarks and semilandmarks, the computation of shape or form variables via superimposition, the visualization of statistical results as actual shapes or forms, the decomposition of shape variation into symmetric and asymmetric components and into different spatial scales, the interpretation of various geometries in shape or form space, and models of the association between shape or form and other variables, such as environmental, genetic, or behavioral data. We focus on recent developments and current methodological challenges, especially those arising from the increasing number of landmarks and semilandmarks, and emphasize the importance of thorough exploratory multivariate analyses rather than single scalar summary statistics. We outline promising directions for further research and for the evaluation of new developments, such as "landmark-free" approaches. To illustrate these methods, we analyze three-dimensional human face shape based on data from the Avon Longitudinal Study of Parents and Children (ALSPAC).

An Overview of Interlocation Sexual Shape Dimorphism in Caquetaia kraussi (Perciformes: Cichlidae) A Geometric Morphometric Approach

C. kraussii is an endemic fish species from Colombia and Venezuela and represents a valuable food resource for local human communities. Due to its economic importance, the management and captive breeding of this species are of special interest. However, the anatomical similarities between sexes have been a problem for visual identification. It is also important to indicate that C. kraussii has cryptic morphological behavior between sexes, a topic that has been one of the main problems for the implementation of management plans. The following research studied individuals from three different localities along the Canal del Dique, Bolívar Department in Colombia, in which the body shape of C. kraussii was analyzed using geometric morphometric analysis. The analyses detected the presence of intralocality sexual dimorphism in two of the three localities analyzed, showing a low morphological variability among males, presenting conserved body shape, as well as a greater morphological disparity among females. This sexual shape dimorphism may be associated with the environmental variation among different locations. These results suggest the presence of two evolutionary forces acting asymmetrically between the sexes of C. kraussii, with males mostly subject to sexual selection pressure, while females are mainly subject to environmental pressures.

Morphological Stasis in Time? A Triatoma brasiliensis brasiliensis Study Using Geometric Morphometrics in the Long Run

Simple Summary

Triatomines are vector insects capable of transmitting the protozoan that causes Chagas disease, thus representing a health risk in several countries, especially in Central and South America. Triatoma brasiliensis brasiliensis, the main triatomine vector in northeastern Brazil, needs frequent monitoring as it is able to colonize various natural and artificial ecotopes as well as to infest domiciles. This research uses geometric morphometrics as a tool to evaluate changes in the morphology and analyze a large temporal dataset of 102 years of collections of T. b. brasiliensis. Finding novelty results which indicate a morphological stasis in the morphology.

Abstract

Triatoma brasiliensis brasiliensis Neiva, 1911 is one of the most important vectors of Chagas disease in the Brazilian semiarid regions in the north-east. The risk imposed by T. b. brasiliensis to the human populations, due to frequent invasions and/or colonization of the domiciles, demands constant monitoring and control actions as well as an understanding of its evolutionary process. In this context, the following research studies the pattern of shape adaptation over time using a large dataset from 102 years of specimen collections in order to identify the morphological plasticity of this vector in Brazil. This dataset was analyzed using geometric morphometrics tools and the timescale was divided into eight different groups, containing specimens from 1912 to 2014. Geometric morphometrics analysis showed an interesting morphological stasis in the wing shape of T. b. brasiliensis, which allowed us to understand the high capacity of adaptation to changes in climate condition through time, and the invasive status which Triatoma species have around the world. Moreover, these results showed novel findings as an interesting phenotypic pattern, with no modifications in more than 100 years, leading us to understand the shape evolution in Triatominae as a vector species of diseases.

Prediction Method of Aeroengine Rotor Assembly Errors Based on a Novel Multi-Axis Measuring and Connecting Mechanism

The aeroengine industry has set strict upper limits for assembly errors in rotor-connecting processes, because assembly errors significantly affect aeroengine stability. Applications of multi-axis mechanisms have the potential to solve the low efficiency of traditional manual connection processes. However, multiple error sources are simultaneously introduced. Thus, an accurate prediction method of rotor assembly error considering multiple error sources is of vital importance, by which the applicability of the new mechanism to rotors can be tested. In this study, a new prediction method for rotor assembly errors is proposed based on the use of a novel multi-axis measuring and connecting mechanism. First, the error propagation among the rotor errors, measurement errors, mechanism errors, and mounting errors is analyzed. Second, reasonable characterization models for these error sources are established using homogeneous transformation matrices. Third, based on the abovementioned error models, a new rotor assembly error prediction algorithm is constructed. It is highly consistent with the actual connection processes. Finally, verification experiments are conducted. The experimental results show that deviation rates of the average values of six types of assembly errors relative to the predictions are all lower than 14%. The proposed prediction method has acceptable accuracy and practical significance.

Mandible shape variation and feeding biomechanics in minks

European and American minks are very similar in ecology, behavior and morphology. Both species hunt terrestrial vertebrates and aquatic prey, but the American mink is a more generalist predator which, among other factors, allows it to outcompete the European mink in areas where it has been introduced. We used 3D geometric morphometrics and estimates of muscle mechanical advantage to assess the degree of variation in mandibular morphology, and to determine whether such variation reflects dietary differences between the two species. The three main axes of variation represented interspecific differences, a common allometric trajectory between species and sexes, and the interspecific effect of sexual size dimorphism, with males having overall stronger bites than females. Differences in mandible shape and biomechanical parameters suggest that American minks are better equipped for preying on terrestrial vertebrates, while the features seen in European mink could be related to tougher prey, fish capture, or both. Additionally, within each species, the larger specimens of each sex present indicators of a higher percentage of terrestrial prey in their diet. These results indicate a low potential dietary overlap between both species, suggesting that factors other than prey competition may have a role in the decline of the European mink.

Thyroid hormone shapes craniofacial bones during postembryonic zebrafish development

Changing the shape of craniofacial bones can profoundly alter ecological function, and understanding how developmental conditions sculpt skeletal phenotypes can provide insight into evolutionary adaptations. Thyroid hormone (TH) stimulates metamorphosis and regulates skeletal morphogenesis across vertebrates. To assess the roles of this hormone in sculpting the craniofacial skeleton of a non-metamorphic vertebrate, we tested zebrafish for developmental periods of TH-induced craniofacial shape change. We analyzed shapes of specific bones that function in prey detection, capture and processing. We quantified these elements from late-larval through adult stages under three developmental TH profiles. Under wild-type conditions, each bone progressively grows allometrically into a mature morphology over the course of postembryonic development. In three of the four bones, TH was required to sculpt an adult shape: hypothyroidism inhibited aspects of shape change, and allowed some components of immature shape to be retained into adulthood. Excess developmental TH stimulated aspects of precocious shape change leading to abnormal morphologies in some bones. Skeletal features with functional importance showed high sensitivities to TH, including the transformator process of the tripus, the mandibular symphysis of the lower jaw, the scutiform lamina of the hyomandibula, and the anterior arm of the pharyngeal jaw. In all, we found that TH is necessary for shaping mature morphology of several essential skeletal elements; this requirement is particularly pronounced during larval development. Altered TH titer leads to abnormal morphologies with likely functional consequences, highlighting the potential of TH and downstream pathways as targets for evolutionary change.

Human semicircular canal form: Ontogenetic changes and variation of shape and size

The semicircular canals (SCCs) transduce angular acceleration of the head into neuronal signals, and their morphology has been used to infer function. Once formed, the bony labyrinth, that surrounds the canals, is tightly regulated and has a very low bone turnover. However, relaxed postnatal inhibition of bone remodelling later in ontogeny may allow for some organised adjustments of shape and size or for greater stochastic variation. In the present study, we test the hypotheses that after birth, the shape and size of the bony canal changes or becomes more variable, or both. We study microCT scans of human perinatal and adult temporal bones using a combination of geometric morphometric analysis and cross-sectional measures. Results revealed marginal differences of size (<5%), of cross-sectional shape and of measurement variability. Geometry of the three canals together and their cross-sectional areas were, however, indistinguishable between perinates and adults. These mixed findings are indicative of diminutive levels of relaxed inhibition superimposed over a constrained template of SCC morphology.

Using virtual reality for anatomical landmark annotation in geometric morphometrics

To study the shape of objects using geometric morphometrics, landmarks are oftentimes collected digitally from a 3D scanned model. The expert may annotate landmarks using software that visualizes the 3D model on a flat screen, and interaction is achieved with a mouse and a keyboard. However, landmark annotation of a 3D model on a 2D display is a tedious process and potentially introduces error due to the perception and interaction limitations of the flat interface. In addition, digital landmark placement can be more time-consuming than direct annotation on the physical object using a tactile digitizer arm. Since virtual reality (VR) is designed to more closely resemble the real world, we present a VR prototype for annotating landmarks on 3D models. We study the impact of VR on annotation performance by comparing our VR prototype to Stratovan Checkpoint, a commonly used commercial desktop software. We use an experimental setup, where four operators placed six landmarks on six grey seal (Halichoerus grypus) skulls in six trials for both systems. This enables us to investigate multiple sources of measurement error. We analyse both for the configuration and for single landmarks. Our analysis shows that annotation in VR is a promising alternative to desktop annotation. We find that annotation precision is comparable between the two systems, with VR being significantly more precise for one of the landmarks. We do not find evidence that annotation in VR is faster than on the desktop, but it is accurate.

Wing morphometrics as a tool for the identification of forensic important Lucilia spp. (Diptera: Calliphoridae)

Blow flies of the genera Lucilia Robineau-Desvoidy (Diptera: Calliphoridae) are considered forensically important species across several regions of the world. Due to the similarity of adults, especially females, the usual methods based on morphology or even molecular techniques can experience some limitations; therefore, alternative or supportive tools are required. Recently, the landmark-based geometric morphometric analysis has been applied to discriminate many insects on genus and species level. Herein, we focus on wing morphometric analysis as a tool in classifying five species of Lucilia; three species from Thailand - L. cuprina (Wiedemann, 1830), L. porphyrina (Walker, 1856) and L. sinensis Aubertin, 1933; and two species from Switzerland - L. caesar (Linnaeus, 1758) and L. illustris (Meigen, 1826). Canonical variate analysis of 233 right wings showed four overlapping clusters of L. cuprina, L. sinensis, L. caesar, and L. illustris with one distinct cluster of L. porphyrina. Eighty-eight to 100 percent of correct classification was achieved, with an UPGMA dendrogram analysis revealing clear-cut branch and sub-branch of five species determined. Results from this study suggested that wing morphometric analysis is a useful tool for the identification of adult Lucilia spp.

Skull morphological variation in a British stranded population of false killer whale (Pseudorca crassidens): a three-dimensional geometric morphometric approach

The false killer whale (Pseudorca crassidens (Owen, 1846)) is a globally distributed delphinid that shows geographical differentiation in its skull morphology. We explored cranial morphological variation in a sample of 85 skulls belonging to a mixed sex population stranded in the Moray Firth, Scotland, in 1927. A three-dimensional digitizer (Microscribe 2GX) was used to record 37 anatomical landmarks on the cranium and 25 on the mandible to investigate size and shape variation and to explore sexual dimorphism using geometric morphometric. Males showed greater overall skull size than females, whereas no sexual dimorphism could be identified in cranial and mandibular shape. Allometric skull changes occurred in parallel for both males and females, supporting the lack of sexual shape dimorphism for this particular sample. Also, fluctuating asymmetry did not differ between crania of males and females. This study confirms the absence of sexual shape dimorphism and the presence of a sexual size dimorphism in this false killer whale population.

How can directional and fluctuating asymmetry help in the prognosis of scoliosis along the course of the condition?

Fluctuating asymmetry (FA) is an indicator of developmental instability referred to random deviations from mean asymmetry. That average asymmetry is the directional asymmetry (DA), which, in the particular case of adolescent idiopathic scoliosis (AIS), corresponds to a right thoracic and left lumbar curves. Investigating the presence of FA and DA in AIS has never been done, and it is a key element of the pathophysiology of the scoliotic condition. Thirty-six X-rays of patients with AIS were digitized and analysed using Geometric Morphometric analyses to test for both statistical effects. The individual FA score for each patient was calculated using Procrustes ANOVA and a methodology based on the components of shape was used to estimate the individual DA score. DA is a stronger effect than FA (2.12 to 1), as it has been found in other clinical conditions. The individual DA score, with an effect size of 0.58, is a better predictor of the Cobb angle than FA score. The methodology presented in this paper to estimate DA score is a valid approach in the study of asymmetries in AIS. FA should be correlated in future studies with environmental covariates to serve as a variable in the medical prognosis, while DA will serve as a good predictor of the Cobb angle during the course of the condition, avoiding the abuse of X-rays. This potential use of DA should be tested on 3D shape due to the three-dimensional clinical presentation of AIS.

Can morphotaxa be assessed with photographs? Estimating the accuracy of two-dimensional cranial geometric morphometrics for the study of threatened populations of African monkeys

The classification of most mammalian orders and families is under debate and the number of species is likely greater than currently recognized. Improving taxonomic knowledge is crucial, as biodiversity is in rapid decline. Morphology is a source of taxonomic knowledge, and geometric morphometrics applied to two dimensional (2D) photographs of anatomical structures is commonly employed for quantifying differences within and among lineages. Photographs are informative, easy to obtain, and low cost. 2D analyses, however, introduce a large source of measurement error when applied to crania and other highly three dimensional (3D) structures. To explore the potential of 2D analyses for assessing taxonomic diversity, we use patas monkeys (Erythrocebus), a genus of large, semi-terrestrial, African guenons, as a case study. By applying a range of tests to compare ventral views of adult crania measured both in 2D and 3D, we show that, despite inaccuracies accounting for up to one-fourth of individual shape differences, results in 2D almost perfectly mirror those in 3D. This apparent paradox might be explained by the small strength of covariation in the component of shape variance related to measurement error. A rigorous standardization of photographic settings and the choice of almost coplanar landmarks are likely to further improve the correspondence of 2D to 3D shapes. 2D geometric morphometrics is, thus, appropriate for taxonomic comparisons of patas ventral crania. Although it is too early to generalize, our results corroborate similar findings from previous research in mammals, and suggest that 2D shape analyses are an effective heuristic tool for morphological investigation of small differences.

Cranial shape variation in mink: Separating two highly similar species

European and American minks (Mustela lutreola and Neovison vison, respectively) are very similar in their ecology, behavior, and morphology. However, the American mink is a generalist predator and seems to adapt better to anthropized environments, allowing it to outcompete the European mink in areas where it has been introduced, threatening the survival of the native species. To assess whether morphological differences may be contributing to the success of the American mink relative to the European mink, we analyzed shape variation in the cranium of both species using 3D geometric morphometrics. A set of 38 landmarks and 107 semilandmarks was used to study shape variation between and within species, and to assess how differences in size factored into that variation. Sexual dimorphism in both size and shape was also studied. Significant differences between species were found in cranial shape, but not in size. Relative to American mink, European mink have a shorter facial region with a rounder forehead and wider orbits, a longer neurocranium with less developed crests and processes, and an antero-medially placed tympanic bullae with an anteriorly expanded cranial border. Within species, size-related sexual dimorphism is highly significant, but sexual dimorphism in shape is only significant in American mink, not in European mink. Additionally, two trends common to both species were discovered, one related to allometric changes and another to sexual size dimorphism. Shape changes related to increasing size can be subdivided into two, probably related, groups: increased muscle force and growth. The first group somewhat parallels the differences between both mink species, while the second group of traits includes an anterodorsal expansion of the face, and the neurocranium shifting from a globous shape in small individuals to a dorsoventrally flattened ellipse in the largest ones. Finally, the sexual dimorphism trend, while also accounting for differences in muscle force, seems to be related to the observed dietary differences between males and females. Overall, differences between species and sexes, and shape changes with increasing size, seem to mainly relate to differences in masticatory-muscle volume and therefore muscle force and bite force, which, in turn, relate to a wider range of potential prey (bigger prey, tougher shells). Thus, muscle force (and dietary range) would be larger in American mink than in European mink, in males than in females, and in larger individuals than in smaller ones.

Measurement error using a SeeMaLab structured light 3D scanner against a Microscribe 3D digitizer

Background

Geometric morphometrics is a powerful approach to capture and quantify morphological shape variation. Both 3D digitizer arms and structured light surface scanners are portable, easy to use, and relatively cheap, which makes these two capturing devices obvious choices for geometric morphometrics. While digitizer arms have been the “gold standard”, benefits of having full 3D models are manifold. We assessed the measurement error and investigate bias associated with the use of an open-source, high-resolution structured light scanner called SeeMaLab against the popular Microscribe 3D digitizer arm.

Methodology

The analyses were based on 22 grey seal (Halichoerus grypus) skulls. 31 fixed anatomical landmarks were annotated both directly using a Microscribe 3D digitizer and on reconstructed 3D digital models created from structured light surface scans. Each skull was scanned twice. Two operators annotated the landmarks, each twice on all the skulls and 3D models, allowing for the investigation of multiple sources of measurement error. We performed multiple Procrustes ANOVAs to compare the two devices in terms of within- and between-operator error, to quantify the measurement error induced by device, to compare between-device error with other sources of variation, and to assess the level of scanning-related error. We investigated the presence of general shape bias due to device and operator.

Results

Similar precision was obtained with both devices. If landmarks that were identified as less clearly defined and thus harder to place were omitted, the scanner pipeline would achieve higher precision than the digitizer. Between-operator error was biased and seemed to be smaller when using the scanner pipeline. There were systematic differences between devices, which was mainly driven by landmarks less clearly defined. The factors device, operator and landmark replica were all statistically significant and of similar size, but were minor sources of total shape variation, compared to the biological variation among grey seal skulls. The scanning-related error was small compared to all other error sources.

Conclusions

As the scanner showed precision similar to the digitizer, a scanner should be used if the advantages of obtaining detailed 3D models of a specimen are desired. To obtain high precision, a pre-study should be conducted to identify difficult landmarks. Due to the observed bias, data from different devices and/or operators should not be combined when the expected biological variation is small, without testing the landmarks for repeatability across platforms and operators. For any study necessitating the combination of landmark measurements from different operators, the scanner pipeline will be better suited. The small scanning-related error indicates that by following the same scanning protocol, different operators can be involved in the scanning process without introducing significant error.

The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote crania

Cranial morphology is remarkably varied in living amniotes and the diversity of shapes is thought to correspond with feeding ecology, a relationship repeatedly demonstrated at smaller phylogenetic scales, but one that remains untested across amniote phylogeny. Using a combination of morphometric methods, we investigate the links between phylogenetic relationships, diet and skull shape in an expansive dataset of extant toothed amniotes: mammals, lepidosaurs and crocodylians. We find that both phylogeny and dietary ecology have statistically significant effects on cranial shape. The three major clades largely partition morphospace with limited overlap. Dietary generalists often occupy clade-specific central regions of morphospace. Some parallel changes in cranial shape occur in clades with distinct evolutionary histories but similar diets. However, members of a given clade often present distinct cranial shape solutions for a given diet, and the vast majority of species retain the unique aspects of their ancestral skull plan, underscoring the limits of morphological convergence due to ecology in amniotes. These data demonstrate that certain cranial shapes may provide functional advantages suited to particular dietary ecologies, but accounting for both phylogenetic history and ecology can provide a more nuanced approach to inferring the ecology and functional morphology of cryptic or extinct amniotes.

Early amphibians evolved distinct vertebrae for habitat invasions

Living tetrapods owe their existence to a critical moment 360-340 million years ago when their ancestors walked on land. Vertebrae are central to locomotion, yet systematic testing of correlations between vertebral form and terrestriality and subsequent reinvasions of aquatic habitats is lacking, obscuring our understanding of movement capabilities in early tetrapods. Here, we quantified vertebral shape across a diverse group of Paleozoic amphibians (Temnospondyli) encompassing different habitats and nearly the full range of early tetrapod vertebral shapes. We demonstrate that temnospondyls were likely ancestrally terrestrial and had several early reinvasions of aquatic habitats. We find a greater diversity in temnospondyl vertebrae than previously known. We also overturn long-held hypotheses centered on weight-bearing, showing that neural arch features, including muscle attachment, were plastic across the water-land divide and do not provide a clear signal of habitat preferences. In contrast, intercentra traits were critical, with temnospondyls repeatedly converging on distinct forms in terrestrial and aquatic taxa, with little overlap between. Through our geometric morphometric study, we have been able to document associations between vertebral shape and environmental preferences in Paleozoic tetrapods and to reveal morphological constraints imposed by vertebrae to locomotion, independent of ancestry.

Evidence of Wing Shape Sexual Dimorphism in Aedes (Stegomyia) albopictus in Mallorca, Spain

The Asian tiger mosquito Aedes albopictus (Skuse, 1894) is a highly invasive species widely distributed on the Spanish Mediterranean coast and the Balearic archipelago. Most studies involving this species in Spain have been focused on surveillance and control methods. However, micro-evolutionary studies for Ae. albopictus in Spain have been traditionally neglected. Morphological diversity could be the result of long-term evolutionary diversification in responses to selective pressures such as temperature, precipitation, food availability, predation, or competition that may influence flight activity, host-seeking, and blood-feeding behavior. Wing geometric morphometric have been used not only to study micro- and macro-evolution in mosquitoes but also in studies of population structuring and sexual dimorphism. Therefore, the main goal of this study was to investigate the wing shape patterns of Ae. albopictus populations to unveil sexual dimorphism that could provide information about their ecology and behavior. Mosquito eggs were collected using oviposition traps at the main campus of the University of the Balearic Islands (Palma de Mallorca, Spain) and reared under laboratory conditions. In order to study wing shape variation patterns in Ae. albopictus males and females, the left wing of each adult mosquito was removed and analyzed based on 18 landmarks. Our results indicated strong levels of sexual dimorphism between Ae. albopictus males and females. Furthermore, according to the cross-validated reclassification test, males were correctly distinguished from females with an accuracy of 84% and females from males 75%. We observed a significant sexual dimorphism in the wing shape patterns of Ae. albopictus when considering different seasonal patterns (spring vs. autumn). Our results suggested that selective pressures may affect males differently to females. Host-seeking, blood-feeding, and oviposition behavior of females may act as a major driver for wing shape sexual dimorphism. These results should be considered for the development of more effective and targeted mosquito control strategies.

Using 2D dental geometric morphometrics to identify modern Perognathus and Chaetodipus specimens (Rodentia, Heteromyidae)

The Heteromyidae (pocket mice and kangaroo rats) are a group of extant small rodents abundant in western North America, as well as in fossil assemblages over the last 20 million years. Two genera of heteromyids, Chaetodipus and Perognathus, share similar tooth morphology and teeth are the primary fossil remains. Previous genetic studies show these extant sister genera likely diverged in the middle Miocene (~16 million years ago); however, the Chaetodipus fossil record starts in the Pleistocene (~2 million years ago). In this study, we asked whether two-dimensional geometric morphometrics on complete dentition and isolated premolars can accurately identify Chaetodipus and Perognathus specimens at the genus and species level. We landmarked the occlusal surface of the upper and lower tooth rows of modern Chaetodipus (n = 83) and Perognathus specimens (n = 80), including 12 of the 26 extant species across the two genera. We ran a canonical variates analysis to investigate whether principal component variation could predict known taxonomic identifications. The morphospace using complete dentition can identify specimens to genus with 90 – 92% accuracy and to species with more variable accuracy. We found an isolated premolar provides sufficient information for genus-level identification (69 – 84% accuracy), but not for species-level identification (26 – 56% accuracy). This morphospace of modern specimens can be used to identify the skeletal remains of Chaetodipus and Perognathus in museum collections, raptor pellets, or middens, to refine our existing knowledge of heteromyid evolutionary history.