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Li P, Xiong C, Huang B, Sun B, Gong X. Terrestrial locomotion characteristics of climbing perch (Anabas testudineus). J Exp Biol 2024; 227:jeb247238. [PMID: 38752366 DOI: 10.1242/jeb.247238] [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: 12/21/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
The evolution and utilization of limbs facilitated terrestrial vertebrate movement on land, but little is known about how other lateral structures enhance terrestrial locomotion in amphibian fishes without terrestrialized limb structures. Climbing perch (Anabas testudineus) exhibit sustained terrestrial locomotion using uniaxial rotating gill covers instead of appendages. To investigate the role of such simple lateral structures in terrestrial locomotion and the motion-generating mechanism of the corresponding locomotor structure configuration (gill covers and body undulation), we measured the terrestrial kinematics of climbing perch and quantitatively analysed its motion characteristics. The digitized locomotor kinematics showed a unique body postural adjustment ability that enables the regulation of the posture of the caudal peduncle for converting lateral bending force into propulsion. An analysis of the coordination characteristics demonstrated that the motion of the gill cover is kinematically independent of axial undulation, suggesting that the gill cover functions as an anchored simple support pole while axial undulation actively mediates body posture and produces propulsive force. The two identified feature shapes explained more than 87% of the complex lateral undulation in multistage locomotion. The kinematic characteristics enhance our understanding of the underlying coordinating mechanism corresponding to locomotor configurations. Our work provides quantitative insight into the terrestrial locomotor adaptation of climbing perch and sheds light on terrestrial motion potential of locomotor configurations containing a typical aquatic body and restricted lateral structure.
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Affiliation(s)
- Peimin Li
- Institute of Medical Equipment Science and Engineering, School of Mechanical Science and Engineering , Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Caihua Xiong
- Institute of Medical Equipment Science and Engineering, School of Mechanical Science and Engineering , Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bo Huang
- Institute of Medical Equipment Science and Engineering, School of Mechanical Science and Engineering , Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Baiyang Sun
- Institute of Medical Equipment Science and Engineering, School of Mechanical Science and Engineering , Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuan Gong
- Institute of Medical Equipment Science and Engineering, School of Mechanical Science and Engineering , Huazhong University of Science and Technology, Wuhan, Hubei, China
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Witzmann F, Fröbisch N. Morphology and ontogeny of carpus and tarsus in stereospondylomorph temnospondyls. PeerJ 2023; 11:e16182. [PMID: 37904842 PMCID: PMC10613440 DOI: 10.7717/peerj.16182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/05/2023] [Indexed: 11/01/2023] Open
Abstract
Skeletal development is well known in temnospondyls, the most diverse group of Paleozoic and Mesozoic amphibians. However, the elements of carpus and tarsus (i.e., the mesopodium) were always the last bones to ossify relative to the other limb bones and with regard to the rest of the skeleton, and are preserved only in rare cases. Thus, in contrast to the other parts of the limb skeleton, little is known about the ontogeny and sequence of ossification of the temnospondyl carpus and tarsus. We intended to close this gap by studying the ontogenies of a number of Permo/Carboniferous stereospondylomorphs, the only temnospondyls with preserved growth series in which the successive ossification of carpals and tarsals can be traced. Studying the degree of mesopodial ossification within the same species show that it is not necessarily correlated with body size. This indicates that individual age rather than size determined the degree of mesopodial ossification in stereospondylomorphs and that the largest individuals are not necessarily the oldest ones. In the stereospondylomorph tarsus, the distal tarsals show preaxial development in accordance with most early tetrapods and salamanders. However, the more proximal mesopodials exhibit postaxial dominance, i.e., the preaxial column (tibiale, centrale 1) consistently started to ossify after the central column (centralia 2-4, intermedium) and the postaxial column (fibulare). Likewise, we observed preaxial development of the distal carpals in the stereospondylomorph carpus, as in most early tetrapods for which a statement can be made. However, in contrast to the tarsus, the more proximal carpals were formed by preaxial development, i.e., the preaxial column (radiale, centrale 1) ossified after the central column (centralia 2-4, intermedium) and before the postaxial column (ulnare). This pattern is unique among known early tetrapods and occurs only in certain extant salamanders. Furthermore, ossification proceeded from distal to proximal in the central column of the stereospondylomorph carpus, whereas the ossification advanced from proximal to distal in the central column of the tarsus. Despite these differences, a general ossification pattern that started from proximolateral (intermedium or centrale 4) to mediodistal (distal tarsal and carpal 1) roughly in a diagonal line is common to all stereospondylomorph mesopodials investigated. This pattern might basically reflect the alignment of stress within the mesopodium during locomotion. Our observations might point to a greater variability in the development of the mesopodium in stereospondylomorphs and probably other early tetrapods than in most extant tetrapods, possibly mirroring a similar variation as seen in the early phases of skeletogenesis in salamander carpus and tarsus.
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Affiliation(s)
- Florian Witzmann
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Nadia Fröbisch
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Department of Biology, Humboldt Universität Berlin, Berlin, Germany
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Wang Z, Peng C, Wu W, Yan C, Lv Y, Li JT. Developmental regulation of conserved non-coding element evolution provides insights into limb loss in squamates. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2399-2414. [PMID: 37256419 DOI: 10.1007/s11427-023-2362-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/09/2023] [Indexed: 06/01/2023]
Abstract
Limb loss shows recurrent phenotypic evolution across squamate lineages. Here, based on three de novo-assembled genomes of limbless lizards from different lineages, we showed that divergence of conserved non-coding elements (CNEs) played an important role in limb development. These CNEs were associated with genes required for limb initiation and outgrowth, and with regulatory signals in the early stage of limb development. Importantly, we identified the extensive existence of insertions and deletions (InDels) in the CNEs, with the numbers ranging from 111 to 756. Most of these CNEs with InDels were lineage-specific in the limbless squamates. Nearby genes of these InDel CNEs were important to early limb formation, such as Tbx4, Fgf10, and Gli3. Based on functional experiments, we found that nucleotide mutations and InDels both affected the regulatory function of the CNEs. Our study provides molecular evidence underlying limb loss in squamate reptiles from a developmental perspective and sheds light on the importance of regulatory element InDels in phenotypic evolution.
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Affiliation(s)
- Zeng Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yunyun Lv
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- College of Life Science, Neijiang Normal University, Neijiang, 641100, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw, 05282, Myanmar.
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Takahashi K. Shelter cleaning of frillfin goby as non-reproductive behaviour. Behav Processes 2023; 208:104875. [PMID: 37061141 DOI: 10.1016/j.beproc.2023.104875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/17/2023]
Abstract
Various animals perform nest cleaning behaviour for breeding and keeping the hygiene of their living environment. Some fishes are also known to clean the nest for breeding and parental care, but it is unclear whether they clean it under non-breeding conditions. This study investigated the shelter cleaning behaviour of frillfin goby (Bathygobius fuscus) during the non-breeding season. All individuals of both males and females removed unknown objects (fishing sinkers) from their shelter, whereas they did not move many sinkers in the feeding area located outside the shelter. Subsequent video observation showed that fish removed sinkers using their tail fin, snout, mouth, and pectoral fins. The results suggest that frillfin goby clean their shelter even under non-breeding conditions. Furthermore, this study found that they can use pectoral fins to move objects, just like other animals use their hands and forelimbs to do so, supporting the developmental relationship between digits and pectoral fins in terms of functionality.
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Affiliation(s)
- Kohji Takahashi
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Japan.
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Rothier PS, Fabre AC, Clavel J, Benson RBJ, Herrel A. Mammalian forelimb evolution is driven by uneven proximal-to-distal morphological diversity. eLife 2023; 12:81492. [PMID: 36700542 PMCID: PMC9908075 DOI: 10.7554/elife.81492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
Vertebrate limb morphology often reflects the environment due to variation in locomotor requirements. However, proximal and distal limb segments may evolve differently from one another, reflecting an anatomical gradient of functional specialization that has been suggested to be impacted by the timing of development. Here, we explore whether the temporal sequence of bone condensation predicts variation in the capacity of evolution to generate morphological diversity in proximal and distal forelimb segments across more than 600 species of mammals. Distal elements not only exhibit greater shape diversity, but also show stronger within-element integration and, on average, faster evolutionary responses than intermediate and upper limb segments. Results are consistent with the hypothesis that late developing distal bones display greater morphological variation than more proximal limb elements. However, the higher integration observed within the autopod deviates from such developmental predictions, suggesting that functional specialization plays an important role in driving within-element covariation. Proximal and distal limb segments also show different macroevolutionary patterns, albeit not showing a perfect proximo-distal gradient. The high disparity of the mammalian autopod, reported here, is consistent with the higher potential of development to generate variation in more distal limb structures, as well as functional specialization of the distal elements.
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Affiliation(s)
- Priscila S Rothier
- Département Adaptations du Vivant, Muséum National d'Histoire NaturelleParisFrance
| | - Anne-Claire Fabre
- Naturhistorisches Museum BernBernSwitzerland
- Institute of Ecology and Evolution, University of BernBernSwitzerland
- Life Sciences Department, Vertebrates Division, Natural History MuseumLondonUnited Kingdom
| | - Julien Clavel
- Life Sciences Department, Vertebrates Division, Natural History MuseumLondonUnited Kingdom
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023VilleurbanneFrance
| | - Roger BJ Benson
- Department of Earth Sciences, University of OxfordOxfordUnited Kingdom
| | - Anthony Herrel
- Département Adaptations du Vivant, Muséum National d'Histoire NaturelleParisFrance
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Early evolution of enamel matrix proteins is reflected by pleiotropy of physiological functions. Sci Rep 2023; 13:1471. [PMID: 36702824 PMCID: PMC9879986 DOI: 10.1038/s41598-023-28388-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Highly specialized enamel matrix proteins (EMPs) are predominantly expressed in odontogenic tissues and diverged from common ancestral gene. They are crucial for the maturation of enamel and its extreme complexity in multiple independent lineages. However, divergence of EMPs occured already before the true enamel evolved and their conservancy in toothless species suggests that non-canonical functions are still under natural selection. To elucidate this hypothesis, we carried out an unbiased, comprehensive phenotyping and employed data from the International Mouse Phenotyping Consortium to show functional pleiotropy of amelogenin, ameloblastin, amelotin, and enamelin, genes, i.e. in sensory function, skeletal morphology, cardiovascular function, metabolism, immune system screen, behavior, reproduction, and respiratory function. Mice in all KO mutant lines, i.e. amelogenin KO, ameloblastin KO, amelotin KO, and enamelin KO, as well as mice from the lineage with monomeric form of ameloblastin were affected in multiple physiological systems. Evolutionary conserved motifs and functional pleiotropy support the hypothesis of role of EMPs as general physiological regulators. These findings illustrate how their non-canonical function can still effect the fitness of modern species by an example of influence of amelogenin and ameloblastin on the bone physiology.
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7
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Gene expression changes during the evolution of the tetrapod limb. Biol Futur 2022; 73:411-426. [PMID: 36355308 DOI: 10.1007/s42977-022-00136-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.
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Abstract
SignificanceAdaptation to more severe ambient temperature fluctuations can be considered one of the key innovations of terrestrial tetrapods. Our study shows the formation of the functional MHR1-3 domain in transient receptor potential melastatin 8 (TRPM8) bestowed the channel with cold sensitivity during the water-to-land transition. The evolved MHR1-3 domain found in terrestrial tetrapods serves as an independent apparatus with cold sensitivity. Furthermore, this domain with independent cold sensitivity is necessary for the regulatory mechanism of the pore domain, where the efficacy of cold activation is largely altered by evolutionary tuning of the hydrophobicity of several residues during the diversification of terrestrial tetrapods. Our findings advance the understanding of cold-sensing emergence during evolution and the thermodynamic basis of TRPM8 cold activation.
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Takeuchi T, Matsubara H, Minamitani F, Satoh Y, Tozawa S, Moriyama T, Maruyama K, Suzuki KIT, Shigenobu S, Inoue T, Tamura K, Agata K, Hayashi T. Newt Hoxa13 has an essential and predominant role in digit formation during development and regeneration. Development 2022; 149:274659. [DOI: 10.1242/dev.200282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/21/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The 5′Hox genes play crucial roles in limb development and specify regions in the proximal-distal axis of limbs. However, there is no direct genetic evidence that Hox genes are essential for limb development in non-mammalian tetrapods or for limb regeneration. Here, we produced single to quadruple Hox13 paralog mutants using the CRISPR/Cas9 system in newts (Pleurodeles waltl), which have strong regenerative capacities, and also produced germline mutants. We show that Hox13 genes are essential for digit formation in development, as in mice. In addition, Hoxa13 has a predominant role in digit formation, unlike in mice. The predominance is probably due to the restricted expression pattern of Hoxd13 in limb buds and the strong dependence of Hoxd13 expression on Hoxa13. Finally, we demonstrate that Hox13 genes are also necessary for digit formation in limb regeneration. Our findings reveal that the general function of Hox13 genes is conserved between limb development and regeneration, and across taxa. The predominance of Hoxa13 function both in newt limbs and fish fins, but not in mouse limbs, suggests a potential contribution of Hoxa13 function in fin-to-limb transition.
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Affiliation(s)
- Takashi Takeuchi
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Haruka Matsubara
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Fumina Minamitani
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Yukio Satoh
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Sayo Tozawa
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Tomoki Moriyama
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Kohei Maruyama
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Ken-ichi T. Suzuki
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Gakushuin University, Toyoshima-Ku, Tokyo 171-8588, Japan
| | - Koji Tamura
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kiyokazu Agata
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Life Science, Faculty of Science, Gakushuin University, Toyoshima-Ku, Tokyo 171-8588, Japan
| | - Toshinori Hayashi
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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10
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Conserved Mechanisms, Novel Anatomies: The Developmental Basis of Fin Evolution and the Origin of Limbs. DIVERSITY 2021. [DOI: 10.3390/d13080384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.
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11
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Dissection of the Fgf8 regulatory landscape by in vivo CRISPR-editing reveals extensive intra- and inter-enhancer redundancy. Nat Commun 2021; 12:439. [PMID: 33469032 PMCID: PMC7815712 DOI: 10.1038/s41467-020-20714-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
Developmental genes are often regulated by multiple elements with overlapping activity. Yet, in most cases, the relative function of those elements and their contribution to endogenous gene expression remain poorly characterized. An example of this phenomenon is that distinct sets of enhancers have been proposed to direct Fgf8 in the limb apical ectodermal ridge and the midbrain-hindbrain boundary. Using in vivo CRISPR/Cas9 genome engineering, we functionally dissect this complex regulatory ensemble and demonstrate two distinct regulatory logics. In the apical ectodermal ridge, the control of Fgf8 expression appears distributed between different enhancers. In contrast, we find that in the midbrain-hindbrain boundary, one of the three active enhancers is essential while the other two are dispensable. We further dissect the essential midbrain-hindbrain boundary enhancer to reveal that it is also composed by a mixture of essential and dispensable modules. Cross-species transgenic analysis of this enhancer suggests that its composition may have changed in the vertebrate lineage.
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12
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Bowman JC, Petrov AS, Frenkel-Pinter M, Penev PI, Williams LD. Root of the Tree: The Significance, Evolution, and Origins of the Ribosome. Chem Rev 2020; 120:4848-4878. [PMID: 32374986 DOI: 10.1021/acs.chemrev.9b00742] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ribosome is an ancient molecular fossil that provides a telescope to the origins of life. Made from RNA and protein, the ribosome translates mRNA to coded protein in all living systems. Universality, economy, centrality and antiquity are ingrained in translation. The translation machinery dominates the set of genes that are shared as orthologues across the tree of life. The lineage of the translation system defines the universal tree of life. The function of a ribosome is to build ribosomes; to accomplish this task, ribosomes make ribosomal proteins, polymerases, enzymes, and signaling proteins. Every coded protein ever produced by life on Earth has passed through the exit tunnel, which is the birth canal of biology. During the root phase of the tree of life, before the last common ancestor of life (LUCA), exit tunnel evolution is dominant and unremitting. Protein folding coevolved with evolution of the exit tunnel. The ribosome shows that protein folding initiated with intrinsic disorder, supported through a short, primitive exit tunnel. Folding progressed to thermodynamically stable β-structures and then to kinetically trapped α-structures. The latter were enabled by a long, mature exit tunnel that partially offset the general thermodynamic tendency of all polypeptides to form β-sheets. RNA chaperoned the evolution of protein folding from the very beginning. The universal common core of the ribosome, with a mass of nearly 2 million Daltons, was finalized by LUCA. The ribosome entered stasis after LUCA and remained in that state for billions of years. Bacterial ribosomes never left stasis. Archaeal ribosomes have remained near stasis, except for the superphylum Asgard, which has accreted rRNA post LUCA. Eukaryotic ribosomes in some lineages appear to be logarithmically accreting rRNA over the last billion years. Ribosomal expansion in Asgard and Eukarya has been incremental and iterative, without substantial remodeling of pre-existing basal structures. The ribosome preserves information on its history.
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Affiliation(s)
- Jessica C Bowman
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton S Petrov
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Moran Frenkel-Pinter
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Petar I Penev
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Loren Dean Williams
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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13
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Chen KQ, Tahara N, Anderson A, Kawakami H, Kawakami S, Nishinakamura R, Pandolfi PP, Kawakami Y. Development of the Proximal-Anterior Skeletal Elements in the Mouse Hindlimb Is Regulated by a Transcriptional and Signaling Network Controlled by Sall4. Genetics 2020; 215:129-141. [PMID: 32156750 PMCID: PMC7198279 DOI: 10.1534/genetics.120.303069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/03/2020] [Indexed: 12/18/2022] Open
Abstract
The vertebrate limb serves as an experimental paradigm to study mechanisms that regulate development of the stereotypical skeletal elements. In this study, we simultaneously inactivated Sall4 using Hoxb6Cre and Plzf in mouse embryos, and found that their combined function regulates development of the proximal-anterior skeletal elements in hindlimbs. The Sall4; Plzf double knockout exhibits severe defects in the femur, tibia, and anterior digits, distinct defects compared to other allelic series of Sall4; Plzf We found that Sall4 regulates Plzf expression prior to hindlimb outgrowth. Further expression analysis indicated that Hox10 genes and GLI3 are severely downregulated in the Sall4; Plzf double knockout hindlimb bud. In contrast, PLZF expression is reduced but detectable in Sall4; Gli3 double knockout limb buds, and SALL4 is expressed in the Plzf; Gli3 double knockout limb buds. These results indicate that Plzf, Gli3, and Hox10 genes downstream of Sall4, regulate femur and tibia development. In the autopod, we show that Sall4 negatively regulates Hedgehog signaling, which allows for development of the most anterior digit. Collectively, our study illustrates genetic systems that regulate development of the proximal-anterior skeletal elements in hindlimbs.
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Affiliation(s)
| | - Naoyuki Tahara
- Department of Genetics, Cell Biology and Development
- Stem Cell Institute, Minneapolis, Minnesota 55455, and
- Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development
- Stem Cell Institute, Minneapolis, Minnesota 55455, and
- Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Sho Kawakami
- Department of Genetics, Cell Biology and Development
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan 860-0811
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development
- Stem Cell Institute, Minneapolis, Minnesota 55455, and
- Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota 55455
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14
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Onimaru K. The evolutionary origin of developmental enhancers in vertebrates: Insights from non‐model species. Dev Growth Differ 2020; 62:326-333. [DOI: 10.1111/dgd.12662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Koh Onimaru
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research (BDR) Wako CitySaitama Japan
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15
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Woltering JM, Holzem M, Meyer A. Lissamphibian limbs and the origins of tetrapod hox domains. Dev Biol 2019; 456:138-144. [DOI: 10.1016/j.ydbio.2019.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/30/2022]
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16
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Darnet S, Dragalzew AC, Amaral DB, Sousa JF, Thompson AW, Cass AN, Lorena J, Pires ES, Costa CM, Sousa MP, Fröbisch NB, Oliveira G, Schneider PN, Davis MC, Braasch I, Schneider I. Deep evolutionary origin of limb and fin regeneration. Proc Natl Acad Sci U S A 2019; 116:15106-15115. [PMID: 31270239 PMCID: PMC6660751 DOI: 10.1073/pnas.1900475116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of paired appendage regeneration, regardless of the amputation level. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in polypterid fishes (Cladistia). Whether this ability evolved independently in sarcopterygians and actinopterygians or has a common origin remains unknown. Here we combine fin regeneration assays and comparative RNA-sequencing (RNA-seq) analysis of Polypterus and axolotl blastemas to provide support for a common origin of paired appendage regeneration in Osteichthyes (bony vertebrates). We show that, in addition to polypterids, regeneration after fin endoskeleton amputation occurs in extant representatives of 2 other nonteleost actinopterygians: the American paddlefish (Chondrostei) and the spotted gar (Holostei). Furthermore, we assessed regeneration in 4 teleost species and show that, with the exception of the blue gourami (Anabantidae), 3 species were capable of regenerating fins after endoskeleton amputation: the white convict and the oscar (Cichlidae), and the goldfish (Cyprinidae). Our comparative RNA-seq analysis of regenerating blastemas of axolotl and Polypterus reveals the activation of common genetic pathways and expression profiles, consistent with a shared genetic program of appendage regeneration. Comparison of RNA-seq data from early Polypterus blastema to single-cell RNA-seq data from axolotl limb bud and limb regeneration stages shows that Polypterus and axolotl share a regeneration-specific genetic program. Collectively, our findings support a deep evolutionary origin of paired appendage regeneration in Osteichthyes and provide an evolutionary framework for studies on the genetic basis of appendage regeneration.
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Affiliation(s)
- Sylvain Darnet
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, Brazil
| | - Aline C Dragalzew
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, Brazil
| | - Danielson B Amaral
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, Brazil
| | - Josane F Sousa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, Brazil
| | - Andrew W Thompson
- Department of Integrative Biology, Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824
| | - Amanda N Cass
- Department of Biology, James Madison University, Harrisonburg, VA 22807
| | - Jamily Lorena
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, Brazil
- Instituto Tecnológico Vale, 66055-090 Belém, Brazil
| | - Eder S Pires
- Instituto Tecnológico Vale, 66055-090 Belém, Brazil
| | - Carinne M Costa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, Brazil
| | - Marcos P Sousa
- Laboratório de Biologia Molecular, Museu Paraense Emílio Goeldi, 66077-530 Belém, Pará, Brazil
| | - Nadia B Fröbisch
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | | | - Patricia N Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, Brazil
| | - Marcus C Davis
- Department of Biology, James Madison University, Harrisonburg, VA 22807
| | - Ingo Braasch
- Department of Integrative Biology, Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, Brazil;
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17
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Wood TWP, Nakamura T. Problems in Fish-to-Tetrapod Transition: Genetic Expeditions Into Old Specimens. Front Cell Dev Biol 2018; 6:70. [PMID: 30062096 PMCID: PMC6054942 DOI: 10.3389/fcell.2018.00070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/15/2018] [Indexed: 12/30/2022] Open
Abstract
The fish-to-tetrapod transition is one of the fundamental problems in evolutionary biology. A significant amount of paleontological data has revealed the morphological trajectories of skeletons, such as those of the skull, vertebrae, and appendages in vertebrate history. Shifts in bone differentiation, from dermal to endochondral bones, are key to explaining skeletal transformations during the transition from water to land. However, the genetic underpinnings underlying the evolution of dermal and endochondral bones are largely missing. Recent genetic approaches utilizing model organisms—zebrafish, frogs, chickens, and mice—reveal the molecular mechanisms underlying vertebrate skeletal development and provide new insights for how the skeletal system has evolved. Currently, our experimental horizons to test evolutionary hypotheses are being expanded to non-model organisms with state-of-the-art techniques in molecular biology and imaging. An integration of functional genomics, developmental genetics, and high-resolution CT scanning into evolutionary inquiries allows us to reevaluate our understanding of old specimens. Here, we summarize the current perspectives in genetic programs underlying the development and evolution of the dermal skull roof, shoulder girdle, and appendages. The ratio shifts of dermal and endochondral bones, and its underlying mechanisms, during the fish-to-tetrapod transition are particularly emphasized. Recent studies have suggested the novel cell origins of dermal bones, and the interchangeability between dermal and endochondral bones, obscuring the ontogenetic distinction of these two types of bones. Assimilation of ontogenetic knowledge of dermal and endochondral bones from different structures demands revisions of the prevalent consensus in the evolutionary mechanisms of vertebrate skeletal shifts.
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Affiliation(s)
- Thomas W P Wood
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Tetsuya Nakamura
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
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18
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Expression of meis and hoxa11 in dipnoan and teleost fins provides new insights into the evolution of vertebrate appendages. EvoDevo 2018; 9:11. [PMID: 29719716 PMCID: PMC5924435 DOI: 10.1186/s13227-018-0099-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/20/2018] [Indexed: 11/22/2022] Open
Abstract
Background The concerted activity of Meis and Hoxa11 transcription factors is essential for the subdivision of tetrapod limbs into proximo-distal (PD) domains; however, little is know about the evolution of this patterning mechanism. Here, we aim to study the expression of meis and hoxa11 orthologues in the median and paired rayed fins of zebrafish and in the lobed fins of the Australian lungfish. Results First, a late phase of expression of meis1.1 and hoxa11b in zebrafish dorsal and anal fins relates with segmentation of endochondral elements in proximal and distal radials. Second, our zebrafish in situ hybridization results reveal spatial and temporal changes between pectoral and pelvic fins. Third, in situ analysis of meis1, meis3 and hoxa11 genes in Neoceratodus pectoral fins identifies decoupled domains of expression along the PD axis. Conclusions Our data raise the possibility that the origin of stylopod and zeugopod lies much deeper in gnathostome evolution and that variation in meis and hoxa11 expression has played a substantial role in the transformation of appendage anatomy. Moreover, these observations provide evidence that the Meis/Hoxa11 profile considered a hallmark of stylopod/zeugopod patterning is present in Neoceratodus. Electronic supplementary material The online version of this article (10.1186/s13227-018-0099-9) contains supplementary material, which is available to authorized users.
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19
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Makanae A, Satoh A. Ectopic Fgf signaling induces the intercalary response in developing chicken limb buds. ZOOLOGICAL LETTERS 2018; 4:8. [PMID: 29721334 PMCID: PMC5907462 DOI: 10.1186/s40851-018-0090-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Intercalary pattern formation is an important regulatory step in amphibian limb regeneration. Amphibian limb regeneration is composed of multiple steps, including wounding, blastema formation, and intercalary pattern formation. Attempts have been made to transfer insights from regeneration-competent animals to regeneration-incompetent animalsat each step in the regeneration process. In the present study, we focused on the intercalary mechanism in chick limb buds. In amphibian limb regeneration, a proximodistal axis is organized as soon as a regenerating blastema is induced. Intermediate structures are subsequently induced (intercalated) between the established proximal and distal identities. Intercalary tissues are derived from proximal tissues. Fgf signaling mediates the intercalary response in amphibian limb regeneration. RESULTS We attempted to transfer insights into intercalary regeneration from amphibian models to the chick limb bud. The zeugopodial part was dissected out, and the distal and proximal parts were conjunct at st. 24. Delivering ectopic Fgf2 + Fgf8 between the distal and proximal parts resulted in induction of zeugopodial elements. Examination of HoxA11 expression, apoptosis, and cell proliferation provides insights to compare with those in the intercalary mechanism of amphibian limb regeneration. Furthermore, the cellular contribution was investigated in both the chicken intercalary response and that of axolotl limb regeneration. CONCLUSIONS We developed new insights into cellular contribution in amphibian intercalary regeneration, and found consistency between axolotl and chicken intercalary responses. Our findings demonstrate that the same principal of limb regeneration functions between regeneration-competent and -incompetent animals. In this context, we propose the feasibility of the induction of the regeneration response in amniotes.
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Affiliation(s)
- Aki Makanae
- Research Core for Interdisciplinary Sciences (RCIS), Okayama University, 3-1-1, Tsushimanaka, Kita-ku, Okayama, 700-8530 Japan
| | - Akira Satoh
- Research Core for Interdisciplinary Sciences (RCIS), Okayama University, 3-1-1, Tsushimanaka, Kita-ku, Okayama, 700-8530 Japan
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20
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Bickelmann C, Frota-Lima GN, Triepel SK, Kawaguchi A, Schneider I, Fröbisch NB. Noncanonical Hox, Etv4, and Gli3 gene activities give insight into unique limb patterning in salamanders. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:138-147. [PMID: 29602205 DOI: 10.1002/jez.b.22798] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 01/08/2023]
Abstract
Limb development in salamanders is unique among tetrapods in significant ways. Not only can salamanders regenerate lost limbs repeatedly and throughout their lives, but also the preaxial zeugopodial element and digits form before the postaxial ones and, hence, with a reversed polarity compared to all other tetrapods. Moreover, in salamanders with free-swimming larval stages, as exemplified by the axolotl (Ambystoma mexicanum), each digit buds independently, instead of undergoing a paddle stage. Here, we report gene expression patterns of Hoxa and d clusters, and other crucial transcription factors during axolotl limb development. During early phases of limb development, expression patterns are mostly similar to those reported for amniotes and frogs. Likewise, Hoxd and Shh regulatory landscapes are largely conserved. However, during late digit-budding phases, remarkable differences are present: (i) the Hoxd13 expression domain excludes developing digits I and IV, (ii) we expand upon previous observation that Hoxa11 expression, which traditionally marks the zeugopodium, extends distally into the developing digits, and (iii) Gli3 and Etv4 show prolonged expression in developing digits. Our findings identify derived patterns in the expression of key transcription factors during late phases of salamander limb development, and provide the basis for a better understanding of the unique patterning of salamander limbs.
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Affiliation(s)
- Constanze Bickelmann
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Gabriela Neiva Frota-Lima
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany.,Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Sandra Karla Triepel
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Akane Kawaguchi
- Research Institute of Molecular Pathology, Campus Vienna Biocenter 1, Vienna, Austria
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Nadia Belinda Fröbisch
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany.,Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
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21
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Jain D, Nemec S, Luxey M, Gauthier Y, Bemmo A, Balsalobre A, Drouin J. Regulatory integration of Hox factor activity with T-box factors in limb development. Development 2018; 145:dev.159830. [PMID: 29490982 DOI: 10.1242/dev.159830] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/16/2018] [Indexed: 01/26/2023]
Abstract
In tetrapods, Tbx4, Tbx5 and Hox cluster genes are crucial for forelimb and hindlimb development and mutations in these genes are responsible for congenital limb defects. The molecular basis of their integrated mechanisms of action in the context of limb development remains poorly understood. We studied Tbx4 and Hoxc10 owing to their overlapping loss-of-function phenotypes and colocalized expression in mouse hindlimb buds. We report an extensive overlap between Tbx4 and Hoxc10 genome occupancy and their putative target genes. Tbx4 and Hoxc10 interact directly with each other, have the ability to bind to a previously unrecognized T-box-Hox composite DNA motif and show synergistic activity when acting on reporter genes. Pitx1, the master regulator for hindlimb specification, also shows extensive genomic colocalization with Tbx4 and Hoxc10. Genome occupancy by Tbx4 in hindlimb buds is similar to Tbx5 occupancy in forelimbs. By contrast, another Hox factor, Hoxd13, also interacts with Tbx4/Tbx5 but antagonizes Tbx4/Tbx5-dependent transcriptional activity. Collectively, the modulation of Tbx-dependent activity by Hox factors acting on common DNA targets may integrate different developmental processes for the balanced formation of proportionate limbs.
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Affiliation(s)
- Deepak Jain
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
| | - Stephen Nemec
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada
| | - Maëva Luxey
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Amandine Bemmo
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada .,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada.,Departement de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, QC, H3J 3J7 Canada
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22
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Lalonde RL, Akimenko MA. Effects of fin fold mesenchyme ablation on fin development in zebrafish. PLoS One 2018; 13:e0192500. [PMID: 29420592 PMCID: PMC5805328 DOI: 10.1371/journal.pone.0192500] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
Abstract
The evolution of the tetrapod limb involved an expansion and elaboration of the endoskeletal elements, while the fish fin rays were lost. Loss of fin-specific genes, and regulatory changes in key appendicular patterning genes have been identified as mechanisms of limb evolution, however their contributions to cellular organization and tissue differences between fins and limbs remains poorly understood. During early larval fin development, hoxa13a/hoxd13a-expressing fin fold mesenchyme migrate through the median and pectoral fin along actinotrichia fibrils, non-calcified skeletal elements crucial for supporting the fin fold. Fin fold mesenchyme migration defects have previously been proposed as a mechanism of fin dermal bone loss during tetrapod evolution as it has been shown they contribute directly to the fin ray osteoblast population. Using the nitroreductase/metronidazole system, we genetically ablated a subset of hoxa13a/hoxd13a-expressing fin fold mesenchyme to assess its contributions to fin development. Following the ablation of fin fold mesenchyme in larvae, the actinotrichia are unable to remain rigid and the median and pectoral fin folds collapse, resulting in a reduced fin fold size. The remaining cells following ablation are unable to migrate and show decreased actinodin1 mesenchymal reporter activity. Actinodin proteins are crucial structural component of the actinotrichia. Additionally, we show a decrease in hoxa13a, hoxd13a, fgf10a and altered shha, and ptch2 expression during larval fin development. A continuous treatment of metronidazole leads to fin ray defects at 30dpf. Fewer rays are present compared to stage-matched control larvae, and these rays are shorter and less defined. These results suggest the targeted hoxa13a/hoxd13a-expressing mesenchyme contribute to their own successful migration through their contributions to actinotrichia. Furthermore, due to their fate as fin ray osteoblasts, we propose their initial ablation, and subsequent disorganization produces truncated fin dermal bone elements during late larval stages.
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Affiliation(s)
- Robert L. Lalonde
- Department of Biology, University of Ottawa, 20 Marie-Curie, Ottawa, Ontario, Canada
| | - Marie-Andrée Akimenko
- Department of Biology, University of Ottawa, 20 Marie-Curie, Ottawa, Ontario, Canada
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23
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Tulenko FJ, Massey JL, Holmquist E, Kigundu G, Thomas S, Smith SME, Mazan S, Davis MC. Fin-fold development in paddlefish and catshark and implications for the evolution of the autopod. Proc Biol Sci 2018; 284:rspb.2016.2780. [PMID: 28539509 DOI: 10.1098/rspb.2016.2780] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 01/04/2023] Open
Abstract
The evolutionary origin of the autopod involved a loss of the fin-fold and associated dermal skeleton with a concomitant elaboration of the distal endoskeleton to form a wrist and digits. Developmental studies, primarily from teleosts and amniotes, suggest a model for appendage evolution in which a delay in the AER-to-fin-fold conversion fuelled endoskeletal expansion by prolonging the function of AER-mediated regulatory networks. Here, we characterize aspects of paired fin development in the paddlefish Polyodon spathula (a non-teleost actinopterygian) and catshark Scyliorhinus canicula (chondrichthyan) to explore aspects of this model in a broader phylogenetic context. Our data demonstrate that in basal gnathostomes, the autopod marker HoxA13 co-localizes with the dermoskeleton component And1 to mark the position of the fin-fold, supporting recent work demonstrating a role for HoxA13 in zebrafish fin ray development. Additionally, we show that in paddlefish, the proximal fin and fin-fold mesenchyme share a common mesodermal origin, and that components of the Shh/LIM/Gremlin/Fgf transcriptional network critical to limb bud outgrowth and patterning are expressed in the fin-fold with a profile similar to that of tetrapods. Together these data draw contrast with hypotheses of AER heterochrony and suggest that limb-specific morphologies arose through evolutionary changes in the differentiation outcome of conserved early distal patterning compartments.
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Affiliation(s)
- Frank J Tulenko
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA.,Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - James L Massey
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309, USA
| | - Elishka Holmquist
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Gabriel Kigundu
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sarah Thomas
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sylvie Mazan
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, UMR7232, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marcus C Davis
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
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24
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Perez LN, Lorena J, Costa CM, Araujo MS, Frota-Lima GN, Matos-Rodrigues GE, Martins RAP, Mattox GMT, Schneider PN. Eye development in the four-eyed fish Anableps anableps: cranial and retinal adaptations to simultaneous aerial and aquatic vision. Proc Biol Sci 2018; 284:rspb.2017.0157. [PMID: 28381624 DOI: 10.1098/rspb.2017.0157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/06/2017] [Indexed: 12/25/2022] Open
Abstract
The unique eyes of the four-eyed fish Anableps anableps have long intrigued biologists. Key features associated with the bulging eye of Anableps include the expanded frontal bone and the duplicated pupils and cornea. Furthermore, the Anableps retina expresses different photoreceptor genes in dorsal and ventral regions, potentially associated with distinct aerial and aquatic stimuli. To gain insight into the developmental basis of the Anableps unique eye, we examined neurocranium and eye ontogeny, as well as photoreceptor gene expression during larval stages. First, we described six larval stages during which duplication of eye structures occurs. Our osteological analysis of neurocranium ontogeny revealed another distinctive Anablepid feature: an ossified interorbital septum partially separating the orbital cavities. Furthermore, we identified the onset of differences in cell proliferation and cell layer density between dorsal and ventral regions of the retina. Finally, we show that differential photoreceptor gene expression in the retina initiates during development, suggesting that it is inherited and not environmentally determined. In sum, our results shed light on the ontogenetic steps leading to the highly derived Anableps eye.
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Affiliation(s)
- Louise N Perez
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Jamily Lorena
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Carinne M Costa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Maysa S Araujo
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | - Rodrigo A P Martins
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - George M T Mattox
- Departamento de Biologia, Universidade Federal de São Carlos, Campus Sorocaba, São Paulo, Brazil
| | - Patricia N Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
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25
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Abstract
Two groups have studied the loss of limbs in snake evolution by focusing on a long-distance cis-acting enhancer of Sonic Hedgehog. They find a progressive degeneration of binding sites for key transcription factors, mirroring the progressive limblessness occurring in these reptiles.
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Affiliation(s)
- Maria M Kaltcheva
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mark Lewandoski
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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26
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Barry SN, Crow KD. The role of HoxA11 and HoxA13 in the evolution of novel fin morphologies in a representative batoid ( Leucoraja erinacea). EvoDevo 2017; 8:24. [PMID: 29214009 PMCID: PMC5709974 DOI: 10.1186/s13227-017-0088-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/21/2017] [Indexed: 01/13/2023] Open
Abstract
Background Batoids exhibit unique body plans with derived fin morphologies, such as the anteriorly expanded pectoral fins that fuse to the head, or distally extended anterior pelvic fin lobes used for a modified swimming technique utilized by skates (Rajidae). The little skate (Leucoraja erinacea), exhibits both of these unique fin morphologies. These fin modifications are not present in a typical shark body plan, and little is known regarding the mechanisms underlying their development. A recent study identified a novel apical ectodermal ridge (AER) associated with the development of the anterior pectoral fin in the little skate, but the role of the posterior HoxA genes was not featured during skate fin development. Results We present the first evidence for HoxA expression (HoxA11 and HoxA13) in novel AER domains associated with the development of three novel fin morphologies in a representative batoid, L. erinacea. We found HoxA13 expression associated with the recently described novel AER in the anterior pectoral fin, and HoxA11 expression in a novel AER domain in the anterior pelvic fin that we describe here. We find that both HoxA11 and HoxA13 are expressed in claspers, and while HoxA11 is expressed in pelvic fins and claspers, HoxA13 is expressed exclusively in developing claspers of males. Finally, HoxA11 expression is associated with the developing fin rays in paired fins. Conclusion Overall, these results indicate that the posterior HoxA genes play an important role in the morphological evolution of paired fins in a representative batoid. These data suggest that the batoids utilize a unique Hox code, where the posterior HoxA genes exhibit distinct expression patterns that are likely associated with specification of novel fin morphologies. Electronic supplementary material The online version of this article (10.1186/s13227-017-0088-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shannon N Barry
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94127 USA
| | - Karen D Crow
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94127 USA
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27
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Zhu J, Mackem S. John Saunders' ZPA, Sonic hedgehog and digit identity - How does it really all work? Dev Biol 2017; 429:391-400. [PMID: 28161524 PMCID: PMC5540801 DOI: 10.1016/j.ydbio.2017.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/28/2017] [Accepted: 02/01/2017] [Indexed: 01/02/2023]
Abstract
Among John Saunders' many seminal contributions to developmental biology, his discovery of the limb 'zone of polarizing activity' (ZPA) is arguably one of the most memorable and ground-breaking. This discovery introduced the limb as a premier model for understanding developmental patterning and promoted the concept of patterning by a morphogen gradient. In the 50 years since the discovery of the ZPA, Sonic hedgehog (Shh) has been identified as the ZPA factor and the basic components of the signaling pathway and many aspects of its regulation have been elucidated. Although much has also been learned about how it regulates growth, the mechanism by which Shh patterns the limb, how it acts to instruct digit 'identity', nevertheless remains an enigma. This review focuses on what has been learned about Shh function in the limb and the outstanding puzzles that remain to be solved.
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Affiliation(s)
- Jianjian Zhu
- Cancer and Developmental Biology Laboratory, CCR, NCI, Frederick, MD 21702, United States
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, CCR, NCI, Frederick, MD 21702, United States.
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28
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Amaral DB, Schneider I. Fins into limbs: Recent insights from sarcopterygian fish. Genesis 2017; 56. [PMID: 28834157 DOI: 10.1002/dvg.23052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/10/2017] [Accepted: 08/15/2017] [Indexed: 02/03/2023]
Abstract
Limbs with digits evolved as sarcopterygian fish transitioned to a terrestrial life, giving rise to modern tetrapods. Since the Devonian, most of the sarcopterygian fish diversity became extinct, with the only surviving representatives being two coelacanth and six lungfish species. As the sister group of tetrapods, sarcopterygian fish constitute the ideal models to address questions regarding the transition of vertebrates from water to land. However, distantly related yet experimentally amenable teleost fish species have instead become the organisms of choice for geneticists and developmental biologists. Comparative studies using teleosts, such as zebrafish, have greatly enriched our knowledge on the genetic and regulatory mechanisms underlying fin development. However, their highly derived fin anatomy provides limited insights on the origin of limbs and the teleost-specific whole-genome duplication represents a further complication to comparisons of gene function and regulation. In recent years, refined morphological and behavioral studies and access to lungfish embryos and availability of genetic resources have underscored the value of nontetrapod sarcopterygians as model organisms. Here we review recent studies using lungfishes and coelacanths that shed light on various aspects of the evolution of the tetrapod limb, including the origin of the tetrapod pelvis, limb musculature, digits, locomotion, and regenerative capacity.
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Affiliation(s)
- Danielson B Amaral
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01, Belém, 66075-900, Brazil
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01, Belém, 66075-900, Brazil
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Kherdjemil Y, Kmita M. Insights on the role of hox genes in the emergence of the pentadactyl ground state. Genesis 2017; 56. [DOI: 10.1002/dvg.23046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/19/2017] [Accepted: 06/22/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Yacine Kherdjemil
- Laboratory of Genetics and Development; Institut de Recherches Cliniques de Montréal (IRCM); 110 avenue des Pins Ouest, Montréal, QC H2W1R7 Canada
- Département de Médecine (Programme de Biologie Moléculaire); Université de Montréal; Montréal QC H3T 1J4 Canada
| | - Marie Kmita
- Laboratory of Genetics and Development; Institut de Recherches Cliniques de Montréal (IRCM); 110 avenue des Pins Ouest, Montréal, QC H2W1R7 Canada
- Département de Médecine (Programme de Biologie Moléculaire); Université de Montréal; Montréal QC H3T 1J4 Canada
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Divergent Hox Coding and Evasion of Retinoid Signaling Specifies Motor Neurons Innervating Digit Muscles. Neuron 2017; 93:792-805.e4. [PMID: 28190640 DOI: 10.1016/j.neuron.2017.01.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 01/20/2017] [Indexed: 11/21/2022]
Abstract
The establishment of spinal motor neuron subclass diversity is achieved through developmental programs that are aligned with the organization of muscle targets in the limb. The evolutionary emergence of digits represents a specialized adaptation of limb morphology, yet it remains unclear how the specification of digit-innervating motor neuron subtypes parallels the elaboration of digits. We show that digit-innervating motor neurons can be defined by selective gene markers and distinguished from other LMC neurons by the expression of a variant Hox gene repertoire and by the failure to express a key enzyme involved in retinoic acid synthesis. This divergent developmental program is sufficient to induce the specification of digit-innervating motor neurons, emphasizing the specialized status of digit control in the evolution of skilled motor behaviors. Our findings suggest that the emergence of digits in the limb is matched by distinct mechanisms for specifying motor neurons that innervate digit muscles.
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Abstract
The limb is a commonly used model system for developmental biology. Given the need for precise control of complex signalling pathways to achieve proper patterning, the limb is also becoming a model system for gene regulation studies. Recent developments in genomic technologies have enabled the genome-wide identification of regulatory elements that control limb development, yielding insights into the determination of limb morphology and forelimb versus hindlimb identity. The modulation of regulatory interactions - for example, through the modification of regulatory sequences or chromatin architecture - can lead to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.
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Affiliation(s)
- Florence Petit
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,University of Lille, CHU Lille, EA 7364-RADEME, F-59000 Lille, France
| | - Karen E Sears
- School of Integrative Biology, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,Institute for Human Genetics, University of California San Francisco, California 94158, USA
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32
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Kherdjemil Y, Lalonde RL, Sheth R, Dumouchel A, de Martino G, Pineault KM, Wellik DM, Stadler HS, Akimenko MA, Kmita M. Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state. Nature 2016; 539:89-92. [PMID: 27706137 PMCID: PMC5558051 DOI: 10.1038/nature19813] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/26/2016] [Indexed: 11/08/2022]
Abstract
The fin-to-limb transition represents one of the major vertebrate morphological innovations associated with the transition from aquatic to terrestrial life and is an attractive model for gaining insights into the mechanisms of morphological diversity between species. One of the characteristic features of limbs is the presence of digits at their extremities. Although most tetrapods have limbs with five digits (pentadactyl limbs), palaeontological data indicate that digits emerged in lobed fins of early tetrapods, which were polydactylous. How the transition to pentadactyl limbs occurred remains unclear. Here we show that the mutually exclusive expression of the mouse genes Hoxa11 and Hoxa13, which were previously proposed to be involved in the origin of the tetrapod limb, is required for the pentadactyl state. We further demonstrate that the exclusion of Hoxa11 from the Hoxa13 domain relies on an enhancer that drives antisense transcription at the Hoxa11 locus after activation by HOXA13 and HOXD13. Finally, we show that the enhancer that drives antisense transcription of the mouse Hoxa11 gene is absent in zebrafish, which, together with the largely overlapping expression of hoxa11 and hoxa13 genes reported in fish, suggests that this enhancer emerged in the course of the fin-to-limb transition. On the basis of the polydactyly that we observed after expression of Hoxa11 in distal limbs, we propose that the evolution of Hoxa11 regulation contributed to the transition from polydactyl limbs in stem-group tetrapods to pentadactyl limbs in extant tetrapods.
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Affiliation(s)
- Yacine Kherdjemil
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Département de Médecine (Programme de Biologie Moléculaire), Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Robert L Lalonde
- Department of Biology and CAREG, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Rushikesh Sheth
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Annie Dumouchel
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Gemma de Martino
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Kyriel M Pineault
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan 48109-2200, USA
| | - Deneen M Wellik
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan 48109-2200, USA
| | | | - Marie-Andrée Akimenko
- Department of Biology and CAREG, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Département de Médecine (Programme de Biologie Moléculaire), Université de Montréal, Montréal, Québec H3T 1J4, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
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33
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Fröbisch NB. Teenage tetrapods. Nature 2016; 537:311-312. [DOI: 10.1038/nature19432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Digits and fin rays share common developmental histories. Nature 2016; 537:225-228. [PMID: 27533041 PMCID: PMC5161576 DOI: 10.1038/nature19322] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/20/2016] [Indexed: 12/14/2022]
Abstract
Understanding the evolutionary transformation of fish fins into tetrapod limbs is a fundamental problem in biology. The search for antecedents of tetrapod digits in fish has remained controversial because the distal skeletons of limbs and fins differ structurally, developmentally, and histologically. Moreover, comparisons of fins with limbs have been limited by a relative paucity of data on the cellular and molecular processes underlying the development of the fin skeleton. Here, we provide a functional analysis, using CRISPR/Cas9 and fate mapping, of 5' hox genes and enhancers in zebrafish that are indispensable for the development of the wrists and digits of tetrapods. We show that cells marked by the activity of an autopodial hoxa13 enhancer exclusively form elements of the fin fold, including the osteoblasts of the dermal rays. In hox13 knockout fish, we find that a marked reduction and loss of fin rays is associated with an increased number of endochondral distal radials. These discoveries reveal a cellular and genetic connection between the fin rays of fish and the digits of tetrapods and suggest that digits originated via the transition of distal cellular fates.
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35
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Reno PL, Kjosness KM, Hines JE. The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:303-21. [DOI: 10.1002/jez.b.22688] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/13/2016] [Accepted: 06/28/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Philip L. Reno
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
| | - Kelsey M. Kjosness
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
| | - Jasmine E. Hines
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
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36
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Marcellini S, González F, Sarrazin AF, Pabón-Mora N, Benítez M, Piñeyro-Nelson A, Rezende GL, Maldonado E, Schneider PN, Grizante MB, Da Fonseca RN, Vergara-Silva F, Suaza-Gaviria V, Zumajo-Cardona C, Zattara EE, Casasa S, Suárez-Baron H, Brown FD. Evolutionary Developmental Biology (Evo-Devo) Research in Latin America. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:5-40. [PMID: 27491339 DOI: 10.1002/jez.b.22687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/29/2022]
Abstract
Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community.
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Affiliation(s)
- Sylvain Marcellini
- Laboratorio de Desarrollo y Evolución, Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Favio González
- Facultad de Ciencias, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Andres F Sarrazin
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Xochimilco, Ciudad de México, México
| | - Gustavo L Rezende
- Universidade Estadual do Norte Fluminense, CBB, LQFPP, Campos dos Goytacazes, RJ, Brazil
| | - Ernesto Maldonado
- EvoDevo Lab, Unidad de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, México
| | | | | | - Rodrigo Nunes Da Fonseca
- Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro, Macae, RJ, Brazil
| | | | | | | | | | - Sofia Casasa
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Federico D Brown
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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Miyake T, Kumamoto M, Iwata M, Sato R, Okabe M, Koie H, Kumai N, Fujii K, Matsuzaki K, Nakamura C, Yamauchi S, Yoshida K, Yoshimura K, Komoda A, Uyeno T, Abe Y. The pectoral fin muscles of the coelacanthLatimeria chalumnae: Functional and evolutionary implications for the fin-to-limb transition and subsequent evolution of tetrapods. Anat Rec (Hoboken) 2016; 299:1203-23. [DOI: 10.1002/ar.23392] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 05/25/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Tsutomu Miyake
- The Graduate School of Science and Technology; Keio University; Tokyo Japan
- Department of Anatomy; The Jikei University School of Medicine; Tokyo Japan
| | | | | | - Ryuichi Sato
- Institute of Biomechanical Control Systems; Kanazawa Institute of Technology; Hakusan Japan
| | - Masataka Okabe
- Department of Anatomy; The Jikei University School of Medicine; Tokyo Japan
| | - Hiroshi Koie
- Department of Veterinary Medicine; Nihon University; Fujisawa Japan
| | - Nori Kumai
- Research Center of Computational Mechanics (RCCM), Inc; Tokyo Japan
| | - Kenichi Fujii
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | - Koji Matsuzaki
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | - Chiho Nakamura
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | | | - Kosuke Yoshida
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | | | - Akira Komoda
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | - Teruya Uyeno
- National Museum of Nature and Science; Tokyo Japan
| | - Yoshitaka Abe
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
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38
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Kelley JL, Brown AP, Therkildsen NO, Foote AD. The life aquatic: advances in marine vertebrate genomics. Nat Rev Genet 2016; 17:523-34. [DOI: 10.1038/nrg.2016.66] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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39
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Lencer ES, Riccio ML, McCune AR. Changes in growth rates of oral jaw elements produce evolutionary novelty in bahamian pupfish. J Morphol 2016; 277:935-47. [DOI: 10.1002/jmor.20547] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 11/11/2022]
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40
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Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FEG, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 2016; 48:427-37. [PMID: 26950095 PMCID: PMC4817229 DOI: 10.1038/ng.3526] [Citation(s) in RCA: 402] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 02/12/2016] [Indexed: 12/16/2022]
Abstract
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Andrew R Gehrke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Jeremy Pasquier
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Aaron M Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S Campbell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Daniel Barrell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, UK
| | - John F Mulley
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Vydianathan Ravi
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Alison P Lee
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Tetsuya Nakamura
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Shaohua Fan
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dustin Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Cristian Cañestro
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Felix E G Beaudry
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Yi Sun
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Mikio Ishiyama
- Department of Dental Hygiene, Nippon Dental University College at Niigata, Niigata, Japan
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steffi Kehr
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Marcia Lara
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John H Letaw
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Ronda T Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Masato Mikami
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Niigata, Niigata, Japan
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Hayama, Japan
| | - Nil Ratan Saha
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Louise Williams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - John S Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Brazil
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
- International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | - Chris T Amemiya
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Yann Guiguen
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Julien Bobe
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Neil H Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | | | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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41
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Dediu D, Christiansen MH. Language Evolution: Constraints and Opportunities From Modern Genetics. Top Cogn Sci 2016; 8:361-70. [DOI: 10.1111/tops.12195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Dan Dediu
- Language and Genetics Department; Max Planck Institute for Psycholinguistics
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42
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HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution. Sci Rep 2016; 6:22720. [PMID: 26940624 PMCID: PMC4778128 DOI: 10.1038/srep22720] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 02/18/2016] [Indexed: 11/24/2022] Open
Abstract
The role of Homeobox transcription factors during fin and limb development have been the focus of recent work investigating the evolutionary origin of limb-specific morphologies. Here we characterize the expression of HoxD genes, as well as the cluster-associated genes Evx2 and LNP, in the paddlefish Polyodon spathula, a basal ray-finned fish. Our results demonstrate a collinear pattern of nesting in early fin buds that includes HoxD14, a gene previously thought to be isolated from global Hox regulation. We also show that in both Polyodon and the catshark Scyliorhinus canicula (a representative chondrichthyan) late phase HoxD transcripts are present in cells of the fin-fold and co-localize with And1, a component of the dermal skeleton. These new data support an ancestral role for HoxD genes in patterning the fin-folds of jawed vertebrates, and fuel new hypotheses about the evolution of cluster regulation and the potential downstream differentiation outcomes of distinct HoxD-regulated compartments.
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43
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HoxA Genes and the Fin-to-Limb Transition in Vertebrates. J Dev Biol 2016; 4:jdb4010010. [PMID: 29615578 PMCID: PMC5831813 DOI: 10.3390/jdb4010010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/27/2016] [Accepted: 02/04/2016] [Indexed: 12/12/2022] Open
Abstract
HoxA genes encode for important DNA-binding transcription factors that act during limb development, regulating primarily gene expression and, consequently, morphogenesis and skeletal differentiation. Within these genes, HoxA11 and HoxA13 were proposed to have played an essential role in the enigmatic evolutionary transition from fish fins to tetrapod limbs. Indeed, comparative gene expression analyses led to the suggestion that changes in their regulation might have been essential for the diversification of vertebrates' appendages. In this review, we highlight three potential modifications in the regulation and function of these genes that may have boosted appendage evolution: (1) the expansion of polyalanine repeats in the HoxA11 and HoxA13 proteins; (2) the origin of +a novel long-non-coding RNA with a possible inhibitory function on HoxA11; and (3) the acquisition of cis-regulatory elements modulating 5' HoxA transcription. We discuss the relevance of these mechanisms for appendage diversification reviewing the current state of the art and performing additional comparative analyses to characterize, in a phylogenetic framework, HoxA11 and HoxA13 expression, alanine composition within the encoded proteins, long-non-coding RNAs and cis-regulatory elements.
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44
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Gehrke AR, Shubin NH. Cis-regulatory programs in the development and evolution of vertebrate paired appendages. Semin Cell Dev Biol 2016; 57:31-39. [PMID: 26783722 DOI: 10.1016/j.semcdb.2016.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/07/2016] [Accepted: 01/11/2016] [Indexed: 02/02/2023]
Abstract
Differential gene expression is the core of development, mediating the genetic changes necessary for determining cell identity. The regulation of gene activity by cis-acting elements (e.g., enhancers) is a crucial mechanism for determining differential gene activity by precise control of gene expression in embryonic space and time. Modifications to regulatory regions can have profound impacts on phenotype, and therefore developmental and evolutionary biologists have increasingly focused on elucidating the transcriptional control of genes that build and pattern body plans. Here, we trace the evolutionary history of transcriptional control of three loci key to vertebrate appendage development (Fgf8, Shh, and HoxD/A). Within and across these regulatory modules, we find both complex and flexible regulation in contrast with more fixed enhancers that appear unchanged over vast timescales of vertebrate evolution. The transcriptional control of vertebrate appendage development was likely already incredibly complex in the common ancestor of fish, implying that subtle changes to regulatory networks were more likely responsible for alterations in phenotype rather than the de novo addition of whole regulatory domains. Finally, we discuss the dangers of relying on inter-species transgenesis when testing enhancer function, and call for more controlled regulatory swap experiments when inferring the evolutionary history of enhancer elements.
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Affiliation(s)
- Andrew R Gehrke
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA.
| | - Neil H Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA.
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Abstract
Novel body structures are often generated by the redeployment of ancestral components of the genome. In this issue of Developmental Cell, Glassford et al. (2015) present a thorough analysis of the co-option of a gene regulatory network in the origin of an evolutionary novelty.
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Affiliation(s)
- Ella Preger-Ben Noon
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Nicolás Frankel
- Departamento de Ecología, Genética y Evolución, IEGEBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires 1428, Argentina.
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46
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Zuniga A. Next generation limb development and evolution: old questions, new perspectives. Development 2015; 142:3810-20. [DOI: 10.1242/dev.125757] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The molecular analysis of limb bud development in vertebrates continues to fuel our understanding of the gene regulatory networks that orchestrate the patterning, proliferation and differentiation of embryonic progenitor cells. In recent years, systems biology approaches have moved our understanding of the molecular control of limb organogenesis to the next level by incorporating next generation ‘omics’ approaches, analyses of chromatin architecture, enhancer-promoter interactions and gene network simulations based on quantitative datasets into experimental analyses. This Review focuses on the insights these studies have given into the gene regulatory networks that govern limb development and into the fin-to-limb transition and digit reductions that occurred during the evolutionary diversification of tetrapod limbs.
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Affiliation(s)
- Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
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47
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Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AWD, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evol Dev 2015; 17:198-219. [PMID: 25963198 DOI: 10.1111/ede.12125] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.
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Affiliation(s)
- Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Karen E Sears
- School of Integrative Biology and Institute for Genomic Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Pamela Diggle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main St. West Hamilton, Ontario, L8S 4K1, Canada
| | - Cristina Ledon-Rettig
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, 412 Life Sciences Building, Stony Brook, NY, 11794-5215, USA
| | - Siegfried Roth
- University of Cologne, Institute of Developmental Biology, Biocenter, Zülpicher Straße 47b, D-50674, Cologne, Germany
| | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal Québec, H3A 1B1, Canada
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, no. 101, 05508-090, São Paulo, Brazil
| | - Chi-Hua Chiu
- Department of Biological Sciences, Kent State University, OH, USA
| | - C Sarah Cohen
- Biology Department, Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | | | - Scott F Gilbert
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA and Biotechnology Institute, University of Helsinki, 00014, Helsinki, Finland
| | - Brian Hall
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CA, B3H 4R2, USA
| | - Alan C Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, USA
| | - Deirdre C Lyons
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Thomas J Sanger
- Department of Molecular Genetics and Microbiology, University of Florida, P.O. Box 103610, Gainesville, FL, 32610, USA
| | - Joel Smith
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Chelsea Specht
- Plant and Microbial Biology, Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, Scotland, UK
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BioLabs 4103, Cambridge, MA, 02138, USA
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48
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The future of the fossil record: Paleontology in the 21st century. Proc Natl Acad Sci U S A 2015; 112:4852-8. [PMID: 25901304 DOI: 10.1073/pnas.1505146112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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49
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Organogenesis in deep time: A problem in genomics, development, and paleontology. Proc Natl Acad Sci U S A 2015; 112:4871-6. [PMID: 25901307 DOI: 10.1073/pnas.1403665112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The fossil record is a unique repository of information on major morphological transitions. Increasingly, developmental, embryological, and functional genomic approaches have also conspired to reveal evolutionary trajectory of phenotypic shifts. Here, we use the vertebrate appendage to demonstrate how these disciplines can mutually reinforce each other to facilitate the generation and testing of hypotheses of morphological evolution. We discuss classical theories on the origins of paired fins, recent data on regulatory modulations of fish fins and tetrapod limbs, and case studies exploring the mechanisms of digit loss in tetrapods. We envision an era of research in which the deep history of morphological evolution can be revealed by integrating fossils of transitional forms with direct experimentation in the laboratory via genome manipulation, thereby shedding light on the relationship between genes, developmental processes, and the evolving phenotype.
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50
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Nödl MT, Fossati SM, Domingues P, Sánchez FJ, Zullo L. The making of an octopus arm. EvoDevo 2015; 6:19. [PMID: 26052417 PMCID: PMC4458049 DOI: 10.1186/s13227-015-0012-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/13/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Most of our current findings on appendage formation and patterning stem from studies on chordate and ecdysozoan model organisms. However, in order to fully understand the evolution of animal appendages, it is essential to include information on appendage development from lophotrochozoan representatives. Here, we examined the basic dynamics of the Octopus vulgaris arm's formation and differentiation - as a highly evolved member of the lophotrochozoan super phylum - with a special focus on the formation of the arm's musculature. RESULTS The octopus arm forms during distinct phases, including an early outgrowth from an epithelial thickening, an elongation, and a late differentiation into mature tissue types. During early arm outgrowth, uniform proliferation leads to the formation of a rounded bulge, which subsequently elongates along its proximal-distal axis by means of actin-mediated epithelial cell changes. Further differentiation of all tissue layers is initiated but end-differentiation is postponed to post-hatching stages. Interestingly, muscle differentiation shows temporal differences in the formation of distinct muscle layers. Particularly, first myocytes appear in the area of the future transverse prior to the longitudinal muscle layer, even though the latter represents the more dominant muscle type at hatching stage. Sucker rudiments appear as small epithelial outgrowths with a mesodermal and ectodermal component on the oral part of the arm. During late differentiation stages, cell proliferation becomes localized to a distal arm region termed the growth zone of the arm. CONCLUSIONS O. vulgaris arm formation shows both, similarities to known model species as well as species-specific patterns of arm formation. Similarities include early uniform cell proliferation and actin-mediated cell dynamics, which lead to an elongation along the proximal-distal axis. Furthermore, the switch to an adult-like progressive distal growth mode during late differentiation stages is reminiscent of the vertebrate progress zone. However, tissue differentiation shows a species-specific delay, which is correlated to a paralarval pelagic phase after hatching and concomitant emerging behavioral modifications. By understanding the general dynamics of octopus arm formation, we established a basis for further studies on appendage patterning, growth, and differentiation in a representative of the lophotrochozoan super phylum.
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Affiliation(s)
- Marie-Therese Nödl
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Sara M Fossati
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Pedro Domingues
- Centro Oceanografico de Vigo, Instituto Español de Oceanografia, Subida Radio Faro, 50 36390 Vigo, Spain
| | - Francisco J Sánchez
- Centro Oceanografico de Vigo, Instituto Español de Oceanografia, Subida Radio Faro, 50 36390 Vigo, Spain
| | - Letizia Zullo
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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