Conventional Morphometric Analysis Research Articles

Identifying geographically differentiated features of Ethopian Nile tilapia (Oreochromis niloticus) morphology with machine learning.

Visual characteristics are among the most important features for characterizing the phenotype of biological organisms. Color and geometric properties define population phenotype and allow assessing diversity and adaptation to environmental conditions. To analyze geometric properties classical morphometrics relies on biologically relevant landmarks which are manually assigned to digital images. Assigning landmarks is tedious and error prone. Predefined landmarks may in addition miss out on information which is not obvious to the human eye. The machine learning (ML) community has recently proposed new data analysis methods which by uncovering subtle features in images obtain excellent predictive accuracy. Scientific credibility demands however that results are interpretable and hence to mitigate the black-box nature of ML methods. To overcome the black-box nature of ML we apply complementary methods and investigate internal representations with saliency maps to reliably identify location specific characteristics in images of Nile tilapia populations. Analyzing fish images which were sampled from six Ethiopian lakes reveals that deep learning improves on a conventional morphometric analysis in predictive performance. A critical assessment of established saliency maps with a novel significance test reveals however that the improvement is aided by artifacts which have no biological interpretation. More interpretable results are obtained by a Bayesian approach which allows us to identify genuine Nile tilapia body features which differ in dependence of the animals habitat. We find that automatically inferred Nile tilapia body features corroborate and expand the results of a landmark based analysis that the anterior dorsum, the fish belly, the posterior dorsal region and the caudal fin show signs of adaptation to the fish habitat. We may thus conclude that Nile tilapia show habitat specific morphotypes and that a ML analysis allows inferring novel biological knowledge in a reproducible manner.

Quaternary Landform Development in the Central segment of tectonically active Kachchh Mainland Fault zone, Western India

The landform aggradation in an arid climatic region is often regulated by external forces, that provide signatures of climate and tectonic perturbations. The landforms in the central segment of Northern Hill Range (NHR), which marks the surface expression of Kachchh Mainland Fault (KMF), are investigated in this study to understand the role of climatic changes and tectonic activity during the time of aggradation and incision. Geomorphologically, the KMF is expressed by the presence of ∼80–150 m high E-W trending escarpment. The central segment of KMF preserves the alluvial fan surfaces which have been truncated at several places with anomalous incision. Conventional morphometric analyses indicate that the KMF is affected by tectonic activity in recent times. The optical chronology of oldest alluvial fan dated from back limb and forelimb of an anticline was around 28 ka (with gradual onset of aridity) and 25 ka (with peak aridity). This arid phase is correlated with enhanced tectonic uplift along the KMF, which is manifested in the form of strath terraces and incision of river valleys. The oldest activity pre-dated to 25 ka and continued till 14 ka and there was a tectonic stability between 14 and 8 ka. The younger activity began soon after 8 ka and continuous till today, which is most likely caused by the manifestation of the Early Holocene climatic optima that lead to severe erosional processes. The younger Middle Holocene (4.3 ka) event is correlated with enhanced uplift and was accountable for the down cutting of the fill sediments and the Mesozoic bedrock. The study suggests that the deformation pattern close to KMF is the result of localized compressive stress generated between two fault segments.

Morphometric analyses of Staurosira inflata comb. nov. (Bacillariophyceae) and the morphologically related Staurosira tabellaria from north-western Russia

ABSTRACTThe morphology and ontogenetic allometric trends of a rare diatom Fragilaria heidenii Østrup and the morphologically related Staurosira tabellaria (W. Smith) Leuduger-Fortmorel were compared using conventional and semilandmark-based geometric morphometric analyses. Fragilaria heidenii was studied in detail by light and electron microscopy using type material and recent samples from Lake Ladoga and Lake Ilmen (north-western Russia). The taxon is transferred into the genus Staurosira Ehrenberg as Staurosira inflata comb. nov. on the basis of its valve morphology. This taxon is characterized by the absence of rimoportulae, lack of perforated copulae, spines located on the interstriae, internal vola occlusion in the areolae and the features of the areolae and apical pore fields. Conventional morphometric analysis showed considerable overlapping of S. inflata and S. tabellaria in their frustule characteristics such as length, width, length-to-width ratio and striae density. Moreover, at later stages of the vegetative life cycle, S. inflata has a tendency to resemble S. tabellaria by its valve outline that makes it difficult to separate these two taxa. The geometric morphometric analysis revealed two shape groups corresponding to S. inflata and S. tabellaria that were separated by a clear gap. Semilandmarks representing shape of the middle part of the valve were primarily responsible for discrimination between species. Apart from differences in valve shapes, S. inflata and S. tabellaria also differed significantly in their ontogenetic allometric trajectories. Overall, our results demonstrate that the semilandmark-based geometric morphometrics is sensitive enough to distinguish species by their outlines, when traditional morphometric parameters are not able to discriminate them with confidence.

Hippodonta fujiannensis sp. nov. (Bacillariophyceae), a new epipsammic diatom from the low intertidal zone, Fujian Province, China

Hippodonta fujiannensis sp. nov., a new small-sized species of Hippodonta (Bacillariophyceae), was described from the low intertidal zone, Fujian Province, China. The morphology and ultrastructure were investigated by light and scanning electron microscopy, which revealed the following results: 1) valves asymmetrical, elliptic-lanceolate to rhombic-lanceolate with non-protracted apices; 2) raphe filiform, with teardrop-shaped and closely spaced central endings; 3) striae uniseriate, evenly spaced throughout the whole valve; 4) single row of lineolae around the valve apices. In particular, this new species is characterized by its dissymmetrical valves with one special column of lineolae which is close to the raphe and positioned perpendicular to the remaining lineolae of the striae, on only one side of the valves. Hippodonta fujiannensis is epipsammic and inhabits the marine environment. Conventional morphometric analyses were employed to elucidate the differences between this new species and several taxa similar in valve morphology, and the results are discussed.

Corresponding morphological and molecular indicators of crude oil toxicity to the developing hearts of mahi mahi.

Crude oils from distinct geological sources worldwide are toxic to developing fish hearts. When oil spills occur in fish spawning habitats, natural resource injury assessments often rely on conventional morphometric analyses of heart form and function. The extent to which visible indicators correspond to molecular markers for cardiovascular stress is unknown for pelagic predators from the Gulf of Mexico. Here we exposed mahi (Coryphaena hippurus) embryos to field-collected crude oil samples from the 2010 Deepwater Horizon disaster. We compared visible heart defects (edema, abnormal looping, reduced contractility) to changes in expression of cardiac-specific genes that are diagnostic of heart failure in humans or associated with loss-of-function zebrafish cardiac mutants. Mahi exposed to crude oil during embryogenesis displayed typical symptoms of cardiogenic syndrome as larvae. Contractility, looping, and circulatory defects were evident, but larval mahi did not exhibit downstream craniofacial and body axis abnormalities. A gradation of oil exposures yielded concentration-responsive changes in morphometric and molecular responses, with relative sensitivity being influenced by age. Our findings suggest that 1) morphometric analyses of cardiac function are more sensitive to proximal effects of crude oil-derived chemicals on the developing heart, and 2) molecular indicators reveal a longer-term adverse shift in cardiogenesis trajectory.

Automated quantification of pancreatic β-cell mass.

β-Cell mass is a parameter commonly measured in studies of islet biology and diabetes. However, the rigorous quantification of pancreatic β-cell mass using conventional histological methods is a time-consuming process. Rapidly evolving virtual slide technology with high-resolution slide scanners and newly developed image analysis tools has the potential to transform β-cell mass measurement. To test the effectiveness and accuracy of this new approach, we assessed pancreata from normal C57Bl/6J mice and from mouse models of β-cell ablation (streptozotocin-treated mice) and β-cell hyperplasia (leptin-deficient mice), using a standardized systematic sampling of pancreatic specimens. Our data indicate that automated analysis of virtual pancreatic slides is highly reliable and yields results consistent with those obtained by conventional morphometric analysis. This new methodology will allow investigators to dramatically reduce the time required for β-cell mass measurement by automating high-resolution image capture and analysis of entire pancreatic sections.

Early subchondral bone changes in an osteoarthritis model in wild type and tgf-alpha knockout mice

Early subchondral bone changes in an osteoarthritis model in wild type and tgf-alpha knockout mice

Morphometric evidence of seismicity around Wagad and Gedi Faults, eastern Kachchh, Gujarat

Recent studies suggest that the eastern Kachchh is a potential zone for major earthquakes in the near future. Particularly, the E-W trending faults are considered capable of generating large magnitude earthquakes is further indicated by the recent concentration of the earthquake shocks, which, show two prominent clustering around west and north of the Wagad upland. In view of this, the conventional morphometric analyses of a terrain bounded by the E-W trending North Wagad Fault (NWF) and the Gedi Fault (GF) has been undertaken to ascertain the influence of seismicity in the evolution of the drainage basin. The study suggests that the fifth order drainage basins responded to the seismicity associated with both the NWF and GF. However, compared to the GF, the NWF seems to be more active. In addition to this, based on the stream morphology, we could identify two lineaments trending N-S and E-W. The former appears to be associated with the activity along the Manfara Fault (MF), whereas, the later seems to be the splays of the NWF. Further, a preferential westward shift of the streams suggests left lateral displacement of the E-W trending faults. Overall it can be suggested that the terrain is in juvenile stage implying tectonic instability.

Morphometric and Electrophoretic Approaches to Discrimination of Capelin (Mallotus villosus) Populations in the Estuary and Gulf of St. Lawrence

The degree of differentiation between capelin (Mallotus villosus) populations in the Estuary and Gulf of St. Lawrence was evaluated using conventional and truss morphometric analyses together with electrophoretic analyses of protein-coding loci. Samples of spawning fish were collected in the same year at eight sites across NAFO divisions 4R, 4S, and 4T. While the results of conventional morphometric analyses were not conclusive, truss and electrophoretic analyses differentiated the sampled sites along an east–west axis. Two samples (one from the Southern Gulf and the other from the Northeastern Gulf) did not follow this trend. Processes are suggested to explain this pattern. Variations in allelic frequencies among age-classes of fish have been observed in some samples and may be attributed to selective environmental pressures. This could explain the apparent population differentiation observed, although the distribution of the alleles revealed a high gene flow.

Neighborhood Analysis of Low Magnification Structures (Glands) in Healthy, Adenomatous, and Carcinomatous Colon Mucos

A new algorithm analyzing neighborhood conditions of adenomatous tissue is is introduced. Using O'Callaghan's definition of neighborhoods, a graph theory approach for measuring histomorphological structures can be created as follows: glands are defined as vertices and the coherence of neighboring glands as edges. The procedure leads to an unoriented, well-defined graph which contains information usually not measurable by conventional morphometric analysis. Measurements on healthy mucosa, tubulo-villous adenoma and highly to moderately differentiated adenocarcinoma of colon revealed statistically significant differences (p less than or equal to 0.05) for the following parameters: number of vertices, number of edges, frequency distribution of n-stars and of n-closed paths. Correct separation and reclassification of 83% of cases could be carried out using discriminant analysis. 11/15 cases (73%) could be classified correctly in a prospective group based upon the learning set. The significance of these findings for automatic pattern recognition in histopathology is discussed.