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Danos N, Staab KL, Whitenack LB. The Core Concepts, Competencies and Grand Challenges of Comparative Vertebrate Anatomy and Morphology. Integr Org Biol 2022; 4:obac019. [PMID: 35919560 PMCID: PMC9338813 DOI: 10.1093/iob/obac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 05/02/2022] [Accepted: 05/18/2022] [Indexed: 12/02/2022] Open
Abstract
Core concepts offer coherence to the discourse of a scientific discipline and facilitate teaching by identifying large unifying themes that can be tailored to the level of the class and expertise of the instructor. This approach to teaching has been shown to encourage deeper learning that can be integrated across subdisciplines of biology and has been adopted by several other biology subdisciplines. However, Comparative Vertebrate Anatomy, although one of the oldest biological areas of study, has not had its core concepts identified. Here, we present five core concepts and seven competencies (skills) for Comparative Vertebrate Anatomy that came out of an iterative process of engagement with the broader community of vertebrate morphologists over a 3-year period. The core concepts are (A) evolution, (B) structure and function, (C) morphological development, (D) integration, and (E) human anatomy is the result of vertebrate evolution. The core competencies students should gain from the study of comparative vertebrate anatomy are (F) tree thinking, (G) observation, (H) dissection of specimens, (I) depiction of anatomy, (J) appreciation of the importance of natural history collections, (K) science communication, and (L) data integration. We offer a succinct description of each core concept and competency, examples of learning outcomes that could be used to assess teaching effectiveness, and examples of relevant resources for both instructors and students. Additionally, we pose a grand challenge to the community, arguing that the field of Comparative Vertebrate Anatomy needs to acknowledge racism, androcentrism, homophobia, genocide, slavery, and other influences in its history and address their lingering effects in order to move forward as a thriving discipline that is inclusive of all students and scientists and continues to generate unbiased knowledge for the betterment of humanity. Despite the rigorous process used to compile these core concepts and competencies, we anticipate that they will serve as a framework for an ongoing conversation that ensures Comparative Vertebrate Anatomy remains a relevant field in discovery, innovation, and training of future generations of scientists.
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Affiliation(s)
- Nicole Danos
- Biology, University of San Diego, 5998 Alcala Park, San Diego, CA 92210
| | - Katie Lynn Staab
- Biology Department, McDaniel College, 2 College Hill, Westminster, MD 21157
| | - Lisa B Whitenack
- Depts. of Biology and Geology, Allegheny College, 520 N. Main St., Meadville, PA 16335
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Abstract
Plants and animals are both important for studies in evolutionary developmental biology (EvoDevo). Plant morphology as a valuable discipline of EvoDevo is set for a paradigm shift. Process thinking and the continuum approach in plant morphology allow us to perceive and interpret growing plants as combinations of developmental processes rather than as assemblages of structural units (“organs”) such as roots, stems, leaves, and flowers. These dynamic philosophical perspectives were already favored by botanists and philosophers such as Agnes Arber (1879–1960) and Rolf Sattler (*1936). The acceptance of growing plants as dynamic continua inspires EvoDevo scientists such as developmental geneticists and evolutionary biologists to move towards a more holistic understanding of plants in time and space. This review will appeal to many young scientists in the plant development research fields. It covers a wide range of relevant publications from the past to present.
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Kim JW, Yang HJ, Oel AP, Brooks MJ, Jia L, Plachetzki DC, Li W, Allison WT, Swaroop A. Recruitment of Rod Photoreceptors from Short-Wavelength-Sensitive Cones during the Evolution of Nocturnal Vision in Mammals. Dev Cell 2017; 37:520-32. [PMID: 27326930 DOI: 10.1016/j.devcel.2016.05.023] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 04/16/2016] [Accepted: 05/24/2016] [Indexed: 01/07/2023]
Abstract
Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinas. In mice, we discovered genetic and epigenetic vestiges of short-wavelength cones in developing rods, and cell-lineage tracing validated the genesis of rods from S cones. Curiously, rods did not derive from S cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution.
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Affiliation(s)
- Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam Phillip Oel
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Matthew John Brooks
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Jia
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Charles Plachetzki
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William Ted Allison
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Rutishauser R. Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification. ANNALS OF BOTANY 2016; 117:811-32. [PMID: 26589968 PMCID: PMC4845801 DOI: 10.1093/aob/mcv172] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/19/2015] [Accepted: 09/25/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND Various groups of flowering plants reveal profound ('saltational') changes of their bauplans (architectural rules) as compared with related taxa. These plants are known as morphological misfits that appear as rather large morphological deviations from the norm. Some of them emerged as morphological key innovations (perhaps 'hopeful monsters') that gave rise to new evolutionary lines of organisms, based on (major) genetic changes. SCOPE This pictorial report places emphasis on released bauplans as typical for bladderworts (Utricularia, approx. 230 secies, Lentibulariaceae) and river-weeds (Podostemaceae, three subfamilies, approx. 54 genera, approx. 310 species). Bladderworts (Utricularia) are carnivorous, possessing sucking traps. They live as submerged aquatics (except for their flowers), as humid terrestrials or as epiphytes. Most Podostemaceae are restricted to rocks in tropical river-rapids and waterfalls. They survive as submerged haptophytes in these extreme habitats during the rainy season, emerging with their flowers afterwards. The recent scientific progress in developmental biology and evolutionary history of both Lentibulariaceae and Podostemaceae is summarized. CONCLUSIONS Lentibulariaceae and Podostemaceae follow structural rules that are different from but related to those of more typical flowering plants. The roots, stems and leaves - as still distinguishable in related flowering plants - are blurred ('fuzzy'). However, both families have stable floral bauplans. The developmental switches to unusual vegetative morphologies facilitated rather than prevented the evolution of species diversity in both families. The lack of one-to-one correspondence between structural categories and gene expression may have arisen from the re-use of existing genetic resources in novel contexts. Understanding what developmental patterns are followed in Lentibulariaceae and Podostemaceae is a necessary prerequisite to discover the genetic alterations that led to the evolution of these atypical plants. Future molecular genetic work on morphological misfits such as bladderworts and river-weeds will provide insight into developmental and evolutionary aspects of more typical vascular plants.
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Affiliation(s)
- Rolf Rutishauser
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
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Wang F, Ballesteros JA, Hormiga G, Chesters D, Zhan Y, Sun N, Zhu C, Chen W, Tu L. Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae). Mol Phylogenet Evol 2015; 91:135-49. [PMID: 25988404 DOI: 10.1016/j.ympev.2015.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 03/03/2015] [Accepted: 05/07/2015] [Indexed: 11/30/2022]
Abstract
For high-level molecular phylogenies, a comprehensive sampling design is a key factor for not only improving inferential accuracy, but also for maximizing the explanatory power of the resulting phylogeny. Two standing problems in molecular phylogenies are the unstable placements of some deep and long branches, and the phylogenetic relationships shown by robust supported clades conflict with recognized knowledge. Empirical and theoretical studies suggest that increasing taxon sampling is expected to ameliorate, if not resolve, both problems; however, sometimes neither the current taxonomic system nor the established phylogeny can provide sufficient information to guide additional sampling design. We examined the phylogeny of the spider family Linyphiidae, and selected ingroup species based on epigynal morphology, which can be reconstructed in a phylogenetic context. Our analyses resulted in seven robustly supported clades within linyphiids. The placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling, suggesting the possibility of long branch attraction artifacts. Results of ancestral state reconstruction indicate that successive state transformations of the epigynal plate are associated with early cladogenetic events in linyphiid diversification. Representatives of different subfamilies were mixed together within well supported clades and examination revealed that their defining characters, as per traditional taxonomy, are homoplastic. Furthermore, our results demonstrated that increasing taxon sampling produced a more informative framework, which in turn helps to study character evolution and interpret the relationships among linyphiid lineages. Additional defining characters are needed to revise the linyphiid taxonomic system based on our phylogenetic hypothesis.
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Affiliation(s)
- Fang Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, PR China
| | - Jesus A Ballesteros
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Douglas Chesters
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yongjia Zhan
- College of Life Sciences, Capital Normal University, Beijing 100048, PR China
| | - Ning Sun
- College of Life Sciences, Capital Normal University, Beijing 100048, PR China
| | - Chaodong Zhu
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wei Chen
- College of Life Sciences, Capital Normal University, Beijing 100048, PR China
| | - Lihong Tu
- College of Life Sciences, Capital Normal University, Beijing 100048, PR China.
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Zamer WE, Scheiner SM. A conceptual framework for organismal biology: linking theories, models, and data. Integr Comp Biol 2014; 54:736-56. [PMID: 24935989 DOI: 10.1093/icb/icu075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Implicit or subconscious theory is especially common in the biological sciences. Yet, theory plays a variety of roles in scientific inquiry. First and foremost, it determines what does and does not count as a valid or interesting question or line of inquiry. Second, theory determines the background assumptions within which inquiries are pursued. Third, theory provides linkages among disciplines. For these reasons, it is important and useful to develop explicit theories for biology. A general theory of organisms is developed, which includes 10 fundamental principles that apply to all organisms, and 6 that apply to multicellular organisms only. The value of a general theory comes from its utility to help guide the development of more specific theories and models. That process is demonstrated by examining two domains: ecoimmunology and development. For the former, a constitutive theory of ecoimmunology is presented, and used to develop a specific model that explains energetic trade-offs that may result from an immunological response of a host to a pathogen. For the latter, some of the issues involved in trying to devise a constitutive theory that covers all of development are explored, and a more narrow theory of phenotypic novelty is presented. By its very nature, little of a theory of organisms will be new. Rather, the theory presented here is a formal expression of nearly two centuries of conceptual advances and practice in research. Any theory is dynamic and subject to debate and change. Such debate will occur as part of the present, initial formulation, as the ideas presented here are refined. The very process of debating the form of the theory acts to clarify thinking. The overarching goal is to stimulate debate about the role of theory in the study of organisms, and thereby advance our understanding of them.
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Affiliation(s)
- William E Zamer
- Biological Sciences Directorate, National Science Foundation, 4201 Wilson Boulevard, Arlington, VA 22230, USA
| | - Samuel M Scheiner
- Biological Sciences Directorate, National Science Foundation, 4201 Wilson Boulevard, Arlington, VA 22230, USA
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Arginine kinase isoforms in the closest protozoan relative of metazoans. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2011; 6:171-7. [PMID: 21439926 DOI: 10.1016/j.cbd.2011.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 02/28/2011] [Accepted: 02/28/2011] [Indexed: 11/21/2022]
Abstract
The genome of the choanoflagellate Monosiga brevicollis contains at least three genes for the phosphoryl transfer enzyme, arginine kinase (AK; EC 2.7.3.3). Bioinformatic analyses of the deduced amino acid sequences of the proteins coded for by two of these genes showed that one of these AKs is cytoplasmic (denoted AK1) while the other appears to have an N-terminal mitochondrial targeting peptide (denoted AK2). Cloning and expression of the cDNA for AK1 yielded considerable soluble AK activity. Three AK2 constructs were expressed - one corresponding to the full length protein and two corresponding to truncated versions in which the signal peptide had been deleted. Expression of the former construct yielded minimal soluble activity. In contrast, significant AK activity was found in both truncated constructs confirming the importance of removal of the targeting peptide for proper folding and catalytic activity. Both AK1 and AK2 are functional oligomers unlike typical AKs which are monomeric. A phylogenetic analysis showed that these choanoflagellate AKs group more closely with a supercluster consisting of cytoplasmic and mitochondrial CKs and invertebrate AKs that evolved secondarily from a CK-like ancestor. Reaction-diffusion constraints in choanoflagellates are likely mitigated by the presence of AK isoforms which facilitate energy transport in these highly polarized cells.
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Abstract
Considerable progress has been made in understanding variations in gene sequence and expression level associated with phenotype, yet how genetic diversity translates into complex phenotypic differences remains poorly understood. Here, we examine the relationship between genetic background and spatial patterns of gene expression across seven strains of mice, providing the most extensive cellular-resolution comparative analysis of gene expression in the mammalian brain to date. Using comprehensive brainwide anatomic coverage (more than 200 brain regions), we applied in situ hybridization to analyze the spatial expression patterns of 49 genes encoding well-known pharmaceutical drug targets. Remarkably, over 50% of the genes examined showed interstrain expression variation. In addition, the variability was nonuniformly distributed across strain and neuroanatomic region, suggesting certain organizing principles. First, the degree of expression variance among strains mirrors genealogic relationships. Second, expression pattern differences were concentrated in higher-order brain regions such as the cortex and hippocampus. Divergence in gene expression patterns across the brain could contribute significantly to variations in behavior and responses to neuroactive drugs in laboratory mouse strains and may help to explain individual differences in human responsiveness to neuroactive drugs.
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Love AC. Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages. Philos Trans R Soc Lond B Biol Sci 2010; 365:679-90. [PMID: 20083642 DOI: 10.1098/rstb.2009.0262] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations.
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Affiliation(s)
- Alan C Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, 831 Heller Hall, 271 19th Avenue South, Minneapolis, MN 55455, USA.
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Berwick DC, Diss JKJ, Budhram-Mahadeo VS, Latchman DS. A simple technique for the prediction of interacting proteins reveals a direct Brn-3a-androgen receptor interaction. J Biol Chem 2010; 285:15286-15295. [PMID: 20228055 DOI: 10.1074/jbc.m109.071456] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The formation of multiprotein complexes constitutes a key step in determining the function of any translated gene product. Thus, the elucidation of interacting partners for a protein of interest is of fundamental importance to cell biology. Here we describe a simple methodology for the prediction of novel interactors. We have applied this to the developmental transcription factor Brn-3a to predict and verify a novel interaction between Brn-3a and the androgen receptor (AR). We demonstrate that these transcription factors form complexes within the nucleus of ND7 neuroblastoma cells, while in vitro pull-down assays show direct association. As a functional consequence of the Brn-3a-AR interaction, the factors bind cooperatively to multiple elements within the promoter of the voltage-gated sodium channel, Nav1.7, leading to a synergistic increase in its expression. Thus, these data define AR as a direct Brn-3a interactor and verify a simple interacting protein prediction methodology that is likely to be useful for many other proteins.
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Affiliation(s)
- Daniel C Berwick
- Medical Molecular Biology Unit, University College London Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom.
| | - James K J Diss
- Medical Molecular Biology Unit, University College London Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
| | - Vishwanie S Budhram-Mahadeo
- Medical Molecular Biology Unit, University College London Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
| | - David S Latchman
- Medical Molecular Biology Unit, University College London Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom; Birkbeck, University of London, Malet Street, London WC1E 7HX, United Kingdom
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Quantitative Genetics, Pleiotropy, and Morphological Integration in the Dentition of Papio hamadryas. Evol Biol 2009; 36:5-18. [PMID: 22919117 DOI: 10.1007/s11692-008-9048-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Variation in the mammalian dentition is highly informative of adaptations and evolutionary relationships, and consequently has been the focus of considerable research. Much of the current research exploring the genetic underpinnings of dental variation can trace its roots to Olson and Miller's 1958 book Morphological Integration. These authors explored patterns of correlation in the post-canine dentitions of the owl monkey and Hyopsodus, an extinct condylarth from the Eocene. Their results were difficult to interpret, as was even noted by the authors, due to a lack of genetic information through which to view the patterns of correlation. Following in the spirit of Olson and Miller's research, we present a quantitative genetic analysis of dental variation in a pedigreed population of baboons. We identify patterns of genetic correlations that provide insight to the genetic architecture of the baboon dentition. This genetic architecture indicates the presence of at least three modules: an incisor module that is genetically independent of the post-canine dentition, and a premolar module that demonstrates incomplete pleiotropy with the molar module. We then compare this matrix of genetic correlations to matrices of phenotypic correlations between the same measurements made on museum specimens of another baboon subspecies and the Southeast Asian colobine Presbytis. We observe moderate significant correlations between the matrices from these three primate taxa. From these observations we infer similarity in modularity and hypothesize a common pattern of genetic integration across the dental arcade in the Cercopithecoidea.
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Mallatt J. The Origin of the Vertebrate Jaw: Neoclassical Ideas Versus Newer, Development-Based Ideas. Zoolog Sci 2008; 25:990-8. [DOI: 10.2108/zsj.25.990] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Bonfante P, Genre A. Plants and arbuscular mycorrhizal fungi: an evolutionary-developmental perspective. TRENDS IN PLANT SCIENCE 2008; 13:492-8. [PMID: 18701339 DOI: 10.1016/j.tplants.2008.07.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 06/12/2008] [Accepted: 07/09/2008] [Indexed: 05/03/2023]
Abstract
Arbuscular mycorrhizas (AMs) are widespread symbiotic associations that are commonly described as the result of co-evolution events between fungi and plants where both partners benefit from the reciprocal nutrient exchange. Here, we review data from fossil records, characterizations of AM fungi in basal plants and live cell imaging of angiosperm colonization processes from an evolutionary-developmental perspective. The uniformity of plant cell responses to AM colonization in haploid gametophytes and diploid sporophytes, in non-root organs, and throughout many seed plant clades highlights the ancient origin of the interaction and suggests the existence of common molecular and cellular processes. The possibility that pre-existing mechanisms involved in plant cell division were recruited by plants to accommodate AM fungi is discussed.
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Affiliation(s)
- Paola Bonfante
- Dipartimento di Biologia Vegetale, Università di Torino - Istituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche, Viale Mattioli 25, 10125, Torino, Italy.
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