Geometric Morphometric Methods Research Articles

Land snail diversity in central China: revision of Laeocathaica Möllendorff, 1899 (Gastropoda, Camaenidae), with descriptions of seven new species.

Central China harbors the native dart-sac-bearing camaenids Laeocathaica. The genus is revised and seven new species are proposed based on museum material and newly collected specimens. This work confirmed that most Laeocathaica species have restricted habitats. The comparison of the dart sac apparatus among the dart-sac-bearing camaenid genera indicated the importance of the presence of the proximal accessory sac that might be analogous to the membranous/muscular sac surrounding the proximal dart sac and/or the distal region of the vagina near the atrium, which also plays a significant role in the diagnosis of Laeocathaica species based on its number, symmetry and position on the dart sac. Species with similar shell morphology were studied using geometric morphometric methods to detect variations in shell shape. A molecular phylogenetic analysis based on 16S and ITS2 sequence data of partial Laeocathaica species and many other dart-sac-bearing taxa suggested that Laeocathaica might be monophyletic. Furthermore, the present phylogeny indicated that Stilpnodiscus, Cathaica, Bradybaena, and Pseudobuliminus might be polyphyletic and therefore the taxonomy of dart-sac-bearing camaenids in this region requires a thorough revision. This work reconfirms that the Southern Gansu Plateau is important as a hotspot for malacodiversity conservation on the Chinese mainland.

Skull variation in different breeds sheep from Balkan countries

The Balkan Peninsula region has a very diverse agricultural and livestock tradition, and almost every country has its own local breed of sheep. Different breeds of sheep and different breeding traditions, despite the small geographical distance, determine the morphological and morphometric variability among animal breeds. In this study, this morphological diversity among the skulls of sheep breeds of some countries in the Balkan region was examined by the geometric morphometric method. 2D images of 86 sheep skulls from five different countries were analyzed from the dorsal view.Sixteen landmarks were used. The Bardhoka and the Ivesi breed have the broadest distributions of skull shape amongst the sheep breeds. The Ruda sheep is the most morphologically conservative. The sheep from Turkey (Ivesi) and Kosovo (Bardhoka) seem to differ mainly from sheep from other Balkan countries. Bardhoka and Ruda differ most from each other (p < 0.0001). The next biggest differences were between Ivesi and Ruda (p < 0.0011) and between Bardhoka and Sharri sheep (p < 0.0016). The sheep breeds Dubska and Lara e Polisit differ the least from each other. Geometrics morphometric analysis is a useful tool to detect differences in the shape of the skull of different sheep breeds and can therefore be used successfully for taxonomic purposes.

Evolutionary roots of the risk of hip fracture in humans

The transition to bipedal locomotion was a fundamental milestone in human evolution. Consequently, the human skeleton underwent substantial morphological adaptations. These adaptations are responsible for many of today’s common physical impairments, including hip fractures. This study aims to reveal the morphological changes in the proximal femur, which increase the risk of intracapsular hip fractures in present-day populations. Our sample includes chimpanzees, early hominins, early Homo Neanderthals, as well as prehistoric and recent humans. Using Geometric Morphometric methods, we demonstrate differences in the proximal femur shape between hominids and populations that practiced different lifestyles. We show that the proximal femur morphology is a risk factor for intracapsular hip fracture independent of osteoporosis. Changes in the proximal femur, such as the shortening of the femoral neck and an increased anterolateral expansion of the greater trochanter, are associated with an increased risk for intracapsular hip fractures. We conclude that intracapsular hip fractures are a trade-off for efficient bipedal walking in humans, and their risk is exacerbated by reduced physical activity.

Investigating the land-to-sea transition in carnivorans from the evolution of sacrum morphology in pinnipeds

The form and function of the sacrum are of great relevance to understand the evolution of locomotion in tetrapods because it is a key piece of the vertebrate skeleton. The sacrum connects the caudal and presacral regions of the vertebral column and the hindlimbs through the pelvis. Here, we investigate sacrum shape evolution in pinnipeds (Carnivora: Pinnipedia) in relation to terrestrial mammalian carnivorans (fissipeds), and we include crown and stem taxa to quantify the morphological changes they experience in relation to the aquatic environment they inhabit. We use 3D geometric morphometric methods to explore the morphological variability and disparity of the sacrum in a set of terrestrial and aquatic carnivoran species. Our results show that the morphology of the sacrum of each pinniped family is remarkably different and that these differences may be related to the aquatic mode of locomotion (pectoral or pelvic oscillation), the use of hindlimbs to support body weight on land (otariids in contrast with phocids), and the presence or absence of a functional tail. In addition, disparity-through-time analyses indicate that the sacrum of pinnipeds is less constrained than that of fissipeds, which suggests a gravitational origin of such constraints in fissipeds. In conclusion, our results give further support to the important role played by this skeletal structure in the locomotory adaptations of mammals.

An evaluation of sexual dimorphism in head size and shape of Red Salamanders (Pseudotriton ruber)

For many secretive species of amphibians and reptiles, observations of reproductive behavior are limited to sparse anecdotes from the field or to animals held in captivity. However, a careful examination of morphological differences between the sexes can help shape hypotheses about behaviors with which they may be correlated. For example, sexual dimorphism in head size and shape are correlated with courtship, territoriality, and mate-defense behaviors in some salamanders. One widespread species with a poorly described reproductive natural history is the Red Salamander (Pseudotriton ruber). Here, we measure head size and employ geometric morphometric methods to evaluate head shape in P. ruber, with the goals of: 1) quantifying and visualizing sexual variation; 2) forming hypotheses about reproductive behavior. We found preliminary evidence for differences in head size and shape that are consistent with mate-guarding behavior, and we remark upon directions for future research.

Geometric Morphometric Analysis of Skull in Honamli, Hair, Kilis and Saanen Goat Using Dorsal Landmarks

The aim of the study was to analyze the dorsal aspect of the skulls of Honamli, Hair, Kilis and Saanen goats by geometric morphometric method. A total of 48 adult goat skulls, 6 male and 6 female, were used for each breed. After the skulls were photographed dorsally, 10 homologous landmarks were marked. As a result of our study, the degree of dorsal separation of the skulls according to sex was found to be limited. Nevertheless, significant separation was seen in the Honamli skulls of females and in the Honamli and Saanen skulls of males. This information may serve as a reference for the skull remains of ruminants.

Analysis of the hard-tissue menton shape variation in adult South Africans using cone-beam computed tomography (CBCT) scans

: In forensic anthropology, the biological profile is based on human variation and can help in the process of personal identification. In order to better understand shape variation of the mental region, this study analyzed the influence of population affinity and sex on the menton in adult black and white South Africans, using geometric morphometric methods (GMM). : We used cone-beam computed tomography (CBCT) scans of 291 adult dental patients with dentition patterns up to Eichner Index B3, retrospectively collected from the Oral and Dental Hospital, University of Pretoria. We placed eleven standard craniometric landmarks on the menton, mandible, and maxilla of three-dimensional (3D) reconstructions by automatic landmarking and analyzed them by applying GMM. In addition, a subtle shape matrix of seven landmarks was created for a focused analysis of the menton only. Finally, we tested the reproducibility of the landmarks placement with a dispersion analysis. : The landmarks used in this study were reproducible, with an overall dispersion of less than 1 mm. Population affinity significantly influenced menton shape, with P-values = 0.001 in the complete sample and within the sex groups. Differences between sexes for these seven landmarks were also statistically significant (P-values between 0.001 to 0.003) in the complete sample, but not within population groups in isolation. The accuracy for estimation of population affinity by discriminant function analysis was 86.9%. : The use of automatic landmarking improved landmark reproducibility. Population affinity and sexual dimorphism significantly influenced menton shape. However, shape analysis, including all eleven landmarks, was not significantly influenced by sex. This study supports further research focusing on the facial approximations for forensic identification in South Africa.

Ontogenetic Variation and Sexual Dimorphism of Beaks among Four Cephalopod Species Based on Geometric Morphometrics.

Investigating the ontogenetic variation of biological individuals helps us to fully understand the characteristics of evolution. In order to explore the ontogenetic variation and sexual dimorphism of the beak shape in Octopus minor, Uroteuthis edulis, Sepia esculenta and Sthenoteuthis oualaniensis of the China's coastal waters, the differences between immature and mature stages and the sex-linked differences in the beak shape and size were analyzed with geometric morphometrics methods in this study. The results of Procrustes analysis of variance, principal component analysis and multivariate regression showed that the shapes of the upper beaks of O. minor, U. edulis and S. esculenta differed significantly among various ontogenetic stages (p < 0.05). The shapes of the lower beaks of U. edulis, S. esculenta and Sthenoteuthis oualaniensis were also significantly different among various ontogenetic stages (p < 0.05). The results of thin-plate spline deformation grids showed that the beaks of the four cephalopod species presented different variation patterns. This study gives us basic beak geometry morphology information for Octopus minor, Uroteuthis edulis, Sepia esculenta and Sthenoteuthis oualaniensis present in China's coastal waters. The ontogenetic differences in beak shape might be related to extrinsic factors (diet difference and intra and interspecific competition) in habitat.

Bilateral ankle deformities affects gait kinematics in chronic stroke patients.

Stroke patients suffer from ankle joint deformities due to spastic ankle muscles. This study evaluated the viability of using 3D scanned surface images of the feet of stroke victims to visually assess the deformities of a hemiparetic foot and investigated the influences of deformed ankle joints on gait kinematics. A total of 30 subjects with stroke-induced hemiparesis and 11 age-matched healthy controls completed the clinical assessments. We analyzed their feet's morphometric characteristics using a 3D scanner, identified convenient anthropometric measurements, and conducted gait trials on even and uneven terrains. The 3D foot morphometric characteristics were evaluated using the geometric morphometrics method (GMM). Results showed that there were significant differences in bilateral foot shapes between the chronic stroke patients and healthy controls and between the paretic and non-paretic sides in the chronic stroke patients. In stroke patients, those with the smaller medial malleoli's vertical tilt angles showed significantly different ankle ranges of motion of dorsi-/plantar flexion during gaits on uneven terrains (p = 0.009). In addition, those with the greater medial malleoli's vertical tilt angles showed significantly different ankle ranges of motion of inversion/eversion during gaits on even and uneven terrains (p < 0.05). Using 3D scanning technology, bilateral morphometric changes in the feet of chronic stroke patients were shown by GMM and the simple anthropometric measurements identified its shape deformities in the feet. Their possible effects on gait kinematics while walking on uneven terrains were investigated. Current methodology can be potentially useful in applying conventional productions of clinically manufactured, patient-fitted ankle-foot-orthosis in orthotics and prosthetics, and in detecting various unidentified pathological deformities in the feet.

Examination of Shape Variation of the Skull in British Shorthair, Scottish Fold, and Van Cats.

A variety of skull shapes are frequently used for discrimination between animal species, breeds, and sexes. In this study, skulls of three different breeds of cats were examined by the geometric morphometric method, with the aim of revealing skull shape differences. For this purpose, 27 cats (6 British Shorthair, 7 Scottish Fold, and 14 Van cats) were used. The skulls of cats were modeled by computed tomography. Geometric morphometrics was applied using dorsal (8 landmarks, 63 semilandmarks) and lateral (8 landmarks, 63 semilandmarks) skull projections on these models. Centroid size differences between the breeds were statistically insignificant. However, the differences in shape were statistically significant for both the dorsal view and lateral view. Shape variation was less in the British Shorthair than in other breeds. Shape differences generally occurred around the orbit. In the skull of Scottish Folds, the orbit was situated more caudally than in other breeds. The British Shorthair had the largest orbital ring. In dorsal view, the Scottish Fold had the largest orbital diameter. The orbital ring of Van cats was smallest in both dorsal and lateral views. In the canonical variate analysis, it was seen that the breeds were separated from each other. The shape difference in the skull between different cat breeds could be revealed by geometric morphometrics. The results of this study provide useful information for taxonomy.

Combined measures of mimetic fidelity explain imperfect mimicry in a brood parasite-host system.

The persistence of imperfect mimicry in nature presents a challenge to mimicry theory. Some hypotheses for the existence of imperfect mimicry make differing predictions depending on how mimetic fidelity is measured. Here, we measure mimetic fidelity in a brood parasite-host system using both trait-based and response-based measures of mimetic fidelity. Cuckoo finches Anomalospiza imberbis lay imperfectly mimetic eggs that lack the fine scribbling characteristic of eggs of the tawny-flanked prinia Prinia subflava, a common host species. A trait-based discriminant analysis based on Minkowski functionals-that use geometric and topological morphometric methods related to egg pattern shape and coverage-reflects this consistent difference between host and parasite eggs. These methods could be applied to quantify other phenotypes including stripes and waved patterns. Furthermore, by painting scribbles onto cuckoo finch eggs and testing their rate of rejection compared to control eggs (i.e. a response-based approach to quantify mimetic fidelity), we show that prinias do not discriminate between eggs based on the absence of scribbles. Overall, our results support relaxed selection on cuckoo finches to mimic scribbles, since prinias do not respond differently to eggs with and without scribbles, despite the existence of this consistent trait difference.

Role of paleoclimatic and paleohydrological processes in lineage divergence in freshwater organisms: A snippet from lentic genus Pila

The Indian subcontinent is extremely diverse in terms of its flora and fauna. However, only a handful of studies have aimed to understand the diversity of freshwater invertebrates using multiple lines of evidence in recent times. Here we aimed to estimate the cryptic diversity of two widespread freshwater snail species within the genus Pila (Röding, 1798) and uncover the processes behind lineage diversification in these species. We sequenced mitochondrial and nuclear markers from a comprehensive sampling of specimens from different river basins in India. We implemented an integrative taxonomy approach to delimit the lineages in these groups, employing phylogenetic, geometric morphometric and niche modelling-based methods. Then, we investigated the drivers of lineage divergence in these species using population genetic tools in conjunction with divergence time estimation. We found that both species consist of several genetically and ecologically distinct lineages. The genetic data showed that several of these lineages are restricted to a single or a few river basins. The divergence time estimation analyses indicated that the time frame of divergence within the species coincided with paleohydrological and paleoclimatic events in the Miocene. The diversification was primarily driven by allopatric isolation into different river basins. To conclude, the study sheds light on the complex interaction between the habitat preference of the species and the environment in shaping the diversification patterns in this group.

Geometric Morphometrics Can Predict Postoperative Visual Acuity Changes in Patients With Epiretinal Membrane: A Retrospective Study.

To investigate the efficacy of the geometric morphometrics method for the evaluation of retinal deformation in patients with epiretinal membrane (ERM) and determine whether the degree of deformation can serve as a predictive factor for postoperative visual outcome. We retrospectively evaluated data from 29 eyes of 29 patients with primary ERM. Preoperative optical coherence tomography images were compared with images of their normal fellow eyes using the geometric morphometrics thin-plate spline technique. Conventional parameters such as retinal layer thickness and previously reported indices were also measured. The correlation between the preoperative parameters and visual acuity was evaluated. Statistical comparisons were performed using a paired t-test, and associations between the optical coherence tomography image parameters and visual acuity were determined using Spearman's rank correlation coefficient. Bending energy, which was calculated using geometric morphometrics, was significantly associated with visual acuity as well as conventional optical coherence tomography parameters and previously reported indices. Multiple regression analysis showed that bending energy was an independent predictive factor for postoperative visual acuity changes. The geometric morphometrics method is an effective approach for evaluating the severity of ERM and predicting the efficacy of surgery. Geometric morphometrics can effectively evaluate retinal deformation in eyes with epiretinal membrane.

Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics.

The methods of geometric morphometrics are commonly used to quantify morphology in a broad range of biological sciences. The application of these methods to large datasets is constrained by manual landmark placement limiting the number of landmarks and introducing observer bias. To move the field forward, we need to automate morphological phenotyping in ways that capture comprehensive representations of morphological variation with minimal observer bias. Here, we present Morphological Variation Quantifier (morphVQ), a shape analysis pipeline for quantifying, analyzing, and exploring shape variation in the functional domain. morphVQ uses descriptor learning to estimate the functional correspondence between whole triangular meshes in lieu of landmark configurations. With functional maps between pairs of specimens in a dataset we can analyze and explore shape variation. morphVQ uses Consistent ZoomOut refinement to improve these functional maps and produce a new representation of shape variation, area-based and conformal (angular) latent shape space differences (LSSDs). We compare this new representation of shape variation to shape variables obtained via manual digitization and auto3DGM, an existing approach to automated morphological phenotyping. We find that LSSDs compare favorably to modern 3DGM and auto3DGM while being more computationally efficient. By characterizing whole surfaces, our method incorporates more morphological detail in shape analysis. We can classify known biological groupings, such as Genus affiliation with comparable accuracy. The shape spaces produced by our method are similar to those produced by modern 3DGM and to auto3DGM, and distinctiveness functions derived from LSSDs show us how shape variation differs between groups. morphVQ can capture shape in an automated fashion while avoiding the limitations of manually digitized landmarks, and thus represents a novel and computationally efficient addition to the geometric morphometrics toolkit.

More than 80 years without new taxa: analysis of morphological variation among members of Mexican Aeneolamia Fennah (Hemiptera, Cercopidae) support a new species in the genus.

The genus Aeneolamia includes eight described species and 32 subspecies widely distributed in America. In Mexico, two species (A.contigua and A.albofasciata) and one subspecies (A.contiguacampecheana) are recognized. In a recent study of Cercopidae in Mexico, a new species of Aeneolamia was noted from Oaxaca, Mexico based on body color and the ornamentation patterns of tegmen, without a formal taxonomic description. To test the hypothesis of an extant new taxon within the genus a comprehensive analysis of intraspecific morphological variation from 46 morphological features was performed, four related to tegmen color patterns in both sexes, six to male genitalia, and 36 continuous characters measured in specimens of both sexes of Mexican Aeneolamia from several geographical localities using traditional univariate, multivariate morphometric, and geometric morphometric methods. This is the first time that this approach has been used in Cercopidae. Aeneolamiadanpecki Castro, Armendáriz & Utrera, sp. nov. from Oaxaca showed pronounced morphological differences in tegmen coloration patterns, the shape of different elements of the male genitalia, and body measurements compared to the other Mexican members of Aeneolamia; therefore, it is described as a new species.

Geometric Morphometrics of the Cranium and Mandible in Social Voles of the “Guentheri” Group (Arvicolinae: Sumeriomys)

We analyzed the cranium dorsal projection and the mandible lateral projection in bone specimens from five Microtus guentheri and Microtus hartingi forms by geometric morphometrics (GM) methods (generalized Procrustes analysis, principal component analysis, canonical variance analysis, and discriminant function analysis). Analyses of the linear size and shapes of the cranium and lower jaw showed clear-cut differentiation among the forms into an eastern cluster and western cluster, matching M. guentheri and M. hartingi, respectively. Differences were revealed both between two subspecies of M. guentheri and between the subspecies M. h. strandzensis and Rhodopean M. hartingi, whose subspecies status has not yet been determined. M. h. ankaraensis bone specimens differ in many parameters of GM from the studied European specimens and to a lesser extent from M. g. guentheri and M. g. philistinus. Calculated morpho-ecological indices of the lower jaw revealed significant differences among all these forms, thereby possibly indicating adaptation of each to a specific habitat and dietary habits. Because of the emergence of impenetrable barriers for voles (the Anatolian Diagonal in the east and the Dardanelles and Bosporus in the west), the resultant vole groups have evolved independently.

Geometric Morphometric Investigation of Incus in Horse (Equus ferus caballus) and Donkey (Equus Asinus)

In this study, it was aimed to determine the shape of the incus in horse and donkey by geometric morphometric method and to evaluate the shape differences between horse’s and donkey’s incus. The left incus bone of 5 adult horses and 5 donkeys were used in the study. Incus were photographed at same lateral direction. Thirteen homologous landmarks were marked from the photographs using TpsUtil (Version 1.79) and TpsDig2 (Version 2.31) software. As a result of the study, the first principal component explained 38,642% of the total shape variation. In the PC1 plot, samples were clearly clustered by group. Acording to canonical varians analysis, in the wire frame warp graphic, the corpus incudis edges (right, left, and bottom) were flatter in donkeys. Angle at the LM13 level was more pronounced on the crus breve. The apex of the crus longum (Landmark 4, 5, and 6) was wider in donkey. In the study, the morphological features of horse’s and donkey’s incus were determined by geometric morphometric method. This study is important in that it is the first geometric morphometric study on the incus that is one of the ossicula auditus in horse and donkey. We think that the study will contribute to the anatomy of the ossicula auditus in the equide family.

Are the mandible shapes of common (Paradoxurus hermaphroditus) and golden (Paradoxurus zeylonensis) palm civets different? A pilot study

In this study adult common and golden palm civet mandibles were analysed by geometric morphometric method. For this purpose, the materials were photographed in accordance with the procedure and analysed using computer programs. No allometric component was detected in the comparison of the mandibles. The first principal component defined 28.657% of the total shape variation in the mandibles of the two groups that were analysed with a total of 19 landmarks. The samples were largely separated from each other in the principal component analysis. The shape differences were mostly in the caudal of the mandible. Also, in the common palm civet mandible, the mental foramina were located more ventrally from the premolars edge than in the golden palm civet. It is thought that the information obtained as a result of the study will contribute to the studies of understanding the taxonomic difference or similarities in terms of two species.

Evaluation of Cold Carcasses of Kıvırcık and Romanov Lambs by Geometric Morphometric Method

Evaluation of Cold Carcasses of Kıvırcık and Romanov Lambs by Geometric Morphometric Method

Covariation in Shapes Between the Sternum and Pelvis in Aquatic Birds with Different Locomotor Modes

Birds associated with aquatic environments have diverse locomotor and foraging strategies. We hypothesize that aquatic birds have different covariation patterns in the shapes of the sternum and pelvis depending on the locomotor mode and the predominant use of wings or hind limbs when moving through the water. The study was conducted on 26 bird species, among which we identified three ecological categories: surface swimmers, wing- and foot-propelled divers. The last two categories included only species that dive from the water surface. Geometric morphometric methods were applied to analyze shapes, and covariance was investigated with two-block PLS analysis. We show that wing- and foot-propelled divers have different patterns of covariation between sternum and pelvis shapes. A narrower, elongated and flattened sternum correlates with a shortened postacetabular region of a pelvis in wing-propelled divers. A widened and shortened sternum with a deep keel correlates with an elongated post-acetabular region of a pelvis in foot-propelled divers. Surface swimmers have a wide variety of combinations of sternum and pelvis shapes, which is apparently explained by their lower specialization for specific aquatic locomotion, and by the influence of diverse ecological factors.