scholarly journals Geometric morphometrics analysis: a complement to the revision of whelk taxonomy in the Arctic

2018 ◽  
Author(s):  
Lisa Treau De Coeli ◽  
Jean-Marc Gagnon ◽  
Philippe Archambault
Keyword(s):  
Phenotypic Plasticity ◽  
Geometric Morphometrics ◽  
Community Dynamics ◽  
The Arctic ◽  
Proof Of Concept ◽  
Benthic Organisms ◽  
Dispersal Capacity ◽  
Reproduction Mode ◽  
3 Dimensional ◽  
Limited Dispersal

Ice cover, food availability, light intensity, limited dispersal capacity, presence of predators and reproduction mode are just a few of the drivers that influence benthic community dynamics, especially in the Arctic. Benthic organisms can respond to such drivers through morphologic variations, referred to as phenotypic plasticity. These variations are however hard to observe on Arctic whelk (genus Buccinum) and their diversity and extensive distribution increase the complexity of their identification. While genetics analyses can address this problem, they are not broadly accessible. More accessible are landmark-based geometric morphometrics which analytically identifies morphologic variations. This technique aims at identifying shape variations and could be used to identify intra- and inter-species morphologic variability in the genus Buccinum. The main objective of this project is to verify whether landmark-based geometric morphometrics, particularly 3-dimensional, could be used on whelk species. If this proof of concept proves successful, the next step will be to identify new morphologic traits to differentiate species and compare this technique to genetics analyses on multiple Buccinum species. This project could allow researchers to efficiently differentiate between whelk species on the basis of morphologic traits rather than through more demanding genetics analyses.

scholarly journals Geometric morphometrics analysis: a complement to the revision of whelk taxonomy in the Arctic

2018 ◽  
Author(s):  
Lisa Treau De Coeli ◽  
Jean-Marc Gagnon ◽  
Philippe Archambault
Keyword(s):  
Phenotypic Plasticity ◽  
Geometric Morphometrics ◽  
Community Dynamics ◽  
The Arctic ◽  
Proof Of Concept ◽  
Benthic Organisms ◽  
Dispersal Capacity ◽  
Reproduction Mode ◽  
3 Dimensional ◽  
Limited Dispersal

Ice cover, food availability, light intensity, limited dispersal capacity, presence of predators and reproduction mode are just a few of the drivers that influence benthic community dynamics, especially in the Arctic. Benthic organisms can respond to such drivers through morphologic variations, referred to as phenotypic plasticity. These variations are however hard to observe on Arctic whelk (genus Buccinum) and their diversity and extensive distribution increase the complexity of their identification. While genetics analyses can address this problem, they are not broadly accessible. More accessible are landmark-based geometric morphometrics which analytically identifies morphologic variations. This technique aims at identifying shape variations and could be used to identify intra- and inter-species morphologic variability in the genus Buccinum. The main objective of this project is to verify whether landmark-based geometric morphometrics, particularly 3-dimensional, could be used on whelk species. If this proof of concept proves successful, the next step will be to identify new morphologic traits to differentiate species and compare this technique to genetics analyses on multiple Buccinum species. This project could allow researchers to efficiently differentiate between whelk species on the basis of morphologic traits rather than through more demanding genetics analyses.

scholarly journals A simple standardized protocol to evaluate the reliability of seed rain estimates

2020 ◽  
pp. 1-6
Author(s):  
André J. Arruda ◽  
Fernando A.O. Silveira ◽  
Elise Buisson
Keyword(s):  
Restoration Ecology ◽  
Community Dynamics ◽  
Size Dependence ◽  
Seed Rain ◽  
Proof Of Concept ◽  
Sticky Traps ◽  
Standardized Protocol ◽  
Funnel Trap ◽  
Seed Trap ◽  
Cross Site

Abstract Seed dispersal has key implications for community dynamics and restoration ecology. However, estimating seed rain (the number and diversity of seeds arriving in a given area) is challenging, and the lack of standardization in measurement prevents cross-site comparisons. Seed trap effectiveness and accuracy of seed sorting methods are key components of seed rain estimates in need of standardization. We propose and describe a standardized protocol for evaluating the effectiveness of two seed trap types (sticky and funnel traps) and the accuracy of a seed sorting method. We used widely available seeds (arugula, quinoa, sesame and sunflower) to produce a gradient of seed size, weight and colour. Proof-of-concept was tested in a tropical grassland, where traps were set for 30 days. Our results suggest that we underestimate dispersal of seeds with less than 2 mm width that can be easily mistaken for debris and soil particles or that fail to adhere to sticky traps. Seeds on sticky traps may be more vulnerable to removal by wind and rain, whereas seeds in funnel traps are more susceptible to decay. We found no evidence of observer bias on seed sorting for funnel trap samples. However, accuracy on seed sorting for funnel trap samples tended to decline for seeds with less than 2 mm width, suggesting a size-dependence in seed retrieval success. Our standardized protocol addressing trap effectiveness and seed sorting methods will increase the reliability of data obtained in seed rain studies and allow more reliable comparisons between datasets.

Allozyme Evidence of Genetic Differentiation Between Populations of Hediste Diversicolor (Polychaeta: Nereididae) from the Western Mediterranean

1996 ◽  
Vol 76 (3) ◽  
pp. 637-647 ◽  
Author(s):  
M. Abbiati ◽  
F. Maltagliati
Keyword(s):  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Western Mediterranean ◽  
Allozyme Electrophoresis ◽  
Isolated Populations ◽  
Hediste Diversicolor ◽  
Dispersal Capacity ◽  
Two Samples ◽  
Distance Model ◽  
Limited Dispersal

The occurrence of genetic differentiation among western Mediterranean Hediste diversicolor (Polychaeta: Nereididae) populations was assessed by allozyme electrophoresis on cellulose acetate. Seventeen loci were analysed in four populations. The level of the genetic variability was markedly low (mean HL range: 0.014–0.034), but comparable to that of other brackish water nereidids. The values of Nei genetic distance index (D) confirm the existence of genetic differentiation between the geographically isolated populations at Venice, Elba, Navicelli and Serchio D range: 0.128–0.356). However, the two samples from Serchio and Navicelli, ~15 km apart, were not genetically different (D=0·00005). The level of genetic differentiation in H. diversicolor populations followed the isolation-by-distance model. Reduced gene flow among H. diversicolor populations may be explained by its limited dispersal capacity and the eco-physiological barriers that occur between different brackish habitats.

Towards A 3D Chromosome Shape Alphabet

2020 ◽  
Author(s):  
Carlos Soto ◽  
Darshan Bryner ◽  
Nicola Neretti ◽  
Anuj Srivastava
Keyword(s):  
Structural Biology ◽  
3D Structure ◽  
Proof Of Concept ◽  
3D Structures ◽  
3 Dimensional ◽  
Topologically Associating Domains ◽  
Independent Test ◽  
Sequence Logos ◽  
Shape Data

AbstractThe study of the 3-dimensional (3D) structure of chromosomes – the largest macromolecules in biology – is one of the most challenging to date in structural biology. Here, we develop a novel representation of chromosomes, as sequences of shape letters from a finite shape alphabet, which provides a compact and efficient way to analyze ensembles of chromosome shape data, akin to the analysis of texts in a language by using letters. We construct a Chromosome Shape Alphabet (CSA) from an ensemble of chromosome 3D structures inferred from Hi-C data – via SIMBA3D or other methods – by segmenting curves based on topologically associating domains (TADs) boundaries, and by clustering all TADs’ 3D structures into groups of similar shapes. The median shapes of these groups, with some pruning and processing, form the Chromosome Shape Letters (CSLs) of the alphabet. We provide a proof-of-concept for these CSLs by reconstructing independent test curves using only CSLs (and corresponding transformations) and comparing these reconstructions with the original curves. Finally, we demonstrate how CSLs can be used to summarize the variability of shapes in an ensemble of chromosome 3D structures using generalized sequence logos.

scholarly journals Divergent scute asymmetry among pure and crossed individuals of Testudo hermanni (Gmelin, 1789)

2020 ◽  
pp. 43-50
Author(s):  
P. M. Parés–Casanova ◽  
J. Minoves ◽  
J. Soler ◽  
A. Martínez–Silvestre
Keyword(s):  
Phenotypic Plasticity ◽  
Geometric Morphometrics ◽  
Key Words ◽  
Fluctuating Asymmetry ◽  
Environmental Changes ◽  
Developmental Stability ◽  
Anatomical Landmarks ◽  
Geometric Morphometric ◽  
Testudo Hermanni ◽  
Left And Right

Fluctuating asymmetry (FA) refers to subtle differences between left and right sides in bilaterally symmetrical organisms or their parts. Both genetic and environmental changes can increase FA, reflecting deterioration in developmental homeostasis of adult morphology due to a loss of developmental stability. In this study, we used geometric morphometric techniques to examine plastral scute asymmetries in a sample of 31 pure and crossed Testudo species (T. hermanni hermanni n = 23 and crosses with T. hermanni boettgeri n = 8) only females by means of 19 anatomical landmarks. Procrustes ANOVA indicated that FA in crossed individuals was significantly higher than that in pure individuals. Crossed individuals also showed a greater degree of phenotypic plasticity than T. hermanni hermanni. We conclude that crosses among T. hermanni hermanni and T. hermanni boettgeri can increase homozygosity and are responsible for greater developmental instabilities. Nonetheless, more information on crossed phenotypes could be of great interest to raise pure Hermann’s tortoises for reintroduction programmes. Key words: Carapace, Geometric morphometrics, Hybridization, Plastron, Testudines

Lissajous-Like Scan Pattern for a Nodding Multi-Beam Lidar

2018 ◽  
Author(s):  
Michael Benson ◽  
Jonathan Nikolaidis ◽  
Garrett M. Clayton
Keyword(s):  
Lidar Data ◽  
Trajectory Design ◽  
Vertical Resolution ◽  
Proof Of Concept ◽  
Lidar System ◽  
Trade Off ◽  
3 Dimensional ◽  
Raster Scan ◽  
Scan Speed ◽  
Scan Pattern

In this paper, trajectory design for a nodding multi-beam Lidar system is studied. While the multi-beam Lidar is inherently 3-dimensional and does not require nodding to create a 3D scan, the vertical resolution of these units can be limited, depending on the number of Lidar beams and their spread. This is especially important when viewing small objects and objects at distance. This vertical resolution can be improved by placing the Lidar on a nodding mechanism, allowing the beams to be repositioned. Typically, this mechansism undergoes a raster scan pattern, where the Lidar is slowly rotated and each line of Lidar data is collected in order. In contrast, this work presents the use of Lissajous-like scan pattern, in which the depth points are collected while the cradle is moving quickly. This trajectory allows for a trade-off between scan speed and resolution that is not possible when using a raster scan. In this paper, relevant theory and prior work is presented, simulations are shown that support the proposed theory, and proof-of-concept experiments are performed to show the feasibility of the approach.

scholarly journals Differences in Mobility and Dispersal Capacity Determine Body Size Clines in Two Common Alpine-Tundra Arthropods

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 74 ◽  
Author(s):  
Beckers ◽  
Hein ◽  
Anneser ◽  
Vanselow ◽  
Löffler
Keyword(s):  
Body Size ◽  
High Mobility ◽  
Carabid Beetles ◽  
Alpine Tundra ◽  
The Arctic ◽  
Dispersal Capacity ◽  
Spatial Gradients ◽  
Temperature And Precipitation ◽  
Underlying Mechanisms ◽  
Possible Cause

The Arctic is projected to be severely impacted by changes in temperature and precipitation. Species react to these changes by shifts in ranges, phenology, and body size. In ectotherms, the patterns of body size clines and their underlying mechanisms are often hard to untangle. Mountains provide a space-for-time substitute to study these shifts along multiple spatial gradients. As such, mobility and dispersal capacity might conceal reactions with elevation. We test this influence on body size clines by comparing two common arthropods of the alpine tundra. We find that high mobility in the lycosid spider Pardosa palustris blurs elevational effects. Partially low mobility at least during development makes the carabid beetle Amara alpina more susceptible to elevational effects. Specific life-history mechanisms, such as brood care in lycosid spiders and holometabolic development in carabid beetles, are the possible cause.

Initial Experience with 3-Dimensional Exoscope-Assisted Transmastoid and Lateral Skull Base Surgery

2019 ◽  
Vol 160 (2) ◽  
pp. 364-367 ◽  
Author(s):  
Sullivan Smith ◽  
Elliott D. Kozin ◽  
Vivek V. Kanumuri ◽  
Samuel R. Barber ◽  
Douglas Backous ◽  
...  
Keyword(s):  
Visual Experience ◽  
Skull Base Surgery ◽  
Perioperative Complications ◽  
Surgical Approaches ◽  
Operating Microscope ◽  
Proof Of Concept ◽  
High Definition ◽  
3 Dimensional ◽  
Lateral Skull Base ◽  
Compact Size

Extracorporeal video microscopes, or “exoscopes,” provide high-definition views of the operative field and are alternatives to the operating microscope or loupes for large-corridor surgical approaches. In this proof-of-concept study, we aim to determine the feasibility of 3-dimensional exoscopes as alternatives to operating microscopes in otology and neurotology, espeically in conjunction with endoscopes. Eleven consecutive cases were performed using 3-dimensional exoscopes in place of, or as adjuncts to, the operating microscope. The exoscope was the sole visualization tool in 7 cases, with 4 including the use of an endoscope or microscope. There were no perioperative complications. Potential subjective advantages include superior ergonomics, compact size, and an equal visual experience for surgeons and observers. Limitations include low lighting in small surgical corridors and pixilation at high magnification. Exoscopes are potentially viable alternatives to the microscope in otologic and neurotologic surgery.

scholarly journals Community dynamics and sensitivity to model structure: towards a probabilistic view of process-based model predictions

2018 ◽  
Vol 15 (149) ◽  
pp. 20180741 ◽  
Author(s):  
Clement Aldebert ◽  
Daniel B. Stouffer
Keyword(s):  
Biological Sciences ◽  
Community Dynamics ◽  
Parametric Uncertainty ◽  
Proof Of Concept ◽  
Predator Prey ◽  
Predictive Uncertainty ◽  
Structural Sensitivity ◽  
Model Predictions ◽  
Complex Models ◽  
Process Based Models

Statistical inference and mechanistic, process-based modelling represent two philosophically different streams of research whose primary goal is to make predictions. Here, we merge elements from both approaches to keep the theoretical power of process-based models while also considering their predictive uncertainty using Bayesian statistics. In environmental and biological sciences, the predictive uncertainty of process-based models is usually reduced to parametric uncertainty. Here, we propose a practical approach to tackle the added issue of structural sensitivity, the sensitivity of predictions to the choice between quantitatively close and biologically plausible models. In contrast to earlier studies that presented alternative predictions based on alternative models, we propose a probabilistic view of these predictions that include the uncertainty in model construction and the parametric uncertainty of each model. As a proof of concept, we apply this approach to a predator–prey system described by the classical Rosenzweig–MacArthur model, and we observe that parametric sensitivity is regularly overcome by structural sensitivity. In addition to tackling theoretical questions about model sensitivity, the proposed approach can also be extended to make probabilistic predictions based on more complex models in an operational context. Both perspectives represent important steps towards providing better model predictions in biology, and beyond.

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