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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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2
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Dhawan SS, Yedavalli V, Massoud TF. Atavistic and vestigial anatomical structures in the head, neck, and spine: an overview. Anat Sci Int 2023:10.1007/s12565-022-00701-7. [PMID: 36680662 DOI: 10.1007/s12565-022-00701-7] [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: 08/07/2022] [Accepted: 12/27/2022] [Indexed: 01/22/2023]
Abstract
Organisms may retain nonfunctional anatomical features as a consequence of evolutionary natural selection. Resultant atavistic and vestigial anatomical structures have long been a source of perplexity. Atavism is when an ancestral trait reappears after loss through an evolutionary change in previous generations, whereas vestigial structures are remnants that are largely or entirely functionless relative to their original roles. While physicians are cognizant of their existence, atavistic and vestigial structures are rarely emphasized in anatomical curricula and can, therefore, be puzzling when discovered incidentally. In addition, the literature is replete with examples of the terms atavistic and vestigial being used interchangeably without careful distinction between them. We provide an overview of important atavistic and vestigial structures in the head, neck, and spine that can serve as a reference for anatomists and clinical neuroscientists. We review the literature on atavistic and vestigial anatomical structures of the head, neck, and spine that may be encountered in clinical practice. We define atavistic and vestigial structures and employ these definitions consistently when classifying anatomical structures. Pertinent anatomical structures are numerous and include human tails, plica semilunaris, the vomeronasal organ, levator claviculae, and external ear muscles, to name a few. Atavistic and vestigial structures are found throughout the head, neck, and spine. Some, such as human tails and branchial cysts may be clinically symptomatic. Literature reports indicate that their prevalence varies across populations. Knowledge of atavistic and vestigial anatomical structures can inform diagnoses, prevent misrecognition of variation for pathology, and guide clinical interventions.
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Affiliation(s)
- Siddhant Suri Dhawan
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, USA
| | - Vivek Yedavalli
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Tarik F Massoud
- Division of Neuroimaging and Neurointervention, and Stanford Initiative for Multimodality Neuro-Imaging in Translational Anatomy Research (SIMITAR), Department of Radiology, Stanford University School of Medicine, Stanford, USA. .,Center for Academic Medicine, Radiology MC: 5659; 453 Quarry Road, Palo Alto, CA, 94304, USA.
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3
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Nojiri T, Werneburg I, Tu VT, Fukui D, Takechi M, Iseki S, Furutera T, Koyabu D. Timing of organogenesis underscores the evolution of neonatal life histories and powered flight in bats. Proc Biol Sci 2023; 290:20221928. [PMID: 36629110 PMCID: PMC9832570 DOI: 10.1098/rspb.2022.1928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
Bats have undergone one of the most drastic limb innovations in vertebrate history, associated with the evolution of powered flight. Knowledge of the genetic basis of limb organogenesis in bats has increased but little has been documented regarding the differences between limb organogenesis in bats and that of other vertebrates. We conducted embryological comparisons of the timelines of limb organogenesis in 24 bat species and 72 non-bat amniotes. In bats, the time invested for forelimb organogenesis has been considerably extended and the appearance timing of the forelimb ridge has been significantly accelerated, whereas the timing of the finger and first appearance of the claw development has been delayed, facilitating the enlargement of the manus. Furthermore, we discovered that bats initiate the development of their hindlimbs earlier than their forelimbs compared with other placentals. Bat neonates are known to be able to cling continuously with their well-developed foot to the maternal bodies or habitat substrates soon after birth. We suggest that this unique life history of neonates, which possibly coevolved with powered flight, has driven the accelerated development of the hindlimb and precocious foot.
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Affiliation(s)
- Taro Nojiri
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Graduate School of Environmental Science, Hokkaido University, North 11, West 10, Sapporo 060-0811, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Ingmar Werneburg
- Senckenberg Centre for Human Evolution and Palaeoenvironment an der Eberhard Karls Universität, Sigwartstraße 10, D-72076 Tübingen, Germany
- Fachbereich Geowissenschaften, Eberhard Karls Universität, Hölderlinstraße 12, 72074 Tübingen, Germany
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet road, Cau Giay district, Hanoi, Vietnam
- Vietnam Academy of Science and Technology, Graduate University of Science and Technology, No. 18, Hoang Quac Viet road, Cau Giay district, Hanoi, Vietnam
| | - Dai Fukui
- The University of Tokyo Hokkaido Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 9-61, Yamabe-Higashimachi, Furano, Hokkaido 079-1563, Japan
| | - Masaki Takechi
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Sachiko Iseki
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Toshiko Furutera
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Daisuke Koyabu
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
- Research and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba-shi, Ibaraki 305-8550, Japan
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4
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Lewis ZR, Kerney R, Hanken J. Developmental basis of evolutionary lung loss in plethodontid salamanders. SCIENCE ADVANCES 2022; 8:eabo6108. [PMID: 35977024 PMCID: PMC9385146 DOI: 10.1126/sciadv.abo6108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
One or more members of four living amphibian clades have independently dispensed with pulmonary respiration and lack lungs, but little is known of the developmental basis of lung loss in any taxon. We use morphological, molecular, and experimental approaches to examine the Plethodontidae, a dominant family of salamanders, all of which are lungless as adults. We confirm an early anecdotal report that plethodontids complete early stages of lung morphogenesis: Transient embryonic lung primordia form but regress by apoptosis before hatching. Initiation of pulmonary development coincides with expression of the lung-specification gene Wnt2b in adjacent mesoderm, and the lung rudiment expresses pulmonary markers Nkx2.1 and Sox9. Lung developmental-genetic pathways are at least partially conserved despite the absence of functional adult lungs for at least 25 and possibly exceeding 60 million years. Adult lung loss appears associated with altered expression of signaling molecules that mediate later stages of tracheal and pulmonary development.
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Affiliation(s)
- Zachary R. Lewis
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Ryan Kerney
- Department of Biology, Gettysburg College, Gettysburg, PA, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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5
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Snake-like limb loss in a Carboniferous amniote. Nat Ecol Evol 2022; 6:614-621. [PMID: 35347258 DOI: 10.1038/s41559-022-01698-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 02/08/2022] [Indexed: 02/08/2023]
Abstract
Among living tetrapods, many lineages have converged on a snake-like body plan, where extreme axial elongation is accompanied by reduction or loss of paired limbs. However, when and how this adaptive body plan first evolved in amniotes remains poorly understood. Here, we provide insights into this question by reporting on a new taxon of molgophid recumbirostran, Nagini mazonense gen. et sp. nov., from the Francis Creek Shale (309-307 million years ago) of Illinois, United States, that exhibits extreme axial elongation and corresponding limb reduction. The molgophid lacks entirely the forelimb and pectoral girdle, thus representing the earliest occurrence of complete loss of a limb in a taxon recovered phylogenetically within amniotes. This forelimb-first limb reduction is consistent with the pattern of limb reduction that is seen in modern snakes and contrasts with the hindlimb-first reduction process found in many other tetrapod groups. Our findings suggest that a snake-like limb-reduction mechanism may be operating more broadly across the amniote tree.
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6
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Pence CH. Whatever happened to reversion? STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2022; 92:97-108. [PMID: 35158173 DOI: 10.1016/j.shpsa.2022.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/14/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
The idea of 'reversion' or 'atavism' has a peculiar history. For many authors in the late-nineteenth and early-twentieth centuries - including Darwin, Galton, Pearson, Weismann, and Spencer, among others - reversion was one of the central phenomena which a theory of heredity ought to explain. By only a few decades later, however, Fisher and others could look back upon reversion as a historical curiosity, a non-problem, or even an impediment to clear theorizing. I explore various reasons that reversion might have appeared to be a central problem for this first group of figures, focusing on their commitment to a variety of conceptual features of evolutionary theory; discuss why reversion might have then ceased to be an interesting phenomenon; and, finally, close with some more general thoughts about the death of scientific problems.
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Affiliation(s)
- Charles H Pence
- Université catholique de Louvain, Institut supérieur de philosophie, Place du Cardinal Mercier 14, bte. L3.06.01, 1348, Louvain-la-Neuve, Belgium.
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7
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Abouheif E. My road to the ants: A model clade for eco-evo-devo. Curr Top Dev Biol 2022; 147:231-290. [PMID: 35337451 DOI: 10.1016/bs.ctdb.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This chapter is the story of how I pioneered ants as a system for studying eco-evo-devo, a field that integrates developmental biology with ecology and evolutionary biology. One aim of eco-evo-devo is to understand how the interactions between genes and their environments during development facilitates the origin and evolution of novel phenotypes. In a series of six parts, I review some of the key discoveries from my lab on how novel worker caste systems in ants--soldiers and supersoldiers--originated and evolved. I also discuss some of the ideas that emerged from these discoveries, including the role that polyphenisms, hidden developmental potentials, and rudimentary organs play in facilitating developmental and evolutionary change. As superorganisms, I argue that ants are uniquely positioned to reveal types of variation that are often difficult to observe in nature. In doing so, they have the potential to transform our view of biology and provide new perspectives in medicine, agriculture, and biodiversity conservation. With my story I hope to inspire the next generation of biologists to continue exploring the unknown regions of phenotypic space to solve some of our most pressing societal challenges.
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Affiliation(s)
- Ehab Abouheif
- Department of Biology, McGill University, Montreal, QC, Canada.
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8
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Randall JG, Gatesy J, Springer MS. Molecular Evolutionary Analyses of Tooth Genes Support Sequential Loss of Enamel and Teeth in Baleen Whales (Mysticeti). Mol Phylogenet Evol 2022; 171:107463. [DOI: 10.1016/j.ympev.2022.107463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/16/2021] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
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9
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Liang N, Deme L, Kong Q, Sun L, Cao Y, Wu T, Huang X, Xu S, Yang G. Divergence of Tbx4 hindlimb enhancer HLEA underlies the hindlimb loss during cetacean evolution. Genomics 2022; 114:110292. [DOI: 10.1016/j.ygeno.2022.110292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/13/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
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10
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Swank S, Sanger TJ, Stuart YE. (Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss. Ecol Evol 2021; 11:15484-15497. [PMID: 34824770 PMCID: PMC8601893 DOI: 10.1002/ece3.8226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/31/2021] [Accepted: 09/21/2021] [Indexed: 01/16/2023] Open
Abstract
Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.
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Affiliation(s)
- Samantha Swank
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Thomas J. Sanger
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Yoel E. Stuart
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
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11
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Camaiti M, Evans AR, Hipsley CA, Chapple DG. A farewell to arms and legs: a review of limb reduction in squamates. Biol Rev Camb Philos Soc 2021; 96:1035-1050. [PMID: 33538028 DOI: 10.1111/brv.12690] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 01/02/2023]
Abstract
Elongated snake-like bodies associated with limb reduction have evolved multiple times throughout vertebrate history. Limb-reduced squamates (lizards and snakes) account for the vast majority of these morphological transformations, and thus have great potential for revealing macroevolutionary transitions and modes of body-shape transformation. Here we present a comprehensive review on limb reduction, in which we examine and discuss research on these dramatic morphological transitions. Historically, there have been several approaches to the study of squamate limb reduction: (i) definitions of general anatomical principles of snake-like body shapes, expressed as varying relationships between body parts and morphometric measurements; (ii) framing of limb reduction from an evolutionary perspective using morphological comparisons; (iii) defining developmental mechanisms involved in the ontogeny of limb-reduced forms, and their genetic basis; (iv) reconstructions of the evolutionary history of limb-reduced lineages using phylogenetic comparative methods; (v) studies of functional and biomechanical aspects of limb-reduced body shapes; and (vi) studies of ecological and biogeographical correlates of limb reduction. For each of these approaches, we highlight their importance in advancing our understanding, as well as their weaknesses and limitations. Lastly, we provide suggestions to stimulate further studies, in which we underscore the necessity of widening the scope of analyses, and of bringing together different perspectives in order to understand better these morphological transitions and their evolution. In particular, we emphasise the importance of investigating and comparing the internal morphology of limb-reduced lizards in contrast to external morphology, which will be the first step in gaining a deeper insight into body-shape variation.
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Affiliation(s)
- Marco Camaiti
- School of Biological Sciences, Monash University, 19 Rainforest Walk, Clayton, VIC, 3800, Australia
| | - Alistair R Evans
- School of Biological Sciences, Monash University, 19 Rainforest Walk, Clayton, VIC, 3800, Australia
| | - Christy A Hipsley
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Department of Sciences, Museums Victoria, 11 Nicholson St, Carlton, Melbourne, VIC, 3053, Australia
| | - David G Chapple
- School of Biological Sciences, Monash University, 19 Rainforest Walk, Clayton, VIC, 3800, Australia
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12
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Uesaka M, Kuratani S, Irie N. The developmental hourglass model and recapitulation: An attempt to integrate the two models. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 338:76-86. [PMID: 33503326 PMCID: PMC9292893 DOI: 10.1002/jez.b.23027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Recapitulation is a hypothetical concept that assumes embryogenesis of an animal parallels its own phylogenetic history, sequentially developing from more ancestral features to more derived ones. This concept predicts that the earliest developmental stage of various animals should represent the most evolutionarily conserved patterns. Recent transcriptome‐based studies, on the other hand, have reported that mid‐embryonic, organogenetic periods show the highest level of conservation (the developmental hourglass model). This, however, does not rule out the possibility that recapitulation would still be detected after the mid‐embryonic period. In accordance with this, recapitulation‐like morphological features are enriched in late developmental stages. Moreover, our recent chromatin accessibility‐based study provided molecular evidence for recapitulation in the mid‐to‐late embryogenesis of vertebrates, as newly evolved gene regulatory elements tended to be activated at late embryonic stages. In this review, we revisit the recapitulation hypothesis, together with recent molecular‐based studies that support the developmental hourglass model. We contend that the recapitulation hypothesis does not entirely contradict the developmental hourglass model and that these two may even coexist in later embryonic stages of vertebrates. Finally, we review possible mechanisms underlying the recapitulation pattern of chromatin accessibility together with the hourglass‐like evolutionary conservation in vertebrate embryogenesis. Recapitulation pattern has been reported for chromatin accessibility during the mid‐to‐late embryogenesis. The observed recapitulation pattern and the developmental hourglass model may coexist. The possible evolutionary mechanisms underlying tendencies of embryonic evolution were discussed.
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Affiliation(s)
- Masahiro Uesaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Laboratory for Evolutionary Morphology, RIKEN Cluster for Pioneering Research, Kobe, Japan
| | - Naoki Irie
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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13
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Bergmann PJ, Morinaga G, Freitas ES, Irschick DJ, Wagner GP, Siler CD. Locomotion and palaeoclimate explain the re-evolution of quadrupedal body form in Brachymeles lizards. Proc Biol Sci 2020; 287:20201994. [PMID: 33171093 DOI: 10.1098/rspb.2020.1994] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Evolutionary reversals, including re-evolution of lost structures, are commonly found in phylogenetic studies. However, we lack an understanding of how these reversals happen mechanistically. A snake-like body form has evolved many times in vertebrates, and occasionally a quadrupedal form has re-evolved, including in Brachymeles lizards. We use body form and locomotion data for species ranging from snake-like to quadrupedal to address how a quadrupedal form could re-evolve. We show that large, quadrupedal species are faster at burying and surface locomotion than snake-like species, indicating a lack of expected performance trade-off between these modes of locomotion. Species with limbs use them while burying, suggesting that limbs are useful for burying in wet, packed substrates. Palaeoclimatological data suggest that Brachymeles originally evolved a snake-like form under a drier climate probably with looser soil in which it was easier to dig. The quadrupedal clade evolved as the climate became humid, where limbs and large size facilitated fossorial locomotion in packed soils.
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Affiliation(s)
- Philip J Bergmann
- Department of Biology, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Gen Morinaga
- Department of Biology, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Elyse S Freitas
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 2401 Chautauqua Ave., Norman, OK 73072, USA
| | - Duncan J Irschick
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Cameron D Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 2401 Chautauqua Ave., Norman, OK 73072, USA
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14
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Stynoski JL, Womack MC, Trama FA, Coloma LA, Hoke KL. Whispers from vestigial nubbins: Arrested development provokes trait loss in toads. Evol Dev 2020; 23:5-18. [PMID: 33107688 DOI: 10.1111/ede.12356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/29/2022]
Abstract
Despite the use of acoustic communication, many species of toads (family Bufonidae) have lost parts of the tympanic middle ear, representing at least 12 independent evolutionary occurrences of trait loss. The comparative development of the tympanic middle ear in toads is poorly understood. Here, we compared middle ear development among two pairs of closely related toad species in the genera Atelopus and Rhinella that have (eared) or lack (earless) middle ear structures. We bred toads in Peru and Ecuador, preserved developmental series from tadpoles to juveniles, and examined ontogenetic timing and volume of the otic capsule, oval window, operculum, opercularis muscle, columella (stapes), and extracolumella in three-dimensional histological reconstructions. All species had similar ontogenesis of the otic capsule, oval window, operculum, and opercularis muscle. Moreover, cell clusters of primordial columella in the oval window appeared just before metamorphosis in both eared and earless lineages. However, in earless lineages, the cell clusters either remained as small nubbins or cell buds in the location of the columella footplate within the oval window or disappeared by juvenile and adult stages. Thus, columella growth began around metamorphosis in all species but was truncated and/or degenerated after metamorphosis in earless species, leaving earless adults with morphology typical of metamorphic anurans. Shifts in the timing or expression of biochemical pathways that regulate the extension or differentiation of the columella after metamorphosis may be the developmental mechanism underlying convergent trait loss among toad lineages.
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Affiliation(s)
- Jennifer L Stynoski
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA.,Instituto Clodomiro Picado, Universidad de Costa Rica, Coronado, Costa Rica
| | - Molly C Womack
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Florencia A Trama
- Grupo de Investigación en Entomología y Medio Ambiente, Universidad San Ignacio de Loyola, Lima, Peru.,Centro de Capacitación en Conservación y Desarrollo Sostenible (CDS/CNEH-Perú), Oxapampa, Peru
| | - Luis A Coloma
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, Quito, Ecuador
| | - Kim L Hoke
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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15
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Cooper LN, Ball HC, Vinyard CJ, Safadi FF, George JC, Thewissen JGM. Linking gene expression and phenotypic changes in the developmental and evolutionary origins of osteosclerosis in the ribs of bowhead whales (Balaena mysticetus). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:339-349. [PMID: 32729176 DOI: 10.1002/jez.b.22990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 12/22/2022]
Abstract
Bowhead whales are among the longest-lived mammals with an extreme lifespan of about 211 years. During the first 25 years of their lives, rib bones increase in mineral density and the medulla transitions from compact to trabecular bone. Molecular drivers associated with these phenotypic changes in bone remain unknown. This study assessed expression levels of osteogenic genes from samples of rib bones of bowheads. Samples were harvested from prenatal to 86-year-old whales, representing the first third of the bowhead lifespan. Fetal to 2-year-old bowheads showed expression levels consistent with the rapid deposition of the bone extracellular matrix. Sexually mature animals showed expression levels associated with low rates of osteogenesis and increased osteoclastogenesis. After the first 25 years of life, declines in osteogenesis corresponded with increased expression of EZH2, an epigenetic regulator of osteogenesis. These findings suggest EZH2 may be at least one epigenetic modifier that contributes to the age-related changes in the rib bone phenotype along with the transition from compact to trabecular bone. Ancient cetaceans and their fossil relatives also display these phenotypes, suggesting EZH2 may have shaped the skeleton of whales in evolutionary history.
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Affiliation(s)
- Lisa N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA.,Department of Anatomy and Neurobiology, Musculoskeletal Research Group, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Hope C Ball
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA.,Department of Anatomy and Neurobiology, Musculoskeletal Research Group, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Christopher J Vinyard
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA.,Department of Anatomy and Neurobiology, Musculoskeletal Research Group, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Fayez F Safadi
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA.,Department of Anatomy and Neurobiology, Musculoskeletal Research Group, Northeast Ohio Medical University, Rootstown, Ohio, USA.,Department of Orthopedics, Rebecca D. Considine Research Institute, Akron Children's Hospital, Akron, Ohio, USA
| | - John C George
- Department of Wildlife Management, The North Slope Borough, Utqiagvik, Alaska, USA
| | - Johannes G M Thewissen
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA.,Department of Anatomy and Neurobiology, Musculoskeletal Research Group, Northeast Ohio Medical University, Rootstown, Ohio, USA
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16
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Bergmann PJ, Mann SDW, Morinaga G, Freitas ES, Siler CD. Convergent Evolution of Elongate Forms in Craniates and of Locomotion in Elongate Squamate Reptiles. Integr Comp Biol 2020; 60:190-201. [DOI: 10.1093/icb/icaa015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Synopsis Elongate, snake- or eel-like, body forms have evolved convergently many times in most major lineages of vertebrates. Despite studies of various clades with elongate species, we still lack an understanding of their evolutionary dynamics and distribution on the vertebrate tree of life. We also do not know whether this convergence in body form coincides with convergence at other biological levels. Here, we present the first craniate-wide analysis of how many times elongate body forms have evolved, as well as rates of its evolution and reversion to a non-elongate form. We then focus on five convergently elongate squamate species and test if they converged in vertebral number and shape, as well as their locomotor performance and kinematics. We compared each elongate species to closely related quadrupedal species and determined whether the direction of vertebral or locomotor change matched in each case. The five lineages examined are obscure species from remote locations, providing a valuable glimpse into their biology. They are the skink lizards Brachymeles lukbani, Lerista praepedita, and Isopachys anguinoides, the basal squamate Dibamus novaeguineae, and the basal snake Malayotyphlops cf. ruficaudus. Our results support convergence among these species in the number of trunk and caudal vertebrae, but not vertebral shape. We also find that the elongate species are relatively slower than their limbed counterparts and move with lower frequency and higher amplitude body undulations, with the exception of Isopachys. This is among the first evidence of locomotor convergence across distantly related, elongate species.
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Affiliation(s)
| | - Sara D W Mann
- Department of Biology, Clark University, Worcester, MA, USA
| | - Gen Morinaga
- Department of Biology, Clark University, Worcester, MA, USA
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Elyse S Freitas
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK, USA
| | - Cameron D Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK, USA
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17
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Accelerated Evolution of Limb-Related Gene Hoxd11 in the Common Ancestor of Cetaceans and Ruminants (Cetruminantia). G3-GENES GENOMES GENETICS 2020; 10:515-524. [PMID: 31792005 PMCID: PMC7003097 DOI: 10.1534/g3.119.400512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Reduced numbers of carpal and tarsal bones (wrist and ankle joints) are extensively observed in the clade of Cetacea and Ruminantia (Cetruminantia). Homebox D11 (Hoxd11) is one of the important genes required for limb development in mammals. Mutations in Hoxd11 can lead to defects in particular bones of limbs, including carpus and tarsus. To test whether evolutionary changes in Hoxd11 underlie the loss of these bones in Cetruminantia, we sequenced and analyzed Hoxd11 coding sequences and compared them with other 5′ HoxA and HoxD genes in a taxonomic coverage of Cetacea, Ruminantia and other mammalian relatives. Statistical tests on the Hoxd11 sequences found an accelerated evolution in the common ancestor of cetaceans and ruminants, which coincided with the reduction of carpal and tarsal bones in this clade. Five amino acid substitutions (G222S, G227A, G229S, A240T and G261V) and one amino acid deletion (G254Del) occurred in this lineage. In contrast, other 5′ HoxA and HoxD genes do not show this same evolutionary pattern, but instead display a highly conserved pattern of evolution in this lineage. Accelerated evolution of Hoxd11, but not other 5′ HoxA and HoxD genes, is probably related to the reduction of the carpal and tarsal bones in Cetruminantia. Moreover, we found two amino acid substitutions (G110S and D223N) in Hoxd11 that are unique to the lineage of Cetacea, which coincided with hindlimb loss in the common ancestor of cetaceans. Our results give molecular evidence of Hoxd11 adaptive evolution in cetaceans and ruminants, which could be correlated with limb morphological adaptation.
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18
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Paparella I, LeBlanc ARH, Doschak MR, Caldwell MW. The iliosacral joint in lizards: an osteological and histological analysis. J Anat 2020; 236:668-687. [PMID: 31903561 DOI: 10.1111/joa.13132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2019] [Indexed: 01/13/2023] Open
Abstract
The development of the iliosacral joint (ISJ) in tetrapods represented a crucial step in the evolution of terrestrial locomotion. This structure is responsible for transferring forces between the vertebral column and appendicular skeleton, thus supporting the bodyweight on land. However, most research dealing with the water-to-land transition and biomechanical studies in general has focused exclusively on the articulation between the pelvic girdle and femur. Our knowledge about the contact between the pelvic girdle and vertebral column (i.e. the ISJ) at a tissue level is restricted so far to human anatomy, with little to no information available on other tetrapods. This lack of data limits our understanding of the development and evolution of such a key structure, and thus on the pattern and processes of the evolution of terrestrial locomotion. Therefore, we investigated the macro- and microanatomy of the ISJ in limb-bearing squamates that, similar to most non-mammalian, non-avian tetrapods, possess only two sacral ribs articulating with the posterior process of the ilium. Using a combination of osteology, micro-computed tomography and histology, we collected data on the ISJ apparatus of numerous specimens, sampling different taxa and different ontogenetic stages. Osteologically, we recorded consistent variability in all three processes of the ilium (preacetabular, supracetabular and posterior) and sacral ribs that correlate with posture and locomotion. The presence of a cavity between the ilium and sacral ribs, abundant articular cartilage and fibrocartilage, and a surrounding membrane of dense fibrous connective tissue allowed us to define this contact as a synovial joint. By comparison, the two sacral ribs are connected to each other mostly by dense fibrous tissue, with some cartilage found more distally along the margins of the two ribs, defining this joint as a combination of a syndesmosis and synchondrosis. Considering the intermediary position of the ISJ between the axial and appendicular skeletons, the shape of the articular surfaces of the sacral ribs and ilium, and the characteristics of the muscles associated with this structure, we argue that the mobility of the ISJ is primarily driven by the movements of the hindlimb during locomotion. We hypothesize that limited torsion of the ilium at the ISJ happens when the hip is abducted, and the joint is likely able to absorb the compressional and extensional forces related to the protraction and retraction of the femur. The mix of fibres and cartilage between the two sacral ribs instead serves primarily as a shock absorber, with the potential for limited vertical translation during locomotion.
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Affiliation(s)
- Ilaria Paparella
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aaron R H LeBlanc
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Michael R Doschak
- Faculty of Pharmacy & Pharmaceutical Sciences and Department of Biomedical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Michael W Caldwell
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
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19
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Pallandre JP, Cornette R, Placide MA, Pelle E, Lavenne F, Abad V, Ribaud M, Bels VL. Iliac auricular surface morphofunctional study in felidae. ZOOLOGY 2019; 138:125714. [PMID: 31756647 DOI: 10.1016/j.zool.2019.125714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/19/2022]
Abstract
Felids show remarkable phenotypic similarities and are conservative in behavioral and ecological traits. In contrast, they display a large range in body mass from around 1kg to more than 300kg. Body size and locomotory specializations correlate to skull, limb and vertebral skeleton morphology. With an increase in body mass, felids prey selection switches from small to large, from using a rapid skull or spine lethal bite for small prey, to sustained suffocating bite for large prey. Dietary specialization correlates to skull and front limbs morphology but no correlation was found on the spine or on the hind limb. The morphology of the sacroiliac junction in relation to ecological factors remained to be described. We are presenting a study of the overall shape of the iliac auricular surface with qualitative and quantitative analyses of its morphology. Our results demonstrate that body mass, prey selection, and bite type, crucially influence the auricular surface, where no significant effect of locomotor specialization was found. The outline of the surface is significantly more elevated dorso-caudally and the joint surface shows an irregular W-shape topography in big cats whereas the surface in small cats is smoother with a C-shape topography and less of an elevated ridge. Biomechanically, we suggest that a complex auricular surface increases joint stiffness and provides more support in heavier cats, an advantage for subduing big prey successfully during a sustained bite.
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Affiliation(s)
- Jean-Pierre Pallandre
- Sorbonne Université, Muséum national d'Histoire naturelle, Institut de Systématique Evolution Biodiversité (UMR 7205 MNHN/CNRNS/UPMC/EPHE), 57 Rue Cuvier, 75005, Paris, France.
| | - Raphaël Cornette
- Sorbonne Université, Muséum national d'Histoire naturelle, Institut de Systématique Evolution Biodiversité (UMR 7205 MNHN/CNRNS/UPMC/EPHE), 57 Rue Cuvier, 75005, Paris, France
| | - Marie-Ange Placide
- Sorbonne Université, Muséum national d'Histoire naturelle, Institut de Systématique Evolution Biodiversité (UMR 7205 MNHN/CNRNS/UPMC/EPHE), 57 Rue Cuvier, 75005, Paris, France
| | - Eric Pelle
- Sorbonne Université, Muséum national d'Histoire naturelle, Direction Générale des collections, 57 Rue Cuvier, 75005, Paris, France
| | - Franck Lavenne
- Centre d'Etude et de Recherche Multimodale Et Pluridisciplinaire en imagerie du vivant (CNRS, INSB), 16-18 avenue Doyen Lépine, 69500, Bron, France
| | - Vincent Abad
- R & D, Manufacture des pneumatiques Michelin, 23 place des Carmes Dechaux, 63040, Clermont-Ferrand, France
| | - Mélina Ribaud
- Université Lyon, Ecole Centrale de Lyon, Institut Camille Jordan, 36 avenue Guy de Collonge, 69134, Ecully, France
| | - Vincent L Bels
- Sorbonne Université, Muséum national d'Histoire naturelle, Institut de Systématique Evolution Biodiversité (UMR 7205 MNHN/CNRNS/UPMC/EPHE), 57 Rue Cuvier, 75005, Paris, France
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20
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Flap-Footed Lizards (Gekkota: Pygopodidae) Have Forelimbs, Albeit During Embryonic Development. J HERPETOL 2019. [DOI: 10.1670/19-002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Macaluso L, Carnevale G, Casu R, Pietrocola D, Villa A, Delfino M. Structural and environmental constraints on reduction of paired appendages among vertebrates. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractBurrowing habits or complex environments have generally been considered as potential drivers acting on reduction and loss of the appendicular skeleton among vertebrates. Herein, we suggest that this might be the case for lissamphibians and squamates, but that fin loss in fishes is usually prevented by important structural constraints, because pectoral fins are commonly used to control rolling and pitching. We provide an overview of the distribution of paired appendage reduction across vertebrates while examining the ecological affinities of finless and limbless clades. We analysed the correlation between lifestyle and fin or limb loss using the discrete comparative analysis. The resulting Bayesian factors indicate strong evidence of correlation between: (1) pectoral-fin loss and coexistence of anguilliform elongation and burrowing habits or complex habitat in teleost fishes; and (2) limb loss and a burrowing or grass-swimming lifestyle in squamate reptiles and lissamphibians. These correlations suggest that a complex environment or a fossorial habit is a driving force leading to appendage loss. The only style of locomotion that is functional even in the absence of paired appendages is the undulatory one, which is typical of all elongated reptiles and lissamphibians, but certainly less common in teleost fishes.
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Affiliation(s)
- Loredana Macaluso
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Raffaello Casu
- Dipartimento di Fisica, Università degli Studi di Torino, Via Pietro Giuria, Torino, Italy
| | - Daniel Pietrocola
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Andrea Villa
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße, München, Germany
| | - Massimo Delfino
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici Z (ICTA-ICP), Carrer de les Columnes s/n, Campus de la UAB, Cerdanyola del Valles, Barcelona, Spain
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22
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Lammers M, Kraaijeveld K, Mariën J, Ellers J. Gene expression changes associated with the evolutionary loss of a metabolic trait: lack of lipogenesis in parasitoids. BMC Genomics 2019; 20:309. [PMID: 31014246 PMCID: PMC6480896 DOI: 10.1186/s12864-019-5673-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/08/2019] [Indexed: 12/24/2022] Open
Abstract
Background Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these cases involve loss-of-function mutations in one or more trait-specific genes. However, in parasitoid insects the evolutionary loss of a metabolic trait is not associated with gene decay. Parasitoids have lost the ability to convert dietary sugars into fatty acids. Earlier research suggests that lack of lipogenesis in the parasitoid wasp Nasonia vitripennis is caused by changes in gene regulation. Results We compared transcriptomic responses to sugar-feeding in the non-lipogenic parasitoid species Nasonia vitripennis and the lipogenic Drosophila melanogaster. Both species adjusted their metabolism within 4 hours after sugar-feeding, but there were sharp differences between the expression profiles of the two species, especially in the carbohydrate and lipid metabolic pathways. Several genes coding for key enzymes in acetyl-CoA metabolism, such as malonyl-CoA decarboxylase (mcd) and HMG-CoA synthase (hmgs) differed in expression between the two species. Their combined action likely blocks lipogenesis in the parasitoid species. Network-based analysis showed connectivity of genes to be negatively correlated to the fold change of gene expression. Furthermore, genes involved in the fatty acid metabolic pathway were more connected than the set of genes of all metabolic pathways combined. Conclusion High connectivity of lipogenesis genes is indicative of pleiotropic effects and could explain the absence of gene degradation. We conclude that modification of expression levels of only a few little-connected genes, such as mcd, is sufficient to enable complete loss of lipogenesis in N. vitripennis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5673-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark Lammers
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Ken Kraaijeveld
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Janine Mariën
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Jacintha Ellers
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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23
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Roston RA, Roth VL. Cetacean Skull Telescoping Brings Evolution of Cranial Sutures into Focus. Anat Rec (Hoboken) 2019; 302:1055-1073. [DOI: 10.1002/ar.24079] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 10/12/2018] [Accepted: 10/21/2018] [Indexed: 01/09/2023]
Affiliation(s)
| | - V. Louise Roth
- Department of Biology; Duke University; Durham North Carolina
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24
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Westphal N, Mahlow K, Head JJ, Müller J. Pectoral myology of limb-reduced worm lizards (Squamata, Amphisbaenia) suggests decoupling of the musculoskeletal system during the evolution of body elongation. BMC Evol Biol 2019; 19:16. [PMID: 30630409 PMCID: PMC6329177 DOI: 10.1186/s12862-018-1303-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 11/20/2018] [Indexed: 01/10/2023] Open
Abstract
Background The evolution of elongated body forms in tetrapods has a strong influence on the musculoskeletal system, including the reduction of pelvic and pectoral girdles, as well as the limbs. However, despite extensive research in this area it still remains unknown how muscles within and around bony girdles are affected by these reductions. Here we investigate this issue using fossorial amphisbaenian reptiles, or worm lizards, as a model system, which show substantial variation in the degree of reductions of girdles and limbs. Using iodine-based contrast-enhanced computed tomography (diceCT), we analyze the composition of the shoulder muscles of the main clades of Amphisbaenia and their outgroups relative to the pectoral skeleton. Results All investigated amphisbaenian taxa retain the full set of 17 shoulder muscles, independent of the degree of limb and girdle reductions, whereas in some cases muscles are fused to complexes or changed in morphology relative to the ancestral condition. Bipes is the only taxon that retains forelimbs and an almost complete pectoral girdle. All other amphisbaenian families show more variation concerning the completeness of the pectoral girdle having reduced or absent girdle elements. Rhineura, which undergoes the most severe bone reductions, differs from all other taxa in possessing elongated muscle strands instead of discrete shoulder muscles. In all investigated amphisbaenians, the shoulder muscle agglomerate is shortened and shifted anteriorly relative to the ancestral position as seen in the outgroups. Conclusions Our results show that pectoral muscle anatomy does not necessarily correspond to the loss or reduction of bones, indicating a decoupling of the musculoskeletal system. Muscle attachment sites change from bones to non-skeletal areas, such as surrounding muscles, skin or connective tissue, whereas muscle origins themselves remain in the same region where the pectoral bones were ancestrally located. Our findings indicate a high degree of developmental autonomy within the musculoskeletal system, we predict that the observed evolutionary rearrangements of amphisbaenian shoulder muscles were driven by functional demands rather than by developmental constraints. Nevertheless, worm lizards display a spatial offset of both pectoral bones and muscles relative to the ancestral position, indicating severe developmental modifications of the amphisbaenian body axis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1303-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natascha Westphal
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstr. 43, 10115, Berlin, Germany.
| | - Kristin Mahlow
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstr. 43, 10115, Berlin, Germany
| | - Jason James Head
- Department of Zoology and University Museum of Zoology, University of Cambridge, Downing St, Cambridge, CB2 3EJ, UK
| | - Johannes Müller
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstr. 43, 10115, Berlin, Germany
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25
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Uesaka M, Kuratani S, Takeda H, Irie N. Recapitulation-like developmental transitions of chromatin accessibility in vertebrates. ZOOLOGICAL LETTERS 2019; 5:33. [PMID: 31807314 PMCID: PMC6857340 DOI: 10.1186/s40851-019-0148-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/06/2019] [Indexed: 05/09/2023]
Abstract
The relationship between development and evolution has been a central theme in evolutionary developmental biology. Across the vertebrates, the most highly conserved gene expression profiles are found at mid-embryonic, organogenesis stages, whereas those at earlier and later stages are more diverged. This hourglass-like pattern of divergence does not necessarily rule out the possibility that gene expression profiles that are more evolutionarily derived appear at later stages of development; however, no molecular-level evidence of such a phenomenon has been reported. To address this issue, we compared putative gene regulatory elements among different species within a phylum. We made a genome-wide assessment of accessible chromatin regions throughout embryogenesis in three vertebrate species (mouse, chicken, and medaka) and estimated the evolutionary ages of these regions to define their evolutionary origins on the phylogenetic tree. In all the three species, we found that genomic regions tend to become accessible in an order that parallels their phylogenetic history, with evolutionarily newer gene regulations activated at later developmental stages. This tendency was restricted only after the mid-embryonic, phylotypic periods. Our results imply a phylogenetic hierarchy of putative regulatory regions, in which their activation parallels the phylogenetic order of their appearance. One evolutionary mechanism that may explain this phenomenon is that newly introduced regulatory elements are more likely to survive if activated at later stages of embryogenesis. Possible relationships between this phenomenon and the so-called recapitulation are discussed.
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Affiliation(s)
- Masahiro Uesaka
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Naoki Irie
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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26
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Bergmann PJ, Morinaga G. The convergent evolution of snake‐like forms by divergent evolutionary pathways in squamate reptiles*. Evolution 2018; 73:481-496. [DOI: 10.1111/evo.13651] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/08/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Philip J. Bergmann
- Department of Biology Clark University 950 Main Street Worcester Massachusetts 01610
| | - Gen Morinaga
- Department of Biology Clark University 950 Main Street Worcester Massachusetts 01610
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27
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Galis F, Metz JA, van Alphen JJ. Development and Evolutionary Constraints in Animals. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062339] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We review the evolutionary importance of developmental mechanisms in constraining evolutionary changes in animals—in other words, developmental constraints. We focus on hard constraints that can act on macroevolutionary timescales. In particular, we discuss the causes and evolutionary consequences of the ancient metazoan constraint that differentiated cells cannot divide and constraints against changes of phylotypic stages in vertebrates and other higher taxa. We conclude that in all cases these constraints are caused by complex and highly controlled global interactivity of development, the disturbance of which has grave consequences. Mutations that affect such global interactivity almost unavoidably have many deleterious pleiotropic effects, which will be strongly selected against and will lead to long-term evolutionary stasis. The discussed developmental constraints have pervasive consequences for evolution and critically restrict regeneration capacity and body plan evolution.
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Affiliation(s)
- Frietson Galis
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Johan A.J. Metz
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
- International Institute for Applied Systems Analysis, A-2361 Laxenburg, Austria
- Mathematical Institute, University of Leiden; 2333 CA Leiden, The Netherlands
| | - Jacques J.M. van Alphen
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
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Espinasa L, Robinson J, Espinasa M. Mc1r gene in Astroblepus pholeter and Astyanax mexicanus: Convergent regressive evolution of pigmentation across cavefish species. Dev Biol 2018; 441:305-310. [DOI: 10.1016/j.ydbio.2018.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 12/28/2022]
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Espinasa L, Robinson J, Soares D, Hoese G, Toulkeridis T, Toomey III R. Troglomorphic features of Astroblepus pholeter, a cavefish from Ecuador, and possible introgressive hybridization. SUBTERRANEAN BIOLOGY 2018. [DOI: 10.3897/subtbiol.27.27098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cave organisms are often characterized by reduced pigmentation, eyesight, and enhanced mechanosensory functions. The stygobitic catfish Astroblepuspholeter is found within some subterranean drainages in Ecuador. The species was first described in 1962 with specimens that were all highly depigmented and troglomorphic. The next observations in the field occurred until 2011, 2015 and 2018. At such dates, specimens examined progressively displayed more surface-like appearance. Appendages in these individuals were progressively shorter and pigmentation levels are now as high as some surface Astroblepus. Based on sampled specimens, it would appear that since 1962, the population has been progressively composed of less troglomorphic individuals. One possibility is that the population has undergone introgressive hybridization in recent years as surface Astroblepus are known to enter the caves and cohabitate with the troglomorphic Astroblepus. Lastly, we report that Individuals are able to detect and respond to light. Histological analyses show that A.pholeter’s eyes have all of the major ocular structures (lens, optic nerve, and all retinal layers).
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Emerling CA, Widjaja AD, Nguyen NN, Springer MS. Their loss is our gain: regressive evolution in vertebrates provides genomic models for uncovering human disease loci. J Med Genet 2017; 54:787-794. [PMID: 28814606 DOI: 10.1136/jmedgenet-2017-104837] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/07/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022]
Abstract
Throughout Earth's history, evolution's numerous natural 'experiments' have resulted in a diverse range of phenotypes. Though de novo phenotypes receive widespread attention, degeneration of traits inherited from an ancestor is a very common, yet frequently neglected, evolutionary path. The latter phenomenon, known as regressive evolution, often results in vertebrates with phenotypes that mimic inherited disease states in humans. Regressive evolution of anatomical and/or physiological traits is typically accompanied by inactivating mutations underlying these traits, which frequently occur at loci identical to those implicated in human diseases. Here we discuss the potential utility of examining the genomes of vertebrates that have experienced regressive evolution to inform human medical genetics. This approach is low cost and high throughput, giving it the potential to rapidly improve knowledge of disease genetics. We discuss two well-described examples, rod monochromacy (congenital achromatopsia) and amelogenesis imperfecta, to demonstrate the utility of this approach, and then suggest methods to equip non-experts with the ability to corroborate candidate genes and uncover new disease loci.
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Affiliation(s)
- Christopher A Emerling
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Biology, University of California, Riverside, California, USA
| | - Andrew D Widjaja
- Department of Biochemistry, University of California, Riverside, California, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA
| | - Nancy N Nguyen
- Department of Bioengineering, University of California, Riverside, California, USA
- Department of Bioengineering, University of California, Los Angeles, California, USA
| | - Mark S Springer
- Department of Biology, University of California, Riverside, California, USA
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Cooper LN, Sears KE, Armfield BA, Kala B, Hubler M, Thewissen JGM. Review and experimental evaluation of the embryonic development and evolutionary history of flipper development and hyperphalangy in dolphins (Cetacea: Mammalia). Genesis 2017; 56. [DOI: 10.1002/dvg.23076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 09/27/2017] [Accepted: 09/29/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Lisa Noelle Cooper
- Department of Anatomy and NeurobiologyNEOMEDRootstown OH44272‐0095
- Department of Anatomy and NeurobiologyMusculoskeletal Biology Research Group at NEOMEDRootstown OH44272‐0095
| | - Karen E. Sears
- Department of Animal BiologyUniversity of IllinoisUrbana IL61801
- University of Illinois, Institute for Genomic BiologyUrbana IL61801
| | - Brooke A. Armfield
- Molecular Genetics and MicrobiologyUniversity of FloridaGainesville FL32610
| | - Bhavneet Kala
- Department of Anatomy and NeurobiologyNEOMEDRootstown OH44272‐0095
| | - Merla Hubler
- Department of Animal BiologyUniversity of IllinoisUrbana IL61801
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Buchholtz EA, Gee JK. Finding sacral: Developmental evolution of the axial skeleton of odontocetes (Cetacea). Evol Dev 2017; 19:190-204. [PMID: 28726248 DOI: 10.1111/ede.12227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emily A. Buchholtz
- Department of Biological Sciences; Wellesley College; Wellesley Massachusetts
| | - Jessica K. Gee
- Department of Biological Sciences; Wellesley College; Wellesley Massachusetts
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Stanley SG, Liniewski RM, Senter PJ. Appendicular skeleton of the vestigial-limbed African skinkEumecia anchietae. AFR J HERPETOL 2016. [DOI: 10.1080/21564574.2016.1258012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shane G. Stanley
- Department of Biology, Fayetteville Technical Community College, PO Box 35236, 2201 Hull Road, Fayetteville, North Carolina 28303, USA
| | - Rachel M. Liniewski
- Department of Biological Sciences, Fayetteville State University, 1200 Murchison Road, Fayetteville, North Carolina 28301, USA
| | - Philip J. Senter
- Department of Biological Sciences, Fayetteville State University, 1200 Murchison Road, Fayetteville, North Carolina 28301, USA
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Espinasa L, Collins E, Finocchiaro A, Kopp J, Robinson J, Rutkowski J. Incipient regressive evolution of the circadian rhythms of a cave amphipod. SUBTERRANEAN BIOLOGY 2016. [DOI: 10.3897/subtbiol.20.10010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Loch C, van Vuuren LJ. Ultrastructure, biomechanical and chemical properties of the vestigial dentition of a Cuvier's beaked whale. NEW ZEALAND JOURNAL OF ZOOLOGY 2016. [DOI: 10.1080/03014223.2015.1133666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- C Loch
- Collections, Research and Education, Otago Museum, Dunedin, New Zealand
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - L Jansen van Vuuren
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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Selection on different genes with equivalent functions: the convergence story told by Hox genes along the evolution of aquatic mammalian lineages. BMC Evol Biol 2016; 16:113. [PMID: 27209096 PMCID: PMC4875654 DOI: 10.1186/s12862-016-0682-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/10/2016] [Indexed: 11/24/2022] Open
Abstract
Background Convergent evolution has been a challenging topic for decades, being cetaceans, pinnipeds and sirenians textbook examples of three independent origins of equivalent phenotypes. These mammalian lineages acquired similar anatomical features correlated to an aquatic life, and remarkably differ from their terrestrial counterparts. Whether their molecular evolutionary history also involved similar genetic mechanisms underlying such morphological convergence nevertheless remained unknown. To test for the existence of convergent molecular signatures, we studied the molecular evolution of Hox genes in these three aquatic mammalian lineages, comparing their patterns to terrestrial mammals. Hox genes are transcription factors that play a pivotal role in specifying embryonic regional identity of nearly any bilateral animal, and are recognized major agents for diversification of body plans. Results We detected few signatures of positive selection on Hox genes across the three aquatic mammalian lineages and verified that purifying selection prevails in these sequences, as expected for pleiotropic genes. Genes found as being positively selected differ across the aquatic mammalian lineages, but we identified a substantial overlap of their developmental functions. Such pattern likely resides on the duplication history of Hox genes, which probably provided different possible evolutionary routes for achieving the same phenotypic solution. Conclusions Our results indicate that convergence occurred at a functional level of Hox genes along three independent origins of aquatic mammals. This conclusion reinforces the idea that different changes in developmental genes may lead to similar phenotypes, probably due to the redundancy provided by the participation of Hox paralogous genes in several developmental functions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0682-4) contains supplementary material, which is available to authorized users.
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Liniewski R, Stanley S, Andrade J, Senter P. Vestigial appendicular skeletons in the African and Malagasy skink speciesFeylinia grandisquamis,Melanoseps ater,Grandidierina lineataandVoeltzkowia mira. AFR J HERPETOL 2016. [DOI: 10.1080/21564574.2015.1133722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Senter P, Moch JG. A critical survey of vestigial structures in the postcranial skeletons of extant mammals. PeerJ 2015; 3:e1439. [PMID: 26623192 PMCID: PMC4662599 DOI: 10.7717/peerj.1439] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/04/2015] [Indexed: 11/20/2022] Open
Abstract
In the Mammalia, vestigial skeletal structures abound but have not previously been the focus of study, with a few exceptions (e.g., whale pelves). Here we use a phylogenetic bracketing approach to identify vestigial structures in mammalian postcranial skeletons and present a descriptive survey of such structures in the Mammalia. We also correct previous misidentifications, including the previous misidentification of vestigial caviid metatarsals as sesamoids. We also examine the phylogenetic distribution of vestigiality and loss. This distribution indicates multiple vestigialization and loss events in mammalian skeletal structures, especially in the hand and foot, and reveals no correlation in such events between mammalian fore and hind limbs.
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Affiliation(s)
- Phil Senter
- Department of Biological Sciences, Fayetteville State University, Fayetteville, NC, United States
| | - John G. Moch
- Department of Chemistry and Physics, Fayetteville State University, Fayetteville, NC, United States
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Adaptive simplification and the evolution of gecko locomotion: morphological and biomechanical consequences of losing adhesion. Proc Natl Acad Sci U S A 2014; 112:809-14. [PMID: 25548182 DOI: 10.1073/pnas.1418979112] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Innovations permit the diversification of lineages, but they may also impose functional constraints on behaviors such as locomotion. Thus, it is not surprising that secondary simplification of novel locomotory traits has occurred several times among vertebrates and could potentially lead to exceptional divergence when constraints are relaxed. For example, the gecko adhesive system is a remarkable innovation that permits locomotion on surfaces unavailable to other animals, but has been lost or simplified in species that have reverted to a terrestrial lifestyle. We examined the functional and morphological consequences of this adaptive simplification in the Pachydactylus radiation of geckos, which exhibits multiple unambiguous losses or bouts of simplification of the adhesive system. We found that the rates of morphological and 3D locomotor kinematic evolution are elevated in those species that have simplified or lost adhesive capabilities. This finding suggests that the constraints associated with adhesion have been circumvented, permitting these species to either run faster or burrow. The association between a terrestrial lifestyle and the loss/reduction of adhesion suggests a direct link between morphology, biomechanics, and ecology.
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Ivanović A, Arntzen JW. Evolution of skull and body shape inTriturusnewts reconstructed from three-dimensional morphometric data and phylogeny. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12314] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ana Ivanović
- Faculty of Biology; Institute for Zoology; University of Belgrade; Studentski trg 16 11000 Belgrade Serbia
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden The Netherlands
| | - Jan W. Arntzen
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden The Netherlands
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41
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Bard J. Generating anatomical variation through mutations in networks - implications for evolution. J Anat 2014; 225:123-31. [PMID: 24934180 DOI: 10.1111/joa.12205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2014] [Indexed: 12/01/2022] Open
Abstract
Genetic mutation leads to anatomical variation only indirectly because many proteins involved in generating anatomical structures in embryos operate cooperatively within molecular networks. These include gene-regulatory or control networks (CNs) for timing, signaling and patterning together with the process networks (PNs) for proliferation, apoptosis, differentiation and morphogenesis that they control. This paper argues that anatomical variation is achieved through a two-stage process: mutation alters the outputs of CNs and perhaps the proliferation network, and such changed outputs alter the ways that PNs construct tissues. This systems-biology approach has several implications: first, because networks contain many cooperating proteins, they amplify the effects of genetic variation so enabling mutation to generate a wider range of phenotypes than a single changed protein acting alone could. Second, this amplification helps explain how novel phenotypes can be produced relatively rapidly. Third, because even organisms with novel anatomical phenotypes derive from variants in standard networks, there is no genetic barrier to their producing viable offspring. This approach also clarifies a terminological difficulty: classical evolutionary genetics views genes in terms of phenotype heritability rather than as DNA sequences. This paper suggests that the molecular phenotype of the classical concept of a gene is often a protein network, with a mutation leading to an alteration in that network's dynamics.
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Affiliation(s)
- Jonathan Bard
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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42
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Bridgham JT, Keay J, Ortlund EA, Thornton JW. Vestigialization of an allosteric switch: genetic and structural mechanisms for the evolution of constitutive activity in a steroid hormone receptor. PLoS Genet 2014; 10:e1004058. [PMID: 24415950 PMCID: PMC3886901 DOI: 10.1371/journal.pgen.1004058] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/08/2013] [Indexed: 11/30/2022] Open
Abstract
An important goal in molecular evolution is to understand the genetic and physical mechanisms by which protein functions evolve and, in turn, to characterize how a protein's physical architecture influences its evolution. Here we dissect the mechanisms for an evolutionary shift in function in the mollusk ortholog of the steroid hormone receptors (SRs), a family of biologically essential transcription factors. In vertebrates, the activity of SRs allosterically depends on binding a hormonal ligand; in mollusks, however, the SR ortholog (called ER, because of high sequence similarity to vertebrate estrogen receptors) activates transcription in the absence of ligand and does not respond to steroid hormones. To understand how this shift in regulation evolved, we combined evolutionary, structural, and functional analyses. We first determined the X-ray crystal structure of the ER of the Pacific oyster Crassostrea gigas (CgER), and found that its ligand pocket is filled with bulky residues that prevent ligand occupancy. To understand the genetic basis for the evolution of mollusk ERs' unique functions, we resurrected an ancient SR progenitor and characterized the effect of historical amino acid replacements on its functions. We found that reintroducing just two ancient replacements from the lineage leading to mollusk ERs recapitulates the evolution of full constitutive activity and the loss of ligand activation. These substitutions stabilize interactions among key helices, causing the allosteric switch to become “stuck” in the active conformation and making activation independent of ligand binding. Subsequent changes filled the ligand pocket without further affecting activity; by degrading the allosteric switch, these substitutions vestigialized elements of the protein's architecture required for ligand regulation and made reversal to the ancestral function more complex. These findings show how the physical architecture of allostery enabled a few large-effect mutations to trigger a profound evolutionary change in the protein's function and shaped the genetics of evolutionary reversibility. An important goal in evolutionary genetics is to understand how genetic mutations cause the evolution of new protein functions and how a protein's structure shapes its evolution. Here we address these questions by studying a dramatic lineage-specific shift in function in steroid hormone receptors (SRs), a physiologically important family of transcription factors. In vertebrates, SRs bind hormones and then undergo a structural change that allows them to activate gene expression. In mollusks, SRs do not bind hormone and are always active. We identified the genetic and structural mechanisms for the evolution of constitutive activity in the mollusk SRs by using X-ray crystallography, ancestral sequence reconstruction, and experimental studies of the effects of ancient mutations on protein structure and function. We found that constitutive activity evolved due to just two historical substitutions that subtly stabilized elements of the active conformation, and subsequent mutations filled the hormone-binding cavity. The structural characteristics required for a hormone-sensitive activator were thus vestigialized, much the same way that a whale's hindlimbs became vestiges of their ancestral form after they became dispensable. Our findings show how the architecture of a protein can shape its evolution, allowing radically different functions to evolve by a few large-effect mutations.
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Affiliation(s)
- Jamie T. Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - June Keay
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Eric A. Ortlund
- Biochemistry Department, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Joseph W. Thornton
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Departments of Human Genetics and Ecology & Evolution, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Marigo J, Pinto NS, Simões-Lopes PC, Leonardo F, Azevedo AF, Lailson-Brito J. Case Report of Flipper Anatomic Anomaly of Sotalia guianensisFrom Sepetiba Bay, Rio de Janeiro. Anat Rec (Hoboken) 2013; 296:1016-8. [DOI: 10.1002/ar.22706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 03/26/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Juliana Marigo
- Laboratório de Mamíferos Aquáticos e Biodindicadores; Universidade do Estado do Rio de Janeiro (MAQUA-UERJ);; Projeto BioPesca, Praia Grande SP Brazil
| | - Nelson S. Pinto
- NSP Clínica Radiológica. Rua Jorge Rudge 15; 20550-220, Vila Isabel Rio de Janeiro Brazil
| | - Paulo C. Simões-Lopes
- Laboratório de Mamíferos Aquáticos (LAMAQ), Departamento de Ecologia e Zoologia; Universidade Federal de Santa Catarina (UFSC); Caixa Postal 5102, 88040-970 Florianópolis Santa Catarina Brazil
| | - Flach Leonardo
- Instituto Boto cinza. Rua Gastão de Carvalho Lote 2; Quadra 4, 23860-000, Itacuruçá, Mangaratiba, RJ,Brasil; Programa de Pós-graduação em Ecologia e Evolução (UERJ) Rio de Janeiro, RJ Brazil
| | - Alexandre F. Azevedo
- Laboratório de Mamíferos Aquáticos e Biodindicadores, Faculdade de Oceanografia; Universidade do Estado do Rio de Janeiro (MAQUA-UERJ); Rua São Francisco Xavier, 524 sala 4002E, 20550-013, Maracanã Rio de Janeiro, RJ Brazil
| | - José Lailson-Brito
- Laboratório de Mamíferos Aquáticos e Biodindicadores, Faculdade de Oceanografia; Universidade do Estado do Rio de Janeiro (MAQUA-UERJ); Rua São Francisco Xavier, 524 sala 4002E, 20550-013, Maracanã Rio de Janeiro, RJ Brazil
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Parés-Casanova PM. Evaluation of Obturator Foramen Suggests No Differences Between Sexes in Young Bovines. Anat Histol Embryol 2013; 42:138-43. [DOI: 10.1111/j.1439-0264.2012.01175.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. M. Parés-Casanova
- Department of Animal Production; University of Lleida; Av. Alcalde Rovira Roure, 191; E-25198; Lleida; Catalunya; Spain
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45
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Don EK, Currie PD, Cole NJ. The evolutionary history of the development of the pelvic fin/hindlimb. J Anat 2013; 222:114-33. [PMID: 22913749 PMCID: PMC3552419 DOI: 10.1111/j.1469-7580.2012.01557.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2012] [Indexed: 12/20/2022] Open
Abstract
The arms and legs of man are evolutionarily derived from the paired fins of primitive jawed fish. Few evolutionary changes have attracted as much attention as the origin of tetrapod limbs from the paired fins of ancestral fish. The hindlimbs of tetrapods are derived from the pelvic fins of ancestral fish. These evolutionary origins can be seen in the examination of shared gene and protein expression patterns during the development of pelvic fins and tetrapod hindlimbs. The pelvic fins of fish express key limb positioning, limb bud induction and limb outgrowth genes in a similar manner to that seen in hindlimb development of higher vertebrates. We are now at a point where many of the key players in the development of pelvic fins and vertebrate hindlimbs have been identified and we can now readily examine and compare mechanisms between species. This is yielding fascinating insights into how the developmental programme has altered during evolution and how that relates to anatomical change. The role of pelvic fins has also drastically changed over evolutionary history, from playing a minor role during swimming to developing into robust weight-bearing limbs. In addition, the pelvic fins/hindlimbs have been lost repeatedly in diverse species over evolutionary time. Here we review the evolution of pelvic fins and hindlimbs within the context of the changes in anatomical structure and the molecular mechanisms involved.
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Affiliation(s)
- Emily K Don
- Department of Anatomy & Histology, School of Medical Sciences and Bosch Institute, University of Sydney, Sydney, NSW, Australia
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46
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van der Velden YU, Wang L, van Lohuizen M, Haramis APG. The Polycomb group protein Ring1b is essential for pectoral fin development. Development 2012; 139:2210-20. [PMID: 22619390 DOI: 10.1242/dev.077156] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polycomb group (PcG) proteins are transcriptional repressors that mediate epigenetic gene silencing by chromatin modification. PcG-mediated gene repression is implicated in development, cell differentiation, stem-cell fate maintenance and cancer. However, analysis of the roles of PcG proteins in orchestrating vertebrate developmental programs in vivo has been hampered by the early embryonic lethality of several PcG gene knockouts in mice. Here, we demonstrate that zebrafish Ring1b, the E3 ligase in Polycomb Repressive Complex 1 (PRC1), is essential for pectoral fin development. We show that differentiation of lateral plate mesoderm (LPM) cells into presumptive pectoral fin precursors is initiated normally in ring1b mutants, but fin bud outgrowth is impaired. Fgf signaling, which is essential for migration, proliferation and cell-fate maintenance during fin development, is not sufficiently activated in ring1b mutants. Exogenous application of FGF4, as well as enhanced stimulation of Fgf signaling by overactivated Wnt signaling in apc mutants, partially restores the fin developmental program. These results reveal that, in the absence of functional Ring1b, fin bud cells fail to execute the pectoral fin developmental program. Together, our results demonstrate that PcG-mediated gene regulation is essential for sustained Fgf signaling in vertebrate limb development.
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Affiliation(s)
- Yme U van der Velden
- Department of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
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47
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Moch JG, Senter P. Vestigial structures in the appendicular skeletons of eight African skink species (Squamata, Scincidae). J Zool (1987) 2011. [DOI: 10.1111/j.1469-7998.2011.00839.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Sears KE. Novel insights into the regulation of limb development from ‘natural’ mammalian mutants. Bioessays 2011; 33:327-31. [DOI: 10.1002/bies.201100005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Holocephalan embryos provide evidence for gill arch appendage reduction and opercular evolution in cartilaginous fishes. Proc Natl Acad Sci U S A 2011; 108:1507-12. [PMID: 21220324 DOI: 10.1073/pnas.1012968108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chondrichthyans possess endoskeletal appendages called branchial rays that extend laterally from their hyoid and gill-bearing (branchial) arches. Branchial ray outgrowth, like tetrapod limb outgrowth, is maintained by Sonic hedgehog (Shh) signaling. In limbs, distal endoskeletal elements fail to form in the absence of normal Shh signaling, whereas shortened duration of Shh expression correlates with distal endoskeletal reduction in naturally variable populations. Chondrichthyans also exhibit natural variation with respect to branchial ray distribution--elasmobranchs (sharks and batoids) possess a series of ray-supported septa on their hyoid and gill arches, whereas holocephalans (chimaeras) possess a single hyoid arch ray-supported operculum. Here we show that the elongate hyoid rays of the holocephalan Callorhinchus milii grow in association with sustained Shh expression within an opercular epithelial fold, whereas Shh is only transiently expressed in the gill arches. Coincident with this transient Shh expression, branchial ray outgrowth is initiated in C. milii but is not maintained, yielding previously unrecognized vestigial gill arch branchial rays. This is in contrast to the condition seen in sharks, where sustained Shh expression corresponds to the presence of fully formed branchial rays on the hyoid and gill arches. Considered in light of current hypotheses of chondrichthyan phylogeny, our data suggest that the holocephalan operculum evolved in concert with gill arch appendage reduction by attenuation of Shh-mediated branchial ray outgrowth, and that chondrichthyan branchial rays and tetrapod limbs exhibit parallel developmental mechanisms of evolutionary reduction.
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50
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Bickels J, Weinstein T, Robinson D, Nevo Z. Common skeletal growth retardation disorders resulting from abnormalities within the mesenchymal stem cells reservoirs in the epiphyseal organs pertaining to the long bones. J Pediatr Endocrinol Metab 2010; 23:1107-22. [PMID: 21284324 DOI: 10.1515/jpem.2010.176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Among the objectives in writing the current chapter were the curiosity and the interest in allocating the sites and routes of migration of the reservoirs of the mesenchymal precartilaginous stem cells of the developing limbs in health and in disease. We chose to emphasize the events believed to initiate in these regions of stem cells, which may lead to growth retardation disorders. Thus, this narrow niche touches an enlarged scope of developmental biology angles and fields. The enclosed coverage sheds light on part of the musculoskeletal system, skeletogenesis, organogenesis of mobile structures and organs, the limbs, joints and digits (arthrology). It appears that the key role of the cartilage-bone regions is their responsibility to replenish the physis with committed chondrocytes, during the developmental, maturation and puberty periods. We shall start by outlining the framework of normal limb formation, the modalities, signals and the agents participating in this biological creation and regulation, illustrating potential sites that might deviate from normal development during the growth periods.
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Affiliation(s)
- Jacob Bickels
- Dept. of Orthopedic-Oncology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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