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Thomas OO, Maga AM. Leveraging Descriptor Learning and Functional Map-based Shape Matching for Automatic Landmark Acquisition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595350. [PMID: 38826373 PMCID: PMC11142217 DOI: 10.1101/2024.05.22.595350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Geometric morphometrics is widely employed across the biological sciences for the quantification of morphological traits. However, the scalability of these methods to large datasets is hampered by the requisite placement of landmarks, which can be laborious and time consuming if done manually. Additionally, the selected landmarks embody a particular hypothesis regarding the critical geometry pertinent to the biological inquiry at hand. Modifying this hypothesis lacks flexibility, necessitating the acquisition of an entirely new set of landmarks on the entire dataset to reflect any theoretical adjustments. In our research, we investigate the precision and accuracy of landmarks derived from the comprehensive set of functional correspondences acquired through the functional map framework of geometry processing. We use a deep functional map network to learn shape descriptors that effectively yield functional map-based and point-to-point correspondences between the specimens in our dataset. We then interrogate these maps to identify corresponding landmarks given manually placed landmarks from the entire dataset. We assess our method by automating the landmarking process on a dataset comprising mandibles from various rodent species, comparing its efficacy against MALPACA, a cutting-edge technique for automatic landmark placement. Compared to MALPACA, our model is notably faster and maintains competitive accuracy. The Root Mean Square Error (RMSE) analysis reveals that while MALPACA generally exhibits the lowest RMSE, our models perform comparably, especially with smaller training datasets, suggesting strong generalizability. Visual evaluations confirm the precision of our landmark placements, with deviations remaining within an acceptable range. These findings underscore the potential of unsupervised learning models in anatomical landmark placement, providing a viable and efficient alternative to traditional methods.
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Affiliation(s)
- Oshane O Thomas
- Center for Development Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - A Murat Maga
- Center for Development Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, United States of America
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
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Parmenter MD, Nelson JP, Gray MM, Weigel S, Vinyard CJ, Payseur BA. A complex genetic architecture underlies mandibular evolution in big mice from Gough Island. Genetics 2022; 220:iyac023. [PMID: 35137059 PMCID: PMC8982026 DOI: 10.1093/genetics/iyac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/31/2022] [Indexed: 01/29/2023] Open
Abstract
Some of the most compelling examples of morphological evolution come from island populations. Alterations in the size and shape of the mandible have been repeatedly observed in murid rodents following island colonization. Despite this pattern and the significance of the mandible for dietary adaptation, the genetic basis of island-mainland divergence in mandibular form remains uninvestigated. To fill this gap, we examined mandibular morphology in 609 F2s from a cross between Gough Island mice, the largest wild house mice on record, and mice from a mainland reference strain (WSB). Univariate genetic mapping identifies 3 quantitative trait loci (QTL) for relative length of the temporalis lever arm and 2 distinct QTL for relative condyle length, 2 traits expected to affect mandibular function that differ between Gough Island mice and WSB mice. Multivariate genetic mapping of coordinates from geometric morphometric analyses identifies 27 QTL contributing to overall mandibular shape. Quantitative trait loci show a complex mixture of modest, additive effects dispersed throughout the mandible, with landmarks including the coronoid process and the base of the ascending ramus frequently modulated by QTL. Additive effects of most shape quantitative trait loci do not align with island-mainland divergence, suggesting that directional selection played a limited role in the evolution of mandibular shape. In contrast, Gough Island mouse alleles at QTL for centroid size and QTL for jaw length increase these measures, suggesting selection led to larger mandibles, perhaps as a correlated response to the evolution of larger bodies.
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Affiliation(s)
| | - Jacob P Nelson
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Melissa M Gray
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Sara Weigel
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Christopher J Vinyard
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
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Jojić V, Čabrilo B, Bjelić-Čabrilo O, Jovanović VM, Budinski I, Vujošević M, Blagojević J. Canalization and developmental stability of the yellow-necked mouse (Apodemus flavicollis) mandible and cranium related to age and nematode parasitism. Front Zool 2021; 18:55. [PMID: 34689812 PMCID: PMC8543932 DOI: 10.1186/s12983-021-00439-4] [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: 06/22/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mammalian mandible and cranium are well-established model systems for studying canalization and developmental stability (DS) as two elements of developmental homeostasis. Nematode infections are usually acquired in early life and increase in intensity with age, while canalization and DS of rodent skulls could vary through late postnatal ontogeny. We aimed to estimate magnitudes and describe patterns of mandibular and cranial canalization and DS related to age and parasite intensity (diversity) in adult yellow-necked mice (Apodemus flavicollis). RESULTS We found the absence of age-related changes in the levels of canalization for mandibular and cranial size and DS for mandibular size. However, individual measures of mandibular and cranial shape variance increased, while individual measures of mandibular shape fluctuating asymmetry (FA) decreased with age. We detected mandibular and cranial shape changes during postnatal ontogeny, but revealed no age-related dynamics of their covariance structure among and within individuals. Categories regarding parasitism differed in the level of canalization for cranial size and the level of DS for cranial shape. We observed differences in age-related dynamics of the level of canalization between non-parasitized and parasitized animals, as well as between yellow-necked mice parasitized by different number of nematode species. Likewise, individual measures of mandibular and cranial shape FA decreased with age for the mandible in the less parasitized category and increased for the cranium in the most parasitized category. CONCLUSIONS Our age-related results partly agree with previous findings. However, no rodent study so far has explored age-related changes in the magnitude of FA for mandibular size or mandibular and cranial FA covariance structure. This is the first study dealing with the nematode parasitism-related canalization and DS in rodents. We showed that nematode parasitism does not affect mandibular and cranial shape variation and covariance structure among and within individuals. However, parasite intensity (diversity) is related to ontogenetic dynamics of the levels of canalization and DS. Overall, additional studies on animals from natural populations are required before drawing some general conclusions.
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Affiliation(s)
- Vida Jojić
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia.
| | - Borislav Čabrilo
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Olivera Bjelić-Čabrilo
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Vladimir M Jovanović
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia.,Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany.,Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
| | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Mladen Vujošević
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jelena Blagojević
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
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Caccavo A, Lemos H, Maroja LS, Gonçalves PR. Does stress mess with rodents' heads? Influence of habitat amount and genetic factors in mandible fluctuating asymmetry in South American water rats ( Nectomys squamipes, Sigmodontinae) from Brazilian Atlantic rainforest remnants. Ecol Evol 2021; 11:7080-7092. [PMID: 34141277 PMCID: PMC8207160 DOI: 10.1002/ece3.7557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/20/2022] Open
Abstract
Loss of developmental stability can lead to deviations from bilateral symmetry (i.e. Fluctuating Asymmetry - FA), and is thought to be caused by environmental and genetic factors associated with habitat loss and stress. Therefore, levels of FA might be a valuable tool to monitor wild populations if FA serves as an indicator of exposure to stress due to impacts of habitat loss and fragmentation. In studies examining FA and habitat fragmentation, FA levels are often explained by loss of genetic variation, though few studies have addressed FA's use as indicator of environmental impact. Here, we investigated whether habitat loss, genetic variation, and/or inbreeding affect the developmental instability in Brazilian Atlantic forest populations of a Neotropical water rat (Nectomys squamipes). We sampled individuals from eight sites within Atlantic forest remnants with different amounts of available forest habitat and assessed FA levels with geometric morphometric techniques using adult mandibles. We used observed heterozygosity (Ho) and inbreeding coefficient (Fis), from seven microsatellite markers, as a proxy of genetic variation at individual and population levels. Populations were not significantly different for shape or size FA levels. Furthermore, interindividual variation in both shape and size FA levels and interpopulational differences in size FA levels were best explained by chance. However, habitat amount was negatively associated with both interpopulational variance and average shape FA levels. This association was stronger in populations living in areas with <28% of forest cover, which presented higher variance and higher average FA, suggesting that Nectomys squamipes might have a tolerance threshold to small availability of habitat. Our work is one of the first to use FA to address environmental stress caused by habitat loss in small mammal populations from a Neotropical biome. We suggest that shape FA might serve as a conservation tool to monitor human impact on natural animal populations.
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Affiliation(s)
- Aldo Caccavo
- Programa de Pós‐Graduação em Ciências Ambientais e ConservaçãoPPGCiAC ‐ Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
- Setor de MastozoologiaDepartamento de VertebradosMuseu NacionalUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
- Museu de História Natural do Ceará Prof. Dias da RochaCentro de Ciências da SaúdeUniversidade Estadual do CearáCearáBrazil
| | - Hudson Lemos
- Programa de Pós‐Graduação em Ciências Ambientais e ConservaçãoPPGCiAC ‐ Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | | | - Pablo Rodrigues Gonçalves
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
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Agbolade O, Nazri A, Yaakob R, Ghani AA, Cheah YK. Morphometric approach to 3D soft-tissue craniofacial analysis and classification of ethnicity, sex, and age. PLoS One 2020; 15:e0228402. [PMID: 32271782 PMCID: PMC7145022 DOI: 10.1371/journal.pone.0228402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/14/2020] [Indexed: 11/18/2022] Open
Abstract
Background The application of three-dimensional scan models offers a useful resource for studying craniofacial variation. The complex mathematical analysis for facial point acquisition in three-dimensional models has made many craniofacial assessments laborious. Method This study investigates three-dimensional (3D) soft-tissue craniofacial variation, with relation to ethnicity, sex and age variables in British and Irish white Europeans. This utilizes a geometric morphometric approach on a subsampled dataset comprising 292 scans, taken from a Liverpool-York Head Model database. Shape variation and analysis of each variable are tested using 20 anchor anatomical landmarks and 480 sliding semi-landmarks. Results Significant ethnicity, sex, and age differences are observed for measurement covering major aspects of the craniofacial shape. The ethnicity shows subtle significant differences compared to sex and age; even though it presents the lowest classification accuracy. The magnitude of dimorphism in sex is revealed in the facial, nasal and crania measurement. Significant shape differences are also seen at each age group, with some distinct dimorphic features present in the age groups. Conclusions The patterns of shape variation show that white British individuals have a more rounded head shape, whereas white Irish individuals have a narrower head shape. White British persons also demonstrate higher classification accuracy. Regarding sex patterns, males are relatively larger than females, especially in the mouth and nasal regions. Females presented with higher classification accuracy than males. The differences in the chin, mouth, nose, crania, and forehead emerge from different growth rates between the groups. Classification accuracy is best for children and senior adult age groups.
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Affiliation(s)
- Olalekan Agbolade
- Department of Computer Science, Faculty of Computer Science & IT, Universiti Putra Malaysia, Seri Kembangan, Selangor, Malaysia
| | - Azree Nazri
- Department of Computer Science, Faculty of Computer Science & IT, Universiti Putra Malaysia, Seri Kembangan, Selangor, Malaysia
- * E-mail:
| | - Razali Yaakob
- Department of Computer Science, Faculty of Computer Science & IT, Universiti Putra Malaysia, Seri Kembangan, Selangor, Malaysia
| | - Abdul Azim Ghani
- Department of Software Engineering, Faculty of Computer Science & IT, Universiti Putra Malaysia, Seri Kembangan, Selangor, Malaysia
| | - Yoke Kqueen Cheah
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Seri Kembangan, Selangor, Malaysia
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Agbolade O, Nazri A, Yaakob R, Ghani AAA, Cheah YK. Landmark-based homologous multi-point warping approach to 3D facial recognition using multiple datasets. PeerJ Comput Sci 2020; 6:e249. [PMID: 33816901 PMCID: PMC7924716 DOI: 10.7717/peerj-cs.249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 12/05/2019] [Indexed: 11/20/2022]
Abstract
Over the years, neuroscientists and psychophysicists have been asking whether data acquisition for facial analysis should be performed holistically or with local feature analysis. This has led to various advanced methods of face recognition being proposed, and especially techniques using facial landmarks. The current facial landmark methods in 3D involve a mathematically complex and time-consuming workflow involving semi-landmark sliding tasks. This paper proposes a homologous multi-point warping for 3D facial landmarking, which is verified experimentally on each of the target objects in a given dataset using 500 landmarks (16 anatomical fixed points and 484 sliding semi-landmarks). This is achieved by building a template mesh as a reference object and applying this template to each of the targets in three datasets using an artificial deformation approach. The semi-landmarks are subjected to sliding along tangents to the curves or surfaces until the bending energy between a template and a target form is minimal. The results indicate that our method can be used to investigate shape variation for multiple datasets when implemented on three databases (Stirling, FRGC and Bosphorus).
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Affiliation(s)
- Olalekan Agbolade
- Department of Computer Science, Faculty of Computer Science & IT, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Azree Nazri
- Department of Computer Science, Faculty of Computer Science & IT, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Razali Yaakob
- Department of Computer Science, Faculty of Computer Science & IT, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abdul Azim Abd Ghani
- Department of Software Engineering, Faculty of Computer Science & IT, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yoke Kqueen Cheah
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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3-Dimensional facial expression recognition in human using multi-points warping. BMC Bioinformatics 2019; 20:619. [PMID: 31791234 PMCID: PMC6889223 DOI: 10.1186/s12859-019-3153-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/11/2019] [Indexed: 11/28/2022] Open
Abstract
Background Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in 3D by machine remains a challenge in computer vision. This is due to the current challenges facing facial data acquisition in 3D; such as lack of homology and complex mathematical analysis for facial point digitization. This study proposes facial expression recognition in human with the application of Multi-points Warping for 3D facial landmark by building a template mesh as a reference object. This template mesh is thereby applied to each of the target mesh on Stirling/ESRC and Bosphorus datasets. The semi-landmarks are allowed to slide along tangents to the curves and surfaces until the bending energy between a template and a target form is minimal and localization error is assessed using Procrustes ANOVA. By using Principal Component Analysis (PCA) for feature selection, classification is done using Linear Discriminant Analysis (LDA). Result The localization error is validated on the two datasets with superior performance over the state-of-the-art methods and variation in the expression is visualized using Principal Components (PCs). The deformations show various expression regions in the faces. The results indicate that Sad expression has the lowest recognition accuracy on both datasets. The classifier achieved a recognition accuracy of 99.58 and 99.32% on Stirling/ESRC and Bosphorus, respectively. Conclusion The results demonstrate that the method is robust and in agreement with the state-of-the-art results.
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8
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Monteiro LR, Mellado B, Nogueira MR, de Morais-Jr MM. Individual asymmetry as a predictor of fitness in the bat Carollia perspicillata. J Evol Biol 2019; 32:1207-1229. [PMID: 31420901 DOI: 10.1111/jeb.13522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 07/08/2019] [Accepted: 08/09/2019] [Indexed: 11/26/2022]
Abstract
The measurement of fitness in wild populations is a challenging task, and a number of proxies have been proposed with different degrees of success. Developmental instability/stability (DI) is an organismal property associated with variance in bilateral asymmetry (fluctuating asymmetry-FA) and a correlated effect on fitness. This study provides evidence to corroborate the hypothesis that asymmetry partly reflects DI and is correlated with a reduction in fitness measured by survival and reproduction in bats. We studied two colonies of the bat Carollia perspicillata in southeastern Brazil over 5 years, marking and recapturing individuals. Gaussian mixture models for signed Forearm Asymmetry (ForA) distribution indicated that ~20% of asymmetry variation was due to DI heterogeneity among individuals. ForA, body condition (Scaled Mass Index-SMI) and Forearm Length (ForL) were used as predictors of survival probability in Cormack-Jolly-Seber models. Asymmetry was negatively associated with survival, whereas SMI and ForL were positively associated. The male C. perspicillata defend sites within the roost that are favoured by female harems, but there are mating opportunities for bachelor males, leading to both territorial disputes and sperm competition. As predicted by sexual selection, ForA was negatively associated with relative Testicle Length, a measure of reproductive potential. In females, ForA was negatively associated with the probability of two pregnancies (as opposed to one) in a given breeding season. The effect magnitudes and directions of associations suggest that asymmetry, even though not perfectly reflecting DI variation, is a useful predictor for fitness components in C. perspicillata.
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Affiliation(s)
- Leandro R Monteiro
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, Brazil
| | - Breno Mellado
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, Brazil
| | - Marcelo R Nogueira
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, Brazil
| | - Marcio M de Morais-Jr
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, Brazil
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Varón-González C, Navarro N. Epistasis regulates the developmental stability of the mouse craniofacial shape. Heredity (Edinb) 2019; 122:501-512. [PMID: 30209292 PMCID: PMC6461946 DOI: 10.1038/s41437-018-0140-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/19/2022] Open
Abstract
Fluctuating asymmetry is a classic concept linked to organismal development. It has traditionally been used as a measure of developmental instability, which is the inability of an organism to buffer environmental fluctuations during development. Developmental stability has a genetic component that influences the final phenotype of the organism and can lead to congenital disorders. According to alternative hypotheses, this genetic component might be either the result of additive genetic effects or a by-product of developmental gene networks. Here we present a genome-wide association study of the genetic architecture of fluctuating asymmetry of the skull shape in mice. Geometric morphometric methods were applied to quantify fluctuating asymmetry: we estimated fluctuating asymmetry as Mahalanobis distances to the mean asymmetry, correcting first for genetic directional asymmetry. We applied the marginal epistasis test to study epistasis among genomic regions. Results showed no evidence of additive effects but several interacting regions significantly associated with fluctuating asymmetry. Among the candidate genes overlapping these interacting regions we found an over-representation of genes involved in craniofacial development. A gene network is likely to be associated with skull developmental stability, and genes originally described as buffering genes (e.g., Hspa2) might occupy central positions within these networks, where regulatory elements may also play an important role. Our results constitute an important step in the exploration of the molecular roots of developmental stability and the first empirical evidence about its genetic architecture.
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Affiliation(s)
- Ceferino Varón-González
- Biogéosciences, UMR CNRS 6282, Université Bourgogne Franche-Comté, 6 Bd Gabriel, 21000, Dijon, France
| | - Nicolas Navarro
- Biogéosciences, UMR CNRS 6282, Université Bourgogne Franche-Comté, 6 Bd Gabriel, 21000, Dijon, France.
- EPHE, PSL University, 6 Bd Gabriel, 21000, Dijon, France.
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10
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Klingenberg CP. Phenotypic Plasticity, Developmental Instability, and Robustness: The Concepts and How They Are Connected. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00056] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Varón-González C, Pallares LF, Debat V, Navarro N. Mouse Skull Mean Shape and Shape Robustness Rely on Different Genetic Architectures and Different Loci. Front Genet 2019; 10:64. [PMID: 30809244 PMCID: PMC6379267 DOI: 10.3389/fgene.2019.00064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
The genetic architecture of skull shape has been extensively studied in mice and the results suggest a highly polygenic and additive basis. In contrast few studies have explored the genetic basis of the skull variability. Canalization and developmental stability are the two components of phenotypic robustness. They have been proposed to be emergent properties of the genetic networks underlying the development of the trait itself, but this hypothesis has been rarely tested empirically. Here we use outbred mice to investigate the genetic architecture of canalization of the skull shape by implementing a genome-wide marginal epistatic test on 3D geometric morphometric data. The same data set had been used previously to explore the genetic architecture of the skull mean shape and its developmental stability. Here, we address two questions: (1) Are changes in mean shape and changes in shape variance associated with the same genomic regions? and (2) Do canalization and developmental stability rely on the same loci and genetic architecture and do they involve the same patterns of shape variation? We found that unlike skull mean shape, among-individual shape variance and fluctuating asymmetry (FA) show a total lack of additive effects. They are both associated with complex networks of epistatic interactions involving many genes (protein-coding and regulatory elements). Remarkably, none of the genomic loci affecting mean shape contribute these networks despite their enrichment for genes involved in craniofacial variation and diseases. We also found that the patterns of shape FA and individual variation are largely similar and rely on similar multilocus epistatic genetic networks, suggesting that the processes channeling variation within and among individuals are largely common. However, the loci involved in these two networks are completely different. This in turn underlines the difference in the origin of the variation at these two levels, and points at buffering processes that may be specific to each level.
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Affiliation(s)
- Ceferino Varón-González
- Institut de Systématique, Évolution, Biodiversité, ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE, UA, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, Dijon, France
| | - Luisa F. Pallares
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States
| | - Vincent Debat
- Institut de Systématique, Évolution, Biodiversité, ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE, UA, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, Dijon, France
- EPHE, PSL University, Dijon, France
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12
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Leonard RJ, Wat KKY, McArthur C, Hochuli DF. Urbanisation and wing asymmetry in the western honey bee ( Apis mellifera, Linnaeus 1758) at multiple scales. PeerJ 2018; 6:e5940. [PMID: 30533293 PMCID: PMC6282947 DOI: 10.7717/peerj.5940] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/16/2018] [Indexed: 01/08/2023] Open
Abstract
Changes in the mean and variance of phenotypic traits like wing and head morphology are frequently used as indicators of environmental stress experienced during development and may serve as a convenient index of urbanization exposure. To test this claim, we collected adult western honey bee (Apis mellifera Linnaeus 1758, Hymenoptera, Apidae) workers from colonies located across an urbanization gradient, and quantified associations between the symmetries of both wing size and wing shape, and several landscape traits associated with urbanization. Landscape traits were assessed at two spatial scales (three km and 500 m) and included vegetation and anthropogenic land cover, total road length, road proximity and, population and dwelling density. We then used geometric morphometric techniques to determine two wing asymmetry scores-centroid size, a measure of wing size asymmetry and Procrustes distance, a measure of wing shape asymmetry. We found colony dependent differences in both wing size and shape asymmetry. Additionally, we found a negative association between wing shape asymmetry and road proximity at the three km buffer, and associations between wing shape asymmetry and road proximity, anthropogenic land cover and vegetation cover at the 500 m buffer. Whilst we were unable to account for additional variables that may influence asymmetry including temperature, pesticide presence, and parasitism our results demonstrate the potential usefulness of wing shape asymmetry for assessing the impact of certain landscape traits associated with urbanization. Furthermore, they highlight important spatial scale considerations that warrant investigation in future phenotypic studies assessing urbanization impact.
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Affiliation(s)
- Ryan J Leonard
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Katie K Y Wat
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Clare McArthur
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Dieter F Hochuli
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
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Dardalhon-Cuménal D, Deraze J, Dupont CA, Ribeiro V, Coléno-Costes A, Pouch J, Le Crom S, Thomassin H, Debat V, Randsholt NB, Peronnet F. Cyclin G and the Polycomb Repressive complexes PRC1 and PR-DUB cooperate for developmental stability. PLoS Genet 2018; 14:e1007498. [PMID: 29995890 PMCID: PMC6065198 DOI: 10.1371/journal.pgen.1007498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 07/27/2018] [Accepted: 06/19/2018] [Indexed: 12/16/2022] Open
Abstract
In Drosophila, ubiquitous expression of a short Cyclin G isoform generates extreme developmental noise estimated by fluctuating asymmetry (FA), providing a model to tackle developmental stability. This transcriptional cyclin interacts with chromatin regulators of the Enhancer of Trithorax and Polycomb (ETP) and Polycomb families. This led us to investigate the importance of these interactions in developmental stability. Deregulation of Cyclin G highlights an organ intrinsic control of developmental noise, linked to the ETP-interacting domain, and enhanced by mutations in genes encoding members of the Polycomb Repressive complexes PRC1 and PR-DUB. Deep-sequencing of wing imaginal discs deregulating CycG reveals that high developmental noise correlates with up-regulation of genes involved in translation and down-regulation of genes involved in energy production. Most Cyclin G direct transcriptional targets are also direct targets of PRC1 and RNAPolII in the developing wing. Altogether, our results suggest that Cyclin G, PRC1 and PR-DUB cooperate for developmental stability.
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Affiliation(s)
- Delphine Dardalhon-Cuménal
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Jérôme Deraze
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Camille A. Dupont
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Valérie Ribeiro
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Anne Coléno-Costes
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Juliette Pouch
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale
supérieure, CNRS, INSERM, PSL Université Paris Paris, France
| | - Stéphane Le Crom
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale
supérieure, CNRS, INSERM, PSL Université Paris Paris, France
- Sorbonne Université, Univ Antilles, Univ Nice Sophia Antipolis, CNRS,
Evolution Paris Seine—Institut de Biologie Paris Seine (EPS - IBPS), Paris,
France
| | - Hélène Thomassin
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Vincent Debat
- Institut de Systematique, Evolution, Biodiversité ISYEB UMR 7205, MNHN,
CNRS, Sorbonne Université, EPHE, Muséum national d'Histoire naturelle, Sorbonne
Universités, Paris, France
| | - Neel B. Randsholt
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Frédérique Peronnet
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
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Niño-Sandoval TC, Morantes Ariza CF, Infante-Contreras C, Vasconcelos BC. Evaluation of natural mandibular shape asymmetry: an approach by using elliptical Fourier analysis. Dentomaxillofac Radiol 2018; 47:20170345. [PMID: 29583032 DOI: 10.1259/dmfr.20170345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES The purpose of this study was to demonstrate that asymmetry is a natural occurring phenomenon in the mandibular shape by using elliptical Fourier analysis. METHODS 164 digital orthopantomographs from Colombian patients of both sexes aged 18 to 25 years were collected. Curves from left and right hemimandible were digitized. An elliptical Fourier analysis was performed with 20 harmonics. In the general sexual dimorphism a principal component analysis (PCA) and a hotelling T2 from the multivariate warp space were employed. Exploratory analysis of general asymmetry and sexual dimorphism by side was made with a Procrustes Fit. A non-parametric multivariate analysis of variance (MANOVA) was applied to assess differentiation of skeletal classes of each hemimandible, and a Procrustes analysis of variance (ANOVA) was applied to search any relation between skeletal class and side in both sexes. RESULTS Significant values were found in general asymmetry, general sexual dimorphism, in dimorphism by side (p < 0.0001), asymmetry by sex, and differences between Class I, II, and III (p < 0.005). However, a relation of skeletal classes and side was not found. CONCLUSIONS The mandibular asymmetry by shape is present in all patients and should not be articulated exclusively to pathological processes, therefore, along with sexual dimorphism and differences between skeletal classes must be taken into account for improving mandibular prediction systems.
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Affiliation(s)
- Tania C Niño-Sandoval
- 1 Department of Oral and Maxillofacial Surgery, University of Pernambuco , Camaragibe , Brazil
| | | | - Clementina Infante-Contreras
- 3 Department of Oral Health, Growth and Development research line, National University of Colombia, Genetics Institute , Bogotá , Colombia
| | - Belmiro Ce Vasconcelos
- 4 Department of Oral and Maxillofacial Surgery, University of Pernambuco , Camaragibe , Brazil
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Ginot S, Agret S, Claude J. Bite Force Performance, Fluctuating Asymmetry and Antisymmetry in the Mandible of Inbred and Outbred Wild-Derived Strains of Mice (Mus musculus domesticus). Evol Biol 2018. [DOI: 10.1007/s11692-018-9450-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Debat V. [Symmetry is beauty - or is it? The rise and fall of fluctuating asymmetry]. Med Sci (Paris) 2016; 32:774-80. [PMID: 27615188 DOI: 10.1051/medsci/20163208028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Fluctuating asymmetry is the stochastic, minor deviation from perfect symmetry in bilaterally symmetrical organisms. It reflects the limit of developmental precision. Such a precision can be influenced by various factors, both internal (genetic mutations, stochastic variation at every levels of development) and external (environmental influences). Fluctuating asymmetry has receive an extreme attention for the past few decades, that culminated in the 90s: it has been used as an estimator of heterozygosity, fitness, environmental stress, and widely applied to human biology, sociobiology and psychology before being more or less discredited in the early 2000s. The reasons for such an extreme popularity and then disgrace are discussed here. Far from suggesting to abandon the study of fluctuating asymmetry, we indicate some of the most promising research avenues. ‡.
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Affiliation(s)
- Vincent Debat
- Institut de systématique, évolution, biodiversité, ISyEB, UMR 7205, CNRS, UPMC, EPHE, Muséum national d'histoire naturelle, Sorbonne universités, 45, rue Buffon, CP50, 75005 Paris, France
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Measurement error in geometric morphometrics. Dev Genes Evol 2016; 226:139-58. [DOI: 10.1007/s00427-016-0537-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
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18
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Postnatal Dynamics of Developmental Stability and Canalization of Lizard Head Shape Under Different Environmental Conditions. Evol Biol 2016. [DOI: 10.1007/s11692-016-9377-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Analyzing Fluctuating Asymmetry with Geometric Morphometrics: Concepts, Methods, and Applications. Symmetry (Basel) 2015. [DOI: 10.3390/sym7020843] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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