A three-dimensional geometric morphometrics view of the cranial shape variation and population history in the New World

2016 ◽  
Vol 28 (5) ◽  
pp. 646-661 ◽  
Author(s):  
Manon Galland ◽  
Martin Friess
Keyword(s):  
Geometric Morphometrics ◽  
New World ◽  
Three Dimensional ◽  
Population History ◽  
Shape Variation ◽  
Cranial Shape

scholarly journals ShapeRotator: an R tool for standardised rigid rotations of articulated Three-Dimensional structures with application for geometric morphometrics

2017 ◽  
Author(s):  
Marta Vidal-García ◽  
Lashi Bandara ◽  
J. Scott Keogh
Keyword(s):  
Geometric Morphometrics ◽  
Phenotypic Diversity ◽  
Three Dimensional ◽  
R Package ◽  
Morphological Data ◽  
List Type ◽  
Shape Variation ◽  
Data Set ◽  
Articulated Structures ◽  
Shape And Size

SummaryThe quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate in to modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures.While there are existing methods for analysing shape variation in articulated structures in Two-Dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research.Here we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space so it can be applied to any morphometric problem that also uses 3D coordinates (e.g. spherical harmonics). We demonstrate the method by applying it to a landmark-based data set for analysing shape variation using geometric morphometrics.We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.

scholarly journals Three-dimensional geometric morphometrics for studying floral shape variation

2010 ◽  
Vol 15 (8) ◽  
pp. 423-426 ◽  
Author(s):  
Timotheüs van der Niet ◽  
Christoph P.E. Zollikofer ◽  
Marcia S. Ponce de León ◽  
Steven D. Johnson ◽  
H. Peter Linder
Keyword(s):  
Geometric Morphometrics ◽  
Three Dimensional ◽  
Shape Variation

scholarly journals Hominoid intraspecific cranial variation mirrors neutral genetic diversity

2018 ◽  
Vol 115 (45) ◽  
pp. 11501-11506 ◽  
Author(s):  
Julia M. Zichello ◽  
Karen L. Baab ◽  
Kieran P. McNulty ◽  
Christopher J. Raxworthy ◽  
Michael E. Steiper
Keyword(s):  
Genetic Diversity ◽  
Homo Sapiens ◽  
Population History ◽  
Cranial Morphology ◽  
Shape Variation ◽  
Evolutionary Processes ◽  
Cranial Variation ◽  
History Of ◽  
Fossil Hominin ◽  
Cranial Shape

Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique toHomo sapiensbut is also broadly evident across extant ape species. Specifically, taxa that exhibit greater intraspecific cranial shape variation also exhibit greater genetic diversity at neutral autosomal loci. Thus, cranial shape variation within hominoid taxa reflects the population history of each species. Our results suggest that neutral evolutionary processes such as mutation, gene flow, and genetic drift have played an important role in generating cranial variation within species. These findings are consistent with previous work on human cranial morphology and improve our understanding of the evolutionary processes that generate intraspecific cranial shape diversity within hominoids. This work has implications for the analysis of selective and developmental pressures on the cranium and for interpreting shape variation in fossil hominin crania.

scholarly journals Morphological variation under domestication: how variable are chickens?

2018 ◽  
Vol 5 (8) ◽  
pp. 180993 ◽  
Author(s):  
Madlen Stange ◽  
Daniel Núñez-León ◽  
Marcelo R. Sánchez-Villagra ◽  
Per Jensen ◽  
Laura A. B. Wilson
Keyword(s):  
Neural Crest ◽  
Geometric Morphometrics ◽  
Multivariate Statistics ◽  
Morphological Variation ◽  
Three Dimensional ◽  
Cranial Vault ◽  
Shape Variation ◽  
Skull Morphology ◽  
Variable Part ◽  
Brain Shape

The process of domestication has long fascinated evolutionary biologists, yielding insights into the rapidity with which selection can alter behaviour and morphology. Previous studies on dogs, cattle and pigeons have demonstrated that domesticated forms show greater magnitudes of morphological variation than their wild ancestors. Here, we quantify variation in skull morphology, modularity and integration in chickens and compare those to the wild fowl using three-dimensional geometric morphometrics and multivariate statistics. Similar to other domesticated species, chickens exhibit a greater magnitude of variation in shape compared with their ancestors. The most variable part of the chicken skull is the cranial vault, being formed by dermal and neural crest-derived bones, its form possibly related to brain shape variation in chickens, especially in crested breeds. Neural crest-derived portions of the skull exhibit a higher amount of variation. Further, we find that the chicken skull is strongly integrated, confirming previous studies in birds, in contrast to the presence of modularity and decreased integration in mammals.

scholarly journals Skull and limb morphology differentially track population history and environmental factors in the transition to agriculture in Europe

2013 ◽  
Vol 280 (1767) ◽  
pp. 20131337 ◽  
Author(s):  
Noreen von Cramon-Taubadel ◽  
Jay T. Stock ◽  
Ron Pinhasi
Keyword(s):  
Population History ◽  
Shape Variation ◽  
Hunter Gatherers ◽  
Neolithic Transition ◽  
Demographic Processes ◽  
Transition To Agriculture ◽  
Spatio Temporal ◽  
Behavioural Factors ◽  
Cranial Shape ◽  
Limb Morphology

The Neolithic transition in Europe was a complex mosaic spatio-temporal process, involving both demic diffusion from the Near East and the cultural adoption of farming practices by indigenous hunter–gatherers. Previous analyses of Mesolithic hunter–gatherers and Early Neolithic farmers suggest that cranial shape variation preserves the population history signature of the Neolithic transition. However, the extent to which these same demographic processes are discernible in the postcranium is poorly understood. Here, for the first time, crania and postcranial elements from the same 11 prehistoric populations are analysed together in an internally consistent theoretical and methodological framework. Results show that while cranial shape reflects the population history differences between Mesolithic and Neolithic lineages, relative limb dimensions exhibit significant congruence with environmental variables such as latitude and temperature, even after controlling for geography and time. Also, overall limb size is found to be consistently larger in hunter–gatherers than farmers, suggesting a reduction in size related to factors other than thermoregulatory adaptation. Therefore, our results suggest that relative limb dimensions are not tracking the same demographic population history as the cranium, and point to the strong influence of climatic, dietary and behavioural factors in determining limb morphology, irrespective of underlying neutral demographic processes.

scholarly journals The Study of Cranial Shape Variation in a Population from Joseon Dynasty using Geometric Morphometrics

2015 ◽  
Vol 28 (1) ◽  
pp. 27
Author(s):  
Hyunwoo Jung ◽  
EunJin Woo ◽  
Sunyoung Pak
Keyword(s):  
Geometric Morphometrics ◽  
Shape Variation ◽  
Joseon Dynasty ◽  
Cranial Shape

scholarly journals A developmentally descriptive method for quantifying shape in gastropod shells

2020 ◽  
Vol 17 (163) ◽  
pp. 20190721
Author(s):  
J. Larsson ◽  
A. M. Westram ◽  
S. Bengmark ◽  
T. Lundh ◽  
R. K. Butlin
Keyword(s):  
Empirical Studies ◽  
Three Dimensional ◽  
Shell Shape ◽  
Large Set ◽  
Littorina Saxatilis ◽  
Shape Variation ◽  
Gastropod Shell ◽  
Geometric Morphometric ◽  
Wide Range ◽  
Descriptive Method

The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.

Comparative analysis of shape variation in the cone scales of Larix dahurica and L. cajanderi (Pinaceae)

2021 ◽  
pp. 47-67
Author(s):  
Valentina P. Vetrova ◽  
◽  
Alexey P. Barchenkov ◽  
Nadezhda V. Sinelnikova ◽  
◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
Geometric Morphometrics ◽  
Baikal Region ◽  
Canonical Discriminant Analysis ◽  
Shape Variation ◽  
Geometric Morphometric ◽  
The North ◽  
Larch Species ◽  
Geometric Morphometric Analysis ◽  
Cone Scale

Geometric morphometric analysis of shape variation in the cone scales of two closely related larch species, Larix dahurica Laws. (=Larix gmelinii (Rupr.) Rupr) and L. cajanderi Mayr, was carried out. The data on the taxonomy and distribution of L. dahurica and L. cajanderi are contradictory. The taxonomic status of L. cajanderi has been confirmed by the genetic and morphological studies performed in Russia and based on considerable evidence, but the species has not been recognized internationally, being considered as a synonym of Larix gmelinii var. gmelinii. In the systematics of larch, morphological characters of the generative organs are mainly used as diagnostic markers, among the most important being the shape variation of the cone scales. The aim of this study was to test geometric morphometrics as a tool for analyzing differentiation of L. dahurica and L. cajanderi in the shape of their cone scales. Characterization of shape variations in cone scales using geometric morphometric methods consists in digitizing points along an outline of scales followed by analysis of partial warps, describing individual differences in coordinates of the outline points. We studied the populations of L. dahurica from Evenkia and the Trans-Baikal region and six L. cajanderi populations from Yakutia and Magadan Oblast. In each population, we analyzed samples of 100-150 cones collected from 20-30 trees. Scales taken from the middle part of the cones were scanned using an Epson Perfection V500 Photo. On the scanned images, outline points were placed with a TPSDig program (Rolf, 2010), using angular algorithm (Oreshkova et al., 2015). The data were processed and analyzed using Integrated Morphometrics Programs (IMP) software (http://www.canisius.edu/~sheets/ morphsoft.html, Sheets, 2001), following the guidelines on geometric morphometrics in biology (Pavlinov, Mikeshina, 2002; Zelditch et al., 2004). Initial coordinates of the scale landmarks were aligned with the mean structure for L. dahurica and L. cajanderi cone scales using Procrustes superimposition in the CoordGen6 program. PCA based on covariances of partial warp scores was applied to reveal directions of variation in the shape of the cone scales. The relative deformations of the cone scales (PCA scores) were used as shape variables for statistical comparisons of these two larch species with canonical discriminant analysis. Morphotypes of the cone scales were distinguished in L. dahurica populations by pairwise comparison of samples from trees in the TwoGroup6h program using Bootstrap resampling-based Goodall’s F-test (Sheets, 2001). Samples from the trees in which the cone scales differed significantly (p < 0.01) were considered to belong to different morphotypes. Morphotypes distinguished in L. dahurica populations were compared with the morphotypes that we had previously determined in L. cajanderi populations. The composition and the frequency of occurrence of morphotypes were used to determine phenotypic distances between populations (Zhivotovskii, 1991). Multidimensional scaling matrix of the phenotypic distances was applied for ordination of larch populations. In this research, we revealed differentiation of L. dahurica and L. cajanderi using geometric morphometric analysis of the shape variation of cone scales. The results of PCA of partial warp scores exposed four principal components, which account for 90% of total explained variance in the shape of the cone scales in the two larch species. Graphical representations of these shape transformations in the vector form characterized directions of shape variability in scales corresponding to the maximum and minimum values of four principal components (See Fig. 2). PCA-ordination of the larch populations revealed some difference in the shape variation of the cone scales in L. dahurica and L. cajanderi (See Fig. 3). The results of canonical discriminant analysis of relative deformations of scales showed differentiation of the populations of the two larch species (See Fig. 4). Eleven morphotypes were identified in L. dahurica cones from Evenkia and nine morphotypes in the Ingoda population, three of the morphotypes being common for both populations (See Fig. 5). The shape of L. dahurica cone scales varied from spatulate to oval and their apical margins from weakly sinuate to distinctly sinuate. The Trans-Baikal population was dominated by scales with obtuse (truncate) and rounded apexes. The obtained morphotypes were compared with 25 cone scale morphotypes previously distinguished in the Yakut and the Magadan L. cajanderi populations (See Fig. 3). Four similar morphotypes of cone scales were revealed in the North-Yeniseisk population of L. dahurica and the Yakut populations of L. cajanderi. The differences between them in the populations of the two larch species were nonsignificant (p > 0.01). All morphotypes of cone scales from the Ingoda population of L. dahurica differed significantly from L. cajanderi cone scale morphotypes. The results of multidimensional scaling phenotypic distance matrix calculated based on the similarity of morphotypes of L. dahurica and L. cajanderi populations were consistent with the results of their differentiation based on relative deformations of scales obtained using canonical discriminant analysis (See Fig. 4 and Fig. 7). In spite of the differences in the shape of the cone scales between the North-Yeniseisk and the Trans-Baikal populations of L. dahurica, they both differed from L. cajanderi populations. Thus, phenotypic analysis confirmed differentiation of these two larch species. Despite the similarities between a number of morphotypes, the Yakut L. cajanderi populations were differentiated from L. dahurica populations. Significant differences were noted between intraspecific groups: between L. cajanderi populations from Okhotsk-Kolyma Upland and Yakutia and between L. dahurica populations from Evenkia and the Trans-Baikal region (See Fig. 4). The similarities between species and intraspecific differences may be attributed to the ongoing processes of hybridization and species formation in the region where the ranges of the larches overlap with the ranges of L. czekanowskii Szafer and L. dahurica×L. cajanderi hybrids. Geometric morphometrics can be used as an effective tool for analyzing differentiation of L. dahurica and L. cajanderi in the shape of their cone scales.

scholarly journals The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

2017 ◽  
Vol 4 (8) ◽  
pp. 170685 ◽  
Author(s):  
Alessandro Palci ◽  
Mark N. Hutchinson ◽  
Michael W. Caldwell ◽  
Michael S. Y. Lee
Keyword(s):  
Geometric Morphometrics ◽  
Inner Ear ◽  
Phylogenetic Signal ◽  
Three Dimensional ◽  
Lizard Species ◽  
Squamate Reptiles ◽  
Strong Affinity ◽  
Ear Morphology

The inner ear morphology of 80 snake and lizard species, representative of a range of ecologies, is here analysed and compared to that of the fossil stem snake Dinilysia patagonica , using three-dimensional geometric morphometrics. Inner ear morphology is linked to phylogeny (we find here a strong phylogenetic signal in the data that can complicate ecological correlations), but also correlated with ecology, with Dinilysia resembling certain semi-fossorial forms ( Xenopeltis and Cylindrophis ), consistent with previous reports. We here also find striking resemblances between Dinilysia and some semi-aquatic snakes, such as Myron (Caenophidia, Homalopsidae). Therefore, the inner ear morphology of Dinilysia is consistent with semi-aquatic as well as semi-fossorial habits: the most similar forms are either semi-fossorial burrowers with a strong affinity to water ( Xenopeltis and Cylindrophis ) or amphibious, intertidal forms which shelter in burrows ( Myron). Notably, Dinilysia does not cluster as closely with snakes with exclusively terrestrial or obligate burrowing habits (e.g. scolecophidians and uropeltids). Moreover, despite the above similarities, Dinilysia also occupies a totally unique morphospace, raising issues with linking it with any particular ecological category.

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