1
|
Welsh IC, Feiler ME, Lipman D, Mormile I, Hansen K, Percival CJ. Palatal segment contributions to midfacial anterior-posterior growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.03.560703. [PMID: 37873353 PMCID: PMC10592893 DOI: 10.1101/2023.10.03.560703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Anterior-posterior (A-P) elongation of the palate is a critical aspect of integrated midfacial morphogenesis. Reciprocal epithelial-mesenchymal interactions drive secondary palate elongation that is coupled to the periodic formation of signaling centers within the rugae growth zone (RGZ). However, the relationship between RGZ driven morphogenetic processes, the differentiative dynamics of underlying palatal bone mesenchymal precursors, and the segmental organization of the upper jaw has remained enigmatic. A detailed ontogenetic study of these relationships is important, because palatal segment growth is a critical aspect of normal midfacial growth, can be modified to produce dysmorphology, and is a likely basis for evolutionary differences in upper jaw morphology. Variation in palatal-segment specific growth may also underlie known differences in palatal segment proportions between inbred mouse strains. We completed a combined whole mount gene expression and morphometric analysis of normal murine palatal growth dynamics and their association with palatal segment elongation and resulting upper jaw morphology. Our results demonstrated that the first formed palatal ruga (ruga 1), found just posterior to the RGZ, maintained an association with important nasal, neurovascular and palatal structures throughout early midfacial development; suggesting that these features are positioned at a proximal source of embryonic midfacial directional growth. Our detailed characterization of midfacial morphogenesis revealed a one-to-one relationship between palatal segments and upper jaw bones during the earliest stages of palatal elongation. Growth of the maxillary anlage within the anterior secondary palate is uniquely coupled to RGZ-driven morphogenesis that more than doubles the length of this palatal segment prior to palatal shelf fusion. Our results also demonstrate that the future maxillary-palatine suture, approximated by the position ruga 1 and consistently associated with the palatine anlage, forms predominantly via the posterior differentiation of the maxilla within the expanding anterior secondary palate. Our complementary ontogenetic comparison of three inbred mouse strains identified small but significant strain-specific differences in early embryonic palatal segment contributions to the upper jaw. Although early palatal segment specific growth is not primarily responsible for adult differences in upper jaw morphology between these strains, our ontogenetic series of measurements provide a useful foundation for understanding the impact of background genetic effects on facial shape and elongation. In combination, our results provide a novel and particularly detailed picture of the earliest spatiotemporal dynamics of intramembranous midfacial skeletal specification and differentiation within the context of the surrounding palatal segment A-P elongation and associated rugae formation.
Collapse
Affiliation(s)
- Ian C. Welsh
- Program in Craniofacial Biology, University of California at San Francisco, San Francisco, California 94143, USA
- Department of Orofacial Sciences, University of California at San Francisco, San Francisco, California 94143, USA
- Department of Anatomy, University of California at San Francisco, San Francisco, California 94143, USA
| | - Maria E. Feiler
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11790
| | - Danika Lipman
- Department of Cell Biology and Anatomy, University of Calgary
| | - Isabel Mormile
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11790
| | - Karissa Hansen
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA 94143
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA 94143
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143
| | | |
Collapse
|
2
|
Liang Y, Song C, Li J, Li T, Zhang C, Zou Y. Morphometric analysis of the size-adjusted linear dimensions of the skull landmarks revealed craniofacial dysmorphology in Mid1-cKO mice. BMC Genomics 2023; 24:68. [PMID: 36759768 PMCID: PMC9912615 DOI: 10.1186/s12864-023-09162-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND The early craniofacial development is a highly coordinated process involving neural crest cell migration, proliferation, epithelial apoptosis, and epithelial-mesenchymal transition (EMT). Both genetic defects and environmental factors can affect these processes and result in orofacial clefts. Mutations in MID1 gene cause X-linked Opitz Syndrome (OS), which is a congenital malformation characterized by craniofacial defects including cleft lip/palate (CLP). Previous studies demonstrated impaired neurological structure and function in Mid1 knockout mice, while no CLP was observed. However, given the highly variable severities of the facial manifestations observed in OS patients within the same family carrying identical genetic defects, subtle craniofacial malformations in Mid1 knockout mice could be overlooked in these studies. Therefore, we propose that a detailed morphometric analysis should be necessary to reveal mild craniofacial dysmorphologies that reflect the similar developmental defects seen in OS patients. RESULTS In this research, morphometric study of the P0 male Mid1-cKO mice were performed using Procrustes superimposition as well as EMDA analysis of the size-adjusted three-dimensional coordinates of 105 skull landmarks, which were collected on the bone surface reconstructed using microcomputed tomographic images. Our results revealed the craniofacial deformation such as the increased dimension of the frontal and nasal bone in Mid1-cKO mice, in line with the most prominent facial features such as hypertelorism, prominent forehead, broad and/or high nasal bridge seen in OS patients. CONCLUSION While been extensively used in evolutionary biology and anthropology in the last decades, geometric morphometric analysis was much less used in developmental biology. Given the high interspecies variances in facial anatomy, the work presented in this research suggested the advantages of morphometric analysis in characterizing animal models of craniofacial developmental defects to reveal phenotypic variations and the underlining pathogenesis.
Collapse
Affiliation(s)
- Yaohui Liang
- grid.258164.c0000 0004 1790 3548The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Chao Song
- grid.258164.c0000 0004 1790 3548The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Jieli Li
- grid.258164.c0000 0004 1790 3548The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Ting Li
- grid.258164.c0000 0004 1790 3548The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Chunlei Zhang
- grid.258164.c0000 0004 1790 3548First Affiliated Hospital, Jinan University, Guangzhou, 510632 China
| | - Yi Zou
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China. .,Department of Biology, School of Life Science and Technology, Jinan University, Guangzhou, China.
| |
Collapse
|
3
|
Harvati K, Ackermann RR. Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins. Nat Ecol Evol 2022; 6:1573-1585. [PMID: 36064759 DOI: 10.1038/s41559-022-01875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.
Collapse
Affiliation(s)
- K Harvati
- Paleoanthropology section, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - R R Ackermann
- Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa.
- Department of Archaeology, University of Cape Town, Cape Town, South Africa.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| |
Collapse
|
4
|
Percival CJ, Devine J, Hassan CR, Vidal‐Garcia M, O'Connor‐Coates CJ, Zaffarini E, Roseman C, Katz D, Hallgrimsson B. The genetic basis of neurocranial size and shape across varied lab mouse populations. J Anat 2022; 241:211-229. [PMID: 35357006 PMCID: PMC9296060 DOI: 10.1111/joa.13657] [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: 07/07/2021] [Revised: 02/11/2022] [Accepted: 03/08/2022] [Indexed: 11/26/2022] Open
Abstract
Brain and skull tissues interact through molecular signalling and mechanical forces during head development, leading to a strong correlation between the neurocranium and the external brain surface. Therefore, when brain tissue is unavailable, neurocranial endocasts are often used to approximate brain size and shape. Evolutionary changes in brain morphology may have resulted in secondary changes to neurocranial morphology, but the developmental and genetic processes underlying this relationship are not well understood. Using automated phenotyping methods, we quantified the genetic basis of endocast variation across large genetically varied populations of laboratory mice in two ways: (1) to determine the contributions of various genetic factors to neurocranial form and (2) to help clarify whether a neurocranial variation is based on genetic variation that primarily impacts bone development or on genetic variation that primarily impacts brain development, leading to secondary changes in bone morphology. Our results indicate that endocast size is highly heritable and is primarily determined by additive genetic factors. In addition, a non-additive inbreeding effect led to founder strains with lower neurocranial size, but relatively large brains compared to skull size; suggesting stronger canalization of brain size and/or a general allometric effect. Within an outbred sample of mice, we identified a locus on mouse chromosome 1 that is significantly associated with variation in several positively correlated endocast size measures. Because the protein-coding genes at this locus have been previously associated with brain development and not with bone development, we propose that genetic variation at this locus leads primarily to variation in brain volume that secondarily leads to changes in neurocranial globularity. We identify a strain-specific missense mutation within Akt3 that is a strong causal candidate for this genetic effect. Whilst it is not appropriate to generalize our hypothesis for this single locus to all other loci that also contribute to the complex trait of neurocranial skull morphology, our results further reveal the genetic basis of neurocranial variation and highlight the importance of the mechanical influence of brain growth in determining skull morphology.
Collapse
Affiliation(s)
| | - Jay Devine
- Cell Biology and AnatomyUniversity of Calgary Cumming School of MedicineCalgaryCanada
| | | | - Marta Vidal‐Garcia
- Cell Biology and AnatomyUniversity of Calgary Cumming School of MedicineCalgaryCanada
| | | | - Eva Zaffarini
- Cell Biology and AnatomyUniversity of Calgary Cumming School of MedicineCalgaryCanada
| | - Charles Roseman
- Department of Evolution, Ecology, and BehaviorUniversity of IllinoisUrbanaIllinoisUSA
| | - David Katz
- Cell Biology and AnatomyUniversity of Calgary Cumming School of MedicineCalgaryCanada
| | - Benedikt Hallgrimsson
- Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
| |
Collapse
|
5
|
Abstract
BACKGROUND The shape of pig scapula is complex and is important for sow robustness and health. To better understand the relationship between 3D shape of the scapula and functional traits, it is necessary to build a model that explains most of the morphological variation between animals. This requires point correspondence, i.e. a map that explains which points represent the same piece of tissue among individuals. The objective of this study was to further develop an automated computational pipeline for the segmentation of computed tomography (CT) scans to incorporate 3D modelling of the scapula, and to develop a genetic prediction model for 3D morphology. RESULTS The surface voxels of the scapula were identified on 2143 CT-scanned pigs, and point correspondence was established by predicting the coordinates of 1234 semi-landmarks on each animal, using the coherent point drift algorithm. A subsequent principal component analysis showed that the first 10 principal components covered more than 80% of the total variation in 3D shape of the scapula. Using principal component scores as phenotypes in a genetic model, estimates of heritability ranged from 0.4 to 0.8 (with standard errors from 0.07 to 0.08). To validate the entire computational pipeline, a statistical model was trained to predict scapula shape based on marker genotype data. The mean prediction reliability averaged over the whole scapula was equal to 0.18 (standard deviation = 0.05) with a higher reliability in convex than in concave regions. CONCLUSIONS Estimates of heritability of the principal components were high and indicated that the computational pipeline that processes CT data to principal component phenotypes was associated with little error. Furthermore, we showed that it is possible to predict the 3D shape of scapula based on marker genotype data. Taken together, these results show that the proposed computational pipeline closes the gap between a point cloud representing the shape of an animal and its underlying genetic components.
Collapse
Affiliation(s)
- Øyvind Nordbø
- Norsvin SA, Storhamargata 44, 2317, Hamar, Norway.
- Geno SA, Storhamargata 44, 2317, Hamar, Norway.
| |
Collapse
|
6
|
Kollmus H, Fuchs H, Lengger C, Haselimashhadi H, Bogue MA, Östereicher MA, Horsch M, Adler T, Aguilar-Pimentel JA, Amarie OV, Becker L, Beckers J, Calzada-Wack J, Garrett L, Hans W, Hölter SM, Klein-Rodewald T, Maier H, Mayer-Kuckuk P, Miller G, Moreth K, Neff F, Rathkolb B, Rácz I, Rozman J, Spielmann N, Treise I, Busch D, Graw J, Klopstock T, Wolf E, Wurst W, Yildirim AÖ, Mason J, Torres A, Balling R, Mehaan T, Gailus-Durner V, Schughart K, Hrabě de Angelis M. A comprehensive and comparative phenotypic analysis of the collaborative founder strains identifies new and known phenotypes. Mamm Genome 2020; 31:30-48. [PMID: 32060626 PMCID: PMC7060152 DOI: 10.1007/s00335-020-09827-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/31/2020] [Indexed: 01/21/2023]
Abstract
The collaborative cross (CC) is a large panel of mouse-inbred lines derived from eight founder strains (NOD/ShiLtJ, NZO/HILtJ, A/J, C57BL/6J, 129S1/SvImJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ). Here, we performed a comprehensive and comparative phenotyping screening to identify phenotypic differences and similarities between the eight founder strains. In total, more than 300 parameters including allergy, behavior, cardiovascular, clinical blood chemistry, dysmorphology, bone and cartilage, energy metabolism, eye and vision, immunology, lung function, neurology, nociception, and pathology were analyzed; in most traits from sixteen females and sixteen males. We identified over 270 parameters that were significantly different between strains. This study highlights the value of the founder and CC strains for phenotype-genotype associations of many genetic traits that are highly relevant to human diseases. All data described here are publicly available from the mouse phenome database for analyses and downloads.
Collapse
Affiliation(s)
- Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Inhoffenstr.7, 38124, Braunschweig, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Christoph Lengger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Manuela A Östereicher
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Marion Horsch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Juan Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Oana Veronica Amarie
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Julia Calzada-Wack
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Lillian Garrett
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Wolfgang Hans
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Tanja Klein-Rodewald
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Holger Maier
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Philipp Mayer-Kuckuk
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Gregor Miller
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Kristin Moreth
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Frauke Neff
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University München, Feodor-Lynen Str. 25, 81377, Munich, Germany
| | - Ildikó Rácz
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Clinic of Neurodegenerative Diseases and Gerontopsychiatry, University of Bonn Medical Center, Bonn, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Nadine Spielmann
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Irina Treise
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Dirk Busch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstrasse 30, 81675, Munich, Germany
| | - Jochen Graw
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Klinikum Der Ludwig-Maximilians-Universität München, Ziemssenstr. 1a, 80336, Munich, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Site Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University München, Feodor-Lynen Str. 25, 81377, Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Site Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Chair of Developmental Genetics, Technische Universität München-Weihenstephan, C/O Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Ali Önder Yildirim
- Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- German Center for Lung Research, Marburg, Germany
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Arturo Torres
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Luxembourg
| | - Terry Mehaan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Inhoffenstr.7, 38124, Braunschweig, Germany.
- University of Veterinary Medicine Hannover, Hanover, Germany.
- University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| |
Collapse
|
7
|
Hallgrímsson B, Katz DC, Aponte JD, Larson JR, Devine J, Gonzalez PN, Young NM, Roseman CC, Marcucio RS. Integration and the Developmental Genetics of Allometry. Integr Comp Biol 2019; 59:1369-1381. [PMID: 31199435 PMCID: PMC6934422 DOI: 10.1093/icb/icz105] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Allometry refers to the ways in which organismal shape is associated with size. It is a special case of integration, or the tendency for traits to covary, in that variation in size is ubiquitous and evolutionarily important. Allometric variation is so commonly observed that it is routinely removed from morphometric analyses or invoked as an explanation for evolutionary change. In this case, familiarity is mistaken for understanding because rarely do we know the mechanisms by which shape correlates with size or understand their significance. As with other forms of integration, allometric variation is generated by variation in developmental processes that affect multiple traits, resulting in patterns of covariation. Given this perspective, we can dissect the genetic and developmental determinants of allometric variation. Our work on the developmental and genetic basis for allometric variation in craniofacial shape in mice and humans has revealed that allometric variation is highly polygenic. Different measures of size are associated with distinct but overlapping patterns of allometric variation. These patterns converge in part on a common genetic basis. Finally, environmental modulation of size often generates variation along allometric trajectories, but the timing of genetic and environmental perturbations can produce deviations from allometric patterns when traits are differentially sensitive over developmental time. These results question the validity of viewing allometry as a singular phenomenon distinct from morphological integration more generally.
Collapse
Affiliation(s)
- Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - David C Katz
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jose D Aponte
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jacinda R Larson
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jay Devine
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Paula N Gonzalez
- Unidad Ejecutora de Estudios en Neurociencias y Sistemas Complejos (CONICET-HEC-UNAJ), Buenos Aires, Argentina
| | - Nathan M Young
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, USA
| | - Charles C Roseman
- Department of Animal Biology, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, USA
| |
Collapse
|
8
|
Ackermann RR, Arnold ML, Baiz MD, Cahill JA, Cortés-Ortiz L, Evans BJ, Grant BR, Grant PR, Hallgrimsson B, Humphreys RA, Jolly CJ, Malukiewicz J, Percival CJ, Ritzman TB, Roos C, Roseman CC, Schroeder L, Smith FH, Warren KA, Wayne RK, Zinner D. Hybridization in human evolution: Insights from other organisms. Evol Anthropol 2019; 28:189-209. [PMID: 31222847 PMCID: PMC6980311 DOI: 10.1002/evan.21787] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/30/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022]
Abstract
During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.
Collapse
Affiliation(s)
- Rebecca R. Ackermann
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | | | - Marcella D. Baiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - James A. Cahill
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Ben J. Evans
- Biology Department, Life Sciences Building, McMaster University, Hamilton, Canada
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy and the Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Robyn A. Humphreys
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | - Clifford J. Jolly
- Center for the Study of Human Origins, Department of Anthropology, New York University, and NYCEP, New York, New York
| | - Joanna Malukiewicz
- Biodesign Institute, Arizona State University, Tempe, Arizona
- Federal University of Vicosa, Department of Animal Biology, Brazil
| | - Christopher J. Percival
- Department of Cell Biology and Anatomy and the Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
- Department of Anthropology, Stony Brook University, New York
| | - Terrence B. Ritzman
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri
- Department of Anthropology, Washington University, St. Louis, Missouri
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
| | - Charles C. Roseman
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Lauren Schroeder
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Canada
| | - Fred H. Smith
- Department of Sociology and Anthropology, Illinois State University, Normal, Illinois
| | - Kerryn A. Warren
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | | | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
| |
Collapse
|
9
|
A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size. G3-GENES GENOMES GENETICS 2019; 9:1613-1622. [PMID: 30877080 PMCID: PMC6505174 DOI: 10.1534/g3.118.200847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Reproductive success in the eight founder strains of the Collaborative Cross (CC) was measured using a diallel-mating scheme. Over a 48-month period we generated 4,448 litters, and provided 24,782 weaned pups for use in 16 different published experiments. We identified factors that affect the average litter size in a cross by estimating the overall contribution of parent-of-origin, heterosis, inbred, and epistatic effects using a Bayesian zero-truncated overdispersed Poisson mixed model. The phenotypic variance of litter size has a substantial contribution (82%) from unexplained and environmental sources, but no detectable effect of seasonality. Most of the explained variance was due to additive effects (9.2%) and parental sex (maternal vs. paternal strain; 5.8%), with epistasis accounting for 3.4%. Within the parental effects, the effect of the dam's strain explained more than the sire's strain (13.2% vs. 1.8%), and the dam's strain effects account for 74.2% of total variation explained. Dams from strains C57BL/6J and NOD/ShiLtJ increased the expected litter size by a mean of 1.66 and 1.79 pups, whereas dams from strains WSB/EiJ, PWK/PhJ, and CAST/EiJ reduced expected litter size by a mean of 1.51, 0.81, and 0.90 pups. Finally, there was no strong evidence for strain-specific effects on sex ratio distortion. Overall, these results demonstrate that strains vary substantially in their reproductive ability depending on their genetic background, and that litter size is largely determined by dam's strain rather than sire's strain effects, as expected. This analysis adds to our understanding of factors that influence litter size in mammals, and also helps to explain breeding successes and failures in the extinct lines and surviving CC strains.
Collapse
|
10
|
Percival CJ, Devine J, Darwin BC, Liu W, van Eede M, Henkelman RM, Hallgrimsson B. The effect of automated landmark identification on morphometric analyses. J Anat 2019; 234:917-935. [PMID: 30901082 DOI: 10.1111/joa.12973] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 01/20/2023] Open
Abstract
Morphometric analysis of anatomical landmarks allows researchers to identify specific morphological differences between natural populations or experimental groups, but manually identifying landmarks is time-consuming. We compare manually and automatically generated adult mouse skull landmarks and subsequent morphometric analyses to elucidate how switching from manual to automated landmarking will impact morphometric analysis results for large mouse (Mus musculus) samples (n = 1205) that represent a wide range of 'normal' phenotypic variation (62 genotypes). Other studies have suggested that the use of automated landmarking methods is feasible, but this study is the first to compare the utility of current automated approaches to manual landmarking for a large dataset that allows the quantification of intra- and inter-strain variation. With this unique sample, we investigated how switching to a non-linear image registration-based automated landmarking method impacts estimated differences in genotype mean shape and shape variance-covariance structure. In addition, we tested whether an initial registration of specimen images to genotype-specific averages improves automatic landmark identification accuracy. Our results indicated that automated landmark placement was significantly different than manual landmark placement but that estimated skull shape covariation was correlated across methods. The addition of a preliminary genotype-specific registration step as part of a two-level procedure did not substantially improve on the accuracy of one-level automatic landmark placement. The landmarks with the lowest automatic landmark accuracy are found in locations with poor image registration alignment. The most serious outliers within morphometric analysis of automated landmarks displayed instances of stochastic image registration error that are likely representative of errors common when applying image registration methods to micro-computed tomography datasets that were initially collected with manual landmarking in mind. Additional efforts during specimen preparation and image acquisition can help reduce the number of registration errors and improve registration results. A reduction in skull shape variance estimates were noted for automated landmarking methods compared with manual landmarking. This partially reflects an underestimation of more extreme genotype shapes and loss of biological signal, but largely represents the fact that automated methods do not suffer from intra-observer landmarking error. For appropriate samples and research questions, our image registration-based automated landmarking method can eliminate the time required for manual landmarking and have a similar power to identify shape differences between inbred mouse genotypes.
Collapse
Affiliation(s)
| | - Jay Devine
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Benjamin C Darwin
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wei Liu
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Matthijs van Eede
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, AB, Canada.,The McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
11
|
Alhajeri BH. Cranial variation in geographically widespread dwarf gerbil
Gerbillus nanus
(Gerbillinae, Rodentia) populations: Isolation by distance versus adaptation to local environments. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12247] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
12
|
Usui K, Tokita M. Creating diversity in mammalian facial morphology: a review of potential developmental mechanisms. EvoDevo 2018; 9:15. [PMID: 29946416 PMCID: PMC6003202 DOI: 10.1186/s13227-018-0103-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
Mammals (class Mammalia) have evolved diverse craniofacial morphology to adapt to a wide range of ecological niches. However, the genetic and developmental mechanisms underlying the diversification of mammalian craniofacial morphology remain largely unknown. In this paper, we focus on the facial length and orofacial clefts of mammals and deduce potential mechanisms that produced diversity in mammalian facial morphology. Small-scale changes in facial morphology from the common ancestor, such as slight changes in facial length and the evolution of the midline cleft in some lineages of bats, could be attributed to heterochrony in facial bone ossification. In contrast, large-scale changes of facial morphology from the common ancestor, such as a truncated, widened face as well as the evolution of the bilateral cleft possessed by some bat species, could be brought about by changes in growth and patterning of the facial primordium (the facial processes) at the early stages of embryogenesis.
Collapse
Affiliation(s)
- Kaoru Usui
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510 Japan
| | - Masayoshi Tokita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510 Japan
| |
Collapse
|
13
|
Warren KA, Ritzman TB, Humphreys RA, Percival CJ, Hallgrímsson B, Ackermann RR. Craniomandibular form and body size variation of first generation mouse hybrids: A model for hominin hybridization. J Hum Evol 2018; 116:57-74. [PMID: 29477182 PMCID: PMC6699179 DOI: 10.1016/j.jhevol.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/04/2017] [Accepted: 12/12/2017] [Indexed: 12/27/2022]
Abstract
Hybridization occurs in a number of mammalian lineages, including among primate taxa. Analyses of ancient genomes have shown that hybridization between our lineage and other archaic hominins in Eurasia occurred numerous times in the past. However, we still have limited empirical data on what a hybrid skeleton looks like, or how to spot patterns of hybridization among fossils for which there are no genetic data. Here we use experimental mouse models to supplement previous studies of primates. We characterize size and shape variation in the cranium and mandible of three wild-derived inbred mouse strains and their first generation (F1) hybrids. The three parent taxa in our analysis represent lineages that diverged over approximately the same period as the human/Neanderthal/Denisovan lineages and their hybrids are variably successful in the wild. Comparisons of body size, as quantified by long bone measurements, are also presented to determine whether the identified phenotypic effects of hybridization are localized to the cranium or represent overall body size changes. The results indicate that hybrid cranial and mandibular sizes, as well as limb length, exceed that of the parent taxa in all cases. All three F1 hybrid crosses display similar patterns of size and form variation. These results are generally consistent with earlier studies on primates and other mammals, suggesting that the effects of hybridization may be similar across very different scenarios of hybridization, including different levels of hybrid fitness. This paper serves to supplement previous studies aimed at identifying F1 hybrids in the fossil record and to introduce further research that will explore hybrid morphologies using mice as a proxy for better understanding hybridization in the hominin fossil record.
Collapse
Affiliation(s)
- Kerryn A Warren
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Terrence B Ritzman
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa; Department of Neuroscience, Washington University School of Medicine, USA; School of Human Evolution and Social Change, Arizona State University, USA
| | - Robyn A Humphreys
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Christopher J Percival
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Canada; The Alberta Children's Hospital Research Institute, University of Calgary, Canada; The McCaig Institute for Bone and Joint Health, University of Calgary, Canada; Department of Anthropology, Stony Brook, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Canada; The Alberta Children's Hospital Research Institute, University of Calgary, Canada; The McCaig Institute for Bone and Joint Health, University of Calgary, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa.
| |
Collapse
|
14
|
Percival CJ, Green R, Roseman CC, Gatti DM, Morgan JL, Murray SA, Donahue LR, Mayeux JM, Pollard KM, Hua K, Pomp D, Marcucio R, Hallgrímsson B. Developmental constraint through negative pleiotropy in the zygomatic arch. EvoDevo 2018; 9:3. [PMID: 29423138 PMCID: PMC5787316 DOI: 10.1186/s13227-018-0092-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/08/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Previous analysis suggested that the relative contribution of individual bones to regional skull lengths differ between inbred mouse strains. If the negative correlation of adjacent bone lengths is associated with genetic variation in a heterogeneous population, it would be an example of negative pleiotropy, which occurs when a genetic factor leads to opposite effects in two phenotypes. Confirming negative pleiotropy and determining its basis may reveal important information about the maintenance of overall skull integration and developmental constraint on skull morphology. RESULTS We identified negative correlations between the lengths of the frontal and parietal bones in the midline cranial vault as well as the zygomatic bone and zygomatic process of the maxilla, which contribute to the zygomatic arch. Through gene association mapping of a large heterogeneous population of Diversity Outbred (DO) mice, we identified a quantitative trait locus on chromosome 17 driving the antagonistic contribution of these two zygomatic arch bones to total zygomatic arch length. Candidate genes in this region were identified and real-time PCR of the maxillary processes of DO founder strain embryos indicated differences in the RNA expression levels for two of the candidate genes, Camkmt and Six2. CONCLUSIONS A genomic region underlying negative pleiotropy of two zygomatic arch bones was identified, which provides a mechanism for antagonism in component bone lengths while constraining overall zygomatic arch length. This type of mechanism may have led to variation in the contribution of individual bones to the zygomatic arch noted across mammals. Given that similar genetic and developmental mechanisms may underlie negative correlations in other parts of the skull, these results provide an important step toward understanding the developmental basis of evolutionary variation and constraint in skull morphology.
Collapse
Affiliation(s)
| | - Rebecca Green
- Alberta Children’s Hospital Institute for Child and Maternal Health, University of Calgary, Calgary, AB Canada
- The McCaig Bone and Joint Institute, University of Calgary, Calgary, AB Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB Canada
| | - Charles C. Roseman
- Program in Ecology Evolution and Conservation Biology, University of Illinois, Urbana, IL USA
| | | | | | | | | | - Jessica M. Mayeux
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - K. Michael Pollard
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Kunjie Hua
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC USA
| | - Daniel Pomp
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC USA
| | - Ralph Marcucio
- The Orthopaedic Trauma Institute, Department of Orthopaedic Surgery, UCSF School of Medicine, San Francisco, CA USA
| | - Benedikt Hallgrímsson
- Alberta Children’s Hospital Institute for Child and Maternal Health, University of Calgary, Calgary, AB Canada
- The McCaig Bone and Joint Institute, University of Calgary, Calgary, AB Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB Canada
| |
Collapse
|
15
|
Maga AM, Tustison NJ, Avants BB. A population level atlas of Mus musculus craniofacial skeleton and automated image-based shape analysis. J Anat 2017; 231:433-443. [PMID: 28656622 PMCID: PMC5554826 DOI: 10.1111/joa.12645] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 02/04/2023] Open
Abstract
Laboratory mice are staples for evo/devo and genetics studies. Inbred strains provide a uniform genetic background to manipulate and understand gene-environment interactions, while their crosses have been instrumental in studies of genetic architecture, integration and modularity, and mapping of complex biological traits. Recently, there have been multiple large-scale studies of laboratory mice to further our understanding of the developmental basis, evolution, and genetic control of shape variation in the craniofacial skeleton (i.e. skull and mandible). These experiments typically use micro-computed tomography (micro-CT) to capture the craniofacial phenotype in 3D and rely on manually annotated anatomical landmarks to conduct statistical shape analysis. Although the common choice for imaging modality and phenotyping provides the potential for collaborative research for even larger studies with more statistical power, the investigator (or lab-specific) nature of the data collection hampers these efforts. Investigators are rightly concerned that subtle differences in how anatomical landmarks were recorded will create systematic bias between studies that will eventually influence scientific findings. Even if researchers are willing to repeat landmark annotation on a combined dataset, different lab practices and software choices may create obstacles for standardization beyond the underlying imaging data. Here, we propose a freely available analysis system that could assist in the standardization of micro-CT studies in the mouse. Our proposal uses best practices developed in biomedical imaging and takes advantage of existing open-source software and imaging formats. Our first contribution is the creation of a synthetic template for the adult mouse craniofacial skeleton from 25 inbred strains and five F1 crosses that are widely used in biological research. The template contains a fully segmented cranium, left and right hemi-mandibles, endocranial space, and the first few cervical vertebrae. We have been using this template in our lab to segment and isolate cranial structures in an automated fashion from a mixed population of mice, including craniofacial mutants, aged 4-12.5 weeks. As a secondary contribution, we demonstrate an application of nearly automated shape analysis, using symmetric diffeomorphic image registration. This approach, which we call diGPA, closely approximates the popular generalized Procrustes analysis (GPA) but negates the collection of anatomical landmarks. We achieve our goals by using the open-source advanced normalization tools (ANT) image quantification library, as well as its associated R library (ANTsR) for statistical image analysis. Finally, we make a plea to investigators to commit to using open imaging standards and software in their labs to the extent possible to increase the potential for data exchange and improve the reproducibility of findings. Future work will incorporate more anatomical detail (such as individual cranial bones, turbinals, dentition, middle ear ossicles) and more diversity into the template.
Collapse
Affiliation(s)
- A. Murat Maga
- Department of PediatricsDivision of Craniofacial MedicineUniversity of WashingtonSeattleWAUSA
- Seattle Children's Research InstituteCenter for Developmental Biology and Regenerative MedicineSeattleWAUSA
| | - Nicholas J. Tustison
- Department of Radiology and Medical ImagingUniversity of VirginiaCharlottesvilleVAUSA
| | | |
Collapse
|
16
|
Motch Perrine SM, Stecko T, Neuberger T, Jabs EW, Ryan TM, Richtsmeier JT. Integration of Brain and Skull in Prenatal Mouse Models of Apert and Crouzon Syndromes. Front Hum Neurosci 2017; 11:369. [PMID: 28790902 PMCID: PMC5525342 DOI: 10.3389/fnhum.2017.00369] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/29/2017] [Indexed: 01/23/2023] Open
Abstract
The brain and skull represent a complex arrangement of integrated anatomical structures composed of various cell and tissue types that maintain structural and functional association throughout development. Morphological integration, a concept developed in vertebrate morphology and evolutionary biology, describes the coordinated variation of functionally and developmentally related traits of organisms. Syndromic craniosynostosis is characterized by distinctive changes in skull morphology and perceptible, though less well studied, changes in brain structure and morphology. Using mouse models for craniosynostosis conditions, our group has precisely defined how unique craniosynostosis causing mutations in fibroblast growth factor receptors affect brain and skull morphology and dysgenesis involving coordinated tissue-specific effects of these mutations. Here we examine integration of brain and skull in two mouse models for craniosynostosis: one carrying the FGFR2c C342Y mutation associated with Pfeiffer and Crouzon syndromes and a mouse model carrying the FGFR2 S252W mutation, one of two mutations responsible for two-thirds of Apert syndrome cases. Using linear distances estimated from three-dimensional coordinates of landmarks acquired from dual modality imaging of skull (high resolution micro-computed tomography and magnetic resonance microscopy) of mice at embryonic day 17.5, we confirm variation in brain and skull morphology in Fgfr2cC342Y/+ mice, Fgfr2+/S252W mice, and their unaffected littermates. Mutation-specific variation in neural and cranial tissue notwithstanding, patterns of integration of brain and skull differed only subtly between mice carrying either the FGFR2c C342Y or the FGFR2 S252W mutation and their unaffected littermates. However, statistically significant and substantial differences in morphological integration of brain and skull were revealed between the two mutant mouse models, each maintained on a different strain. Relative to the effects of disease-associated mutations, our results reveal a stronger influence of the background genome on patterns of brain-skull integration and suggest robust genetic, developmental, and evolutionary relationships between neural and skeletal tissues of the head.
Collapse
Affiliation(s)
- Susan M Motch Perrine
- Department of Anthropology, Pennsylvania State UniversityUniversity Park, PA, United States
| | - Tim Stecko
- Center for Quantitative Imaging, Penn State Institutes for Energy and the Environment, Pennsylvania State UniversityUniversity Park, PA, United States
| | - Thomas Neuberger
- High Field MRI Facility, Huck Institutes of the Life Sciences, Pennsylvania State UniversityUniversity Park, PA, United States.,Department of Bioengineering, Pennsylvania State UniversityUniversity Park, PA, United States
| | - Ethylin W Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew York, NY, United States
| | - Timothy M Ryan
- Department of Anthropology, Pennsylvania State UniversityUniversity Park, PA, United States.,Center for Quantitative Imaging, Penn State Institutes for Energy and the Environment, Pennsylvania State UniversityUniversity Park, PA, United States
| | - Joan T Richtsmeier
- Department of Anthropology, Pennsylvania State UniversityUniversity Park, PA, United States
| |
Collapse
|
17
|
Percival CJ, Marangoni P, Tapaltsyan V, Klein O, Hallgrímsson B. The Interaction of Genetic Background and Mutational Effects in Regulation of Mouse Craniofacial Shape. G3 (BETHESDA, MD.) 2017; 7:1439-1450. [PMID: 28280213 PMCID: PMC5427488 DOI: 10.1534/g3.117.040659] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/03/2017] [Indexed: 11/18/2022]
Abstract
Inbred genetic background significantly influences the expression of phenotypes associated with known genetic perturbations and can underlie variation in disease severity between individuals with the same mutation. However, the effect of epistatic interactions on the development of complex traits, such as craniofacial morphology, is poorly understood. Here, we investigated the effect of three inbred backgrounds (129X1/SvJ, C57BL/6J, and FVB/NJ) on the expression of craniofacial dysmorphology in mice (Mus musculus) with loss of function in three members of the Sprouty family of growth factor negative regulators (Spry1, Spry2, or Spry4) in order to explore the impact of epistatic interactions on skull morphology. We found that the interaction of inbred background and the Sprouty genotype explains as much craniofacial shape variation as the Sprouty genotype alone. The most severely affected genotypes display a relatively short and wide skull, a rounded cranial vault, and a more highly angled inferior profile. Our results suggest that the FVB background is more resilient to Sprouty loss of function than either C57 or 129, and that Spry4 loss is generally less severe than loss of Spry1 or Spry2 While the specific modifier genes responsible for these significant background effects remain unknown, our results highlight the value of intercrossing mice of multiple inbred backgrounds to identify the genes and developmental interactions that modulate the severity of craniofacial dysmorphology. Our quantitative results represent an important first step toward elucidating genetic interactions underlying variation in robustness to known genetic perturbations in mice.
Collapse
Affiliation(s)
- Christopher J Percival
- Alberta Children's Hospital Institute for Child and Maternal Health, University of Calgary, Alberta T2N 4N1, Canada
- The McCaig Bone and Joint Institute, University of Calgary, Alberta T2N 4Z6, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Alberta T2N 4N1, Canada
| | - Pauline Marangoni
- Department of Orofacial Sciences, University of California, San Francisco, California 94143
- Program in Craniofacial Biology, University of California, San Francisco, California 94143
| | - Vagan Tapaltsyan
- Department of Orofacial Sciences, University of California, San Francisco, California 94143
- Program in Craniofacial Biology, University of California, San Francisco, California 94143
- Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, California 94143
| | - Ophir Klein
- Department of Orofacial Sciences, University of California, San Francisco, California 94143
- Program in Craniofacial Biology, University of California, San Francisco, California 94143
- Department of Pediatrics, University of California, San Francisco, California 94143
- Institute for Human Genetics, University of California, San Francisco, California 94143
| | - Benedikt Hallgrímsson
- Alberta Children's Hospital Institute for Child and Maternal Health, University of Calgary, Alberta T2N 4N1, Canada
- The McCaig Bone and Joint Institute, University of Calgary, Alberta T2N 4Z6, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Alberta T2N 4N1, Canada
| |
Collapse
|
18
|
Osborn MJ, Webber BR, McElmurry RT, Rudser KD, DeFeo AP, Muradian M, Petryk A, Hallgrimsson B, Blazar BR, Tolar J, Braunlin EA. Angiotensin receptor blockade mediated amelioration of mucopolysaccharidosis type I cardiac and craniofacial pathology. J Inherit Metab Dis 2017; 40:281-289. [PMID: 27743312 PMCID: PMC5335863 DOI: 10.1007/s10545-016-9988-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/23/2016] [Accepted: 09/27/2016] [Indexed: 11/26/2022]
Abstract
Mucopolysaccharidosis type I (MPS IH) is a lysosomal storage disease (LSD) caused by inactivating mutations to the alpha-L-iduronidase (IDUA) gene. Treatment focuses on IDUA enzyme replacement and currently employed methods can be non-uniform in their efficacy particularly for the cardiac and craniofacial pathology. Therefore, we undertook efforts to better define the pathological cascade accounting for treatment refractory manifestations and demonstrate a role for the renin angiotensin system (RAS) using the IDUA-/- mouse model. Perturbation of the RAS in the aorta was more profound in male animals suggesting a causative role in the observed gender dimorphism and angiotensin receptor blockade (ARB) resulted in improved cardiac function. Further, we show the ability of losartan to prevent shortening of the snout, a common craniofacial anomaly in IDUA-/- mice. These data show a key role for the RAS in MPS associated pathology and support the inclusion of losartan as an augmentation to current therapies.
Collapse
Affiliation(s)
- Mark J Osborn
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
- Asan-Minnesota Institute for Innovating Transplantation, Seoul, Republic of Korea.
- School of Public Health, University of Minnesota, Minneapolis, MN, USA.
| | - Beau R Webber
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA
| | - Ronald T McElmurry
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA
| | - Kyle D Rudser
- Department of Cell Biology and Anatomy and the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Anthony P DeFeo
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA
| | - Michael Muradian
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA
| | - Anna Petryk
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy and the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Bruce R Blazar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA
| | - Jakub Tolar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Asan-Minnesota Institute for Innovating Transplantation, Seoul, Republic of Korea
- School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Braunlin
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, 420 Delaware ST SE, MMC 366, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
19
|
Pavličev M, Mitteroecker P, Gonzalez PM, Rolian C, Jamniczky H, Villena FPM, Marcucio R, Spritz R, Hallgrimsson B. Development Shapes a Consistent Inbreeding Effect in Mouse Crania of Different Line Crosses. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 326:474-488. [PMID: 28097826 DOI: 10.1002/jez.b.22722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 11/19/2016] [Accepted: 11/22/2016] [Indexed: 11/11/2022]
Abstract
Development translates genetic variation into a multivariate pattern of phenotypic variation, distributing it among traits in a nonuniform manner. As developmental processes are largely shared within species, this suggests that heritable phenotypic variation will be patterned similarly, in spite of the different segregating alleles. To investigate developmental effect on the variational pattern in the shape of the mouse skull across genetically differentiated lines, we employed the full set of reciprocal crosses (a.k.a. diallel) between eight inbred mouse strains of the Collaborative Cross Project. We used geometric morphometrics and multivariate analysis to capture cranial size and shape changes in 8 parentals and their 54 F1 crosses. The high heterozygosity generated in the F1 crosses allowed us to compare the multivariate deviations of the F1 phenotypes from the expected midparental phenotypes in different haplotype combinations. In contrast to body weight, we found a high degree of nonadditive deviation in craniofacial shape. Whereas the phenotypic and genetic divergence of parental strains manifested in high dimensionality of additive effects, the nonadditive deviations exhibited lesser dimensionality and in particular a strikingly coherent direction in shape space. We interpret this finding as evidence for a strong structuring effect of a relatively small set of developmental processes on the mapping of genetic to phenotypic variation.
Collapse
Affiliation(s)
- Mihaela Pavličev
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | | | - Paula M Gonzalez
- Instituto de Genetica Veterinaria, University of La Plata, La Plata, Argentina
| | - Campbell Rolian
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Heather Jamniczky
- Department of Cell Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta.,McCaig Bone and Joint Institute, University of Calgary, Calgary, Alberta, Canada
| | | | - Ralph Marcucio
- Department of Orthopedic Surgery, University of California San Francisco, California
| | - Richard Spritz
- Department of Pediatrics and Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Denver, Colorado
| | - Benedikt Hallgrimsson
- Department of Cell Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta.,McCaig Bone and Joint Institute, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Alberta, Canada
| |
Collapse
|
20
|
Abstract
A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and Diversity Outcross to relatively simple crosses such as sets of consomic strains and reduced complexity crosses. This protocol is intended to help investigators make more informed decisions about choices of resources given different types of questions. We consider factors such as costs, availability, and ease of breeding for common scenarios. In general, we recommend using complementary resources and minimizing depth of resampling of any given genome or strain.
Collapse
Affiliation(s)
- Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, 77 S. Manassas Street, Memphis, TN, 38163, USA.
| | - Evan G Williams
- Department of Biology, Institute for Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
21
|
Human Facial Shape and Size Heritability and Genetic Correlations. Genetics 2016; 205:967-978. [PMID: 27974501 DOI: 10.1534/genetics.116.193185] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/08/2016] [Indexed: 01/24/2023] Open
Abstract
The human face is an array of variable physical features that together make each of us unique and distinguishable. Striking familial facial similarities underscore a genetic component, but little is known of the genes that underlie facial shape differences. Numerous studies have estimated facial shape heritability using various methods. Here, we used advanced three-dimensional imaging technology and quantitative human genetics analysis to estimate narrow-sense heritability, heritability explained by common genetic variation, and pairwise genetic correlations of 38 measures of facial shape and size in normal African Bantu children from Tanzania. Specifically, we fit a linear mixed model of genetic relatedness between close and distant relatives to jointly estimate variance components that correspond to heritability explained by genome-wide common genetic variation and variance explained by uncaptured genetic variation, the sum representing total narrow-sense heritability. Our significant estimates for narrow-sense heritability of specific facial traits range from 28 to 67%, with horizontal measures being slightly more heritable than vertical or depth measures. Furthermore, for over half of facial traits, >90% of narrow-sense heritability can be explained by common genetic variation. We also find high absolute genetic correlation between most traits, indicating large overlap in underlying genetic loci. Not surprisingly, traits measured in the same physical orientation (i.e., both horizontal or both vertical) have high positive genetic correlations, whereas traits in opposite orientations have high negative correlations. The complex genetic architecture of facial shape informs our understanding of the intricate relationships among different facial features as well as overall facial development.
Collapse
|
22
|
Nachshon A, Abu-Toamih Atamni HJ, Steuerman Y, Sheikh-Hamed R, Dorman A, Mott R, Dohm JC, Lehrach H, Sultan M, Shamir R, Sauer S, Himmelbauer H, Iraqi FA, Gat-Viks I. Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains. Front Genet 2016; 7:172. [PMID: 27761138 PMCID: PMC5050206 DOI: 10.3389/fgene.2016.00172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/09/2016] [Indexed: 12/26/2022] Open
Abstract
A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions. We then leveraged a reference collection of metabolic biotransformation pathways to map potential relations between drugs and their underlying expression quantitative trait loci (eQTLs). By applying this approach on proximal eQTLs, including eQTLs acting on the overall expression of genes and on the expression of particular transcript isoforms, we were able to construct the organization of hepatic eQTL-drug connectivity across the CC population. The analysis revealed a substantial impact of genetic variation acting on drug biotransformation, allowed mapping of potential joint genetic effects in the context of individual drugs, and demonstrated crosstalk between drug metabolism and lipid metabolism. Our findings provide a resource for investigating drug disposition in the CC strains, and offer a new paradigm for integrating biotransformation reactions to corresponding variations in DNA sequences.
Collapse
Affiliation(s)
- Aharon Nachshon
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel-Aviv University Tel-Aviv, Israel
| | - Hanifa J Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel- Aviv University Tel-Aviv, Israel
| | - Yael Steuerman
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel-Aviv University Tel-Aviv, Israel
| | - Roa'a Sheikh-Hamed
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel- Aviv University Tel-Aviv, Israel
| | - Alexandra Dorman
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel- Aviv University Tel-Aviv, Israel
| | - Richard Mott
- Genetics Institute, University College of London London, UK
| | - Juliane C Dohm
- Genomics Unit, Center for Genomic RegulationBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU)Vienna, Austria
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Marc Sultan
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University Tel Aviv, Israel
| | - Sascha Sauer
- Department of Vertebrate Genomics, Max Planck Institute for Molecular GeneticsBerlin, Germany; CU Systems Medicine, University of WürzburgWürzburg, Germany
| | - Heinz Himmelbauer
- Genomics Unit, Center for Genomic RegulationBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU)Vienna, Austria
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel- Aviv University Tel-Aviv, Israel
| | - Irit Gat-Viks
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel-Aviv University Tel-Aviv, Israel
| |
Collapse
|
23
|
Gonzalez PN, Pavlicev M, Mitteroecker P, Pardo-Manuel de Villena F, Spritz RA, Marcucio RS, Hallgrímsson B. Genetic structure of phenotypic robustness in the collaborative cross mouse diallel panel. J Evol Biol 2016; 29:1737-51. [PMID: 27234063 DOI: 10.1111/jeb.12906] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 05/11/2016] [Accepted: 05/22/2016] [Indexed: 12/19/2022]
Abstract
Developmental stability and canalization describe the ability of developmental systems to minimize phenotypic variation in the face of stochastic micro-environmental effects, genetic variation and environmental influences. Canalization is the ability to minimize the effects of genetic or environmental effects, whereas developmental stability is the ability to minimize the effects of micro-environmental effects within individuals. Despite much attention, the mechanisms that underlie these two components of phenotypic robustness remain unknown. We investigated the genetic structure of phenotypic robustness in the collaborative cross (CC) mouse reference population. We analysed the magnitude of fluctuating asymmetry (FA) and among-individual variation of cranial shape in reciprocal crosses among the eight parental strains, using geometric morphometrics and a diallel analysis based on a Bayesian approach. Significant differences among genotypes were found for both measures, although they were poorly correlated at the level of individuals. An overall positive effect of inbreeding was found for both components of variation. The strain CAST/EiJ exerted a positive additive effect on FA and, to a lesser extent, among-individual variance. Sex- and other strain-specific effects were not significant. Neither FA nor among-individual variation was associated with phenotypic extremeness. Our results support the existence of genetic variation for both developmental stability and canalization. This finding is important because robustness is a key feature of developmental systems. Our finding that robustness is not related to phenotypic extremeness is consistent with theoretical work that suggests that its relationship to stabilizing selection is not straightforward.
Collapse
Affiliation(s)
- P N Gonzalez
- Instituto de Genética Veterinaria, CCT-CONICET, La Plata, Argentina
| | - M Pavlicev
- Department of Pediatrics, Cincinnati Children's Hospital Medical Centre, Cincinnati, OH, USA
| | - P Mitteroecker
- Department of Theoretical Biology, University of Vienna, Wien, Austria
| | | | - R A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - R S Marcucio
- Department of Orthopaedic Surgery, Orthopaedic Trauma Institute, San Francisco General Hospital, University of California San Francisco, San Francisco, CA, USA
| | - B Hallgrímsson
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
24
|
Pallares LF, Turner LM, Tautz D. Craniofacial shape transition across the house mouse hybrid zone: implications for the genetic architecture and evolution of between-species differences. Dev Genes Evol 2016; 226:173-86. [PMID: 27216933 PMCID: PMC4896993 DOI: 10.1007/s00427-016-0550-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022]
Abstract
Craniofacial shape differences between taxa have often been linked to environmental adaptation, e.g., new food sources, or have been studied in the context of domestication. Evidence for the genetic basis of such phenotypic differences to date suggests that between-species as well as between-population variation has an oligogenic basis, i.e., few loci of large effect explain most of the variation. In mice, it has been shown that within-population craniofacial variation has a highly polygenic basis, but there are no data regarding the genetic basis of between-species differences in natural populations. Here, we address this question using a phenotype-focused approach. Using 3D geometric morphometrics, we phenotyped a panel of mice derived from a natural hybrid zone between Mus musculus domesticus and Mus mus musculus and quantify the transition of craniofacial shape along the hybridization gradient. We find a continuous shape transition along the hybridization gradient and unaltered developmental stability associated with hybridization. This suggests that the morphospace between the two subspecies is continuous despite reproductive isolation and strong barriers to gene flow. We show that quantitative changes in overall genome composition generate quantitative changes in craniofacial shape; this supports a highly polygenic basis for between-species craniofacial differences in the house mouse. We discuss our findings in the context of oligogenic versus polygenic models of the genetic architecture of morphological traits.
Collapse
Affiliation(s)
- Luisa F Pallares
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemannstr. 2, 24306, Plön, Germany
| | - Leslie M Turner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemannstr. 2, 24306, Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemannstr. 2, 24306, Plön, Germany.
| |
Collapse
|
25
|
Navarro N, Maga AM. Does 3D Phenotyping Yield Substantial Insights in the Genetics of the Mouse Mandible Shape? G3 (BETHESDA, MD.) 2016; 6:1153-63. [PMID: 26921296 PMCID: PMC4856069 DOI: 10.1534/g3.115.024372] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/16/2016] [Indexed: 02/07/2023]
Abstract
We describe the application of high-resolution 3D microcomputed tomography, together with 3D landmarks and geometric morphometrics, to validate and further improve previous quantitative genetic studies that reported QTL responsible for variation in the mandible shape of laboratory mice using a new backcross between C57BL/6J and A/J inbred strains. Despite the increasing availability of 3D imaging techniques, artificial flattening of the mandible by 2D imaging techniques seems at first an acceptable compromise for large-scale phenotyping protocols, thanks to an abundance of low-cost digital imaging systems such as microscopes or digital cameras. We evaluated the gain of information from considering explicitly this additional third dimension, and also from capturing variation on the bone surface where no precise anatomical landmark can be marked. Multivariate QTL mapping conducted with different landmark configurations (2D vs. 3D; manual vs. semilandmarks) broadly agreed with the findings of previous studies. Significantly more QTL (23) were identified and more precisely mapped when the mandible shape was captured with a large set of semilandmarks coupled with manual landmarks. It appears that finer phenotypic characterization of the mandibular shape with 3D landmarks, along with higher density genotyping, yields better insights into the genetic architecture of mandibular development. Most of the main variation is, nonetheless, preferentially embedded in the natural 2D plane of the hemi-mandible, reinforcing the results of earlier influential investigations.
Collapse
Affiliation(s)
- Nicolas Navarro
- Biogéosciences, UMR CNRS 6282, Univ Bourgogne Franche-Comté, EPHE, PSL Research University, F-21000 Dijon, France
| | - A Murat Maga
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98105 Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington 98101
| |
Collapse
|
26
|
Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
Collapse
Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| |
Collapse
|