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Zelditch ML, Swiderski DL. Effects of Procrustes Superimposition and Semilandmark Sliding on Modularity and Integration: An Investigation Using Simulations of Biological Data. Evol Biol 2023. [DOI: 10.1007/s11692-023-09600-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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2
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Sansalone G, Paolo C, Riccardo C, Stephen W, Silvia C, Pasquale R. Trapped in the morphospace: The relationship between morphological integration and functional performance. Evolution 2022; 76:2020-2031. [PMID: 35864587 PMCID: PMC9542761 DOI: 10.1111/evo.14575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 01/22/2023]
Abstract
The evolution of complex morphological structures can be characterized by the interplay between different anatomical regions evolving under functional integration in response to shared selective pressures. Using the highly derived humeral morphology of talpid moles as a model, here we test whether functional performance is linked to increased levels of evolutionary integration between humerus subunits and, if so, what the strength is of the relationship. Combining two-dimensional geometric morphometrics, phylogenetic comparative methods, and functional landscape modeling, we demonstrate that the high biomechanical performance of subterranean moles' humeri is coupled with elevated levels of integration, whereas taxa with low-performance values show intermediate or low integration. Theoretical morphs occurring in high-performance areas of the functional landscape are not occupied by any species, and show a marked drop in covariation levels, suggesting the existence of a strong relationship between integration and performance in the evolution of talpid moles' humeri. We argue that the relative temporal invariance of the subterranean environment may have contributed to stabilize humeral morphology, trapping subterranean moles in a narrow region of the landscape and impeding any attempt to reposition on a new ascending slope.
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Affiliation(s)
- Gabriele Sansalone
- Function, Evolution and Anatomy Research Lab, Zoology Division, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia,Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessina98122Italy
| | - Colangelo Paolo
- Research Institute on Terrestrial EcosystemsNational Research CouncilMontelibretti00015Italy
| | - Castiglia Riccardo
- Department of Biology and Biotechnology “Charles Darwin,”“La Sapienza” University of RomeRoma00161Italy
| | - Wroe Stephen
- Function, Evolution and Anatomy Research Lab, Zoology Division, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia
| | - Castiglione Silvia
- Department of Earth Sciences, Environment and ResourcesUniversità degli Studi di Napoli Federico IINaples80138Italy
| | - Raia Pasquale
- Department of Earth Sciences, Environment and ResourcesUniversità degli Studi di Napoli Federico IINaples80138Italy
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Mitteroecker P, Schaefer K. Thirty years of geometric morphometrics: Achievements, challenges, and the ongoing quest for biological meaningfulness. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 178 Suppl 74:181-210. [PMID: 36790612 PMCID: PMC9545184 DOI: 10.1002/ajpa.24531] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/28/2022] [Accepted: 04/17/2022] [Indexed: 12/30/2022]
Abstract
The foundations of geometric morphometrics were worked out about 30 years ago and have continually been refined and extended. What has remained as a central thrust and source of debate in the morphometrics community is the shared goal of meaningful biological inference through a tight connection between biological theory, measurement, multivariate biostatistics, and geometry. Here we review the building blocks of modern geometric morphometrics: the representation of organismal geometry by landmarks and semilandmarks, the computation of shape or form variables via superimposition, the visualization of statistical results as actual shapes or forms, the decomposition of shape variation into symmetric and asymmetric components and into different spatial scales, the interpretation of various geometries in shape or form space, and models of the association between shape or form and other variables, such as environmental, genetic, or behavioral data. We focus on recent developments and current methodological challenges, especially those arising from the increasing number of landmarks and semilandmarks, and emphasize the importance of thorough exploratory multivariate analyses rather than single scalar summary statistics. We outline promising directions for further research and for the evaluation of new developments, such as "landmark-free" approaches. To illustrate these methods, we analyze three-dimensional human face shape based on data from the Avon Longitudinal Study of Parents and Children (ALSPAC).
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Affiliation(s)
- Philipp Mitteroecker
- Department of Evolutionary Biology, Unit for Theoretical BiologyUniversity of ViennaViennaAustria
| | - Katrin Schaefer
- Department of Evolutionary AnthropologyUniversity of ViennaViennaAustria,Human Evolution and Archaeological Sciences (HEAS)University of ViennaViennaAustria
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4
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MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Sci Data 2022; 9:230. [PMID: 35614082 PMCID: PMC9133120 DOI: 10.1038/s41597-022-01338-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/13/2022] [Indexed: 11/08/2022] Open
Abstract
Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase ( www.facebase.org , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).
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Mitteroecker P, Stansfield E. A model of developmental canalization, applied to human cranial form. PLoS Comput Biol 2021; 17:e1008381. [PMID: 33591964 PMCID: PMC7909690 DOI: 10.1371/journal.pcbi.1008381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/26/2021] [Accepted: 01/14/2021] [Indexed: 11/26/2022] Open
Abstract
Developmental mechanisms that canalize or compensate perturbations of organismal development (targeted or compensatory growth) are widely considered a prerequisite of individual health and the evolution of complex life, but little is known about the nature of these mechanisms. It is even unclear if and how a “target trajectory” of individual development is encoded in the organism’s genetic-developmental system or, instead, emerges as an epiphenomenon. Here we develop a statistical model of developmental canalization based on an extended autoregressive model. We show that under certain assumptions the strength of canalization and the amount of canalized variance in a population can be estimated, or at least approximated, from longitudinal phenotypic measurements, even if the target trajectories are unobserved. We extend this model to multivariate measures and discuss reifications of the ensuing parameter matrix. We apply these approaches to longitudinal geometric morphometric data on human postnatal craniofacial size and shape as well as to the size of the frontal sinuses. Craniofacial size showed strong developmental canalization during the first 5 years of life, leading to a 50% reduction of cross-sectional size variance, followed by a continual increase in variance during puberty. Frontal sinus size, by contrast, did not show any signs of canalization. Total variance of craniofacial shape decreased slightly until about 5 years of age and increased thereafter. However, different features of craniofacial shape showed very different developmental dynamics. Whereas the relative dimensions of the nasopharynx showed strong canalization and a reduction of variance throughout postnatal development, facial orientation continually increased in variance. Some of the signals of canalization may owe to independent variation in developmental timing of cranial components, but our results indicate evolved, partly mechanically induced mechanisms of canalization that ensure properly sized upper airways and facial dimensions. Developmental mechanisms that canalize or compensate perturbations of organismal development are a prerequisite of individual health and the evolution of complex life. However, surprisingly little is known about these mechanisms, partly because the “target trajectories” of individual development cannot be directly observed. Here we develop a statistical model of developmental canalization that allows one to estimate the strength of canalization and the amount of canalized variance in a population even if the target trajectories are unobserved. We applied these approaches to data on human postnatal craniofacial growth. Whereas overall craniofacial size was strongly canalized during the first 5 years of age, frontal sinus size did not show any signs of canalization. The relative dimensions of the nasopharynx showed strong canalization and a reduction of variance throughout postnatal development, whereas other shape features, such as facial orientation, continually increased in variance. Our results indicate evolved, partly mechanically induced mechanisms of canalization that ensure properly sized upper airways and facial dimensions.
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Affiliation(s)
- Philipp Mitteroecker
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- * E-mail:
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6
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Grunstra NDS, Bartsch SJ, Le Maître A, Mitteroecker P. Detecting Phylogenetic Signal and Adaptation in Papionin Cranial Shape by Decomposing Variation at Different Spatial Scales. Syst Biol 2020; 70:694-706. [PMID: 33337483 PMCID: PMC8208804 DOI: 10.1093/sysbio/syaa093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 11/22/2020] [Accepted: 11/26/2020] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic reconstruction based on morphometric data is hampered by homoplasies. For example, many similarities in cranial form between primate taxa more strongly reflect ecological similarities rather than phylogenetic relatedness. However, the way in which the different cranial bones constitute cranial form is, if at all, of less functional relevance and thus largely hidden from selection. We propose that these “constructional details” are better indicators of phylogenetic history than any large-scale shape feature or raw form variable. Within a geometric morphometric context, we show how to analyze the relative extent of bones independently of differences in overall shape. We also show how to decompose total shape variation into small-scale and large-scale shape variation. We apply both methods to the midsagittal cranial morphology of papionin monkeys, which are well known for the discrepancy between morphological similarities and phylogenetic relationships. We study phylogenetic signal and functional adaptation using a molecular phylogeny and contextual data on feeding ecology and locomotor behavior. As expected, total cranial shape, bone outline shape, and large-scale shape features were only weakly associated with phylogenetic distance. But the relative bone contributions and small-scale shape features were both highly correlated with phylogenetic distances. By contrast, the association with ecological and behavioral variables was strongest for the outline shape and large-scale shape features. Studies of morphological adaptation and phylogenetic history thus profit from a decomposition of shape variation into different spatial scales. [Adaptation; canalization; cranial shape; geometric morphometrics; papionini; partial warps; phylogeny.]
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Affiliation(s)
- Nicole D S Grunstra
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria.,Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.,Mammal Collection, Natural History Museum Vienna, Vienna, Austria
| | - Silvester J Bartsch
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria.,Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Anne Le Maître
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria.,PALEVOPRIM - UMR 7262 CNRS INEE, Université de Poitiers, Poitiers, France
| | - Philipp Mitteroecker
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria.,Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
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7
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Le Verger K, Hautier L, Bardin J, Gerber S, Delsuc F, Billet G. Ontogenetic and static allometry in the skull and cranial units of nine-banded armadillos (Cingulata: Dasypodidae: Dasypus novemcinctus). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
A large part of extant and past mammalian morphological diversity is related to variation in size through allometric effects. Previous studies suggested that craniofacial allometry is the dominant pattern underlying mammalian skull shape variation, but cranial allometries were rarely characterized within cranial units such as individual bones. Here, we used 3D geometric morphometric methods to study allometric patterns of the whole skull (global) and of cranial units (local) in a postnatal developmental series of nine-banded armadillos (Dasypus novemcinctus ssp.). Analyses were conducted at the ontogenetic and static levels, and for successive developmental stages. Our results support craniofacial allometry as the global pattern along with more local allometric trends, such as the relative posterior elongation of the infraorbital canal, the tooth row reduction on the maxillary, and the marked development of nuchal crests on the supraoccipital with increasing skull size. Our study also reports allometric proportions of shape variation varying substantially among cranial units and across ontogenetic stages. The multi-scale approach advocated here allowed unveiling previously unnoticed allometric variations, indicating an untapped complexity of cranial allometric patterns to further explain mammalian morphological evolution.
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Affiliation(s)
- Kévin Le Verger
- Museum national d’Histoire naturelle, Centre de Recherche en Paléontologie – Paris, UMR 7207 CR2P MNHN/CNRS/UPMC, Sorbonne Universités, Paris, France
| | - Lionel Hautier
- Institut des Sciences de l’Evolution, Université de Montpellier, UMR 5554 ISEM CNRS/IRD/EPHE, Montpellier cedex, France
- Natural History Museum of London, Department of Life Sciences, Mammal Section, London, UK
| | - Jérémie Bardin
- Museum national d’Histoire naturelle, Centre de Recherche en Paléontologie – Paris, UMR 7207 CR2P MNHN/CNRS/UPMC, Sorbonne Universités, Paris, France
| | - Sylvain Gerber
- Muséum national d’Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, Paris, France
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution, Université de Montpellier, UMR 5554 ISEM CNRS/IRD/EPHE, Montpellier cedex, France
| | - Guillaume Billet
- Museum national d’Histoire naturelle, Centre de Recherche en Paléontologie – Paris, UMR 7207 CR2P MNHN/CNRS/UPMC, Sorbonne Universités, Paris, France
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Schuh A, Gunz P, Villa C, Kupczik K, Hublin JJ, Freidline SE. Intraspecific variability in human maxillary bone modeling patterns during ontogeny. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:655-670. [PMID: 33029815 DOI: 10.1002/ajpa.24153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 08/12/2020] [Accepted: 09/15/2020] [Indexed: 11/08/2022]
Abstract
OBJECTIVES This study compares the ontogenetic bone modeling patterns of the maxilla to the related morphological changes in three human populations to better understand how morphological variability within a species is established during ontogeny at both micro- and macroscopic levels. MATERIALS AND METHODS The maxillary bones of an ontogenetic sample of 145 subadult and adult individuals from Greenland (Inuit), Western Europe (France, Germany, and Portugal), and South Africa (Khoekhoe and San) were analyzed. Bone formation and resorption were quantified using histological methods to visualize the bone modeling patterns. In parallel, semilandmark geometric morphometric techniques were used on 3D models of the same individuals to capture the morphological changes. Multivariate statistics were applied and shape differences between age groups were visualized through heat maps. RESULTS The three populations show differences in the degree of shape change acquired during ontogeny, leading to divergences in the developmental trajectories. Only subtle population differences in the bone modeling patterns were found, which were maintained throughout ontogeny. Bone resorption in adults mirrors the pattern found in subadults, but is expressed at lower intensities. DISCUSSION Our data demonstrate that maxillary morphological differences observed in three geographically distinct human populations are also reflected at the microscopic scale. However, we suggest that these differences are mostly driven by changes in rates and timings of the cellular activities, as only slight discrepancies in the location of bone resorption could be observed. The shared general bone modeling pattern is likely characteristic of all Homo sapiens, and can be observed throughout ontogeny.
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Affiliation(s)
- Alexandra Schuh
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp Gunz
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Chiara Villa
- Laboratory of Advanced Imaging and 3D modelling, Section of Forensic Pathology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kornelius Kupczik
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Max Planck Weizmann Center for Integrative Archaeology and Anthropology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah E Freidline
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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9
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Le Maître A, Grunstra NDS, Pfaff C, Mitteroecker P. Evolution of the Mammalian Ear: An Evolvability Hypothesis. Evol Biol 2020; 47:187-192. [PMID: 32801400 PMCID: PMC7399675 DOI: 10.1007/s11692-020-09502-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
Encapsulated within the temporal bone and comprising the smallest elements of the vertebrate skeleton, the ear is key to multiple senses: balance, posture control, gaze stabilization, and hearing. The transformation of the primary jaw joint into the mammalian ear ossicles is one of the most iconic transitions in vertebrate evolution, but the drivers of this complex evolutionary trajectory are not fully understood. We propose a novel hypothesis: The incorporation of the bones of the primary jaw joint into the middle ear has considerably increased the genetic, regulatory, and developmental complexity of the mammalian ear. This increase in the number of genetic and developmental factors may, in turn, have increased the evolutionary degrees of freedom for independent adaptations of the different functional ear units. The simpler ear anatomy in birds and reptiles may be less susceptible to developmental instabilities and disorders than in mammals but also more constrained in its evolution. Despite the tight spatial entanglement of functional ear components, the increased "evolvability" of the mammalian ear may have contributed to the evolutionary success and adaptive diversification of mammals in the vast diversity of ecological and behavioral niches observable today. A brief literature review revealed supporting evidence for this hypothesis.
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Affiliation(s)
- Anne Le Maître
- Department of Evolutionary Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Department of Palaeontology, University of Vienna, Vienna, Austria
- PALEVOPRIM - UMR 7262CNRS INEE, Université de Poitiers, Poitiers, France
| | - Nicole D. S. Grunstra
- Department of Evolutionary Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- KLI Institute for Evolution and Cognition Research, Klosterneuburg, Austria
- Mammal Collection, Natural History Museum Vienna, Vienna, Austria
| | - Cathrin Pfaff
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Philipp Mitteroecker
- Department of Evolutionary Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- KLI Institute for Evolution and Cognition Research, Klosterneuburg, Austria
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Pélabon C, Hilde CH, Einum S, Gamelon M. On the use of the coefficient of variation to quantify and compare trait variation. Evol Lett 2020; 4:180-188. [PMID: 32547779 PMCID: PMC7293077 DOI: 10.1002/evl3.171] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/06/2020] [Accepted: 03/31/2020] [Indexed: 11/29/2022] Open
Abstract
Meaningful comparison of variation in quantitative trait requires controlling for both the dimension of the varying entity and the dimension of the factor generating variation. Although the coefficient of variation (CV; standard deviation divided by the mean) is often used to measure and compare variation of quantitative traits, it only accounts for the dimension of the former, and its use for comparing variation may sometimes be inappropriate. Here, we discuss the use of the CV to compare measures of evolvability and phenotypic plasticity, two variational properties of quantitative traits. Using a dimensional analysis, we show that contrary to evolvability, phenotypic plasticity cannot be meaningfully compared across traits and environments by mean‐scaling trait variation. We further emphasize the need of remaining cognizant of the dimensions of the traits and the relationship between mean and standard deviation when comparing CVs, even when the scales on which traits are expressed allow meaningful calculation of the CV.
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Affiliation(s)
- Christophe Pélabon
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology (NTNU) Trondheim 7491 Norway
| | - Christoffer H Hilde
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology (NTNU) Trondheim 7491 Norway
| | - Sigurd Einum
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology (NTNU) Trondheim 7491 Norway
| | - Marlène Gamelon
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology (NTNU) Trondheim 7491 Norway
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