Testing the accuracy of 3D automatic landmarking via genome-wide association studies

Various advances in 3D automatic phenotyping and landmark-based geometric morphometric methods have been made. While it is generally accepted that automatic landmarking compromises the capture of the biological variation, no studies have directly tested the actual impact of such landmarking approaches in analyses requiring a large number of specimens and for which the precision of phenotyping is crucial to extract an actual biological signal adequately. Here, we use a recently developed 3D atlas-based automatic landmarking method to test its accuracy in detecting QTLs associated with craniofacial development of the house mouse skull and lower jaws for a large number of specimens (circa 700) that were previously phenotyped via a semi-automatic landmarking method complemented with manual adjustment. We compare both landmarking methods with univariate and multivariate mapping of the skull and the lower jaws. We find that most significant SNPs and QTLs are not recovered based on the data derived from the automatic landmarking method. Our results thus confirm the notion that information is lost in the automated landmarking procedure although somewhat dependent on the analyzed structure. The automatic method seems to capture certain types of structures slightly better, such as lower jaws whose shape is almost entirely summarized by its outline and could be assimilated as a 2D flat object. By contrast, the more apparent 3D features exhibited by a structure such as the skull are not adequately captured by the automatic method. We conclude that using 3D atlas-based automatic landmarking methods requires careful consideration of the experimental question.

Morphological characteristic of premature infants’s kidneys with opened Ductus Arteriosis (by the autopsy).

Background. Kidney has protracted nephrogenesis and depend on hemodynamic changes on the highest level in support of natural transition to extrauterine circulation. Fetal communications like Ductus Arteriosus take part in the shunting from the aorta to the pulmonary artery. Increase of this shunting of the blood leads to hyperperfusion with hypoxic changes of some development systems of organs with protracted morphogenesis so like kidneys. Objective. To determine the features of postnatal morphogenesis of the kidneys in premature infants with a gestational age of 25 to 35 weeks on the background of an open ductus arteriosus. Methods. 21 autopsy material premature infant’s kidney which were fixed by 10%-formalin and then were subjected to the standard histological procedures. Slides were stained by hematoxylin and eosin. We used the complex of histological and morphometric methods. There were created 3-demenshional models of kidney’s fragments. We carried out biometrical and statistical analysis. Results. During our research it was determines that the changes of the volume of the functional parenchyma of the kidney and the diameter of the Ductus Arteriosus became in inverse relationship. The wider the duct the smaller the volume of the functional parenchyma because of atrophic and necrotic changes during the late stages of glomerulo- and tubulogenesis. These changes could be distinguished by the quantitative density of development on three germinate layers of the cortex of kidney. Сonclusion. Summing up, it determined the retardation of glomerulogenesis particularly superficial area of the cortex because of the opened Ductus Arteriosus.

Towards accurate and simple morphometric sex differentiation in Bonelli’s Eagle Aquila fasciata nestlings: Interpopulation variations and influence of growth conditions

Morphometric methods of sex differentiation may be cheap, simple, quick, and reliable alternatives to molecular approaches. However, there are still important uncertainties regarding the use of morphometric methods in birds, particularly regarding their applicability to different populations and environmental conditions. Between 2004 and 2019, we sampled 245 Bonelli´s Eagle Aquila fasciata nestlings, 197 from nests in Catalonia (northeastern Spain) and Andalusia (southeastern Spain) and 56 that were partially or totally raised in captivity. Our objective was to develop morphometry-based sexing methods for Bonelli’s Eagle nestlings that can be applied in situ to different subpopulations and growth conditions. We recorded up to nine measures related to nestling body mass, bill, tarsus, and claw length. Tail and wing length were used to control for the age of nestlings, and all individuals were sexed genetically. We found important morphometric differences between the two natural subpopulations. According to our discriminant analyses, body mass and claw length were the most discriminant variables, both in wild and captivity conditions. Differences between sexes were more prominent during the flight feathers’ growing period. Feeding ad libitum in captivity conditions led to larger nestlings and reduced between-sexes differences. We provide different models for sexing Bonelli’s Eagle nestlings that can be applied according to the studied geographic location, growth conditions (wild versus captive), and balance between accuracy and simplicity. Overall, our findings highlight that extrapolating sex discriminant functions to different subpopulations and growth conditions may be risky.

Medfly Phenotypic Plasticity as a Prerequisite for Invasiveness and Adaptation

The hypothesis of this study was that different plant hosts of the medfly Ceratitis capitata may cause variability as a prerequisite for its invasiveness. The main objective was to determine population variability based on medfly wing shape in three favorable medfly host plants (peach, fig and mandarin) from different agroecological growing areas with different pest management practices, and to evaluate phenotypic plasticity as a basis for future expansion into new areas and new hosts. Using geometric morphometric methods across 14 specific landmarks on the medfly wings, 10 populations were tested from infested peach, fig and mandarin fruits, as well as laboratory-grown sterile populations. The studies led to the following main findings: (1) all of the medfly populations that were studied exhibited sexual dimorphism in wing shape; (2) the hosts in which the medfly develops influence wing shape and condition its variability; (3) there is significant variability between laboratory mass-reared sterile and wild individuals in male and female populations; (4) a high phenotypic plasticity of medfly populations was observed along the study sites. Even the low but clearly detected variability between different agroecological conditions and localized variability indicate genotypic stability and high phenotypic plasticity, which can be considered as a prerequisite for medfly invasiveness and dispersal to new areas.

Shape-changing chains for morphometric analysis of 2D and 3D, open or closed outlines

Morphometrics is a multivariate technique for shape analysis widely employed in biological, medical, and paleoanthropological applications. Commonly used morphometric methods require analyzing a huge amount of variables for problems involving a large number of specimens or complex shapes. Moreover, the analysis results are sometimes difficult to interpret and assess. This paper presents a methodology to synthesize a shape-changing chain for 2D or 3D curve fitting and to employ the chain parameters in stepwise discriminant analysis (DA). The shape-changing chain is comprised of three types of segments, including rigid segments that have fixed length and shape, scalable segments with a fixed shape, and extendible segments with constant curvature and torsion. Three examples are presented, including 2D mandible profiles of fossil hominin, 2D leaf outlines, and 3D suture curves on infant skulls. The results demonstrate that the shape-changing chain has several advantages over common morphometric methods. Specifically, it can be applied to a wide range of 2D or 3D profiles, including open or closed curves, and smooth or serrated curves. Additionally, the segmentation of profiles is a flexible and automatic protocol that can consider both biological and geometric features, the number of variables obtained from the fitting results for statistical analysis is modest, and the chain parameters that characterize the profiles can have physical meaning.

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.

Exploratory Analysis of Color Forms’ Variability in the Invasive Asian Lady Beetle Harmonia axyridis (Pallas 1773)

The Asian ladybird (Harmonia axyridis Pallas), native to Asia, is one of the 100 most invasive species in the world and has spread worldwide. This study aimed to characterize color forms of H. axyridis in Croatia and to analyze the variability of wing shape between populations and indicated forms. Geometric morphometric methods were used to analyze a total of 129 left and right wings in males and 126 left and right wings in females of H. axyridis collected from four different sites in Croatia. The results show a significant difference in wing shapes between the studied forms. Each form had its own specific morphotype that likely originated under the influence of genetic changes in the species. This study demonstrates that the use of geometric morphometric analysis is effective in studying the variability in H. axyridis populations. As this study is the first of its kind, for further clarity, it is necessary to conduct additional studies on a larger number of sites and an equal number of individuals of all forms.

Efficiency is Doing Things Right: High Throughput, Automated, 3D Methods in the Modern Era of Otolith Morphometrics

The morphometrics of fish otoliths have been commonly used to investigate population structures and the environmental impacts on ontogeny. These studies can require hundreds if not thousands of otoliths to be collected and processed. Processing these otoliths takes up valuable time, money, and resources that can be saved by automation. These structures also contain relevant information in three dimensions that is lost with 2D morphometric methods from photographic analysis. In this study, the otoliths of three populations of Coho Salmon (Oncorhynchus kisutch) were examined with manual 2D, automated 2D, and automated 3D otolith measurement methods. The automated 3D method was able to detect an 8% difference in average otolith density, while 2D methods could not. Due to the loss of information in the z-axis, and the longer processing time, 2D methods can take up to 100 times longer to reach the same statistical power as automated 3D methods. Automated 3D methods are faster, can answer a wider range of questions, and allow fisheries scientists to automate rather monotonous tasks.

Morphological differentiation of Peromyscus leucopus and P. maniculatus in East Texas

The white-footed deer mouse (Peromyscus leucopus) and the North American deer mouse (P. maniculatus) are widely distributed throughout North America, often with overlapping distributions. These species are believed to be sympatric east of the Balcones fault zone in Texas, but records from natural history collections indicate that P. maniculatus is not common from this region. Given that these two species are notoriously difficult to differentiate morphologically, it is possible that specimens have been incorrectly identified and that P. maniculatus may be rare or not present in East Texas. This study aims to determine if P. leucopus and P. maniculatus can be differentiated morphologically east of the Balcones fault zone in Texas. Cranial and external characters from genetically identified specimens representing each species were analyzed using traditional and geometric morphometric methods. Morphological analyses revealed that genetically identified specimens of P. leucopus and P. maniculatus from east of the Balcones fault zone could be differentiated using a suite of morphological characters. Many of the specimens of P. leucopus used in this study were originally misidentified, suggesting that P. maniculatus is rare in East Texas.