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Alicea B, Bastani S, Gordon NK, Crawford-Young S, Gordon R. The Molecular Basis of Differentiation Wave Activity in Embryogenesis. Biosystems 2024; 243:105272. [PMID: 39033973 DOI: 10.1016/j.biosystems.2024.105272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
As development varies greatly across the tree of life, it may seem difficult to suggest a model that proposes a single mechanism for understanding collective cell behaviors and the coordination of tissue formation. Here we propose a mechanism called differentiation waves, which unify many disparate results involving developmental systems from across the tree of life. We demonstrate how a relatively simple model of differentiation proceeds not from function-related molecular mechanisms, but from so-called differentiation waves. A phenotypic model of differentiation waves is introduced, and its relation to molecular mechanisms is proposed. These waves contribute to a differentiation tree, which is an alternate way of viewing cell lineage and local action of the molecular factors. We construct a model of differentiation wave-related molecular mechanisms (genome, epigenome, and proteome) based on bioinformatic data from the nematode Caenorhabditis elegans. To validate this approach across different modes of development, we evaluate protein expression across different types of development by comparing Caenorhabditis elegans with several model organisms: fruit flies (Drosophila melanogaster), yeast (Saccharomyces cerevisiae), and mouse (Mus musculus). Inspired by gene regulatory networks, two Models of Interactive Contributions (fully-connected MICs and ordered MICs) are used to suggest potential genomic contributions to differentiation wave-related proteins. This, in turn, provides a framework for understanding differentiation and development.
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Affiliation(s)
- Bradly Alicea
- Orthogonal Research and Education Lab, Champaign-Urbana, IL, USA; OpenWorm Foundation, Boston, MA, USA; University of Illinois Urbana-Champaign, USA.
| | - Suroush Bastani
- Orthogonal Research and Education Lab, Champaign-Urbana, IL, USA.
| | | | | | - Richard Gordon
- Gulf Specimen Marine Laboratory & Aquarium, Panacea, FL, USA.
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2
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Iwata R, Vanderhaeghen P. Metabolic mechanisms of species-specific developmental tempo. Dev Cell 2024; 59:1628-1639. [PMID: 38906137 PMCID: PMC11266843 DOI: 10.1016/j.devcel.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/27/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024]
Abstract
Development consists of a highly ordered suite of steps and transitions, like choreography. Although these sequences are often evolutionarily conserved, they can display species variations in duration and speed, thereby modifying final organ size or function. Despite their evolutionary significance, the mechanisms underlying species-specific scaling of developmental tempo have remained unclear. Here, we will review recent findings that implicate global cellular mechanisms, particularly intermediary and protein metabolism, as species-specific modifiers of developmental tempo. In various systems, from somitic cell oscillations to neuronal development, metabolic pathways display species differences. These have been linked to mitochondrial metabolism, which can influence the species-specific speed of developmental transitions. Thus, intermediary metabolic pathways regulate developmental tempo together with other global processes, including proteostasis and chromatin remodeling. By linking metabolism and the evolution of developmental trajectories, these findings provide opportunities to decipher how species-specific cellular timing can influence organism fitness.
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Affiliation(s)
- Ryohei Iwata
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KUL, 3000 Leuven, Belgium
| | - Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KUL, 3000 Leuven, Belgium.
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3
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McCoy JCS, Spicer JI, Rundle SD, Tills O. Comparative phenomics: a new approach to study heterochrony. Front Physiol 2023; 14:1237022. [PMID: 38028775 PMCID: PMC10658192 DOI: 10.3389/fphys.2023.1237022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Understanding the links between development and evolution is one of the major challenges of biology. 'Heterochronies', evolutionary alterations in the timings of development are posited as a key mechanism of evolutionary change, but their quantification requires gross simplification of organismal development. Consequently, how changes in event timings influence development more broadly is poorly understood. Here, we measure organismal development as spectra of energy in pixel values of video, creating high-dimensional landscapes integrating development of all visible form and function. This approach we termed 'Energy proxy traits' (EPTs) is applied alongside previously identified heterochronies in three freshwater pulmonate molluscs (Lymnaea stagnalis, Radix balthica and Physella acuta). EPTs were calculated from time-lapse video of embryonic development to construct a continuous functional time series. High-dimensional transitions in phenotype aligned with major sequence heterochronies between species. Furthermore, differences in event timings between conspecifics were associated with changes in high-dimensional phenotypic space. We reveal EPTs as a powerful approach to considering the evolutionary importance of alterations to developmental event timings. Reimagining the phenotype as energy spectra enabled continuous quantification of developmental changes in high-dimensional phenotypic space, rather than measurement of timings of discrete events. This approach has the possibility to transform how we study heterochrony and development more generally.
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4
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Paolino A, Haines EH, Bailey EJ, Black DA, Moey C, García-Moreno F, Richards LJ, Suárez R, Fenlon LR. Non-uniform temporal scaling of developmental processes in the mammalian cortex. Nat Commun 2023; 14:5950. [PMID: 37741828 PMCID: PMC10517946 DOI: 10.1038/s41467-023-41652-5] [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: 06/09/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
The time that it takes the brain to develop is highly variable across animals. Although staging systems equate major developmental milestones between mammalian species, it remains unclear how distinct processes of cortical development scale within these timeframes. Here, we compare the timing of cortical development in two mammals of similar size but different developmental pace: eutherian mice and marsupial fat-tailed dunnarts. Our results reveal that the temporal relationship between cell birth and laminar specification aligns to equivalent stages between these species, but that migration and axon extension do not scale uniformly according to the developmental stages, and are relatively more advanced in dunnarts. We identify a lack of basal intermediate progenitor cells in dunnarts that likely contributes in part to this timing difference. These findings demonstrate temporal limitations and differential plasticity of cortical developmental processes between similarly sized Therians and provide insight into subtle temporal changes that may have contributed to the early diversification of the mammalian brain.
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Affiliation(s)
- Annalisa Paolino
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Elizabeth H Haines
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Evan J Bailey
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Dylan A Black
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Ching Moey
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Fernando García-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 48013, Bilbao, Spain
| | - Linda J Richards
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
- Washington University in St Louis School of Medicine, Department of Neuroscience, St Louis, MO, 63108, USA
| | - Rodrigo Suárez
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia.
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia.
| | - Laura R Fenlon
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia.
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia.
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5
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Kyomen S, Murillo-Rincón AP, Kaucká M. Evolutionary mechanisms modulating the mammalian skull development. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220080. [PMID: 37183900 PMCID: PMC10184257 DOI: 10.1098/rstb.2022.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Mammals possess impressive craniofacial variation that mirrors their adaptation to diverse ecological niches, feeding behaviour, physiology and overall lifestyle. The spectrum of craniofacial geometries is established mainly during embryonic development. The formation of the head represents a sequence of events regulated on genomic, molecular, cellular and tissue level, with each step taking place under tight spatio-temporal control. Even minor variations in timing, position or concentration of the molecular drivers and the resulting events can affect the final shape, size and position of the skeletal elements and the geometry of the head. Our knowledge of craniofacial development increased substantially in the last decades, mainly due to research using conventional vertebrate model organisms. However, how developmental differences in head formation arise specifically within mammals remains largely unexplored. This review highlights three evolutionary mechanisms acknowledged to modify ontogenesis: heterochrony, heterotopy and heterometry. We present recent research that links changes in developmental timing, spatial organization or gene expression levels to the acquisition of species-specific skull morphologies. We highlight how these evolutionary modifications occur on the level of the genes, molecules and cellular processes, and alter conserved developmental programmes to generate a broad spectrum of skull shapes characteristic of the class Mammalia. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Stella Kyomen
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| | - Andrea P Murillo-Rincón
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| | - Markéta Kaucká
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
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6
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Wildenberg G, Li H, Kasthuri N. The Development of Synapses in Mouse and Macaque Primary Sensory Cortices. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528564. [PMID: 36824798 PMCID: PMC9949058 DOI: 10.1101/2023.02.15.528564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
We report that the rate of synapse development in primary sensory cortices of mice and macaques is unrelated to lifespan, as was previously thought. We analyzed 28,084 synapses over multiple developmental time points in both species and find, instead, that net excitatory synapse development of mouse and macaque neurons primarily increased at similar rates in the first few postnatal months, and then decreased over a span of 1-1.5 years of age. The development of inhibitory synapses differed qualitatively across species. In macaques, net inhibitory synapses first increase and then decrease on excitatory soma at similar ages as excitatory synapses. In mice, however, such synapses are added throughout life. These findings contradict the long-held belief that the cycle of synapse formation and pruning occurs earlier in shorter-lived animals. Instead, our results suggest more nuanced rules, with the development of different types of synapses following different timing rules or different trajectories across species.
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Affiliation(s)
- Gregg Wildenberg
- Department of Neurobiology, The University of Chicago
- Argonne National Laboratory, Biosciences Division
| | - Hanyu Li
- Department of Neurobiology, The University of Chicago
- Argonne National Laboratory, Biosciences Division
| | - Narayanan Kasthuri
- Department of Neurobiology, The University of Chicago
- Argonne National Laboratory, Biosciences Division
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7
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Nojiri T, Werneburg I, Tu VT, Fukui D, Takechi M, Iseki S, Furutera T, Koyabu D. Timing of organogenesis underscores the evolution of neonatal life histories and powered flight in bats. Proc Biol Sci 2023; 290:20221928. [PMID: 36629110 PMCID: PMC9832570 DOI: 10.1098/rspb.2022.1928] [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: 09/27/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
Bats have undergone one of the most drastic limb innovations in vertebrate history, associated with the evolution of powered flight. Knowledge of the genetic basis of limb organogenesis in bats has increased but little has been documented regarding the differences between limb organogenesis in bats and that of other vertebrates. We conducted embryological comparisons of the timelines of limb organogenesis in 24 bat species and 72 non-bat amniotes. In bats, the time invested for forelimb organogenesis has been considerably extended and the appearance timing of the forelimb ridge has been significantly accelerated, whereas the timing of the finger and first appearance of the claw development has been delayed, facilitating the enlargement of the manus. Furthermore, we discovered that bats initiate the development of their hindlimbs earlier than their forelimbs compared with other placentals. Bat neonates are known to be able to cling continuously with their well-developed foot to the maternal bodies or habitat substrates soon after birth. We suggest that this unique life history of neonates, which possibly coevolved with powered flight, has driven the accelerated development of the hindlimb and precocious foot.
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Affiliation(s)
- Taro Nojiri
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Graduate School of Environmental Science, Hokkaido University, North 11, West 10, Sapporo 060-0811, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Ingmar Werneburg
- Senckenberg Centre for Human Evolution and Palaeoenvironment an der Eberhard Karls Universität, Sigwartstraße 10, D-72076 Tübingen, Germany
- Fachbereich Geowissenschaften, Eberhard Karls Universität, Hölderlinstraße 12, 72074 Tübingen, Germany
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet road, Cau Giay district, Hanoi, Vietnam
- Vietnam Academy of Science and Technology, Graduate University of Science and Technology, No. 18, Hoang Quac Viet road, Cau Giay district, Hanoi, Vietnam
| | - Dai Fukui
- The University of Tokyo Hokkaido Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 9-61, Yamabe-Higashimachi, Furano, Hokkaido 079-1563, Japan
| | - Masaki Takechi
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Sachiko Iseki
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Toshiko Furutera
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Daisuke Koyabu
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
- Research and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba-shi, Ibaraki 305-8550, Japan
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8
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Molecular divergence with major morphological consequences: development and evolution of organ size and shape. Essays Biochem 2022; 66:707-716. [PMID: 36373649 DOI: 10.1042/ebc20220118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
Understanding the causes of the morphological diversity among organisms is a topic of great interest to evolutionary developmental biologists. Although developmental biologists have had great success in identifying the developmental mechanisms and molecular processes that specify organ size and shape within species, only relatively recently have the molecular tools become available to study how variation in these mechanisms gives rise to the phenotypic differences that are observed among closely related species. In addition to these technological advances, researchers interested in understanding how molecular variation gives rise to phenotypic variation have used three primary strategies to identify the molecular differences underlying species-specific traits: the candidate gene approach, differential gene expression screens, and between-species genetic mapping experiments. In this review, we discuss how these approaches have been successful in identifying the genes and the cellular mechanisms by which they specify variation in one of the most recognizable examples of the evolution of organ size, the adaptive variation in beak morphology among Darwin's finches. We also discuss insect reproductive structures as a model with great potential to advance our understanding of the specification and evolution of organ size and shape differences among species. The results from these two examples, and those from other species, show that species-specific variation in organ size and shape typically evolves via changes in the timing, location, and amount of gene/protein expression that act on tissue growth processes.
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9
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Genevcius BC, Calandriello DC, Torres TT. Molecular and Developmental Signatures of Genital Size Macro-Evolution in Bugs. Mol Biol Evol 2022; 39:6742344. [PMID: 36181434 PMCID: PMC9585474 DOI: 10.1093/molbev/msac211] [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] [Indexed: 12/15/2022] Open
Abstract
Our understanding of the genetic architecture of phenotypic traits has experienced drastic growth over the last years. Nevertheless, the majority of studies associating genotypes and phenotypes have been conducted at the ontogenetic level. Thus, we still have an elusive knowledge of how these genetic-developmental architectures evolve themselves and how their evolution is mirrored in the phenotypic change across evolutionary time. We tackle this gap by reconstructing the evolution of male genital size, one of the most complex traits in insects, together with its underlying genetic architecture. Using the order Hemiptera as a model, spanning over 350 million years of evolution, we estimate the correlation between genitalia and three features: development rate, body size, and rates of DNA substitution in 68 genes associated with genital development. We demonstrate that genital size macro-evolution has been largely dependent on body size and weakly influenced by development rate and phylogenetic history. We further revealed significant correlations between mutation rates and genital size for 19 genes. Interestingly, these genes have diverse functions and participate in distinct signaling pathways, suggesting that genital size is a complex trait whose fast evolution has been enabled by molecular changes associated with diverse morphogenetic processes. Our data further demonstrate that the majority of DNA evolution correlated with the genitalia has been shaped by negative selection or neutral evolution. Thus, in terms of sequence evolution, changes in genital size are predominantly facilitated by relaxation of constraints rather than positive selection, possibly due to the high pleiotropic nature of the morphogenetic genes.
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Affiliation(s)
| | - Denis C Calandriello
- Department of Genetics and Evolutionary Biology, University of Sao Paulo, Sao Paulo (SP), Brazil
| | - Tatiana T Torres
- Department of Genetics and Evolutionary Biology, University of Sao Paulo, Sao Paulo (SP), Brazil
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10
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Patel R, Galagali H, Kim JK, Frand AR. Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans. eLife 2022; 11:e80010. [PMID: 35968765 PMCID: PMC9377799 DOI: 10.7554/elife.80010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Animal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying timing mechanisms are not well understood. Caenorhabditis elegans undergoes four molts at regular 8 to 10 hour intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-yet unknown factors. Cessation of the cycle in young adults is controlled by the let-7 family of microRNAs and downstream transcription factors in the heterochronic pathway. Here, we characterize a negative feedback loop between NHR-23, the worm homolog of mammalian retinoid-related orphan receptors (RORs), and the let-7 family of microRNAs that regulates both the frequency and finite number of molts. The molting cycle is decelerated in nhr-23 knockdowns and accelerated in let-7(-) mutants, but timed similarly in let-7(-) nhr-23(-) double mutants and wild-type animals. NHR-23 binds response elements (ROREs) in the let-7 promoter and activates transcription. In turn, let-7 dampens nhr-23 expression across development via a complementary let-7-binding site (LCS) in the nhr-23 3' UTR. The molecular interactions between NHR-23 and let-7 hold true for other let-7 family microRNAs. Either derepression of nhr-23 transcripts by LCS deletion or high gene dosage of nhr-23 leads to protracted behavioral quiescence and extra molts in adults. NHR-23 and let-7 also coregulate scores of genes required for execution of the molts, including lin-42. In addition, ROREs and LCSs isolated from mammalian ROR and let-7 genes function in C. elegans, suggesting conservation of this feedback mechanism. We propose that this feedback loop unites the molting timer and the heterochronic gene regulatory network, possibly by functioning as a cycle counter.
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Affiliation(s)
- Ruhi Patel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Himani Galagali
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Alison R Frand
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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11
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Itgen MW, Natalie GR, Siegel DS, Sessions SK, Mueller RL. Genome size drives morphological evolution in organ-specific ways. Evolution 2022; 76:1453-1468. [PMID: 35657770 PMCID: PMC9545640 DOI: 10.1111/evo.14519] [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: 08/19/2021] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 01/22/2023]
Abstract
Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested whether variation in genome and body size is related to morphological variation in the heart and liver using nine species of the salamander genus Plethodon (genome sizes 29-67 gigabases). Our results show that overall organ size is a function of body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force-producing mass and greater intertrabecular space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness may be negligible because low metabolic rates in salamanders relax selective pressure on function of key metabolic organs. Overall, this study suggests large genome and cell size influence the developmental systems involved in heart and liver morphogenesis.
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Affiliation(s)
- Michael W. Itgen
- Department of BiologyColorado State UniversityFort CollinsColorado80523USA
| | | | - Dustin S. Siegel
- Department of BiologySoutheast Missouri State UniversityCape GirardeauMissouri63701USA
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12
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Shkil FN, Borisov V, Seleznev D, Kapitanova D, Abdissa B, Dzerzhinskii K, Smirnov S. Intra- and interspecific variability of the cranial ossification sequences in Barbus sensu lato. Evol Biol 2022. [DOI: 10.1007/s11692-022-09563-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Richardson MK, Keuck G. The revolutionary developmental biology of Wilhelm His, Sr. Biol Rev Camb Philos Soc 2022; 97:1131-1160. [PMID: 35106889 PMCID: PMC9304566 DOI: 10.1111/brv.12834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
Abstract
Swiss‐born embryologist Wilhelm His, Sr. (1831–1904) was the first scientist to study embryos using paraffin histology, serial sectioning and three‐dimensional modelling. With these techniques, His made many important discoveries in vertebrate embryology and developmental neurobiology, earning him two Nobel Prize nominations. He also developed several theories of mechanical and evolutionary developmental biology. His argued that adult form is determined by the differential growth of developmental primordia. Furthermore, he suggested that changes in the growth parameters of those primordia are responsible for generating new phenotypes during evolution. His developed these theories in his book ‘Our Bodily Form’ (Unsere Körperform). Here, we review His's work with special emphasis on its potential importance to the disciplines of evolutionary developmental biology (evo‐devo) and mechanobiology.
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Affiliation(s)
- Michael K Richardson
- Institute of Biology, University of Leiden, Sylvius Laboratory, Sylviusweg 72, Leiden, 2333 BE, The Netherlands
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14
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Dobreva MP, Camacho J, Abzhanov A. Time to synchronize our clocks: Connecting developmental mechanisms and evolutionary consequences of heterochrony. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:87-106. [PMID: 34826199 DOI: 10.1002/jez.b.23103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Heterochrony, defined as a change in the timing of developmental events altering the course of evolution, was first recognized by Ernst Haeckel in 1866. Haeckel's original definition was meant to explain the observed parallels between ontogeny and phylogeny, but the interpretation of his work became a source of controversy over time. Heterochrony took its modern meaning following the now classical work in the 1970-80s by Steven J. Gould, Pere Alberch, and co-workers. Predicted and described heterochronic scenarios emphasize the many ways in which developmental changes can influence evolution. However, while important examples of heterochrony detected with comparative morphological methods have multiplied, the more mechanistic understanding of this phenomenon lagged conspicuously behind. Considering the rapid progress in imaging and molecular tools available now for developmental biologists, this review aims to stress the need to take heterochrony research to the next level. It is time to synchronize the different levels of heterochrony research into a single analysis flow: from studies on organismal-level morphology to cells to molecules and genes, using complementary techniques. To illustrate how to achieve a more comprehensive understanding of phyletic morphological diversification associated with heterochrony, we discuss several recent case studies at various phylogenetic scales that combine morphological, cellular, and molecular analyses. Such a synergistic approach offers to more fully integrate phylogenetic and ontogenetic dimensions of the fascinating evolutionary phenomenon of heterochrony.
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Affiliation(s)
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Arkhat Abzhanov
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
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15
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Richardson MK. Theories, laws, and models in evo-devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 338:36-61. [PMID: 34570438 PMCID: PMC9292786 DOI: 10.1002/jez.b.23096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/01/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary developmental biology (evo‐devo) is the study of the evolution of developmental mechanisms. Here, I review some of the theories, models, and laws in evo‐devo, past and present. Nineteenth‐century evo‐devo was dominated by recapitulation theory and archetypes. It also gave us germ layer theory, the vertebral theory of the skull, floral organs as modified leaves, and the “inverted invertebrate” theory, among others. Newer theories and models include the frameshift theory, the genetic toolkit for development, the ABC model of flower development, the developmental hourglass, the zootype, Urbilateria, and the hox code. Some of these new theories show the influence of archetypes and recapitulation. Interestingly, recent studies support the old “primordial leaf,” “inverted invertebrate,” and “segmented head” theories. Furthermore, von Baer's first three laws may now need to be rehabilitated, and the hourglass model modified, in view of what Abzhanov has pointed out about the maternal‐zygotic transition. There are many supposed “laws” of evo‐devo but I argue that these are merely generalizations about trends in particular lineages. I argue that the “body plan” is an archetype, and is often used in such a way that it lacks any scientific meaning. Looking to the future, one challenge for evo‐devo will be to develop new theories and models to accommodate the wealth of new data from high‐throughput sequencing, including single‐cell sequencing. One step in this direction is the use of sophisticated in silico analyses, as in the “transcriptomic hourglass” models. Laws and other universal concepts, past and present, are reviewed. I show that many concepts focus on conserved aspects of development. The puzzle remains as to how embryonic phenotype, natural selection, and developmental mechanisms can be aligned to give an integrated view of evolution and development.
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Affiliation(s)
- Michael K Richardson
- Sylvius Laboratory, Institute of Biology, University of Leiden, Leiden, The Netherlands
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16
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Nguyen P, Pease NA, Kueh HY. Scalable control of developmental timetables by epigenetic switching networks. J R Soc Interface 2021; 18:20210109. [PMID: 34283940 DOI: 10.1098/rsif.2021.0109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
During development, progenitor cells follow timetables for differentiation that span many cell generations. These developmental timetables are robustly encoded by the embryo, yet scalably adjustable by evolution, facilitating variation in organism size and form. Epigenetic switches, involving rate-limiting activation steps at regulatory gene loci, control gene activation timing in diverse contexts, and could profoundly impact the dynamics of gene regulatory networks controlling developmental lineage specification. Here, we develop a mathematical framework to model regulatory networks with genes controlled by epigenetic switches. Using this framework, we show that such epigenetic switching networks uphold developmental timetables that robustly span many cell generations, and enable the generation of differentiated cells in precisely defined numbers and fractions. Changes to epigenetic switching networks can readily alter the timing of developmental events within a timetable, or alter the overall speed at which timetables unfold, enabling scalable control over differentiated population sizes. With their robust, yet flexibly adjustable nature, epigenetic switching networks could represent central targets on which evolution acts to manufacture diversity in organism size and form.
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Affiliation(s)
- Phuc Nguyen
- Molecular Engineering and Sciences Program, University of Washington, Seattle, WA, USA
| | - Nicholas A Pease
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA, USA.,Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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17
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Burggren W. Developmental Physiology: Grand Challenges. Front Physiol 2021; 12:706061. [PMID: 34177630 PMCID: PMC8225327 DOI: 10.3389/fphys.2021.706061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022] Open
Affiliation(s)
- Warren Burggren
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, TX, United States
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18
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Walla A, Wilma van Esse G, Kirschner GK, Guo G, Brünje A, Finkemeier I, Simon R, von Korff M. An Acyl-CoA N-Acyltransferase Regulates Meristem Phase Change and Plant Architecture in Barley. PLANT PHYSIOLOGY 2020; 183:1088-1109. [PMID: 32376761 PMCID: PMC7333700 DOI: 10.1104/pp.20.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/19/2020] [Indexed: 05/04/2023]
Abstract
The modification of shoot architecture and increased investment into reproductive structures is key for crop improvement and is achieved through coordinated changes in the development and determinacy of different shoot meristems. A fundamental question is how the development of different shoot meristems is genetically coordinated to optimize the balance between vegetative and reproductive organs. Here we identify the MANY NODED DWARF1 (HvMND1) gene as a major regulator of plant architecture in barley (Hordeum vulgare). The mnd1.a mutant displayed an extended vegetative program with increased phytomer, leaf, and tiller production but a reduction in the number and size of grains. The induction of vegetative structures continued even after the transition to reproductive growth, resulting in a marked increase in longevity. Using mapping by RNA sequencing, we found that the HvMND1 gene encodes an acyl-CoA N-acyltransferase that is predominately expressed in developing axillary meristems and young inflorescences. Exploration of the expression network modulated by HvMND1 revealed differential expression of the developmental microRNAs miR156 and miR172 and several key cell cycle and developmental genes. Our data suggest that HvMND1 plays a significant role in the coordinated regulation of reproductive phase transitions, thereby promoting reproductive growth and whole plant senescence in barley.
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Affiliation(s)
- Agatha Walla
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
| | - G Wilma van Esse
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Laboratory for Molecular Biology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Gwendolyn K Kirschner
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
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19
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Smirnov SV, Merkulova KM, Vassilieva AB. Skull development in the Iberian newt,
Pleurodeles waltl
(Salamandridae: Caudata: Amphibia): timing, sequence, variations, and thyroid hormone mediation of bone appearance. J Anat 2020; 237:543-555. [DOI: 10.1111/joa.13210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sergei V. Smirnov
- A. N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Ksenia M. Merkulova
- A. N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Anna B. Vassilieva
- A. N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
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20
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Leung JYS, McAfee D. Stress across life stages: Impacts, responses and consequences for marine organisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134491. [PMID: 31629264 DOI: 10.1016/j.scitotenv.2019.134491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/10/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
Population dynamics of marine organisms are strongly driven by their survival in early life stages. As life stages are tightly linked, environmental stress experienced by organisms in the early life stage can worsen their performance in the subsequent life stage (i.e. carry-over effect). However, stressful events can be ephemeral and hence organisms may be able to counter the harmful effects of transient stress. Here, we analysed the published data to examine the relative strength of carry-over effects on the juvenile growth of marine organisms, caused by different stressors (hypoxia, salinity, starvation, ocean acidification and stress-induced delayed metamorphosis) confronted in their larval stage. Based on 31 relevant published studies, we revealed that food limitation had the greatest negative carry-over effect on juvenile growth. In the laboratory, we tested the effects of short-term early starvation and hypoxia on the larval growth and development of a model organism, polychaete Hydroides elegans, and assessed whether the larvae can accommodate the early stress to maintain their performance as juveniles (settlement and juvenile growth). Results showed that early starvation for 3 days (∼50% of normal larval period) retarded larval growth and development, leading to subsequent reduced settlement rate and juvenile growth. When the starvation period decreased to 1 day, however, the larvae could recover from early starvation through compensatory growth and performed normal as juveniles (c.f. control). Early exposure to hypoxia for 3 days did not affect larval growth (body length) and juvenile growth (tube length), but caused malformation of larvae and reduced settlement rate. We conclude that the adverse effects of transient stress can be carried across life stages (e.g. larval to juvenile stage), but depend on the duration of stressful events relative to larval period. As carry-over effects are primarily driven by energy acquisition, how food availability varies over time and space is fundamental to the population dynamics of marine organisms.
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Affiliation(s)
- Jonathan Y S Leung
- Faculty of Materials and Energy, Southwest University, Chongqing 400715, China; School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; Department of Biology and Chemistry, City University of Hong Kong, Hong Kong Special Administrative Region.
| | - Dominic McAfee
- School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
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21
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Catalano SA, Segura V, Vera Candioti F. PASOS: a method for the phylogenetic analysis of shape ontogenies. Cladistics 2019; 35:671-687. [PMID: 34618936 DOI: 10.1111/cla.12373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2018] [Indexed: 12/17/2022] Open
Abstract
We present a novel phylogenetic approach to infer ancestral ontogenies of shape characters described as landmark configurations. The method is rooted in previously published theoretical developments to analyse landmark data in a phylogenetic context with parsimony as the optimality criterion, in this case using the minimization of differences in landmark position to define not only ancestral shapes but also the changes in developmental timing between ancestor-descendant shape ontogenies. Evolutionary changes along the tree represent changes in relative developmental timing between ontogenetic trajectories (possible heterochronic events) and changes in shape within each stage. The method requires the user to determine the shape of the specimens between two standard events, for instance birth and onset of sexual maturity. Once the ontogenetic trajectory is discretized into a series of consecutive stages, the method enables the user to identify changes in developmental timing associated with changes in the offset and/or onset of the shape ontogenetic trajectories. The method is implemented in a C language program called SPASOS. The analysis of two empirical examples (anurans and felids) using this novel method yielded results in agreement with previous hypotheses about shape evolution in these groups based on non-phylogenetic analyses.
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Affiliation(s)
- Santiago A Catalano
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, Miguel Lillo 251, 4000, S. M. de Tucumán, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000, S. M. de Tucumán, Argentina
| | - Valentina Segura
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, Miguel Lillo 251, 4000, S. M. de Tucumán, Argentina
| | - Florencia Vera Candioti
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, Miguel Lillo 251, 4000, S. M. de Tucumán, Argentina
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22
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Martínez-Méndez R, Pérez-Torres D, Gómez-Chavarín M, Padilla-Cortés P, Fiordelisio T, Gutiérrez-Ospina G. Bilateral enucleation at birth modifies calcium spike amplitude, but not frequency, in neurons of the somatosensory thalamus and cortex: Implications for developmental cross-modal plasticity. IBRO Rep 2019; 7:108-116. [PMID: 31799470 PMCID: PMC6881598 DOI: 10.1016/j.ibror.2019.11.003] [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: 03/10/2019] [Accepted: 11/07/2019] [Indexed: 11/17/2022] Open
Abstract
Bilateral eye enucleation at birth (BE) leads to an expansion of the primary somatosensory cortex (S1) in rat pups. Although increased growth of the somatosensory thalamo-cortical afferents (STCAs) in part explains S1 expansion, timing mechanisms governing S1 formation are also involved. In this work, we begin the search of a developmental clock by intending to document the existence of putative clock neurons in the somatosensory thalamus (VPM) and S1 based upon changes of spontaneous spike amplitude; a biophysical property sensitive to circadian regulation; the latter known to be shifted by enucleation. In addition, we also evaluated whether STCAs growth rate and segregation timing were modified, as parameters the clock might time. We found that spontaneous spike amplitude transiently, but significantly, increased or decreased in VPM and S1 neurons of BE rat pups, respectively, as compared to their control counterparts. The growth rate and segregation timing of STCAs was, however, unaffected by BE. These results support the existence of a developmental clock that ticks differently in the VPM and S1 after BE. This observation, together with the fact that STCAs growth rate and segregation timing is unchanged, suggests that S1 expansion in BE rats may in part be controlled at the cortical level.
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Key Words
- ACSF, artificial cerebrospinal fluid
- AChE, acetylcholinesterase
- BE, birth-enucleated
- Barrel formation
- Blind
- CP, cortical plate
- DAPI, 4′,6-diamidino-2-phenylindole
- Developmental clock
- Developmental timing
- DiI, 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine Perchlorate
- PD, postnatal day
- S, sighted
- S1, primary somatosensory cortex
- SEM, standard error of the mean
- STCAs, somatosensory thalamo-cortical afferents
- Somatosensory cortex specification
- Spontaneous activity
- VPM, ventral posteromedial nucleus
- τd, decay time constant
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Affiliation(s)
- Raquel Martínez-Méndez
- Laboratorio de Biología de Sistemas, Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Daniel Pérez-Torres
- Laboratorio de Biología de Sistemas, Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Margarita Gómez-Chavarín
- Laboratorio de Biología de Sistemas, Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Patricia Padilla-Cortés
- Unidad de Cromatografía de Alta Resolución, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Tatiana Fiordelisio
- Laboratorio de Neuroendocrinología, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Gabriel Gutiérrez-Ospina
- Laboratorio de Biología de Sistemas, Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
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23
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Chong J, Amourda C, Saunders TE. Temporal development of Drosophila embryos is highly robust across a wide temperature range. J R Soc Interface 2019; 15:rsif.2018.0304. [PMID: 29997261 PMCID: PMC6073635 DOI: 10.1098/rsif.2018.0304] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/18/2018] [Indexed: 11/12/2022] Open
Abstract
Development is a process precisely coordinated in both space and time. Spatial precision has been quantified in a number of developmental systems, and such data have contributed significantly to our understanding of, for example, morphogen gradient interpretation. However, comparatively little quantitative analysis has been performed on timing and temporal coordination during development. Here, we use Drosophila to explore the temporal robustness of embryonic development within physiologically normal temperatures. We find that development is temporally very precise across a wide range of temperatures in the three Drosophila species investigated. However, we find temperature dependence in the timing of developmental events. A simple model incorporating history dependence can explain the developmental temporal trajectories. Interestingly, history dependence is temperature-specific, with either effective negative or positive feedback at different temperatures. We also find that embryos are surprisingly robust to shifting temperatures during embryogenesis. We further identify differences between tropical and temperate species, potentially due to different mechanisms regulating temporal development that depend on the local environment. Our data show that Drosophila embryonic development is temporally robust across a wide range of temperatures. This robustness shows interesting species-specific differences that are suggestive of different sensitivity to temperature fluctuations between Drosophila species.
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Affiliation(s)
- Jeronica Chong
- Mechanobiology Institute, National University of Singapore, Singapore, Republic of Singapore
| | - Christopher Amourda
- Mechanobiology Institute, National University of Singapore, Singapore, Republic of Singapore
| | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, Singapore, Republic of Singapore .,Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore.,Institute of Molecular and Cell Biology, A*Star, Proteos, Singapore, Republic of Singapore
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24
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Komarovsky Gulman N, Armon L, Shalit T, Urbach A. Heterochronic regulation of lung development via the Lin28-Let-7 pathway. FASEB J 2019; 33:12008-12018. [PMID: 31373834 DOI: 10.1096/fj.201802702r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The heterochronic gene Lin28 regulates diverse developmental processes. It was shown previously that global Lin28A overexpression during mouse embryogenesis results in perinatal lethality. However, the reason for this early lethality has not been elucidated. Here, we showed that Lin28A overexpression prevents normal lung development via the inhibition of the Let-7 micro RNAs, thus causing the perinatal lethality. We further found that Lin28A overexpression in lung mesenchymal cells, but not epithelial cells, is sufficient to recapitulate the lung phenotype. Moreover, we defined the specific time window wherein Lin28A expression exerts its effect. Deep characterization of the transgenic lungs suggests that the Lin28A-Let-7 pathway delays the transition from one developmental stage to another but does not completely abrogate the differentiation capacity of the lung progenitor cells. Finally, we suggested that the effect of Lin28A-Let-7 on embryonic lung development is mediated at least in part through the TGF-β1-signaling pathway. Altogether, these findings define for the first time the Lin28-Let-7 pathway as a critical heterochronic regulator of lung development.-Komarovsky Gulman, N., Armon, L., Shalit, T., Urbach, A. Heterochronic regulation of lung development via the Lin28-Let-7 pathway.
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Affiliation(s)
- Nelly Komarovsky Gulman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Leah Armon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Tali Shalit
- The Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Achia Urbach
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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25
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López-Aguirre C, Hand SJ, Koyabu D, Son NT, Wilson LAB. Postcranial heterochrony, modularity, integration and disparity in the prenatal ossification in bats (Chiroptera). BMC Evol Biol 2019; 19:75. [PMID: 30866800 PMCID: PMC6417144 DOI: 10.1186/s12862-019-1396-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/21/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Self-powered flight is one of the most energy-intensive types of locomotion found in vertebrates. It is also associated with a range of extreme morpho-physiological adaptations that evolved independently in three different vertebrate groups. Considering that development acts as a bridge between the genotype and phenotype on which selection acts, studying the ossification of the postcranium can potentially illuminate our understanding of bat flight evolution. However, the ontogenetic basis of vertebrate flight remains largely understudied. Advances in quantitative analysis of sequence heterochrony and morphogenetic growth have created novel approaches to study the developmental basis of diversification and the evolvability of skeletal morphogenesis. Assessing the presence of ontogenetic disparity, integration and modularity from an evolutionary approach allows assessing whether flight may have resulted in evolutionary differences in the magnitude and mode of development in bats. RESULTS We quantitatively compared the prenatal ossification of the postcranium (24 bones) between bats (14 species), non-volant mammals (11 species) and birds (14 species), combining for the first time prenatal sequence heterochrony and developmental growth data. Sequence heterochrony was found across groups, showing that bat postcranial development shares patterns found in other flying vertebrates but also those in non-volant mammals. In bats, modularity was found as an axial-appendicular partition, resembling a mammalian pattern of developmental modularity and suggesting flight did not repattern prenatal postcranial covariance in bats. CONCLUSIONS Combining prenatal data from 14 bat species, this study represents the most comprehensive quantitative analysis of chiropteran ossification to date. Heterochrony between the wing and leg in bats could reflect functional needs of the newborn, rather than ecological aspects of the adult. Bats share similarities with birds in the development of structures involved in flight (i.e. handwing and sternum), suggesting that flight altriciality and early ossification of pedal phalanges and sternum are common across flying vertebrates. These results indicate that the developmental modularity found in bats facilitates intramodular phenotypic diversification of the skeleton. Integration and disparity increased across developmental time in bats. We also found a delay in the ossification of highly adaptable and evolvable regions (e.g. handwing and sternum) that are directly associated with flight performance.
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Affiliation(s)
- Camilo López-Aguirre
- PANGEA Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Suzanne J. Hand
- PANGEA Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Daisuke Koyabu
- University Museum, University of Tokyo, Tokyo, Japan
- Department of Humanities and Sciences, Musashino Art University, Tokyo, Japan
| | - Nguyen Truong Son
- Department of Vertebrate Zoology, Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, Hanoi, Vietnam
- Vietnam Academy of Science and Technology, Graduate University of Science and Technology, Hanoi, Vietnam
| | - Laura A. B. Wilson
- PANGEA Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
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26
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Choi S, Ambros V. The C. elegans heterochronic gene lin-28 coordinates the timing of hypodermal and somatic gonadal programs for hermaphrodite reproductive system morphogenesis. Development 2019; 146:dev164293. [PMID: 30745431 PMCID: PMC6432661 DOI: 10.1242/dev.164293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 02/04/2019] [Indexed: 12/17/2022]
Abstract
C. elegans heterochronic genes determine the timing of expression of specific cell fates in particular stages of developing larvae. However, their broader roles in coordinating developmental events across diverse tissues have been less well investigated. Here, we show that loss of lin-28, a central heterochronic regulator of hypodermal development, causes reduced fertility associated with abnormal somatic gonadal morphology. In particular, the abnormal spermatheca-uterine valve morphology of lin-28(lf) hermaphrodites traps embryos in the spermatheca, which disrupts ovulation and causes embryonic lethality. The same genes that act downstream of lin-28 in the regulation of hypodermal developmental timing also act downstream of lin-28 in somatic gonadal morphogenesis and fertility. Importantly, we find that hypodermal expression, but not somatic gonadal expression, of lin-28 is sufficient for restoring normal somatic gonadal morphology in lin-28(lf) mutants. We propose that the abnormal somatic gonadal morphogenesis of lin-28(lf) hermaphrodites results from temporal discoordination between the accelerated hypodermal development and normally timed somatic gonadal development. Thus, our findings exemplify how a cell-intrinsic developmental timing program can also control proper development of other interacting tissues, presumably by cell non-autonomous signal(s). This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Sungwook Choi
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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27
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Avidor-Reiss T, Turner K. The Evolution of Centriole Structure: Heterochrony, Neoteny, and Hypermorphosis. Results Probl Cell Differ 2019; 67:3-15. [PMID: 31435789 DOI: 10.1007/978-3-030-23173-6_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Centrioles are subcellular organelles that were present in the last eukaryotic common ancestor, where the centriole's ancestral role was to form cilia. Centrioles have maintained a remarkably conserved structure in eukaryotes that have cilia, while groups that lack cilia have lost their centrioles, highlighting the structure-function relationship that exists between the centriole and the cilium. In contrast, animal sperm cells, a ciliated cell, exhibit remarkable structural diversity in the centriole. Understanding how this structural diversity evolved may provide insight into centriole assembly and function, as well as their unique role in sperm. Here, we apply concepts used in the study of the evolution of animal morphology to gain insight into the evolution of centriole structure. We propose that centrioles with an atypical structure form because of changes in the timing of centriole assembly events, which can be described as centriolar "heterochrony." Atypical centrioles of insects and mammals appear to have evolved through different types of heterochrony. Here, we discuss two particular types of heterochrony: neoteny and hypermorphosis. The centriole assembly of insect sperm cells exhibits the retention of "juvenile" centriole structure, which can be described as centriolar "neoteny." Mammalian sperm cells have an extended centriole assembly program through the addition of novel steps such as centrosome reduction and centriole remodeling to form atypical centrioles, a form of centriole "hypermorphosis." Overall, centriole heterochrony appears to be a common mechanism for the development of the atypical centriole during the evolution of centriole assembly of various animals' sperm.
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Affiliation(s)
- Tomer Avidor-Reiss
- Department of Biological Sciences, University of Toledo, Toledo, OH, USA.
| | - Katerina Turner
- Department of Biological Sciences, University of Toledo, Toledo, OH, USA
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Sun L, Sang M, Zheng C, Wang D, Shi H, Liu K, Guo Y, Cheng T, Zhang Q, Wu R. The genetic architecture of heterochrony as a quantitative trait: lessons from a computational model. Brief Bioinform 2018; 19:1430-1439. [PMID: 28575183 DOI: 10.1093/bib/bbx056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Indexed: 11/14/2022] Open
Abstract
Heterochrony is known as a developmental change in the timing or rate of ontogenetic events across phylogenetic lineages. It is a key concept synthesizing development into ecology and evolution to explore the mechanisms of how developmental processes impact on phenotypic novelties. A number of molecular experiments using contrasting organisms in developmental timing have identified specific genes involved in heterochronic variation. Beyond these classic approaches that can only identify single genes or pathways, quantitative models derived from current next-generation sequencing data serve as a more powerful tool to precisely capture heterochronic variation and systematically map a complete set of genes that contribute to heterochronic processes. In this opinion note, we discuss a computational framework of genetic mapping that can characterize heterochronic quantitative trait loci that determine the pattern and process of development. We propose a unifying model that charts the genetic architecture of heterochrony that perceives and responds to environmental perturbations and evolves over geologic time. The new model may potentially enhance our understanding of the adaptive value of heterochrony and its evolutionary origins, providing a useful context for designing new organisms that can best use future resources.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Mengmeng Sang
- Computational Genetics in the Center for Computational Biology at Beijing Forestry University
| | - Chenfei Zheng
- Computational Genetics in the Center for Computational Biology at Beijing Forestry University
| | - Dongyang Wang
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Hexin Shi
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Kaiyue Liu
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Yanfang Guo
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Tangren Cheng
- National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Qixiang Zhang
- National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Rongling Wu
- Center for Computational Biology at Beijing Forestry University
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Wei K, Wang Q, Gan J, Zhang S, Ye M, Gragnoli C, Wu R. Mapping genes for drug chronotherapy. Drug Discov Today 2018; 23:1883-1888. [PMID: 29964181 DOI: 10.1016/j.drudis.2018.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/20/2018] [Accepted: 06/12/2018] [Indexed: 12/29/2022]
Abstract
Genome-wide association studies have been increasingly used to map and characterize genes that contribute to interindividual variation in drug response. Some studies have integrated the pharmacokinetic (PK) and pharmacodynamic (PD) processes of drug reactions into association mapping, gleaning new insight into how genes determine the dynamic relationship of drug effect and drug dose. Here, we present an evolutionary framework by which two distinct concepts, chronopharmacodynamics and heterochrony (describing variation in the timing and rate of developmental events), are married to comprehend the pharmacogenetic architecture of drug response. The resulting new concept, heterochronopharmacodynamics (HCPD), can better interpret how genes influence drug efficacy and drug toxicity according to the circadian rhythm of the body and changes in drug concentration.
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Affiliation(s)
- Kun Wei
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qian Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jingwen Gan
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shilong Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Claudia Gragnoli
- Division of Endocrinology, Diabetes, and Metabolic Disease, Translational Medicine, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; Molecular Biology Laboratory, Bios Biotech Multi Diagnostic Health Center, Rome 00197, Italy
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, Pennsylvania State University, Hershey, PA 17033, USA.
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Abstract
The small RNA regulatory molecules called microRNAs (miRNAs) play key roles in the development of most organisms. The expression of many different miRNAs has been described in the developing and mature vertebrate retina. The ability of miRNAs to regulate a diversity of messenger RNA targets allows them to have effects on many different developmental processes, but the functions of only a few miRNAs have been documented to date. Developmental transitions between cell states appear to be particularly sensitive to miRNA loss of function, as evidenced by specific miRNA knockdowns or from global perturbations in miRNA levels (e.g., Dicer deletion). However, we are still in only the very early stages of understanding the range of cellular functions miRNAs control during development.
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Affiliation(s)
- Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA;
| | - Robert Hindges
- Centre for Developmental Neurobiology, MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, United Kingdom;
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31
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Zhan Y, Huang Y, Chen J, Cao Z, He J, Zhang J, Huang H, Ruan H, Luo L, Li L. The caudal dorsal artery generates hematopoietic stem and progenitor cells via the endothelial-to-hematopoietic transition in zebrafish. J Genet Genomics 2018; 45:S1673-8527(18)30099-7. [PMID: 29929848 DOI: 10.1016/j.jgg.2018.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/25/2017] [Accepted: 02/11/2018] [Indexed: 11/22/2022]
Abstract
Zebrafish hematopoietic stem and progenitor cells (HSPCs) originate from the hemogenic endothelium of the ventral wall of the dorsal aorta (DA) through the endothelial-to-hematopoietic transition (EHT) from approximately 30 to 60 hours post fertilization (hpf). However, whether other artery sites can generate HSPCs de novo remains unclear. In this study, using live imaging and lineage tracing, we found that the caudal dorsal artery (CDA) in the caudal hematopoietic tissue directly gave rise to HSPCs through EHT. This process initiated from approximately 60 hpf and terminated at approximately 156 hpf. Compared with that in the DA, fewer EHT events were observed in the CDA. The EHT events in the DA and CDA were similarly regulated by Runx1 but differentially influenced by blood flow (i.e., the EHT frequency in CDA was affected to a lesser extent when circulation was compromised in the tnnt2a-/- mutant). Therefore, the whole artery, including both DA and CDA, was endowed with the ability to produce HSPCs during a much longer time period. Coincidently, the lineage tracing results indicated that adult hematopoietic cells originated from the embryonic endothelium, and those produced later preferentially colonized the adult thymus. Collectively, our study revealed that the CDA serves as an additional source of hematopoiesis, and it shows similar but not identical properties with the DA.
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Affiliation(s)
- Yandong Zhan
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Youkui Huang
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jingying Chen
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zigang Cao
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jianbo He
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Honghui Huang
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hua Ruan
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lingfei Luo
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Li Li
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China.
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32
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Bard JBL. Tinkering and the Origins of Heritable Anatomical Variation in Vertebrates. BIOLOGY 2018; 7:E20. [PMID: 29495378 PMCID: PMC5872046 DOI: 10.3390/biology7010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 02/16/2018] [Accepted: 02/18/2018] [Indexed: 11/16/2022]
Abstract
Evolutionary change comes from natural and other forms of selection acting on existing anatomical and physiological variants. While much is known about selection, little is known about the details of how genetic mutation leads to the range of heritable anatomical variants that are present within any population. This paper takes a systems-based view to explore how genomic mutation in vertebrate genomes works its way upwards, though changes to proteins, protein networks, and cell phenotypes to produce variants in anatomical detail. The evidence used in this approach mainly derives from analysing anatomical change in adult vertebrates and the protein networks that drive tissue formation in embryos. The former indicate which processes drive variation-these are mainly patterning, timing, and growth-and the latter their molecular basis. The paper then examines the effects of mutation and genetic drift on these processes, the nature of the resulting heritable phenotypic variation within a population, and the experimental evidence on the speed with which new variants can appear under selection. The discussion considers whether this speed is adequate to explain the observed rate of evolutionary change or whether other non-canonical, adaptive mechanisms of heritable mutation are needed. The evidence to hand suggests that they are not, for vertebrate evolution at least.
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Affiliation(s)
- Jonathan B L Bard
- Department of Anatomy, Physiology & Genetics, University of Oxford, Oxford OX313QX, UK.
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Buendía-Monreal M, Gillmor CS. The Times They Are A-Changin': Heterochrony in Plant Development and Evolution. FRONTIERS IN PLANT SCIENCE 2018; 9:1349. [PMID: 30283473 PMCID: PMC6157392 DOI: 10.3389/fpls.2018.01349] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 08/27/2018] [Indexed: 05/16/2023]
Abstract
Alterations in the timing of developmental programs during evolution, that lead to changes in the shape, or size of organs, are known as heterochrony. Heterochrony has been widely studied in animals, but has often been neglected in plants. During plant evolution, heterochronic shifts have played a key role in the origin and diversification of leaves, roots, flowers, and fruits. Heterochrony that results in a juvenile or simpler outcome is known as paedomorphosis, while an adult or more complex outcome is called peramorphosis. Mechanisms that alter developmental timing at the cellular level affect cell proliferation or differentiation, while those acting at the tissue or organismal level change endogenous aging pathways, morphogen signaling, and metabolism. We believe that wider consideration of heterochrony in the context of evolution will contribute to a better understanding of plant development.
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Suárez R, Paolino A, Kozulin P, Fenlon LR, Morcom LR, Englebright R, O’Hara PJ, Murray PJ, Richards LJ. Development of body, head and brain features in the Australian fat-tailed dunnart (Sminthopsis crassicaudata; Marsupialia: Dasyuridae); A postnatal model of forebrain formation. PLoS One 2017; 12:e0184450. [PMID: 28880940 PMCID: PMC5589244 DOI: 10.1371/journal.pone.0184450] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022] Open
Abstract
Most of our understanding of forebrain development comes from research of eutherian mammals, such as rodents, primates, and carnivores. However, as the cerebral cortex forms largely prenatally, observation and manipulation of its development has required invasive and/or ex vivo procedures. Marsupials, on the other hand, are born at comparatively earlier stages of development and most events of forebrain formation occur once attached to the teat, thereby permitting continuous and non-invasive experimental access. Here, we take advantage of this aspect of marsupial biology to establish and characterise a resourceful laboratory model of forebrain development: the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-sized carnivorous Australian marsupial. We present an anatomical description of the postnatal development of the body, head and brain in dunnarts, and provide a staging system compatible with human and mouse developmental stages. As compared to eutherians, the orofacial region develops earlier in dunnarts, while forebrain development is largely protracted, extending for more than 40 days versus ca. 15 days in mice. We discuss the benefits of fat-tailed dunnarts as laboratory animals in studies of developmental biology, with an emphasis on how their accessibility in the pouch can help address new experimental questions, especially regarding mechanisms of brain development and evolution.
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Affiliation(s)
- Rodrigo Suárez
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- * E-mail: (RS); (LJR)
| | - Annalisa Paolino
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Peter Kozulin
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Laura R. Fenlon
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Laura R. Morcom
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Robert Englebright
- The University of Queensland, School of Agriculture & Food Science, Gatton, Queensland, Australia
| | - Patricia J. O’Hara
- The University of Queensland, School of Agriculture & Food Science, Gatton, Queensland, Australia
| | - Peter J. Murray
- The University of Queensland, School of Agriculture & Food Science, Gatton, Queensland, Australia
| | - Linda J. Richards
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- The University of Queensland, School of Biomedical Sciences, Brisbane, Queensland, Australia
- * E-mail: (RS); (LJR)
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35
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Jablonski D. Approaches to Macroevolution: 1. General Concepts and Origin of Variation. Evol Biol 2017; 44:427-450. [PMID: 29142333 PMCID: PMC5661017 DOI: 10.1007/s11692-017-9420-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022]
Abstract
Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities-i.e., an uneven density distribution-of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, "punctuated equilibrium" and "phyletic gradualism" simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.
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Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637 USA
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36
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Pham T, Day SM, Glassford WJ, Williams TM, Rebeiz M. The evolutionary origination of a novel expression pattern through an extreme heterochronic shift. Evol Dev 2017; 19:43-55. [PMID: 28116844 DOI: 10.1111/ede.12215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The evolutionary origins of morphological structures are thought to often depend upon the redeployment of old genes into new developmental settings. Although many examples of cis-regulatory divergence have shown how pre-existing patterns of gene expression have been altered, only a small number of case studies have traced the origins of cis-regulatory elements that drive new expression domains. Here, we elucidate the evolutionary history of a novel expression pattern of the yellow gene within the Zaprionus genus of fruit flies. We observed a unique pattern of yellow transcript accumulation in the wing disc during the third larval instar, a stage that precedes its typical expression pattern associated with cuticular melanization by about a week. The region of the Zaprionus wing disc that expresses yellow subsequently develops into a portion of the thorax, a tissue for which yellow expression has been reported for several fruit fly species. Tests of GFP reporter transgenes containing the Zaprionus yellow regulatory region revealed that the wing disc pattern arose by changes in the cis-regulatory region of yellow. Moreover, the wing disc enhancer activity of yellow depends upon a short conserved sequence with ancestral thoracic functions, suggesting that the pupal thorax regulatory sequence was genetically reprogrammed to drive expression that commences much earlier during development. These results highlight how novel domains of gene expression may arise by extreme shifts in timing during the origins of novel traits.
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Affiliation(s)
- Thomas Pham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephanie M Day
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - William J Glassford
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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37
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Signore IA, Concha ML. Heterochrony and Morphological Variation of Epithalamic Asymmetry. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:157-164. [PMID: 27659033 DOI: 10.1002/jez.b.22698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 06/23/2016] [Accepted: 08/16/2016] [Indexed: 12/17/2022]
Abstract
Heterochrony is one proposed mechanism to explain how morphological variation and novelty arise during evolution. To experimentally approach heterochrony in a comprehensive manner, we must consider all three aspects of developmental time (sequence, timing, duration). This task is only possible in developmental models that allow the acquisition of high-quality temporal data in the context of normalized developmental time. Here we propose that epithalamic asymmetry of teleosts is one such model. Comparative studies among related teleost species have revealed heterochronic shifts in the timing of ontogenic events leading to the development of epithalamic asymmetry. Such temporal changes involve neural structures critical for tissue-tissue interactions underlying the generation of asymmetry and are concurrent with the appearance of morphological differences in the pattern of asymmetry between species. Based on these findings, we hypothesize that interspecies variation of epithalamic asymmetry results from changes in the timing of tissue-tissue interactions critical for the establishment of asymmetry during ontogeny. Importantly, this hypothesis can be tested by systematic comparative approaches among teleosts species based on normalized developmental time, combined with experimental manipulation of epithalamic asymmetry development.
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Affiliation(s)
- Iskra A Signore
- Anatomy and Developmental Biology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Independencia, Santiago, Chile
| | - Miguel L Concha
- Anatomy and Developmental Biology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
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38
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Subdivision of the lateral plate mesoderm and specification of the forelimb and hindlimb forming domains. Semin Cell Dev Biol 2016; 49:102-8. [DOI: 10.1016/j.semcdb.2015.11.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/17/2015] [Accepted: 11/21/2015] [Indexed: 11/15/2022]
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39
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Martínez-Torres M, Rubio-Morales B, Piña-Amado JJ, Luis J. Hemipenes in females of the mexican viviparous lizardBarisia imbricata(Squamata: Anguidae): an example of heterochrony in sexual development. Evol Dev 2015; 17:270-7. [DOI: 10.1111/ede.12134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martín Martínez-Torres
- Laboratorio de Biología de la Reproducción; Facultad de Estudios Superiores Iztacala; Universidad Nacional Autónoma de México; Avenida de los Barrios #1, Los Reyes Iztacala A. P. 314 Tlalnepantla Estado de México CP 54090 México
| | - Beatriz Rubio-Morales
- Laboratorio de Herpetología (Vivario); Facultad de Estudios Superiores Iztacala; Universidad Nacional Autónoma de México; Los Reyes Iztacala AP 314 Tlalnepantla Estado de México CP 54090 México
| | - José Juan Piña-Amado
- Laboratorio de Biología de la Reproducción; Facultad de Estudios Superiores Iztacala; Universidad Nacional Autónoma de México; Avenida de los Barrios #1, Los Reyes Iztacala A. P. 314 Tlalnepantla Estado de México CP 54090 México
| | - Juana Luis
- Laboratorio de Biología de la Reproducción; Facultad de Estudios Superiores Iztacala; Universidad Nacional Autónoma de México; Avenida de los Barrios #1, Los Reyes Iztacala A. P. 314 Tlalnepantla Estado de México CP 54090 México
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40
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Bertrand S, Aldea D, Oulion S, Subirana L, de Lera AR, Somorjai I, Escriva H. Evolution of the Role of RA and FGF Signals in the Control of Somitogenesis in Chordates. PLoS One 2015; 10:e0136587. [PMID: 26371756 PMCID: PMC4570818 DOI: 10.1371/journal.pone.0136587] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/05/2015] [Indexed: 11/18/2022] Open
Abstract
During vertebrate development, the paraxial mesoderm becomes segmented, forming somites that will give rise to dermis, axial skeleton and skeletal muscles. Although recently challenged, the "clock and wavefront" model for somitogenesis explains how interactions between several cell-cell communication pathways, including the FGF, RA, Wnt and Notch signals, control the formation of these bilateral symmetric blocks. In the cephalochordate amphioxus, which belongs to the chordate phylum together with tunicates and vertebrates, the dorsal paraxial mesendoderm also periodically forms somites, although this process is asymmetric and extends along the whole body. It has been previously shown that the formation of the most anterior somites in amphioxus is dependent upon FGF signalling. However, the signals controlling somitogenesis during posterior elongation in amphioxus are still unknown. Here we show that, contrary to vertebrates, RA and FGF signals act independently during posterior elongation and that they are not mandatory for posterior somites to form. Moreover, we show that RA is not able to buffer the left/right asymmetry machinery that is controlled through the asymmetric expression of Nodal pathway actors. Our results give new insights into the evolution of the somitogenesis process in chordates. They suggest that RA and FGF pathways have acquired specific functions in the control of somitogenesis in vertebrates. We propose that the "clock and wavefront" system was selected specifically in vertebrates in parallel to the development of more complex somite-derived structures but that it was not required for somitogenesis in the ancestor of chordates.
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Affiliation(s)
- Stéphanie Bertrand
- UPMC Univ Paris 06, UMR 7232, BIOM, Observatoire Océanologique de Banyuls sur Mer, F-66650, Banyuls/Mer, France
- * E-mail: (SB); (HE)
| | - Daniel Aldea
- UPMC Univ Paris 06, UMR 7232, BIOM, Observatoire Océanologique de Banyuls sur Mer, F-66650, Banyuls/Mer, France
| | - Silvan Oulion
- UPMC Univ Paris 06, UMR 7232, BIOM, Observatoire Océanologique de Banyuls sur Mer, F-66650, Banyuls/Mer, France
| | - Lucie Subirana
- UPMC Univ Paris 06, UMR 7232, BIOM, Observatoire Océanologique de Banyuls sur Mer, F-66650, Banyuls/Mer, France
| | - Angel R. de Lera
- Departamento de Química Orgánica, Facultade de Química, CINBIO, Universidade de Vigo, and Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain
| | - Ildiko Somorjai
- UPMC Univ Paris 06, UMR 7232, BIOM, Observatoire Océanologique de Banyuls sur Mer, F-66650, Banyuls/Mer, France
| | - Hector Escriva
- UPMC Univ Paris 06, UMR 7232, BIOM, Observatoire Océanologique de Banyuls sur Mer, F-66650, Banyuls/Mer, France
- * E-mail: (SB); (HE)
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41
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Feldmeyer B, Greshake B, Funke E, Ebersberger I, Pfenninger M. Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix. BMC Evol Biol 2015; 15:164. [PMID: 26281847 PMCID: PMC4539673 DOI: 10.1186/s12862-015-0434-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/24/2015] [Indexed: 01/09/2023] Open
Abstract
Background Life history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related European Radix species. Results Snails of the genus Radix occupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural selection driven speciation based on ecological niche differentiation. We then inferred phylogenetic relationships among the four Radix species based on whole mt-genomes plus 23 nuclear loci. Three different tests to infer selection and changes in amino acid properties yielded a total of 134 genes with signatures of positive selection. The majority of these genes belonged to the functional gene ontology categories “reproduction” and “genitalia” with an overrepresentation of the functions “development” and “growth rate”. Conclusions We show here that Radix species divergence may be primarily enforced by selection on life history traits such as (larval-) development and growth rate. We thus hypothesise that life history differences may confer advantages under the according climate regimes, e.g., species occupying warmer and dryer habitats might have a fitness advantage with fast developing susceptible life stages, which are more tolerant to habitat desiccation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0434-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Barbara Feldmeyer
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany. .,Evolutionary Biology, Johannes Gutenberg University Mainz, Müllerweg 6, Mainz, 55099, Germany.
| | - Bastian Greshake
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany. .,Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Maxvon-Laue Str. 13, Frankfurt am Main, 60438, Germany.
| | - Elisabeth Funke
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany.
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Maxvon-Laue Str. 13, Frankfurt am Main, 60438, Germany.
| | - Markus Pfenninger
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany.
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Jiang L, Clavijo JA, Sun L, Zhu X, Bhakta MS, Gezan SA, Carvalho M, Vallejos CE, Wu R. Plastic expression of heterochrony quantitative trait loci (hQTLs) for leaf growth in the common bean (Phaseolus vulgaris). THE NEW PHYTOLOGIST 2015; 207:872-82. [PMID: 25816915 PMCID: PMC6681149 DOI: 10.1111/nph.13386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/25/2015] [Indexed: 05/14/2023]
Abstract
Heterochrony, that is, evolutionary changes in the relative timing of developmental events and processes, has emerged as a key concept that links evolution and development. Genes associated with heterochrony encode molecular components of developmental timing mechanisms. However, our understanding of how heterochrony genes alter the expression of heterochrony in response to environmental changes remains very limited. We applied functional mapping to find quantitative trait loci (QTLs) responsible for growth trajectories of leaf area and leaf mass in the common bean (Phaseolus vulgaris) grown in two contrasting environments. We identified three major QTLs pleiotropically expressed under the two environments. Further characterization of the temporal pattern of these QTLs indicates that they are heterochrony QTLs (hQTLs) in terms of their role in influencing four heterochronic parameters: the timing of the inflection point, the timing of maximum acceleration and deceleration, and the duration of linear growth. The pattern of gene action by the hQTLs on each parameter was unique, being environmentally dependent and varying between two allometrically related leaf growth traits. These results provide new insights into the complexity of genetic mechanisms that control trait formation in plants and provide novel findings that will be of use in studying the evolutionary trends.
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Affiliation(s)
- Libo Jiang
- Center for Computational BiologyCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing100083China
| | - Jose A. Clavijo
- Department of Horticultural SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular BreedingNational Engineering Research Center for FloricultureBeijing Laboratory of Urban and Rural Ecological Environment and College of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Xuli Zhu
- Center for Computational BiologyCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing100083China
| | - Mehul S. Bhakta
- Department of Horticultural SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Salvador A. Gezan
- School of Forest Resources and ConservationUniversity of FloridaGainesvilleFL32611USA
| | - Melissa Carvalho
- School of Forest Resources and ConservationUniversity of FloridaGainesvilleFL32611USA
| | - C. Eduardo Vallejos
- Department of Horticultural SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Rongling Wu
- Center for Computational BiologyCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing100083China
- Center for Statistical GeneticsThe Pennsylvania State UniversityHersheyPA17033USA
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43
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Torday JS. Pleiotropy as the Mechanism for Evolving Novelty: Same Signal, Different Result. BIOLOGY 2015; 4:443-59. [PMID: 26103090 PMCID: PMC4498309 DOI: 10.3390/biology4020443] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/02/2015] [Accepted: 06/10/2015] [Indexed: 11/22/2022]
Abstract
In contrast to the probabilistic way of thinking about pleiotropy as the random expression of a single gene that generates two or more distinct phenotypic traits, it is actually a deterministic consequence of the evolution of complex physiology from the unicellular state. Pleiotropic novelties emerge through recombinations and permutations of cell-cell signaling exercised during reproduction based on both past and present physical and physiologic conditions, in service to the future needs of the organism for its continued survival. Functional homologies ranging from the lung to the kidney, skin, brain, thyroid and pituitary exemplify the evolutionary mechanistic strategy of pleiotropy. The power of this perspective is exemplified by the resolution of evolutionary gradualism and punctuated equilibrium in much the same way that Niels Bohr resolved the paradoxical duality of light as Complementarity.
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Affiliation(s)
- John S Torday
- Harbor-UCLA Medical Center, 1124 West Carson Street, Torrance, CA 90502-2006, USA.
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44
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Cheatle Jarvela AM, Hinman VF. Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks. EvoDevo 2015; 6:3. [PMID: 25685316 PMCID: PMC4327956 DOI: 10.1186/2041-9139-6-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/18/2014] [Indexed: 11/10/2022] Open
Abstract
The form that an animal takes during development is directed by gene regulatory networks (GRNs). Developmental GRNs interpret maternally deposited molecules and externally supplied signals to direct cell-fate decisions, which ultimately leads to the arrangements of organs and tissues in the organism. Genetically encoded modifications to these networks have generated the wide range of metazoan diversity that exists today. Most studies of GRN evolution focus on changes to cis-regulatory DNA, and it was historically theorized that changes to the transcription factors that bind to these cis-regulatory modules (CRMs) contribute to this process only rarely. A growing body of evidence suggests that changes to the coding regions of transcription factors play a much larger role in the evolution of developmental gene regulatory networks than originally imagined. Just as cis-regulatory changes make use of modular binding site composition and tissue-specific modules to avoid pleiotropy, transcription factor coding regions also predominantly evolve in ways that limit the context of functional effects. Here, we review the recent works that have led to this unexpected change in the field of Evolution and Development (Evo-Devo) and consider the implications these studies have had on our understanding of the evolution of developmental processes.
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Affiliation(s)
- Alys M Cheatle Jarvela
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA 15213 USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA 15213 USA
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45
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Kratochwil CF, Meyer A. Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts. Mol Ecol Resour 2014; 15:761-71. [PMID: 25403420 DOI: 10.1111/1755-0998.12350] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 10/29/2014] [Accepted: 11/15/2014] [Indexed: 01/08/2023]
Abstract
Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For nonmodel organisms with adaptive key innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has been primarily used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genomewide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation.
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Affiliation(s)
- Claudius F Kratochwil
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany
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Keyte AL, Alonzo-Johnsen M, Hutson MR. Evolutionary and developmental origins of the cardiac neural crest: building a divided outflow tract. ACTA ACUST UNITED AC 2014; 102:309-23. [PMID: 25227322 DOI: 10.1002/bdrc.21076] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 08/22/2014] [Indexed: 12/14/2022]
Abstract
The cardiac neural crest cells (CNCCs) have played an important role in the evolution and development of the vertebrate cardiovascular system: from reinforcement of the developing aortic arch arteries early in vertebrate evolution, to later orchestration of aortic arch artery remodeling into the great arteries of the heart, and finally outflow tract septation in amniotes. A critical element necessary for the evolutionary advent of outflow tract septation was the co-evolution of the cardiac neural crest cells with the second heart field. This review highlights the major transitions in vertebrate circulatory evolution, explores the evolutionary developmental origins of the CNCCs from the third stream cranial neural crest, and explores candidate signaling pathways in CNCC and outflow tract evolution drawn from our knowledge of DiGeorge Syndrome.
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Affiliation(s)
- Anna L Keyte
- Brumley Neonatal Perinatal Research Institute, Department of Pediatrics, Duke University, Durham, North Carolina
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