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Ağaç DK, Onuk B, Gündemir O, Kabak M, Manuta N, Çakar B, Janeczek M, Crampton DA, Szara T. Comparative Cranial Geometric Morphometrics among Wistar Albino, Sprague Dawley, and WAG/Rij Rat Strains. Animals (Basel) 2024; 14:1274. [PMID: 38731278 PMCID: PMC11083316 DOI: 10.3390/ani14091274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
This research utilizes geometric morphometrics to investigate shape variation in the skull, mandible, and teeth among three rat strains: Wistar Albino (WA), Sprague Dawley (SD), and WAG/Rij (WR). Through the analysis of 48 rats using 2D geometric morphometric techniques, significant differences in their skull morphology were identified. This study indicates a shift from a rectangular to an oval cranial shape across strains, with notable size and morphological variances. Particularly, the WR strain's skull shape significantly differs from the SD and WA strains, suggesting distinct ecological or genetic pathways. Compared to the skull, mandible shape differences are less pronounced, but still significant. The WR strain exhibits a distinct mandible shape, potentially reflecting ecological adaptations like dietary habits. The teeth shape of WR rats is the most distinct. SD rats consistently exhibited larger sizes in both skull and mandible measurements, while WR rats were notably smaller. Interestingly, sexual dimorphism was not statistically significant in skull and teeth sizes, aligning with findings from previous studies. However, the mandible showed clear size differences between sexes, underscoring its potential for adaptive or behavioral studies. In summary, this study provides a comprehensive analysis of morphological variations in rat strains, highlighting the intricate interplay of size, shape, and ecological factors. These findings lay a foundation for deeper explorations into the adaptive, ecological, or genetic narratives influencing rat morphology.
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Affiliation(s)
- Duygu Küçük Ağaç
- Department of Veterinary, Şiran Mustafa Beyaz Vocational School, Gümüşhane University, 29700 Gümüşhane, Türkiye;
| | - Burcu Onuk
- Department of Anatomy, Faculty of Veterinary Medicine, Ondokuz Mayıs University, 55270 Samsun, Türkiye; (B.O.); (M.K.)
| | - Ozan Gündemir
- Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34500 Istanbul, Türkiye
| | - Murat Kabak
- Department of Anatomy, Faculty of Veterinary Medicine, Ondokuz Mayıs University, 55270 Samsun, Türkiye; (B.O.); (M.K.)
| | - Nicoleta Manuta
- Institute of Graduate Studies, Istanbul University-Cerrahpaşa, 34500 Istanbul, Türkiye; (N.M.); (B.Ç.)
| | - Buket Çakar
- Institute of Graduate Studies, Istanbul University-Cerrahpaşa, 34500 Istanbul, Türkiye; (N.M.); (B.Ç.)
| | - Maciej Janeczek
- Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland;
| | - Denise Amber Crampton
- Research Centre in Evolutionary Anthropology and Palaeoecology, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK;
| | - Tomasz Szara
- Department of Morphological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland
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Greer SE, Haller SJ, Lee D, Dudley AT. N-cadherin and β1 integrin coordinately regulate growth plate cartilage architecture. Mol Biol Cell 2024; 35:ar49. [PMID: 38294852 PMCID: PMC11064670 DOI: 10.1091/mbc.e23-03-0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/07/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
Spatial and temporal regulation of chondrocyte maturation in the growth plate drives growth of many bones. One essential event to generate the ordered cell array characterizing growth plate cartilage is the formation of chondrocyte columns in the proliferative zone via 90-degree rotation of daughter cells to align with the long axis of the bone. Previous studies have suggested crucial roles for cadherins and integrin β1 in column formation. The purpose of this study was to determine the relative contributions of cadherin- and integrin-mediated cell adhesion in column formation. Here we present new mechanistic insights generated by application of live time-lapse confocal microscopy of cranial base explant cultures, robust genetic mouse models, and new quantitative methods to analyze cell behavior. We show that conditional deletion of either the cell-cell adhesion molecule Cdh2 or the cell-matrix adhesion molecule Itgb1 disrupts column formation. Compound mutants were used to determine a potential reciprocal regulatory interaction between the two adhesion surfaces and identified that defective chondrocyte rotation in a N-cadherin mutant was restored by a heterozygous loss of integrin β1. Our results support a model for which integrin β1, and not N-cadherin, drives chondrocyte rotation and for which N-cadherin is a potential negative regulator of integrin β1 function.
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Affiliation(s)
- Sydney E. Greer
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE 68198
| | - Stephen J. Haller
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE 68198
| | - Donghee Lee
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE 68198
| | - Andrew T. Dudley
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE 68198
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Horbaly H, Hubbe M, Sylvester AD, Steadman DW, Auerbach BM. Variation in human limb joint articular morphology. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:388-400. [PMID: 37702986 DOI: 10.1002/ajpa.24829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 06/08/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023]
Abstract
OBJECTIVES Synovial joints in human limbs strike a balance between mobility, stability, and articular fit, yet little is known about how these conflicting demands pattern intraspecific variation in articular shape. In this study, we use geometric morphometrics to establish the apportionment and magnitude of morphological variance of the articular surfaces of the human shoulder, elbow, hip, and knee. We hypothesize that variances will be comparable between articulating surfaces within a joint and will be larger in joints with smaller ranges of motion, given their plurality of functional demands. MATERIALS AND METHODS Three-dimensional landmarks were taken on the articular surfaces of the glenohumeral, humeroulnar, acetabulofemoral, and tibiofemoral joints from CT scans of 200 skeletons from the University of Tennessee Donated Skeletal Collection (84 females, 116 males). Root mean-squared distances between articulations calculated from Procrustes shape coordinates were used to determine variance distributions. RESULTS We found no difference in variances for each articular surface between the sexes or between left and right articular surfaces. A high range of motion is associated with greater morphological variance; however, this pattern is largely driven by the concave articular surfaces of each joint, which consistently exhibit statistically greater variance than their convex counterparts. DISCUSSION The striking pattern of differential variance between articulating morphologies points to potential disparities in development between them. Consistently higher variance in concave surfaces may relate to chondral modeling theory for the formation of joints. Establishing intraspecific morphological variance patterns is a first step in understanding coordinated evolution among articular features.
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Affiliation(s)
- Haley Horbaly
- Department of Health and Human Performance, Congdon School of Health Sciences, High Point University, High Point, North Carolina, USA
- Department of Physician Assistant Studies, Congdon School of Health Sciences, High Point University, High Point, North Carolina, USA
| | - Mark Hubbe
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA
| | - Adam D Sylvester
- Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Benjamin M Auerbach
- Department of Anthropology, The University of Tennessee, Knoxville, Tennessee, USA
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, Tennessee, USA
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Horbaly H. Covariance in human limb joint articular morphology. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:401-411. [PMID: 37702982 DOI: 10.1002/ajpa.24826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 06/12/2023] [Accepted: 06/23/2023] [Indexed: 09/14/2023]
Abstract
OBJECTIVES Limb synovial joints exhibit complex shapes that must accommodate often-antagonistic demands of function, mobility, and stability. These demands presumably dictate coordination among joint articular shapes, but the structure of morphological covariance within and among joints is unknown. This study analyzes the human shoulder, elbow, hip, and knee to determine how articular covariance is structured in relation to joint structure, accessory cartilage, and function. MATERIALS AND METHODS Surface models were created from the CT scans of 200 modern skeletons from the University of Tennessee Donated Skeletal Collection. Three-dimensional landmarks were collected on the shoulder, elbow, hip, and knee joints. Two-block partial least squares were conducted to determine associations between surfaces of conarticular shapes, functionally analogous articulations, and articulations belonging to the same bone. RESULTS Except for the components of the shoulder, all conarticular pairs exhibit covariance, though the strength of these relationships appears unrelated to the amount of accessory cartilage in the joint. Only the analogous articulations of the humerus and femur exhibit significant covariance, but it is unlikely that this pattern is due to function alone. Stronger covariance within the lower limb than the upper limb is consistent broader primate patterns of within-limb integration. DISCUSSION With the exception of the elbow, complementary joint function does not appear to promote strong covariance between articulations. Analogous humeral and femoral surfaces are also serially homologous, which may result in the articular associations observed between these bones. Broadly, these patterns highlight the indirect relationship between joint congruence and covariance.
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Affiliation(s)
- Haley Horbaly
- Department of Health and Human Performance, Congdon School of Health Sciences, High Point University, High Point, North Carolina, USA
- Department of Physician Assistant Studies, Congdon School of Health Sciences, High Point University, High Point, North Carolina, USA
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Tsai DY, Chen JJ, Su PC, Liu IM, Yeh SHH, Chen CK, Cheng HC, Chen CF, Li WH, Ng CS. Chicken HOXC8 and HOXC10 genes may play a role in the altered skull morphology associated with the Crest phenotype. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:392-402. [PMID: 37039065 DOI: 10.1002/jez.b.23194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/12/2023]
Abstract
One of the most intriguing traits found in domestic chickens is the Crest phenotype. This trait, characterized by a tuft of elongated feathers sprouted from the head, is found in breeds such as Polish chickens and Silkie chickens. Moreover, some crested chicken breeds also exhibit a protuberance in their anterodorsal skull region. Previous studies have strived to identify the causative factors of this trait. This study aimed to elucidate the role of chicken HOXC8 and HOXC10 in the formation of the Crest phenotype. We explored the effect of ectopic expression of HOXC8 or HOXC10 on the chicken craniofacial morphology using the RCAS retrovirus transformation system. Microcomputed tomography scanning was conducted to measure the 3D structure of the cranial bone of transgenic embryos for geometric morphometric analysis. We found that the ectopic expression of HOXC8 or HOXC10 in chicken heads caused mild morphological changes in the skull compared with the GFP-transgenic control group. Geometric morphometric analysis showed that HOXC8 and HOXC10 transgenic groups expressed a mild upward shape change in the frontal region of the skull compared with the control group, which is similar to what is seen in the crested chicken breeds. In conclusion, this study supports findings in previous studies in which HOX genes play a role in the formation of the altered skull morphology related to the Crest phenotype. It also supports that mutations in HOX genes may contribute to intra- and inter-specific variation in morphological traits in vertebrates.
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Affiliation(s)
- Dien-Yu Tsai
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Jiun-Jie Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Chi Su
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - I-Ming Liu
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Skye Hsin-Hsien Yeh
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Hsu-Chen Cheng
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Feng Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- Bioresource Conservation Research Center, National Tsing Hua University, Hsinchu, Taiwan
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Devine J, Kurki HK, Epp JR, Gonzalez PN, Claes P, Hallgrímsson B. Classifying high-dimensional phenotypes with ensemble learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542750. [PMID: 37398168 PMCID: PMC10312448 DOI: 10.1101/2023.05.29.542750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Classification is a fundamental task in biology used to assign members to a class. While linear discriminant functions have long been effective, advances in phenotypic data collection are yielding increasingly high-dimensional datasets with more classes, unequal class covariances, and non-linear distributions. Numerous studies have deployed machine learning techniques to classify such distributions, but they are often restricted to a particular organism, a limited set of algorithms, and/or a specific classification task. In addition, the utility of ensemble learning or the strategic combination of models has not been fully explored.We performed a meta-analysis of 33 algorithms across 20 datasets containing over 20,000 high-dimensional shape phenotypes using an ensemble learning framework. Both binary (e.g., sex, environment) and multi-class (e.g., species, genotype, population) classification tasks were considered. The ensemble workflow contains functions for preprocessing, training individual learners and ensembles, and model evaluation. We evaluated algorithm performance within and among datasets. Furthermore, we quantified the extent to which various dataset and phenotypic properties impact performance.We found that discriminant analysis variants and neural networks were the most accurate base learners on average. However, their performance varied substantially between datasets. Ensemble models achieved the highest performance on average, both within and among datasets, increasing average accuracy by up to 3% over the top base learner. Higher class R2 values, mean class shape distances, and between- vs. within-class variances were positively associated with performance, whereas higher class covariance distances were negatively associated. Class balance and total sample size were not predictive.Learning-based classification is a complex task driven by many hyperparameters. We demonstrate that selecting and optimizing an algorithm based on the results of another study is a flawed strategy. Ensemble models instead offer a flexible approach that is data agnostic and exceptionally accurate. By assessing the impact of various dataset and phenotypic properties on classification performance, we also offer potential explanations for variation in performance. Researchers interested in maximizing performance stand to benefit from the simplicity and effectiveness of our approach made accessible via the R package pheble.
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Affiliation(s)
- Jay Devine
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB T2N 4N1, CANADA
| | - Helen K. Kurki
- Department of Anthropology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, CANADA
| | - Jonathan R. Epp
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB T2N 4N1, CANADA
| | - Paula N. Gonzalez
- Institute for Studies in Neuroscience and Complex Systems (ENyS) CONICET, Universidad Nacional de La Plata, Av. Calchaquí 5402, Florencio Varela, Buenos Aires, ARGENTINA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, 3000 Leuven, BELGIUM
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, 3000 Leuven, BELGIUM
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB T2N 4N1, CANADA
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Auerbach BM, Savell KRR, Agosto ER. Morphology, evolution, and the whole organism imperative: Why evolutionary questions need multi-trait evolutionary quantitative genetics. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 37060292 DOI: 10.1002/ajpa.24733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
Since Washburn's New Physical Anthropology, researchers have sought to understand the complexities of morphological evolution among anatomical regions in human and non-human primates. Researchers continue, however, to preferentially use comparative and functional approaches to examine complex traits, but these methods cannot address questions about evolutionary process and often conflate function with fitness. Moreover, researchers also tend to examine anatomical elements in isolation, which implicitly assumes independent evolution among different body regions. In this paper, we argue that questions asked in primate evolution are best examined using multiple anatomical regions subjected to model-bound methods built from an understanding of evolutionary quantitative genetics. A nascent but expanding number of studies over the last two decades use this approach, examining morphological integration, evolvability, and selection modeling. To help readers learn how to use these methods, we review fundamentals of evolutionary processes within a quantitative genetic framework, explore the importance of neutral evolutionary theory, and explain the basics of evolutionary quantitative genetics, namely the calculation of evolutionary potential for multiple traits in response to selection. Leveraging these methods, we demonstrate their use to understand non-independence in possible evolutionary responses across the limbs, limb girdles, and basicranium of humans. Our results show that model-bound quantitative genetic methods can reveal unexpected genetic covariances among traits that create a novel but measurable understanding of evolutionary complexity among multiple traits. We advocate for evolutionary quantitative genetic methods to be a standard whenever appropriate to keep studies of primate morphological evolution relevant for the next seventy years and beyond.
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Affiliation(s)
- Benjamin M Auerbach
- Department of Anthropology, The University of Tennessee, Knoxville, Tennessee, USA
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, Tennessee, USA
| | - Kristen R R Savell
- Department of Biology, Sacred Heart University, Fairfield, Connecticut, USA
| | - Elizabeth R Agosto
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Life History Traits of Sperm Whales Physeter macrocephalus Linnaeus, 1758 Stranded along Italian Coasts (Cetartiodactyla: Physeteridae). Animals (Basel) 2022; 13:ani13010079. [PMID: 36611689 PMCID: PMC9817511 DOI: 10.3390/ani13010079] [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: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
We investigated the relationship between age and body length, and age at sexual maturity of Physeter macrocephalus individuals stranded along the Italian coast. Our molecular analysis shows that all our samples belong to the C.001.002 haplotype, shared between Atlantic and Mediterranean populations. We show that males attain sexual maturity at 10 years, similar to those from other marine areas. However, considering the same body length class, Mediterranean males are older than Atlantic ones. Our finding of a Mediterranean pregnant female of only 6.5 m in length and an assessed age of 24-26 years is particularly noteworthy, considering that females reach sexual maturity at about 9 years and 9 m of total length in other regions. Comparing our results with the literature data, we highlight the positive correlation between lifespan, adult body length and weight of males from the Mediterranean and Atlantic Ocean. Regardless of whether the relatively small size of Mediterranean specimens is a consequence of an inbreeding depression or an adaptation to less favorable trophic conditions, we recommend to closely monitor this population from a conservation perspective. In fact, its low genetic diversity likely corresponds to a relatively limited ability to respond to environmental changes compared with other populations.
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MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Sci Data 2022; 9:230. [PMID: 35614082 PMCID: PMC9133120 DOI: 10.1038/s41597-022-01338-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/13/2022] [Indexed: 11/08/2022] Open
Abstract
Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase ( www.facebase.org , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).
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