scholarly journals Complex genetic architecture of three‐dimensional craniofacial shape variation in domestic pigeons

2021 ◽  
Author(s):  
Elena F. Boer ◽  
Emily T. Maclary ◽  
Michael D. Shapiro
Keyword(s):  
Genetic Architecture ◽  
Three Dimensional ◽  
Shape Variation ◽  
Domestic Pigeons

scholarly journals Complex genetic architecture of three-dimensional craniofacial shape variation in domestic pigeons

2021 ◽  
Author(s):  
Elena F. Boer ◽  
Emily T. Maclary ◽  
Michael D. Shapiro
Keyword(s):  
Life Histories ◽  
Phenotypic Diversity ◽  
Three Dimensional ◽  
Single Species ◽  
Columba Livia ◽  
Craniofacial Morphology ◽  
Shape Variation ◽  
Human Pathology ◽  
Craniofacial Variation ◽  
Domestic Pigeons

AbstractDeciphering the genetic basis of vertebrate craniofacial variation is a longstanding biological problem with broad implications in evolution, development, and human pathology. One of the most stunning examples of craniofacial diversification is the adaptive radiation of birds, in which the beak serves essential roles in virtually every aspect of their life histories. The domestic pigeon (Columba livia) provides an exceptional opportunity to study the genetic underpinnings of craniofacial variation because of its unique balance of experimental accessibility and extraordinary phenotypic diversity within a single species. We used traditional and geometric morphometrics to quantify craniofacial variation in an F2 laboratory cross derived from the straight-beaked Pomeranian Pouter and curved-beak Scandaroon pigeon breeds. Using a combination of genome-wide quantitative trait locus scans and multi-locus modeling, we identified a set of genetic loci associated with complex shape variation in the craniofacial skeleton, including beak curvature, braincase shape, and mandible shape. Some of these loci control coordinated changes between different structures, while others explain variation in the size and shape of specific skull and jaw regions. We find that in domestic pigeons, a complex blend of both independent and coupled genetic effects underlie three-dimensional craniofacial morphology.

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.

scholarly journals Positional variation rather than salt stress dominates changes in three-dimensional leaf shape patterns in cucumber canopies

2019 ◽  
Author(s):  
Dominik Schmidt ◽  
Katrin Kahlen
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Leaf Shape ◽  
Three Dimensional ◽  
Size Variation ◽  
Canopy Architecture ◽  
Shape Variation ◽  
Stress Study ◽  
Salinity Levels ◽  
Adaptation Processes

Abstract Leaf shape plays a key role in the interaction of a plant with its environment, best-known in the plant’s light harvest. Effects of the environment on the interplay of canopy architecture and physiological functioning can be estimated using functional-structural plant models (FSPMs). In order to reduce the complexity of canopy simulations, leaf shape models used in FSPMs are often simple prototypes scaled to match current leaf area. L-Cucumber is such an FSPM, whose leaf prototype mimics average real leaf shape of unstressed cucumber plants well. However, adaptation processes or stress responses may lead to non-proportional changes in leaf geometries, which, for example, could affect length to width ratios or curvatures. The current leaf shape model in L-Cucumber is static and hence does not incorporate changes in leaf shape within or between plants. Thus, the aim of this study was to estimate leaf shape variation and exemplarily study its effects on FSPM simulations. Three-dimensional leaf coordinate data from a salt stress study were analysed with a robust Bayesian mixed-effects model for estimating leaf shape depending on rank, size and salinity. Results showed that positional and size variation rather than salinity levels dominated 3D leaf shape patterns of cucumber. Considering variable leaf shapes in relation to this main sources of variation in L-Cucumber simulations, only minor effects compared to a realistic, yet static average shape were found. However, with similar computational demands variation in shapes other studies highly sensitive to shape dynamics, for example, pesticide spraying might be affected more strongly.

Intervertebral Disc Shape Variation and its Relationship to Degeneration Using Principal Components Analysis of a Population of MR Images

2012 ◽  
Author(s):  
John M. Peloquin ◽  
Jonathon H. Yoder ◽  
Nathan T. Jacobs ◽  
Sung M. Moon ◽  
Alexander C. Wright ◽  
...  
Keyword(s):  
Stress Distribution ◽  
Intervertebral Disc ◽  
Material Properties ◽  
Three Dimensional ◽  
Low Back ◽  
Shape Variation ◽  
Mr Images ◽  
Physiological Basis ◽  
Prevalent Disease ◽  
Components Analysis

Degeneration of the intervertebral disc (IVD) is implicated in low back pain, which is a costly and prevalent disease. Since the IVD is a mechanically active organ, it is important to consider its mechanical behavior as one factor in the degenerate pathology. Strain can be measured directly by imaging methods, but the stress distribution within the disc must be calculated. The stress distribution for a particular strain state is dependent on the IVD’s material properties and its geometry. While the material properties of the tissues comprising IVD have been extensively studied, its three-dimensional geometry remains incompletely characterized. Prior whole-disc models have been constructed from single IVDs. While this approach ensures that the geometry has a physiological basis, it is uncertain the degree to which results from a single IVD shape can be generalized to the entire population.

scholarly journals Turbulence Modeling in Three-Dimensional Stenosed Arterial Bifurcations

2006 ◽  
Vol 129 (1) ◽  
pp. 40-50 ◽  
Author(s):  
J. Banks ◽  
N. W. Bressloff
Keyword(s):  
Carotid Artery ◽  
Turbulence Modeling ◽  
Turbulent Viscosity ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Shape Variation ◽  
Severe Stenosis ◽  
Carotid Artery Bifurcation ◽  
Inflow Turbulence ◽  
Flow Through

Under normal healthy conditions, blood flow in the carotid artery bifurcation is laminar. However, in the presence of a stenosis, the flow can become turbulent at the higher Reynolds numbers during systole. There is growing consensus that the transitional k−ω model is the best suited Reynolds averaged turbulence model for such flows. Further confirmation of this opinion is presented here by a comparison with the RNG k−ϵ model for the flow through a straight, nonbifurcating tube. Unlike similar validation studies elsewhere, no assumptions are made about the inlet profile since the full length of the experimental tube is simulated. Additionally, variations in the inflow turbulence quantities are shown to have no noticeable affect on downstream turbulence intensity, turbulent viscosity, or velocity in the k−ϵ model, whereas the velocity profiles in the transitional k−ω model show some differences due to large variations in the downstream turbulence quantities. Following this validation study, the transitional k−ω model is applied in a three-dimensional parametrically defined computer model of the carotid artery bifurcation in which the sinus bulb is manipulated to produce mild, moderate, and severe stenosis. The parametric geometry definition facilitates a powerful means for investigating the effect of local shape variation while keeping the global shape fixed. While turbulence levels are generally low in all cases considered, the mild stenosis model produces higher levels of turbulent viscosity and this is linked to relatively high values of turbulent kinetic energy and low values of the specific dissipation rate. The severe stenosis model displays stronger recirculation in the flow field with higher values of vorticity, helicity, and negative wall shear stress. The mild and moderate stenosis configurations produce similar lower levels of vorticity and helicity.

scholarly journals Three-dimensional shape variation of talar surface morphology in hominoid primates

2014 ◽  
Vol 225 (1) ◽  
pp. 42-59 ◽  
Author(s):  
W. C. H. Parr ◽  
C. Soligo ◽  
J. Smaers ◽  
H. J. Chatterjee ◽  
A. Ruto ◽  
...  
Keyword(s):  
Surface Morphology ◽  
Three Dimensional ◽  
Shape Variation ◽  
Dimensional Shape ◽  
Three Dimensional Shape

scholarly journals Dose-response surface fits to drought and nitrogen limitation applied together allow mapping of loci that exhibit nonlinear responses

2017 ◽  
Author(s):  
Megan M. Chang ◽  
Danielle Allery Nail ◽  
Toni Kazic ◽  
Susan J. Simmons ◽  
Ann E. Stapleton
Keyword(s):  
Response Surface ◽  
Dose Response ◽  
Genetic Architecture ◽  
Environmental Changes ◽  
Crop Improvement ◽  
Crop Protection ◽  
Three Dimensional ◽  
Response Surfaces ◽  
Protection Measures ◽  
Different Response

ABSTRACTCrop improvement must accelerate to feed an increasing human population in the face of environmental changes. Breeding programs can include anticipated climatic changes and genetic architecture to optimize improvement strategies. We analyzed the genetic architecture underlying the response of Zea mays to combinations of water and nitrogen stresses. Recombinant inbreds were subjected to nine combinations of the two stresses using an optimized response surface design, and their growth was measured. Three-dimensional dose response surfaces were fit globally and to each polymorphic allele to determine which genetic markers were associated with different response surfaces. Three quantitative trait loci that produced nonlinear surfaces were mapped. Alleles that performed better in combinations of mid-range stresses were typically not the alleles that performed best under combinations of extreme stresses. To develop physiologically relevant models for future genetic analyses, we modeled the network that explains the response surfaces. The network contains two components, an elliptical paraboloid and a plane, that each combine the nitrogen and water inputs. The relative weighting of the two components and the inputs is governed by five parameters. We estimated parameter values for the smoothed surfaces from the experimental lines using a set of points that covered the most distinctive regions of the three-dimensional surfaces. Surfaces computed using these values reproduced the smoothed experimental surfaces well, especially in the neighborhood of the peaks, as judged by three different criteria. The parameters exaggerated the amplitudes of the simulated surfaces. Experiments using single stresses could misestimate responses to their combinations and disguise loci that respond nonlinearly. The three-dimensional shape evaluation strategy used here more thoroughly compares nonlinear, nonplanar responses. We encourage the application of our findings and methods to experiments that mix crop protection measures, stresses, or both, on elite and landrace germplasm.

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.

Detection and comparison of breast shape variation among different three-dimensional body scan conditions: nude, with a structured bra, and with a soft bra

2019 ◽  
Vol 89 (21-22) ◽  
pp. 4595-4606 ◽  
Author(s):  
Jie Pei ◽  
Jintu Fan ◽  
Susan P Ashdown
Keyword(s):  
Regression Models ◽  
Breast Tissue ◽  
Three Dimensional ◽  
Shape Variation ◽  
Breast Asymmetry ◽  
Spider Web ◽  
Contour Maps ◽  
Breast Shape ◽  
3D Scans ◽  
The Impact

To investigate the effect of structured bras and soft bras on breast shape, 46 female participants (Caucasian, BMI < 30, aged 18–45) were recruited for three-dimensional (3D) scanning. Participants were scanned in three conditions: wearing a provided structured bra, a provided soft bra, and nude. The impact of the bras on breast asymmetry was quantitatively studied. The change in breast shape and position from the nude condition to the condition when shaped by the bras was also explored. Contour maps that show the topographic shapes of the scans were generated to analyze these comparisons. Thirty-five measurements were extracted from spider web structures that were derived from the contour maps, and were used for statistical analysis. Eight measurements were found to be especially indicative of the shape variations introduced by the bras. Regression models were built to predict the in-bra shape given only the nude breast shape. Lastly, heat maps that visualize the shape variations from the nude-to-bra condition via colors were plotted on the surfaces of the 3D scans of the participants in bras, and were used for qualitative analysis. This study is helpful in understanding how bras interact with breast tissue, and can provide useful information for the improvement of bra designs for enhanced fitting or desired shaping effects.

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