scholarly journals Development and Assessment of Fully Automated and Globally Transitive Geometric Morphometric Methods, With Application to a Biological Comparative Dataset With High Interspecific Variation

2017 ◽  
Vol 301 (4) ◽  
pp. 636-658 ◽  
Author(s):  
Tingran Gao ◽  
Gabriel S. Yapuncich ◽  
Ingrid Daubechies ◽  
Sayan Mukherjee ◽  
Doug M. Boyer
Keyword(s):  
Interspecific Variation ◽  
Geometric Morphometric ◽  
Morphometric Methods

scholarly journals Development and assessment of fully automated and globally transitive geometric morphometric methods, with application to a biological comparative dataset with high interspecific variation

2016 ◽  
Author(s):  
Tingran Gao ◽  
Gabriel S. Yapuncich ◽  
Ingrid Daubechies ◽  
Sayan Mukherjee ◽  
Doug M. Boyer
Keyword(s):  
Ground Truth ◽  
Interspecific Variation ◽  
Shape Space ◽  
Substantial Fraction ◽  
Geometric Morphometric ◽  
Full Sample ◽  
Morphometric Methods ◽  
Automated Methods ◽  
Variance Structure

AbstractAutomated geometric morphometric methods are promising tools for shape analysis in comparative biology: they improve researchers’ abilities to quantify biological variation extensively (by permitting more specimens to be analyzed) and intensively (by characterizing shapes with greater fidelity). Although use of these methods has increased, automated methods have some notable limitations: pairwise correspondences are frequently inaccurate or lack transitivity (i.e., they are not defined with reference to the full sample). In this study, we reassess the accuracy of two previously published automated methods, cPDist [1] and auto3Dgm [2], and evaluate several modifications to these methods. We show that a substantial fraction of alignments and pairwise maps between specimens of highly dissimilar geometries were inaccurate in the study of Boyer et al. [1], despite a taxonomically sensitive variance structure of continuous Procrustes distances. We also show these inaccuracies can be remedied by utilizing a globally informed methodology within a collection of shapes, instead of only comparing shapes in a pairwise manner (c.f. [2]). Unfortunately, while global information generally enhances maps between dissimilar objects, it can degrade the quality of correspondences between similar objects due to the accumulation of numerical error. We explore a number of approaches to mitigate this degradation, quantify the performance of these approaches, and compare the generated pairwise maps (as well as the shape space characterized by these maps) to a “ground truth” obtained from landmarks manually collected by geometric morphometricians. Novel methods both improve the quality of the pairwise correspondences relative to cPDist, and achieve a taxonomic distinctiveness comparable to auto3Dgm.

scholarly journals Arothron: An R package for geometric morphometric methods and virtual anthropology applications

2021 ◽  
Author(s):  
Profico Antonio ◽  
Buzi Costantino ◽  
Castiglione Silvia ◽  
Melchionna Marina ◽  
Piras Paolo ◽  
...  
Keyword(s):  
R Package ◽  
Geometric Morphometric ◽  
Morphometric Methods ◽  
Virtual Anthropology

scholarly journals Comparing skull formation of the Hungarian (Hortobágy) Zackel sheep breed by geometrics morphometrics

2015 ◽  
pp. 29-33
Author(s):  
Zsuzsanna Csóri ◽  
András Gáspárdy ◽  
András Jávor
Keyword(s):  
Morphological Changes ◽  
Time Change ◽  
Carpathian Basin ◽  
Sheep Breed ◽  
Geometric Morphometric ◽  
The Past ◽  
Morphometric Methods ◽  
Skull Formation ◽  
Over Time

This work seeks to explore the morphological changes of the Hungarian (Hortobágy) Zackel sheep's skull, which occurred in the past 50–70 years. In this study, we compared individuals skull forms by geometric morphometric methods. The origin of the breed is not known, we do not know when entering the Carpathian Basin. Therefore, the comparison involved the only known early archaeological findings. We have shown that there is no difference between each period colour variations, but over time change has occurred in the skull formation of the breed.

scholarly journals Geometric Morphometric Analyses Support Incorporating the Goshen Point Type into Plainview

2019 ◽  
Vol 85 (1) ◽  
pp. 171-181 ◽  
Author(s):  
Briggs Buchanan ◽  
Mark Collard ◽  
Michael J. O'Brien
Keyword(s):  
Recent Work ◽  
Social Dynamics ◽  
Spatiotemporal Variation ◽  
Single Type ◽  
Geometric Morphometric ◽  
Morphometric Analyses ◽  
Morphometric Methods ◽  
Point Type

Recent work has demonstrated that Goshen points overlap in time with another group of unfluted lanceolate points from the Plains, Plainview points. This has raised the question of whether the two types should be kept separate or consolidated into a single type. We sought to resolve this issue by applying geometric morphometric methods to a sample of points from well-documented Goshen and Plainview assemblages. We found that their shapes were statistically indistinguishable, which indicates that Goshen and Plainview points should be assigned to the same type. Because Plainview points were recognized before Goshen points, it is the latter type name that should be dropped. Sinking Goshen into Plainview allows us to move beyond taxonomic issues and toward understanding both the spatiotemporal variation that exists among Plainview assemblages and what it can tell us about the adaptations and social dynamics of Plainview groups.

Morphometric variation of fish scales among some species of rattail fish from New Zealand waters

2018 ◽  
Vol 98 (8) ◽  
pp. 1991-1998
Author(s):  
A. L. Ibáñez ◽  
L. A. Jawad
Keyword(s):  
New Zealand ◽  
Discriminant Analysis ◽  
Morphological Evolution ◽  
Procrustes Analysis ◽  
Fish Scales ◽  
Geometric Morphometric ◽  
Morphometric Variation ◽  
Generalized Procrustes Analysis ◽  
Morphometric Methods ◽  
Components Analysis

New Zealand rattail fish are of great interest both to biologists who study their phylogenetics and in fisheries. In contrast, their morphological evolution is little studied and poorly understood. Geometric morphometric methods based on scale shape were applied in this study to determine differences among species and genera. Scale shapes were described using seven landmarks, the coordinates of which were subjected to a generalized Procrustes analysis, followed by a principal components analysis. A cross-validated discriminant analysis was applied to assess and compare the size-shape (centroid size plus shape variables) efficacy in the species and the discrimination of the genera. Two main phenetic groups were identified: cluster no. 1 with eight species and cluster no. 2 with six species. Coelorhinchus aspercephalus and Mesovagus antipodum were more separated from the other species in the first cluster. The cross-validated canonical discriminant analysis correctly classified 74% at the genus level, with most misclassifications occurring between Coelorhinchus and Coryphaenoides, whereas the best classified genera were Mesovagus and Trachyrincus. The discrimination of correctly classified species ranged from 41.2 to 100%. The highest correct classification rates were recorded for Coryphaenoides armatus, Coelorhinchus innotabilis, Trachyrincus longirostris and Mesovagus antipodum.

scholarly journals Heterochronic Shifts Mediate Ecomorphological Convergence in Skull Shape of Microcephalic Sea Snakes

2019 ◽  
Vol 59 (3) ◽  
pp. 616-624 ◽  
Author(s):  
Emma Sherratt ◽  
Kate L Sanders ◽  
Amy Watson ◽  
Mark N Hutchinson ◽  
Michael S Y Lee ◽  
...  
Keyword(s):  
Morphological Changes ◽  
Shape Variation ◽  
Micro Computed Tomography ◽  
Trophic Specialization ◽  
Evolutionary Patterns ◽  
Dietary Specialization ◽  
Geometric Morphometric ◽  
Sea Snakes ◽  
Morphometric Methods ◽  
Cranial Shape

Abstract Morphological variation among the viviparous sea snakes (Hydrophiinae), a clade of fully aquatic elapid snakes, includes an extreme “microcephalic” ecomorph that has a very small head atop a narrow forebody, while the hind body is much thicker (up to three times the forebody girth). Previous research has demonstrated that this morphology has evolved at least nine times as a consequence of dietary specialization on burrowing eels, and has also examined morphological changes to the vertebral column underlying this body shape. The question addressed in this study is what happens to the skull during this extreme evolutionary change? Here we use X-ray micro-computed tomography and geometric morphometric methods to characterize cranial shape variation in 30 species of sea snakes. We investigate ontogenetic and evolutionary patterns of cranial shape diversity to understand whether cranial shape is predicted by dietary specialization, and examine whether cranial shape of microcephalic species may be a result of heterochronic processes. We show that the diminutive cranial size of microcephalic species has a convergent shape that is correlated with trophic specialization to burrowing prey. Furthermore, their cranial shape is predictable for their size and very similar to that of juvenile individuals of closely related but non-microcephalic sea snakes. Our findings suggest that heterochronic changes (resulting in pedomorphosis) have driven cranial shape convergence in response to dietary specializations in sea snakes.

Larval anatomy of Andean tadpoles of Telmatobius (Anura: Ceratophryidae) from Northwestern Argentina

Zootaxa ◽  
2008 ◽  
Vol 1938 (1) ◽  
pp. 40-60 ◽  
Author(s):  
M. FLORENCIA VERA CANDIOTI
Keyword(s):  
Intraspecific Variation ◽  
Characteristic Pattern ◽  
Species Discrimination ◽  
Shape Variation ◽  
Geometric Morphometric ◽  
Northwestern Argentina ◽  
Preliminary Results ◽  
Internal Morphology ◽  
Morphometric Methods ◽  
Interspecific And Intraspecific Variation

In this paper I study the oral, buccopharyngeal, and musculoskeletal configuration in tadpoles of nine Telmatobius species from Northwestern Argentina (T. atacamensis, T. ceiorum, T. laticeps, T. oxycephalus, T. pinguiculus, T. pisanoi, T. cf. schreiteri, T. scrocchii, and T. stephani; N = 30, Gosner stages 31–36). Specimens were prepared according to standard clearing and staining protocols; additionally, I applied landmark and outline-based geometric morphometric methods in order to quantify shape variation in chondrocrania, hyobranchial skeletons, and suprarostral cartilages. Although preliminary, results show a marked morphological uniformity on the analyzed levels, and overlapping interspecific and intraspecific variation, which renders species discrimination difficult. Some distinctive traits for the genus are bicuspidate buccal spurs, peculiar arrangement of buccal roof and floor papillae, tetrapartite suprarostral, adrostral cartilages, a lateral slip of the m. subarcualis rectus II-IV invading branchial septum IV, and a characteristic pattern of muscles inserted on the diaphragm. The conservative larval internal morphology in this genus could be explained by a recent speciation and a development possibly characterized by the postmetamorphic appearance of specific features.En este trabajo estudio la morfología oral, bucofaríngea y musculoesquelética de larvas de nueve especies de Telmatobius del Noroeste argentino (T. atacamensis, T. ceiorum, T. laticeps, T. oxycephalus, T. pinguiculus, T. pisanoi, T. cf. schreiteri, T. scrocchii y T. stephani; N = 30, estadios de Gosner 31–36). Los especímenes se prepararon siguiendo protocolos clásicos de transparentación y coloración diferencial; adicionalmente, apliqué métodos de morfometría geométrica basada en landmarks y contornos para cuantificar la variación de formas en condrocráneos, esqueletos hiobranquiales y cartílagos suprarostrales. Aunque de carácter preliminar, los resultados muestran una notable uniformidad morfológica en los niveles analizados, y una variación intraespecífica que se superpone con la interespecífica, dificultando la distinción entre especies. Algunos rasgos distintivos del género son un par de espolones bucales bífidos, un arreglo particular de las papilas del techo y piso bucales, suprarostral tetrapartito, adrostrales, un haz del m. subarcualis rectus II-IV invadiendo el septo branquial IV, y un patrón aparentemente característico de los músculos insertos en el diafragma. La morfología larval interna conservadora en el género podría explicarse por una especiación reciente y un desarrollo posiblemente caracterizado por la aparición postmetamórfica de los rasgos específicos.

scholarly journals The Utility of Geometric Morphometrics to Elucidate Pathways of Cichlid Fish Evolution

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Michaela Kerschbaumer ◽  
Christian Sturmbauer
Keyword(s):  
Geometric Morphometrics ◽  
Evolutionary Biology ◽  
Body Shape ◽  
Cichlid Fish ◽  
Anatomical Landmarks ◽  
Trophic Specialization ◽  
Geometric Morphometric ◽  
The Family ◽  
Morphometric Methods ◽  
Head Morphology

Fishes of the family Cichlidae are famous for their spectacular species flocks and therefore constitute a model system for the study of the pathways of adaptive radiation. Their radiation is connected to trophic specialization, manifested in dentition, head morphology, and body shape. Geometric morphometric methods have been established as efficient tools to quantify such differences in overall body shape or in particular morphological structures and meanwhile found wide application in evolutionary biology. As a common feature, these approaches define and analyze coordinates of anatomical landmarks, rather than traditional counts or measurements. Geometric morphometric methods have several merits compared to traditional morphometrics, particularly for the distinction and analysis of closely related entities. Cichlid evolutionary research benefits from the efficiency of data acquisition, the manifold opportunities of analyses, and the potential to visualize shape changes of those landmark-based methods. This paper briefly introduces to the concepts and methods of geometric morphometrics and presents a selection of publications where those techniques have been successfully applied to various aspects of cichlid fish diversification.

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