Measurement error in geometric morphometrics

Lack of assortative mating might explain reduced phenotypic differentiation where two grasshopper species meet

Hybridization is an evolutionary process with wide‐ranging potential outcomes, from providing populations with important genetic variation for adaptation to being a substantial fitness cost leading to extinction. Here, we focussed on putative hybridization between two morphologically distinct species of New Zealand grasshopper. We collected Phaulacridium marginale and Phaulacridium otagoense specimens from a region where mitochondrial introgression had been detected and where their habitat has been modified by introduced mammals eating the natural vegetation and by the colonization of many non‐native plant species. In contrast to observations in the 1970s, our sampling of wild pairs of grasshoppers in copula provided no evidence of assortative mating with respect to species. Geometric morphometrics on pronotum shape of individuals from areas of sympatry detected phenotypically intermediate specimens (putative hybrids), and the distribution of phenotypes in most areas of sympatry was found to be unimodal. These results suggest that hybridization associated with anthropogenic habitat changes has led to these closely related species forming a hybrid swarm, with random mating. Without evidence of hybrid disadvantage, we suggest a novel hybrid lineage might eventually result from the merging of these two species.

scAnt-an open-source platform for the creation of 3D models of arthropods (and other small objects)

We present scAnt, an open-source platform for the creation of digital 3D models of arthropods and small objects. scAnt consists of a scanner and a Graphical User Interface, and enables the automated generation of Extended Depth Of Field images from multiple perspectives. These images are then masked with a novel automatic routine which combines random forest-based edge-detection, adaptive thresholding and connected component labelling. The masked images can then be processed further with a photogrammetry software package of choice, including open-source options such as Meshroom, to create high-quality, textured 3D models. We demonstrate how these 3D models can be rigged to enable realistic digital specimen posing, and introduce a novel simple yet effective method to include semi-realistic representations of approximately planar and transparent structures such as wings. As a result of the exclusive reliance on generic hardware components, rapid prototyping and open-source software, scAnt costs only a fraction of available comparable systems. The resulting accessibility of scAnt will (i) drive the development of novel and powerful methods for machine learning-driven behavioural studies, leveraging synthetic data; (ii) increase accuracy in comparative morphometric studies as well as extend the available parameter space with area and volume measurements; (iii) inspire novel forms of outreach; and (iv) aid in the digitisation efforts currently underway in several major natural history collections.

Selection for increased tibia length in mice alters skull shape through parallel changes in developmental mechanisms

Bones in the vertebrate cranial base and limb skeleton grow by endochondral ossification, under the control of growth plates. Mechanisms of endochondral ossification are conserved across growth plates, which increases covariation in size and shape among bones, and in turn may lead to correlated changes in skeletal traits not under direct selection. We used micro-CT and geometric morphometrics to characterize shape changes in the cranium of the Longshanks mouse, which was selectively bred for longer tibiae. We show that Longshanks skulls became longer, flatter, and narrower in a stepwise process. Moreover, we show that these morphological changes likely resulted from developmental changes in the growth plates of the Longshanks cranial base, mirroring changes observed in its tibia. Thus, indirect and non-adaptive morphological changes can occur due to developmental overlap among distant skeletal elements, with important implications for interpreting the evolutionary history of vertebrate skeletal form.

Unraveling the Morphological Variation of Triatoma infestans in the Peridomestic Habitats of Chuquisaca Bolivia: A Geometric Morphometric Approach

Morphometrics has been used on Triatomines, a well-known phenotypically variable insect, to understand the process of morphological plasticity and infer the changes of this phenomenon. The following research was carried out in two regions of the inter-Andean valleys and two Chaco regions of Chuquisaca-Bolivia. Triatoma infestans adults were collected from the peridomestic (pens and chicken coops) along a geographic gradient in order to evaluate the morphological differentiation between groups and their pattern of sexual shape dimorphism. Geometric morphometric methods were applied on the wings and heads of T. infestans. The main findings include that we proved sexual dimorphism in heads and wings, determined the impact of environmental factors on size and shape and validated the impact of nutrition on head shape variation. These results show that geometric morphometric procedures can be used to provide key insight into the biological adaptation of T. infestans on different biotic (nutrition) and abiotic (environment) conditions, which could serve in understanding and evaluating infestation processes and further vector control programs.

Optimizing digitalization effort in morphometrics

Quantifying phenotypes is a common practice for addressing questions regarding morphological variation. The time dedicated to data acquisition can vary greatly depending on methods and on the required quantity of information. Optimizing digitization effort can be done either by pooling datasets among users, by automatizing data collection, or by reducing the number of measurements. Pooling datasets among users is not without risk since potential errors arising from multiple operators in data acquisition prevent combining morphometric datasets. We present an analytical workflow to estimate within and among operator biases and to assess whether morphometric datasets can be pooled. We show that pooling and sharing data requires careful examination of the errors occurring during data acquisition, that the choice of morphometric approach influences amount of error, and that in some cases pooling data should be avoided. The demonstration is based on a worked example (Sus scrofa teeth) using a combinations of 18 morphometric approaches and datasets for which we identified and quantified several potential sources of errors in the workflow. We show that it is possible to estimate the analytical power of a study using a small subset of data to select the best morphometric protocol and to optimize the number of variables necessary for analysis. In particular, we focus on semi-landmarks, which often produce an inflation of variables in contrast to the number of available observations use in statistical testing. We show how the workflow can be used for optimizing digitization efforts and provide recommendations for best practices in error management.

Freshwater Testate Amoebae (Arcellinida) Response to Eutrophication as Revealed by Test Size and Shape Indices

We review the potential for applying traits-based approaches to freshwater testate amoeba, a diverse protist group that are abundant in lakes and are valuable ecological indicators. We investigated the efficacy of geometric morphometric analysis to define Arcellinida test size and shape indices that could summarize freshwater testate amoeba community dynamics along a temporal gradient of eutrophication in Loch Leven, Scotland (United Kingdom). A cluster analysis of test size and shape indices yielded three clusters, each dominated by a single shape: elongate, spherical and ovoid. When plotted stratigraphically, we observed increases in spherical tests, decreases in elongate tests and shrinking of test size coeval with eutrophication in Loch Leven. Decreases in the elongate cluster may reflect benthic conditions with reduced oxygen levels, while increases in the spherical cluster are likely associated with an expanding macrophyte community that promoted pelagic and epibiotic life habits. Shrinking of test size may be a stress response to eutrophication and/or warming temperatures. Tracking community dynamics using test size and shape indices was found to be as effective as using species-based approaches to summarize key palaeolimnological changes, with the added benefits of being free from taxonomic bias and error. The approach thus shows significant potential for future studies of aquatic community change in nutrient impacted lakes.

The intraspecific diversity of tooth morphology in the large-spotted catshark Scyliorhinus stellaris: insights into the ontogenetic cues driving sexual dimorphism

Teeth in sharks are shed and replaced throughout their lifetime. Morphological dental changes through ontogeny have been identified in several species and have been correlated with shifts in diet and the acquisition of sexual maturity. However, these changes were rarely quantified in detail along multiple ontogenetic stages, which makes it difficult to infer the developmental processes responsible for the observed plasticity. In this work, we use micro-computed tomography and 3D geometric morphometrics to describe and analyze the tooth size and shape diversity across three ontogenetic stages (hatchling, juvenile, and sexually mature) in the large-spotted catshark Scyliorhinus stellaris (Linnaeus, 1758). We first describe the intra-individual variation of tooth form for each sex at each ontogenetic stage. We provide a tooth morphospace for palatoquadrate and Meckelian teeth and identify dental features, such as relative size and number of cusps, involved in the range of variation of the observed morphologies. We then use these shape data to draw developmental trajectories between ontogenetic stages and for each tooth position within the jaw to characterize ontogenetic patterns of sexual dimorphism. We highlight the emergence of gynandric heterodonty between the juvenile and mature ontogenetic stages, with mature females having tooth morphologies more similar to juveniles' than mature males that display regression in the number of accessory cusps. From these data, we speculate on the developmental processes that could account for such developmental plasticity in S. stellaris.

How Exactly Did the Nose Get That Long? A Critical Rethinking of the Pinocchio Effect and How Shape Changes Relate to Landmarks

The Pinocchio effect has long been discussed in the literature on geometric morphometrics. It denotes the observation that Procrustes superimposition tends to distribute shape changes over many landmarks, even though a different superimposition may exist for the same landmark configurations that concentrates changes in just one or a few landmarks. This is widely seen as a flaw of Procrustes methods. Visualizations illustrating the Pinocchio effect use a comparison of the same pair of shapes superimposed in two different ways: in a resistant-fit superimposition that concentrates the shape difference in just one or a few landmarks, and in Procrustes superimposition, which distributes differences over most or all landmarks. Because these superimpositions differ only in the non-shape aspects of size, position and orientation, they are equivalent from the perspective of shape analysis. Simulation studies of the Pinocchio effect usually generate data, either single pairs or larger samples of landmark configurations, in a particular superimposition so that differences occur mostly or exclusively at just one or a few landmarks, but no steps are taken to remove variation from size, position and orientation. When these configurations are then compared with Procrustes-superimposed data, differences appear and are attributed to the Pinocchio effect. Overall, it is ironic that all manifestations of the Pinocchio effect in one way or another rely on differences in the non-shape properties of position and orientation. Rigorous thinking about shape variation and careful choice of visualization methods can prevent confusion over this issue.

Australian Rodents Reveal Conserved Cranial Evolutionary Allometry across 10 Million Years of Murid Evolution

AbstractAmong vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes.

Effect of altitude on wing metric variation of Aedes aegypti (Diptera: Culicidae) in a region of the Colombian Central Andes

In mosquitoes of medical importance, wing shape and size can vary with altitude, an aspect that can influence dispersion and, consequently, their vector capacity. Using geometric morphometry analysis, Aedes aegypti wing size and shape variation of males and females was studied in four altitudes in the second-smallest department in Colombia: 1,200 m (Tebaida), 1,400 m (Armenia), 1,500 m (Calarcá), and 1,700 m (Filandia). Wing shape in males (P < 0.001) and females (P < 0.001) was significantly different through the altitudinal gradient; in turn, wing size in males followed the altitudinal gradient males (R² = 0.04946, P = 0.0002), females (R² = 0.0011, P = 0.46). Wing allometry for males (P < 0.001) and females (P < 0.001) was significant. Likewise, the shape and size of the wings of males (P < 0.001) and females (P < 0.001) had significant fluctuating asymmetry. It is concluded that, in a small scale with an altitudinal variation of 500 meters, it is detected that the size and shape of the wings varied in A. aegypti, main vector the agents that cause dengue, chikungunya, and Zika. The fluctuating asymmetry is present in the individuals studied and could be associated with environmental effects caused by vector control campaigns present in some sampling locations.

Plasticity and evolutionary convergence in the locomotor skeleton of Greater Antillean Anolis lizards

Plasticity can put evolution on repeat if development causes species to generate similar morphologies in similar environments. Anolis lizards offer the opportunity to put this role of developmental plasticity to the test. Following colonization of the four Greater Antillean islands, Anolis lizards independently and repeatedly evolved six ecomorphs adapted to manoeuvring different microhabitats. By quantifying the morphology of the locomotor skeleton of 95 species, we demonstrate that ecomorphs on different islands have diverged along similar trajectories. However, microhabitat-induced morphological plasticity differed between species and did not consistently improve individual locomotor performance. Consistent with this decoupling between morphological plasticity and locomotor performance, highly plastic features did not show greater evolvability, and plastic responses to microhabitat were poorly aligned with evolutionary divergence between ecomorphs. The locomotor skeleton of Anolis may have evolved within a subset of possible morphologies that are highly accessible through genetic change, enabling adaptive convergence independently of plasticity.

Do we need the third dimension? Quantifying the effect of the z-axis in 3D geometric morphometrics based on sailfin silversides (Telmatherinidae)

This study investigated the impact of the third dimension in geometric morphometrics (GM) using sailfin silversides (Telmatherinidae) from the Malili Lakes of Sulawesi (Indonesia). The three morphospecies of the monophyletic "roundfin" radiation are laterally compressed and vary in shape traits. The results of 2D and 3D GM were compared and quantified to discuss the advantages and disadvantages of both methods for closely related species and their sexes. This approach focused on the head because it is far more complex and three-dimensionally structured than the trunk or the caudal region. The results revealed no significant benefit concerning repeatability and measurement error in 3D GM compared to 2D GM. The z-axis contributed substantially to the variance of the 3D data set but was irrelevant for discrimination of species and sexes in the approach. Limited gain in information was contrasted by substantially higher effort for 3D compared to the 2D analyses. The study concluded that 2D GM is the more efficient shape analysis approach for discriminating roundfins. Broader studies are needed to test which of the two methods is more efficient in distinguishing laterally compressed fishes in general. For future studies, due to the high investment required, this study recommends carefully evaluating the necessity of 3D GM. If in doubt, this study suggests testing for congruence between 2D and 3D GM with a subsample and consequently applying 2D GM in the case of high congruence.

Testing repeatability, measurement error and species differentiation when using geometric morphometrics on complex shapes: a case study of Patagonian lizards of the genus Liolaemus (Squamata: Liolaemini)

The repeatability of findings is the key factor behind scientific reliability, and the failure to reproduce scientific findings has been termed the ‘replication crisis’. Geometric morphometrics is an established tool in evolutionary biology. However, different operators (and/or different methods) could act as large sources of variation in the data obtained. Here, we investigated inter-operator error in geometric morphometric protocols on complex shapes of Liolaemus lizards, as well as measurement error in three taxa varying in their difficulty of digitalization. We also examined the potential for these protocols to discriminate among complex shapes in closely related species. We found a wide range of inter-operator error, contributing between 19.5% and 60% to the total variation. Moreover, measurement error increased with the complexity of the quantified shape. All protocols were able to discriminate between species, but the use of more landmarks did not imply better performance. We present evidence that complex shapes reduce repeatability, highlighting the need to explore different sources of variation that could lead to such low repeatability. Lastly, we suggest some recommendations to improve the repeatability and reliability of geometric morphometrics results.

Measuring the Inter and Intraspecific Sexual Shape Dimorphism and Body Shape Variation in Generalist Ground Beetles in Russia

Ground beetles in multiple species vary greatly in the expression of the shape on sexual traits, resulting in a sexual shape dimorphism as a consequence of sexual selection differences. The present research focuses on the study of inter and intrasexual sexual shape dimorphism of two generalist genera of ground beetles Pterostichus and Carabus. Geometric morphometric methods were applied to five generalist species of ground beetles Carabus exaratus, C. granulatus, Pterostichus melanarius, P. niger, and P. oblongopunctatus and several multivariate analyses were applied for two different traits, abdomen and elytra. Three of the five species analyzed showed high levels of sex-based shape dimorphism. However, the most generalist species, P. melanarius and P. oblongopunctatus, did not evidence shape-based sexual dimorphism differentiation in both of the analyzed traits, as statistically confirmed based on the permutation of pairwise comparison of the Mahalanobis distances of a sex–species classifier. It is generally known that environmental stress in natural populations can affect the fitness expression, principally related to sexual fecundity, being that this pattern is more evident in non-generalist species. In our results, the contrary pattern was found, with the absence of sexual shape dimorphism for two of the three generalist species analyzed. On the other hand, the interspecies shape variation was clearly identified using principal component analysis of both of the analyzed traits. Finally, this research is the first to analyze the relationship between sexual shape dimorphism in Russian ground beetles, evidencing the lack of understanding of the mechanism underlying the sexual dimorphism, especially in species living in extreme environments.

Advanced procedures for skull sex estimation using sexually dimorphic morphometric features

This paper introduces an automated method for estimating sex from cranial sex diagnostic traits by extracting and evaluating specialized morphometric features from the glabella, the supraorbital ridge, the occipital protuberance, and the mastoid process. The proposed method was developed and evaluated using two European population samples, a Czech sample comprising 170 crania reconstructed from anonymized CT scans and a Greek sample of 156 crania from the Athens Collection. It is based on a fully automatic algorithm applied on 3D models for extracting sex diagnostic morphometric features which are further processed by computer vision and machine learning algorithms. Classification accuracy was evaluated in a population specific and a population generic 2-way cross-validation scheme. Population-specific accuracy for individual morphometric features ranged from 78.5 to 96.7%, whereas population generic correct classification ranged from 71.7 to 90.8%. Combining all sex diagnostic traits in multi-feature sex estimation yielded correct classification performance in excess of 91% for the entire sample, whereas the sex of about three fourths of the sample could be determined with 100% accuracy according to posterior probability estimates. The proposed method provides an efficient and reliable way to estimate sex from cranial remains, and it offers significant advantages over existing methods. The proposed method can be readily implemented with the skullanalyzer computer program and the estimate_sex.m GNU Octave function, which are freely available under a suitable license.

Assessment of Shape Variation Patterns in Triatoma infestans (Klug 1834) (Hemiptera: Reduviidae: Triatominae): A First Report in Populations from Bolivia

The morphological variations of four populations of geographically isolated Triatoma infestans located in the area of inter-Andean valleys and Chaco of Chuquisaca, Bolivia, were evaluated. Fifty-three females and sixty-one males were collected in the peri-domicile and analyzed with geometric morphometrics tools to study the patterns of the head and wing shape variation. The principal component analysis and canonical variate analysis revealed morphological variations between the populations studied, which were then confirmed by the permutation test of the differences between populations using Mahalanobis and Procustes distances. The multivariate regression analysis shows that the centroid size influences the shape of the heads and wings. T. infestans of the inter-Andean valleys are longer in the head and wings compared to the population of the Chaco. We propose that the geometric shape variation may be explained by geographical changes in climatic conditions, peri-domiciliar habitats, food source quality, and the use of insecticides.

Developmental instability is associated with estrogenic endocrine disruption in the Chilean native fish species, Trichomycterus areolatus

Endocrine disrupting compounds (EDCs) are widespread contaminants that alter the normal functioning of the endocrine system. While they cause dysfunctions in essential biological processes, it is unclear whether EDCs also impact developmental stability. In the present study, we investigated the occurrence of estrogenic endocrine disrupting compounds in a small watershed of south-central Chile impacted by anthropogenic activities. Then, we assessed their relationship with internal levels of estrogenic active compounds and fluctuating asymmetry (FA), a proxy of developmental stability in organisms with bilateral symmetry, in a native fish species (Trichomycterus areolatus). Yeast estrogenic screen assays were performed to measure estrogenic activity in river sediments and in male fish tissues collected from 17 sites along the Chillán watershed, and geometric morphometrics used to estimate fluctuating asymmetry based on the shapes of 248 fish skulls. Estrogenic activity was detected both in sediments and male fish tissues at concentrations of up to 1005 ng and 83 ng 17β-estradiol equivalent/kg dw, respectively. No significant correlation was found between the two. However, fish tissue estrogenicity, water temperature and dissolved oxygen explained >80% of the FA population variation. By showing a significant relationship between estrogenic activity and FA of T. areolatus, our results indicate that developmental stability can be altered by estrogenic endocrine disruption, and that FA can be a useful indicator of sub-lethal stress in T. areolatus populations.

Morphometric approach to 3D soft-tissue craniofacial analysis and classification of ethnicity, sex, and age

Background

The application of three-dimensional scan models offers a useful resource for studying craniofacial variation. The complex mathematical analysis for facial point acquisition in three-dimensional models has made many craniofacial assessments laborious.

Method

This study investigates three-dimensional (3D) soft-tissue craniofacial variation, with relation to ethnicity, sex and age variables in British and Irish white Europeans. This utilizes a geometric morphometric approach on a subsampled dataset comprising 292 scans, taken from a Liverpool-York Head Model database. Shape variation and analysis of each variable are tested using 20 anchor anatomical landmarks and 480 sliding semi-landmarks.

Results

Significant ethnicity, sex, and age differences are observed for measurement covering major aspects of the craniofacial shape. The ethnicity shows subtle significant differences compared to sex and age; even though it presents the lowest classification accuracy. The magnitude of dimorphism in sex is revealed in the facial, nasal and crania measurement. Significant shape differences are also seen at each age group, with some distinct dimorphic features present in the age groups.

Conclusions

The patterns of shape variation show that white British individuals have a more rounded head shape, whereas white Irish individuals have a narrower head shape. White British persons also demonstrate higher classification accuracy. Regarding sex patterns, males are relatively larger than females, especially in the mouth and nasal regions. Females presented with higher classification accuracy than males. The differences in the chin, mouth, nose, crania, and forehead emerge from different growth rates between the groups. Classification accuracy is best for children and senior adult age groups.

Modern morphometrics and the study of population differences: Good data behind clever analyses and cool pictures?

The study of phenotypic variation in time and space is central to evolutionary biology. Modern geometric morphometrics is the leading family of methods for the quantitative analysis of biological forms. This set of techniques relies heavily on technological innovation for data acquisition, often in the form of 2D or 3D digital images, and on powerful multivariate statistical tools for their analysis. However, neither the most sophisticated device for computerized imaging nor the best statistical test can produce accurate, robust and reproducible results, if it is not based on really good samples and an appropriate use of the 'measurements' extracted from the data. Using examples mostly from my own work on mammal craniofacial variation and museum specimens, I will show how easy it is to forget these most basic assumptions, while focusing heavily on analytical and visualization methods, and much less on the data that generate potentially powerful analyses and visually appealing diagrams.

Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification

Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data acquisition sources: specimen presentation, imaging devices, interobserver variation, and intraobserver variation. We then evaluated the impact of those errors on linear discriminant analysis-based classifications of the five species using recent specimens of known species affinity and fossil specimens of unknown species affinity. Results indicate that data acquisition error can be substantial, sometimes explaining >30% of the total variation among datasets. Comparisons of datasets digitized by different individuals exhibit the greatest discrepancies in landmark precision, and comparison of datasets photographed from different presentation angles yields the greatest discrepancies in species classification results. All error sources impact statistical classification to some extent. For example, no two landmark dataset replicates exhibit the same predicted group memberships of recent or fossil specimens. Our findings emphasize the need to mitigate error as much as possible during geometric morphometric data collection. Though the impact of measurement error on statistical fidelity is likely analysis-specific, we recommend that all geometric morphometric studies standardize specimen imaging equipment, specimen presentations (if analyses are 2D), and landmark digitizers to reduce error and subsequent analytical misinterpretations.

Sources of variation in the 3dMDface and Vectra H1 3D facial imaging systems

As technology advances and collaborations grow, our ability to finely quantify and explore morphological variation in 3D structures can enable important discoveries and insights into clinical, evolutionary, and genetic questions. However, it is critical to explore and understand the relative contribution of potential sources of error to the structures under study. In this study, we isolated the level of error in 3D facial images attributable to four sources, using the 3dMDface and Vectra H1 camera systems. When the two camera systems are used separately to image human participants, this analysis finds an upper bound of error potentially introduced by the use of the 3dMDface or Vectra H1 camera systems, in conjunction with the MeshMonk registration toolbox, at 0.44 mm and 0.40 mm, respectively. For studies using both camera systems, this upper bound increases to 0.85 mm, on average, and there are systematic differences in the representation of the eyelids, nostrils, and mouth by the two camera systems. Our results highlight the need for careful assessment of potential sources of error in 3D images, both in terms of magnitude and position, especially when dealing with very small measurements or performing many tests.

Does sediment composition sort kinorhynch communities? An ecomorphological approach through geometric morphometrics

Ecomorphology studies the relationship between organisms' morphology and environment features. To better understand whether the shape of the body and the appendages involved in the movement is correlated to sediment composition in meiofaunal organisms, we study the evolved morphological adaptations to environment in selected taxa of the phylum Kinorhyncha: the allomalorhagid families Dracoderidae and Pycnophyidae, and the cyclorhagid genus Echinoderes. The selected taxa include the most diverse groups of Kinorhyncha worldwide, representing the 75.5% of the total phylum diversity. Widened, plump bodies and lateral terminal spines may be adaptive for species living in coarse, more heterogeneous sediments, as they could maintain a more powerful musculature to actively displace the sediment grains applying a greater force. Conversely, slender, vermiform bodies and lateral terminal spines would represent an adaptation of species inhabiting fine, more homogeneous sediments where there would not be much need to exert a high force to displace the sediment particles, and a more vermiform shape would even favour the burrowing of the animal through the smaller interstices. The studied kinorhynch taxa would also be adapted to the higher velocity of the sea-water and the intense erosion and transportation of heterogeneous sediments by possessing more robust bodies, avoiding getting laid off substratum under these conditions. These findings provide evolutionary evidence that body shape in the studied kinorhynch groups is adapted to environment.

How flat can a horse be? Exploring 2D approximations of 3D crania in equids

Quantitative analyses of morphological variation using geometric morphometrics are often performed on 2D photos of 3D structures. It is generally assumed that the error due to the flattening of the third dimension is negligible. However, despite hundreds of 2D studies, few have actually tested this assumption and none has done it on large animals, such as those typically classified as megafauna. We explore this issue in living equids, focusing on ventral cranial variation at both micro- and macro-evolutionary levels. By comparing 2D and 3D data, we found that size is well approximated, whereas shape is more strongly impacted by 2D inaccuracies, as it is especially evident in intra-specific analyses. The 2D approximation improves when shape differences are larger, as in macroevolution, but even at this level precise inter-individual similarity relationships are altered. Despite this, main patterns of sex, species and allometric variation in 2D were the same as in 3D, thus suggesting that 2D may be a source of 'noise' that does not mask the main signal in the data. However, the picture that emerges from this and other recent studies on 2D approximation of 3D structures is complex and any generalization premature. Morphometricians should therefore test the appropriateness of 2D using preliminary investigations in relation to the specific study questions in their own samples. We discuss whether this might be feasible using a reduced landmark configuration and smaller samples, which would save time and money. In an exploratory analysis, we found that in equids results seem robust to sampling, but become less precise and, with fewer landmarks, may slightly overestimate 2D inaccuracies.

Landmark-based homologous multi-point warping approach to 3D facial recognition using multiple datasets

Over the years, neuroscientists and psychophysicists have been asking whether data acquisition for facial analysis should be performed holistically or with local feature analysis. This has led to various advanced methods of face recognition being proposed, and especially techniques using facial landmarks. The current facial landmark methods in 3D involve a mathematically complex and time-consuming workflow involving semi-landmark sliding tasks. This paper proposes a homologous multi-point warping for 3D facial landmarking, which is verified experimentally on each of the target objects in a given dataset using 500 landmarks (16 anatomical fixed points and 484 sliding semi-landmarks). This is achieved by building a template mesh as a reference object and applying this template to each of the targets in three datasets using an artificial deformation approach. The semi-landmarks are subjected to sliding along tangents to the curves or surfaces until the bending energy between a template and a target form is minimal. The results indicate that our method can be used to investigate shape variation for multiple datasets when implemented on three databases (Stirling, FRGC and Bosphorus).

The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids

Hybridization and polyploidization are important evolutionary processes whose impacts range from the alteration of gene expression and phenotypic variation to the triggering of asexual reproduction. We investigated fishes of the Cobitis taenia-elongatoides hybrid complex, which allowed us to disentangle the direct effects of both processes, due to the co-occurrence of parental species with their diploid and triploid hybrids. Employing morphological, ecological, and RNAseq approaches, we investigated the molecular determinants of hybrid and polyploid forms. In contrast with other studies, hybridization and polyploidy induced relatively very little transgressivity. Instead, Cobitis hybrids appeared intermediate with a clear effect of genomic dosing when triploids expressed higher similarity to the parent contributing two genome sets. This dosage effect was symmetric in the germline (oocyte gene expression), interestingly though, we observed an overall bias toward C. taenia in somatic tissues and traits. At the level of individual genes, expression-level dominance vastly prevailed over additivity or transgressivity. Also, trans-regulation of gene expression was less efficient in diploid hybrids than in triploids, where the expression modulation of homoeologs derived from the "haploid" parent was stronger than those derived from the "diploid" parent. Our findings suggest that the apparent intermediacy of hybrid phenotypes results from the combination of individual genes with dominant expression rather than from simple additivity. The efficiency of cross-talk between trans-regulatory elements further appears dosage dependent. Important effects of polyploidization may thus stem from changes in relative concentrations of trans-regulatory elements and their binding sites between hybridizing genomes. Links between gene regulation and asexuality are discussed.

3-Dimensional facial expression recognition in human using multi-points warping

Background

Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in 3D by machine remains a challenge in computer vision. This is due to the current challenges facing facial data acquisition in 3D; such as lack of homology and complex mathematical analysis for facial point digitization. This study proposes facial expression recognition in human with the application of Multi-points Warping for 3D facial landmark by building a template mesh as a reference object. This template mesh is thereby applied to each of the target mesh on Stirling/ESRC and Bosphorus datasets. The semi-landmarks are allowed to slide along tangents to the curves and surfaces until the bending energy between a template and a target form is minimal and localization error is assessed using Procrustes ANOVA. By using Principal Component Analysis (PCA) for feature selection, classification is done using Linear Discriminant Analysis (LDA).

Result

The localization error is validated on the two datasets with superior performance over the state-of-the-art methods and variation in the expression is visualized using Principal Components (PCs). The deformations show various expression regions in the faces. The results indicate that Sad expression has the lowest recognition accuracy on both datasets. The classifier achieved a recognition accuracy of 99.58 and 99.32% on Stirling/ESRC and Bosphorus, respectively.

Conclusion

The results demonstrate that the method is robust and in agreement with the state-of-the-art results.

Automatic landmarking as a convenient prerequisite for geometric morphometrics. Validation on cone beam computed tomography (CBCT)- based shape analysis of the nasal complex

Manual landmarking is used in several manual and semi-automated prediction guidelines for approximation of the nose. The manual placement of landmarks may, however, render the analysis less repeatable due to observer subjectivity and, consequently, have an impact on the accuracy of the human facial approximation. In order to address this subjectivity and thereby improve facial approximations, we are developing an automated three-dimensional (3D) method based on an automatic dense landmarking procedure using non-rigid surface registration. The aim of this study was to validate the automatic landmarking method by comparing the intra-observer errors (INTRA-OE) and inter-observer errors (INTER-OE) between automatic and manual landmarking. Cone beam computed tomography (CBCT) scans of adult South Africans were selected from the Oral and Dental Hospital, University of Pretoria, South Africa. In this study, the validation of the automatic landmarking was performed on 20 3D surfaces. INTRA-OE and INTER-OE were analyzed by registering 41 craniometric landmarks from 10 hard-tissue surfaces and 21 capulometric landmarks from 10 soft-tissue surfaces of the same individuals. Absolute precision of the landmark positioning (both on the samples as well as the template) was assessed by calculating the measurement error (ME) for each landmark over different observers. Systematic error (bias) and relative random error (precision) was further quantified through repeated measures ANOVA (ANOVA-RM). The analysis showed that the random component of the ME in landmark positioning between the automatic observations were on average on par with the manual observations, except for the soft-tissue landmarks where automatic landmarking showed lower ME compared to manual landmarking. No bias was observed within the craniometric landmarking methods, but some bias was observed for capulometric landmarking. In conclusion, this research provides a first validation of the precision and accuracy of the automatic placement of landmarks on 3D hard- and soft-tissue surfaces and demonstrates its utilization as a convenient prerequisite for geometric morphometrics based shape analysis of the nasal complex.

Tissue preservation can affect geometric morphometric analyses: a case study using fish body shape

In geometric morphometrics, the extent of variation attributable to non-biological causes (i.e. measurement error) is sometimes overlooked. The effects of this variation on downstream statistical analyses are also largely unknown. In particular, it is unclear whether specimen preservation induces substantial variation in shape and whether such variation affects downstream statistical inference. Using a combination of empirical fish body shape data and realistic simulations, we show that preservation introduces substantial artefactual variation and significant non-random error (i.e. bias). Most changes in shape occur when fresh fish are frozen and thawed, whereas a smaller change in shape is observed when frozen and thawed fish are fixed in formalin and transferred to ethanol. Surprisingly, we also show that, in our case, preservation produces only minor effects on three downstream analyses of shape variation: classification using canonical variate analysis, permutation tests of differences in means and computations of differences in mean shape between groups. Even mixing of differently preserved specimens has a relatively small effect on downstream analyses. However, we suggest that mixing fish with different preservation should still be avoided and discuss the conditions in which this practice might be justified.

Variability, agreement and reliability of MRI knee landmarks

Surface mesh reconstructions of bones are often required to define landmark-based coordinate systems, regions of interest and morphological features when studying the soft tissues of the knee from MRI scans. This study reports the variability, agreement and reliability of osseous landmarks to better understand their downstream effects. Fifteen landmarks were defined on the distal femur and twelve on the proximal tibia. Surface meshes were created from twenty right knee MRI scans with a mean subject age of 30.9 years. A single observer identified landmarks on all twenty knees, while three observers repeated the observations three times on a subset of eight knees. All observations were aligned to the Procrustes mean shapes. Principal component analysis was used to study inter-subject variability and two-way ANOVA for inter- and intra-observer agreement and reliability. Inter-subject landmark variation ranged from 0.6 to 5.26 mm, while inter- and intra-observer agreement were at most 5.1 and 5.69 mm respectively. Between-observer reliability ranged from 0.07 to 0.98 while within-observer values were between 0.51 and 0.98. Landmarks derived from fitted spheres or circles often performed well, while most others had their poorest agreement or greatest variation limited to only one or two cardinal directions.

The multifactorial nature of beak and skull shape evolution in parrots and cockatoos (Psittaciformes)

Background

The Psittaciformes (parrots and cockatoos) are characterised by their large beaks, and are renowned for their ability to produce high bite forces. These birds also possess a suite of modifications to their cranial architecture interpreted to be adaptations for feeding on mechanically resistant foods, yet the relationship between cranial morphology and diet has never been explicitly tested. Here, we provide a three-dimensional geometric morphometric analysis of the developmental and biomechanical factors that may be influencing the evolution of psittaciformes’ distinctive cranial morphologies.

Results

Contrary to our own predictions, we find that dietary preferences for more- or less- mechanically resistant foods have very little influence on beak and skull shape, and that diet predicts only 2.4% of the shape variation in psittaciform beaks and skulls. Conversely, evolutionary allometry and integration together predict almost half the observed shape variation, with phylogeny remaining an important factor in shape identity throughout our analyses, particularly in separating cockatoos (Cacatuoidea) from the true parrots (Psittacoidea).

Conclusions

Our results are similar to recent findings about the evolutionary trajectories of skull and beak shape in other avian families. We therefore propose that allometry and integration are important factors causing canalization of the avian head, and while diet clearly has an influence on beak shape between families, this may not be as important at driving evolvability within families as is commonly assumed.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1432-1) contains supplementary material, which is available to authorized users.

Measurement error in μCT-based three-dimensional geometric morphometrics introduced by surface generation and landmark data acquisition

Computed-tomography-derived (CT-derived) polymesh surfaces are widely used in geometric morphometric studies. This approach is inevitably associated with decisions on scanning parameters, resolution, and segmentation strategies. Although the underlying processing steps have been shown to potentially contribute artefactual variance to three-dimensional landmark coordinates, their effects on measurement error have rarely been assessed systematically in CT-based geometric morphometric studies. The present study systematically assessed artefactual variance in landmark data introduced by the use of different voxel sizes, segmentation strategies, surface simplification degrees, and by inter- and intra-observer differences, and compared their magnitude to true biological variation. Multiple CT-derived surface variants of the anuran (Amphibia: Anura) pectoral girdle were generated by systematic changes in the factors that potentially influence the surface geometries. Twenty-four landmarks were repeatedly acquired by different observers. The contribution of all factors to the total variance in the landmark data was assessed using random-factor nested permanovas. Selected sets of Euclidean distances between landmark sets served further to compare the variance among factor levels. Landmark precision was assessed by landmark standard deviation and compared among observers and days. Results showed that all factors, except for voxel size, significantly contributed to measurement error in at least some of the analyses performed. In total, 6.75% of the variance in landmark data that mimicked a realistic biological study was caused by measurement error. In this landmark dataset, intra-observer error was the major source of artefactual variance followed by inter-observer error; the factor segmentation contributed < 1% and slight surface simplification had no significant effect. Inter-observer error clearly exceeded intra-observer error in a different landmark dataset acquired by six partly inexperienced observers. The results suggest that intra-observer error can potentially be reduced by including a training period prior to the actual landmark acquisition task and by acquiring landmarks in as few sessions as possible. Additionally, the application of moderate and careful surface simplification and, potentially, also the use of case-specific optimal combinations of automatic local thresholding algorithms and parameters for segmentation can help reduce intra-observer error. If landmark data are to be acquired by several observers, it is important to ensure that all observers are consistent in landmark identification. Despite the significant amount of artefactual variance, we have shown that landmark data acquired from microCT-derived surfaces are precise enough to study the shape of anuran pectoral girdles. Yet, a systematic assessment of measurement error is advisable for all geometric morphometric studies.

Exploratory study of the three-dimensional morphological variation of the jaw associated to teeth loss

PURPOSE

The aim of this study is to evaluate the morphological variability in mandibles with different types of edentulism, comparing the use of traditional morphometrics and tridimensional geometric morphometrics.

METHODS

Traditional morphometrics and geometric morphometrics (GM) exploratory analysis, by principal components (PCs) and PC scores, were performed on a sample of 24 cadaveric hemi mandibles. A digital reconstruction of 3D surfaces of each specimen was obtained by CT scans segmentation. The mandibles were divided in three groups: full dentition (G1), partial edentition (G2) and total edentition (G3). The results of the two methods were compared in relation to the morphological variability determined with each method.

RESULTS

Both methods were consistent in terms of morphological variability between the defined groups. The main shape variations observed were a decrease in mandibular body height, a widening of the cross sectional morphology on the symphysis, a shorten-narrowed Ramus and a deeper sigmoid notch, in the partially or totally edentition groups, compared to the full dentition group.

DISCUSSION

The general patterns of morphological variations associated with edentulism that have been reported in literature could be visualized with GM method, which had not been previously used for this purpose. The GM methods could offer a more detailed definition of shape variations, which is critical in a clinical context. Moreover, GM allowed defining configurations of mean morphologies and an image library with different types of morphological variations.

Effect of preservation on fish morphology over time: Implications for morphological studies

It has long been recognized that the process of preserving biological specimens results in alterations of body shape, though detailed studies examining the degree to which morphological changes occur throughout the preservation process are lacking. We utilize geometric morphometric analyses, an increasingly common tool for examining shape variation in a wide variety of biological disciplines, to examine the effects of formalin and ethanol preservation on the body shape of 10 freshwater fish species over time: from fresh specimens to eight weeks after preservation. We found significant changes in body shape among fresh and formalin fixed specimens. Furthermore, changes in body shape continue to occur after subsequent ethanol preservation. Two fish species collected at multiple localities show significant morphological differences for a limited number of morphometric characters. However, the significance, or lack thereof, often changed inconsistently from one stage of preservation to another. We conclude that morphometric analyses would ideally be performed on fresh specimens. However, recognizing that this is not always feasible, it is important to be aware of the morphometric changes that can occur during preservation.

Host-specific phenotypic variation of a parasite co-introduced with invasive Burmese pythons

Invasive Burmese pythons (Python bivittatus Kuhl, 1820) have introduced a lung parasite, Raillietiella orientalis, (Hett, 1915) from the python's native range in Southeast Asia to its introduced range in Florida, where parasite spillover from pythons to two families and eight genera of native snakes has occurred. Because these novel host species present a diversity of ecological and morphological traits, and because these parasites attach to their hosts with hooks located on their cephalothorax, we predicted that R. orientalis would exhibit substantial, host-associated phenotypic plasticity in cephalothorax shape. Indeed, geometric morphometric analyses of 39 parasites from five host species revealed significant variation among host taxa in R. orientalis cephalothorax shape. We observed differences associated with host ecology, where parasites from semi-aquatic and aquatic snakes exhibited the greatest morphological similarity. Morphological analyses of R. orientalis recovered from invasive pythons, native pit vipers, and terrestrial snakes each revealed distinct shapes. Our results suggest R. orientalis can exhibit significant differences in morphology based upon host species infected, and this plasticity may facilitate infection with this non-native parasite in a wide array of novel squamate host species.

A Step-by-Step Guide for Geometric Morphometrics of Floral Symmetry

This paper provides a step-by-step guide for the morphological analysis of corolla and the decomposition of corolla shape variation into its symmetric and asymmetric components. The shape and symmetric organisation of corolla are key traits in the developmental and evolutionary biology of flowering plants. The various spatial layout of petals can exhibit bilateral symmetry, rotational symmetry or more complex combination of symmetry types. Here, I describe a general landmark-based geometric morphometric framework for the full statistical shape analysis of corolla and exemplify its use with four fully worked out case studies including tissue treatment, imaging, landmark data collection, file formatting, and statistical analyses: (i) bilateral symmetry (Fedia graciliflora), (ii) two perpendicular axes of bilateral symmetry (Erysimum mediohispanicum), (iii) rotational symmetry (Vinca minor), and (iv) combined bilateral and rotational symmetry (Trillium undulatum). The necessary tools for such analyses are not implemented in standard morphometric software and they are therefore provided here as functions running in the R environment. Principal Component Analysis is used to separate symmetric and asymmetric components of variation, respectively, quantifying variation among and within individuals. For bilaterally symmetric flowers, only one component of left-right asymmetric variation is extracted, while flowers with more complex symmetric layout have components of asymmetric variation associated with each symmetry operator implied (e.g., left-right asymmetry and adaxial-abaxial asymmetry). Fundamental information on the genetic, developmental, and environmental determinants of shape variation can be inferred from this decomposition (e.g., directional asymmetry, fluctuating asymmetry) and further exploited to document patterns of canalization, developmental stability, developmental modularity and morphological integration. Even if symmetry and asymmetry are not the primary interest of a study on corolla shape variation, statistical and anatomical arguments support the use of the framework advocated. This didactic protocol will help both morphometricians and non-morphometricians to further understand the role of symmetry in the development, variation and adaptive evolution of flowers.

A 3D characterization method of geometric variation in edentulous mandibles

PURPOSE

The aim of this study was to perform an exploratory analysis of the morphological variations of mandibles at diverse states of edentulousness using tridimensional geometric morphometrics.

METHODS

Twelve cadaveric mandibles were selected and divided in three groups: dentate (G1), partially edentate (G2) and totally edentate (G3). CT scans, segmentation and digital reconstruction of 3D surfaces of each specimen was made. Thirteen landmarks were defined; the measurement error was determined and 3D morphometrics exploratory analysis by principal components (PCs) and PC scores was performed.

RESULTS

The principal shape variations in G2 and G3 compared to G1 can be summarized as follows: (1) decrease in the mid body mandibular height of 24% in G2 and 41% in G3, (2) decrease of symphysis height of 16% in G2 and 37% in G3, (3) a decrease in posterior mandibular height of 30% in both G1 and G2, (4) a deeper sigmoid notch also in both groups and finally (5) a widening of 7.7% in the cross sectional morphology on the symphysis in G3.

CONCLUSIONS

The 3D morphometric methods, combined with surface morphing tools confirmed the main patterns of bone changes in edentulous mandibles, referenced in the literature. The average 3D mandibular morphologies of each edentulousness state group was also defined. These methods could offer more accurate definition of shape variations, which is critical in a clinical context. This study provides clinicians with highlights of 3D morphological mandibular variations at different states of edentulism and not only in 2D projections as they are currently described. The 3D surface model for each group in PDF3D file format, are include in supplementary material.

Geometric morphometric analyses of sexual dimorphism and allometry in two sympatric snakes: Natrix helvetica (Natricidae) and Vipera berus (Viperidae)

The non-venomous grass snake (Natrix helvetica) and the venomous adder (Vipera berus) are two native species that are often found in sympatry in Great Britain and Europe. They occupy partially overlapping ecological niches and prey on small vertebrates, but use different feeding strategies. Here, we investigated the morphologies of grass snakes and adders from Dorset (UK) using two-dimensional geometric morphometrics to assess the degree of sexual dimorphism in size and shape together with the relative impact of allometry and general body dimensions on head shape. Both species showed significant sexual dimorphism in head size, but not in head shape. We found a clear allometric pattern in N. helvetica, whereas allometry in V. berus was generally less pronounced. Body dimensions were strongly correlated with head shape in the grass snake, but not in the adder. The fact that V. berus is venomous appears to explain the lack of allometric patterns and the lack of an association between body dimensions and head shape. The high degree of size dimorphism identified in both species could originate from the advantages of reduced intraspecific competition that are conveyed by a partial differentiation in feeding morphology.

Repeatability, reproducibility and consistency of horse shape data and its association with linearly described conformation traits in Franches-Montagnes stallions

Linear description (LD) of conformation traits was introduced in horse breeding to minimise subjectivity in scoring. However, recent studies have shown that LD traits show essentially the same problems as traditionally scored traits, such as data converging around the mean value with very small standard deviations. To improve the assessment of conformation traits of horses, we investigated the application of the recently described horse shape space model based upon 403 digitised photographs of 243 Franches-Montagnes (FM) stallions and extracted joint angles based on specific landmark triplets. Repeatability, reproducibility and consistency of the resulting shape data and joint angles were assessed with Procrustes ANOVA (Rep) and intra-class correlation coefficients (ICC). Furthermore, we developed a subjective score to classify the posture of the horses on each photograph. We derived relative warp scores (PCs) based upon the digitised photos conducting a principal component analysis (PCA). The PCs of the shapes and joint angles were compared to the posture scores and to the linear description data using linear mixed effect models including significant posture scores as random factors. The digitisation process was highly repeatable and reproducible for the shape (Rep = 0.72–0.99, ICC = 0.99). The consistency of the shape was limited by the age and posture (p < 0.05). The angle measurements were highly repeatable within one digitiser. Between digitisers, we found a higher variability of ICC values (ICC = 0.054–0.92), indicating digitising error in specific landmarks (e.g. shoulder point). The posture scores were highly repeatable (Fleiss’ kappa = 0.713–0.857). We identified significant associations (p_(X²₎ < 0.05) with traits describing the withers height, shoulder length and incline, overall leg conformation, walk and trot step length. The horse shape data and angles provide additional information to explore the morphology of horses and therefore can be applied to improve the knowledge of the genetic architecture of LD traits.

Gene(s) and individual feeding behavior: Exploring eco-evolutionary dynamics underlying left-right asymmetry in the scale-eating cichlid fish Perissodus microlepis

The scale‐eating cichlid fish Perissodus microlepis is a textbook example of bilateral asymmetry due to its left or right‐bending heads and of negative frequency‐dependent selection, which is proposed to maintain this stable polymorphism. The mechanisms that underlie this asymmetry remain elusive. Several studies had initially postulated a simple genetic basis for this trait, but this explanation has been questioned, particularly by reports observing a unimodal distribution of mouth shapes. We hypothesize that this unimodal distribution might be due to a combination of genetic and phenotypically plastic components. Here, we expanded on previous work by investigating a formerly identified candidate SNP associated to mouth laterality, documenting inter‐individual variation in feeding preference using stable isotope analyses, and testing their association with mouth asymmetry. Our results suggest that this polymorphism is influenced by both a polygenic basis and inter‐individual non‐genetic variation, possibly due to feeding experience, individual specialization, and intraspecific competition. We introduce a hypothesis potentially explaining the simultaneous maintenance of left, right, asymmetric and symmetric mouth phenotypes due to the interaction between diverse eco‐evolutionary dynamics including niche construction and balancing selection. Future studies will have to further tease apart the relative contribution of genetic and environmental factors and their interactions in an integrated fashion.