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Morris ZS, Colbert MW, Rowe TB. Variation and Variability in Skeletal Ossification of the Gray Short-tailed Opossum, Monodelphis domestica. Integr Org Biol 2024; 6:obae024. [PMID: 39114377 PMCID: PMC11305135 DOI: 10.1093/iob/obae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 06/06/2024] [Accepted: 07/02/2024] [Indexed: 08/10/2024] Open
Abstract
By reconstructing and comparing the sequence of ontogenetic (embryonic development and post-natal growth) events across species, developmental biologists have gained unique insights into the key processes underlying the evolution of modern lineages and their extinct relatives. However, despite the importance of intraspecific variation to evolutionary transformation and lineage divergence, variation in the sequence of developmental events is seldom acknowledged. Thus, how much variation or variability should be expected during ontogeny remains poorly understood and it is an open question to what extent it impacts interspecific comparisons of developmental patterns. To address this crucial question, we studied the skeletal development of the important biomedical and developmental model organism, Monodelphis domestica. We investigated cranial, forelimb, and hindlimb elements using ontogenetic sequence analysis (OSA) to quantify and assess the full range of variation and variability in the sequence of ossification. Our study documented that previously unrecognized variation exists during M. domestica ontogeny-with over 5000 sequences for the full 92 event analysis. Further, OSA revealed unexpectedly high variability (i.e., the propensity to express variation) in the sequence of ossification for the skull and across the entire skeleton. Reconstructed modal sequences were generally in agreement with previously recognized patterns, including earlier ossification of the facial skeleton and a slight offset between forelimb and hindlimb development. However, the full range of variation shows that the majority of specimens in our analysis followed developmental trajectories distinct from those recovered by prior studies. This level of variation is quite remarkable and demonstrates the importance of assessing intraspecific ontogenetic variation. By quantifying sequence polymorphism and studying how developmental variation and variability differ among species, we can clarify more precisely how developmental patterns differ among species and gain insights into how ontogeny itself evolves.
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Affiliation(s)
- Z S Morris
- Jackson School of Geosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Dinosaur Institute, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - M W Colbert
- Jackson School of Geosciences, The University of Texas at Austin, Austin, TX 78712, USA
- University of Texas High‐Resolution X‐Ray CT Facility, The University of Texas, Austin, TX 78712, USA
| | - T B Rowe
- Jackson School of Geosciences, The University of Texas at Austin, Austin, TX 78712, USA
- University of Texas High‐Resolution X‐Ray CT Facility, The University of Texas, Austin, TX 78712, USA
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2
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Howenstine AO, Sadier A, Anthwal N, Lau CL, Sears KE. Non-model systems in mammalian forelimb evo-devo. Curr Opin Genet Dev 2021; 69:65-71. [PMID: 33684847 PMCID: PMC8364859 DOI: 10.1016/j.gde.2021.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 01/09/2023]
Abstract
Mammal forelimbs are highly diverse, ranging from the elongated wing of a bat to the stout limb of the mole. The mammal forelimb has been a long-standing system for the study of early developmental patterning, proportional variation, shape change, and the reduction of elements. However, most of this work has been performed in mice, which neglects the wide variation present across mammal forelimbs. This review emphasizes the critical role of non-model systems in limb evo-devo and highlights new emerging models and their potential. We discuss the role of gene networks in limb evolution, and touch on functional analyses that lay the groundwork for further developmental studies. Mammal limb evo-devo is a rich field, and here we aim to synthesize the findings of key recent works and the questions to which they lead.
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Affiliation(s)
- Aidan O Howenstine
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, 90095, United States
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, 90095, United States
| | - Neal Anthwal
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, 90095, United States; Centre for Craniofacial and Regenerative Biology, King's CollegeLondon, 27th Floor Guy's Tower, London, SE1 9RT, UK
| | - Clive Lf Lau
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, 90095, United States
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, 90095, United States.
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3
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Hayden L, Lochovska K, Sémon M, Renaud S, Delignette-Muller ML, Vilcot M, Peterkova R, Hovorakova M, Pantalacci S. Developmental variability channels mouse molar evolution. eLife 2020; 9:50103. [PMID: 32048989 PMCID: PMC7182435 DOI: 10.7554/elife.50103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 02/02/2020] [Indexed: 12/30/2022] Open
Abstract
Do developmental systems preferentially produce certain types of variation that orient phenotypic evolution along preferred directions? At different scales, from the intra-population to the interspecific, the murine first upper molar shows repeated anterior elongation. Using a novel quantitative approach to compare the development of two mouse strains with short or long molars, we identified temporal, spatial and functional differences in tooth signaling center activity, that arise from differential tuning of the activation-inhibition mechanisms underlying tooth patterning. By tracing their fate, we could explain why only the upper first molar reacts via elongation of its anterior part. Despite a lack of genetic variation, individuals of the elongated strain varied in tooth length and the temporal dynamics of their signaling centers, highlighting the intrinsic instability of the upper molar developmental system. Collectively, these results reveal the variational properties of murine molar development that drive morphological evolution along a line of least resistance. Over time species develop random mutations in their genetic sequence that causes their form to change. If this new form increases the survival of a species it will become favored through natural selection and is more likely to get passed on to future generations. But, the evolution of these new traits also depends on what happens during development. Developmental mechanisms control how an embryo progresses from a single cell to an adult organism made of many cells. Mutations that alter these processes can influence the physical outcome of development, and cause a new trait to form. This means that if many different mutations alter development in a similar way, this can lead to the same physical change, making it ‘easy’ for a new trait to repeatedly occur. Most of the research has focused on finding the mutations that underlie repeated evolution, but rarely on identifying the role of the underlying developmental mechanisms. To bridge this gap, Hayden et al. investigated how changes during development influence the shape and size of molar teeth in mice. In some wild species of mice, the front part of the first upper molar is longer than in other species. This elongation, which is repeatedly found in mice from different islands, likely came from developmental mechanisms. Tooth development in mice has been well-studied in the laboratory, and Hayden et al. started by identifying two strains of laboratory mice that mimic the teeth seen in their wild cousins, one with elongated upper first molars and another with short ones. Comparing how these two strains of mice developed their elongated or short teeth revealed key differences in the embryonic structures that form the upper molar and cause it to elongate. Further work showed that variations in these embryonic structures can even cause mice that are genetically identical to have longer or shorter upper first molars. These findings show how early differences during development can lead to small variations in form between adult species of mice. This study highlights how studying developmental differences as well as genetic sequences can further our understanding of how different species evolved.
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Affiliation(s)
- Luke Hayden
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, INSERM U1210, Lyon, France.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Katerina Lochovska
- 1st Department of Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marie Sémon
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, INSERM U1210, Lyon, France
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, VetAgro Sup, Villeurbanne, France
| | - Marie-Laure Delignette-Muller
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, VetAgro Sup, Villeurbanne, France
| | - Maurine Vilcot
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
| | - Renata Peterkova
- Department of Histology and Embryology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Maria Hovorakova
- Department of Developmental Biology, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic
| | - Sophie Pantalacci
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, INSERM U1210, Lyon, France
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4
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Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences University of Chicago Chicago Illinois
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5
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Ferraz T, Rossoni DM, Althoff SL, Pissinatti A, Paixão-Cortês VR, Bortolini MC, González-José R, Marroig G, Salzano FM, Gonçalves GL, Hünemeier T. Contrasting patterns of RUNX2 repeat variations are associated with palate shape in phyllostomid bats and New World primates. Sci Rep 2018; 8:7867. [PMID: 29777172 PMCID: PMC5959863 DOI: 10.1038/s41598-018-26225-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
Establishing the genetic basis that underlies craniofacial variability in natural populations is one of the main topics of evolutionary and developmental studies. One of the genes associated with mammal craniofacial variability is RUNX2, and in the present study we investigated the association between craniofacial length and width and RUNX2 across New World bats (Phyllostomidae) and primates (Catarrhini and Platyrrhini). Our results showed contrasting patterns of association between the glutamate/alanine ratios (Q/A ratio) and palate shape in these highly diverse groups. In phyllostomid bats, we found an association between shorter/broader faces and increase of the Q/A ratio. In New World monkeys (NWM) there was a positive correlation of increasing Q/A ratios to more elongated faces. Our findings reinforced the role of the Q/A ratio as a flexible genetic mechanism that would rapidly change the time of skull ossification throughout development. However, we propose a scenario in which the influence of this genetic adjustment system is indirect. The Q/A ratio would not lead to a specific phenotype, but throughout the history of a lineage, would act along with evolutionary constraints, as well as other genes, as a facilitator for adaptive morphological changes.
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Affiliation(s)
- Tiago Ferraz
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Daniela M Rossoni
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | | | | | | | - Maria Cátira Bortolini
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Rolando González-José
- Patagonian Institute of Social and Human Sciences, National Council for Scientific and Technological Research-CONICET, U9120ACD, Puerto Madryn, Argentina
| | - Gabriel Marroig
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Francisco M Salzano
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Gislene L Gonçalves
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil.,Department of Environmental Resources, Faculty of Agrarian Sciences, University of Tarapacá, Arica, Chile
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil.
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Sears K, Maier JA, Sadier A, Sorensen D, Urban DJ. Timing the developmental origins of mammalian limb diversity. Genesis 2017; 56. [PMID: 29095555 DOI: 10.1002/dvg.23079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 12/31/2022]
Abstract
Mammals have highly diverse limbs that have contributed to their occupation of almost every niche. Researchers have long been investigating the development of these diverse limbs, with the goals of identifying developmental processes and potential biases that shape mammalian limb diversity. To date, researchers have used techniques ranging from the genomic to the anatomic to investigate the developmental processes shaping the limb morphology of mammals from five orders (Marsupialia, Chiroptera, Rodentia, Cetartiodactyla, and Perissodactyla). Results of these studies suggest that the differential expression of genes controlling diverse cellular processes underlies mammalian limb diversity. Results also suggest that the earliest development of the limb tends to be conserved among mammalian species, while later limb development tends to be more variable. This research has established the mammalian limb as a model system for evolutionary developmental biology, and set the stage for more in-depth, cross-disciplinary research into the genetic controls, tissue-level cellular behaviors, and selective pressures that have driven the developmental evolution of mammalian limbs. Ideally, these studies will be performed in a diverse suite of mammalian species within a comparative, phylogenetic framework.
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Affiliation(s)
- Karen Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, 90095
| | - Jennifer A Maier
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, 90095
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, 90095
| | - Daniel Sorensen
- Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Daniel J Urban
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, 90095.,Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801.,Department of Mammalogy, American Museum of Natural History, New York, New York, 10024
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7
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Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLoS Genet 2017; 13:e1006867. [PMID: 28704372 PMCID: PMC5509106 DOI: 10.1371/journal.pgen.1006867] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/13/2017] [Indexed: 12/29/2022] Open
Abstract
Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.
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Affiliation(s)
- Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Kayla Stefanko
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Caitlyn Cubba
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States of America
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Martínez-Abadías N, Mateu R, Niksic M, Russo L, Sharpe J. Geometric Morphometrics on Gene Expression Patterns Within Phenotypes: A Case Example on Limb Development. Syst Biol 2015; 65:194-211. [PMID: 26377442 PMCID: PMC4748747 DOI: 10.1093/sysbio/syv067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/11/2015] [Indexed: 01/12/2023] Open
Abstract
How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are associated with changes in morphology using the limb as a case example. Our method combines molecular biology techniques, such as whole-mount in situ hybridization, with image and shape analysis, extending the use of Geometric Morphometrics to the analysis of nonanatomical shapes, such as gene expression domains. Elliptical Fourier and Procrustes-based semilandmark analyses were used to analyze the variation and covariation patterns of the limb bud shape with the expression patterns of two relevant genes for limb morphogenesis, Hoxa11 and Hoxa13. We devised a multiple thresholding method to semiautomatically segment gene domains at several expression levels in large samples of limb buds from C57Bl6 mouse embryos between 10 and 12 postfertilization days. Besides providing an accurate phenotyping tool to quantify the spatiotemporal dynamics of gene expression patterns within developing structures, our morphometric analyses revealed high, non-random, and gene-specific variation undergoing canalization during limb development. Our results demonstrate that Hoxa11 and Hoxa13, despite being paralogs with analogous functions in limb patterning, show clearly distinct dynamic patterns, both in shape and size, and are associated differently with the limb bud shape. The correspondence between our results and already well-established molecular processes underlying limb development confirms that this morphometric approach is a powerful tool to extract features of development regulating morphogenesis. Such multilevel analyses are promising in systems where not so much molecular information is available and will advance our understanding of the genotype–phenotype map. In systematics, this knowledge will increase our ability to infer how evolution modified a common developmental pattern to generate a wide diversity of morphologies, as in the vertebrate limb.
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Affiliation(s)
- Neus Martínez-Abadías
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roger Mateu
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Martina Niksic
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lucia Russo
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Sharpe
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Fusco G. For a new dialogue between theoretical and empirical studies in evo-devo. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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