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de Bakker MAG, van der Vos W, de Jager K, Chung WY, Fowler DA, Dondorp E, Spiekman SNF, Chew KY, Xie B, Jiménez R, Bickelmann C, Kuratani S, Blazek R, Kondrashov P, Renfree MB, Richardson MK. Selection on phalanx development in the evolution of the bird wing. Mol Biol Evol 2021; 38:4222-4237. [PMID: 34164688 PMCID: PMC8476175 DOI: 10.1093/molbev/msab150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 05/03/2021] [Indexed: 11/12/2022] Open
Abstract
The frameshift hypothesis is a widely-accepted model of bird wing evolution. This hypothesis postulates a shift in positional values, or molecular-developmental identity, that caused a change in digit phenotype. The hypothesis synthesised developmental and palaeontological data on wing digit homology. The 'most anterior digit' (MAD) hypothesis presents an alternative view based on changes in transcriptional regulation in the limb. The molecular evidence for both hypotheses is that the most anterior digit expresses Hoxd13 but not Hoxd11 and Hoxd12. This digit I 'signature' is thought to characterise all amniotes. Here, we studied Hoxd expression patterns in a phylogenetic sample of 18 amniotes. Instead of a conserved molecular signature in digit I, we find wide variation of Hoxd11, Hoxd12 and Hoxd13 expression in digit I. Patterns of apoptosis, and Sox9 expression, a marker of the phalanx-forming region, suggest that phalanges were lost from wing digit IV because of early arrest of the phalanx-forming region followed by cell death. Finally, we show that multiple amniote lineages lost phalanges with no frameshift. Our findings suggest that the bird wing evolved by targeted loss of phalanges under selection. Consistent with our view, some recent phylogenies based on dinosaur fossils eliminate the need to postulate a frameshift in the first place. We suggest that the phenotype of the Archaeopteryx lithographica wing is also consistent with phalanx loss. More broadly, our results support a gradualist model of evolution based on tinkering with developmental gene expression.
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Affiliation(s)
- Merijn A G de Bakker
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Wessel van der Vos
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72.,Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Kaylah de Jager
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Wing Yu Chung
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Donald A Fowler
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Esther Dondorp
- Naturalis Biodiversity Center, 2300 RA Leiden, PO Box 9517, The Netherlands
| | - Stephan N F Spiekman
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Keng Yih Chew
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Bing Xie
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Rafael Jiménez
- Departamento de Genética, Universidad de Granada, Lab 127 Centro de Investigación Biomédica, Avenida del Conocimiento S/N, 1810018016 Armilla, Granada, Spain
| | - Constanze Bickelmann
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,RIKEN Cluster for Pioneering Research, Kobe, Japan
| | - Radim Blazek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna, 603 65, Czech Republic 8, Brno
| | - Peter Kondrashov
- Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, 63501, MO USA)
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Michael K Richardson
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
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2
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Fowler DA, Larsson HCE. The tissues and regulatory pattern of limb chondrogenesis. Dev Biol 2020; 463:124-134. [PMID: 32417169 DOI: 10.1016/j.ydbio.2020.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022]
Abstract
Initial limb chondrogenesis offers the first differentiated tissues that resemble the mature skeletal anatomy. It is a developmental progression of three tissues. The limb begins with undifferentiated mesenchyme-1, some of which differentiates into condensations-2, and this tissue then transforms into cartilage-3. Each tissue is identified by physical characteristics of cell density, shape, and extracellular matrix composition. Tissue specific regimes of gene regulation underlie the diagnostic physical and chemical properties of these three tissues. These three tissue based regimes co-exist amid a background of other gene regulatory regimes within the same tissues and time-frame of limb development. The bio-molecular indicators of gene regulation reveal six identifiable patterns. Three of these patterns describe the unique bio-molecular indicators of each of the three tissues. A fourth pattern shares bio-molecular indicators between condensation and cartilage. Finally, a fifth pattern is composed of bio-molecular indicators that are found in undifferentiated mesenchyme prior to any condensation differentiation, then these bio-molecular indicators are upregulated in condensations and downregulated in undifferentiated mesenchyme. The undifferentiated mesenchyme that remains in between the condensations and cartilage, the interdigit, contains a unique set of bio-molecular indicators that exhibit dynamic behaviour during chondrogenesis and therefore argue for its own inclusion as a tissue in its own right and for more study into this process of differentiation.
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Affiliation(s)
- Donald A Fowler
- Redpath Museum, McGill University, 859 Sherbrooke St W, Montréal, QC, H3A 0C4, Canada; Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield, Montréal, QC, H3A 1B1, Canada.
| | - Hans C E Larsson
- Redpath Museum, McGill University, 859 Sherbrooke St W, Montréal, QC, H3A 0C4, Canada.
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3
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Stewart TA, Liang C, Cotney JL, Noonan JP, Sanger TJ, Wagner GP. Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings. Nat Commun 2019; 10:3244. [PMID: 31324809 PMCID: PMC6642197 DOI: 10.1038/s41467-019-11215-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/28/2019] [Indexed: 02/03/2023] Open
Abstract
In crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan. However, testing hypotheses of digit homology is challenging because it is unclear whether digits represent distinct and conserved gene regulatory states. Here we show dramatic evolutionary dynamism in the gene expression profiles of digits, challenging the notion that five digits have conserved developmental identities across amniotes. Transcriptomics shows diversity in the patterns of gene expression differentiation of digits, although the anterior-most digit of the pentadactyl limb has a unique, conserved expression profile. Further, we identify a core set of transcription factors that are differentially expressed among the digits of amniote limbs; their spatial expression domains, however, vary between species. In light of these results, we reevaluate the frame shift hypothesis of avian wing evolution and conclude only the identity of the anterior-most digit has shifted position, suggesting a 1,3,4 digit identity in the bird wing.
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Affiliation(s)
- Thomas A Stewart
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA. .,Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN, 55455, USA. .,Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, 60637, USA.
| | - Cong Liang
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA.,Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, 06030, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Thomas J Sanger
- Department of Biology, Loyola University in Chicago, Chicago, IL, 60660, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA. .,Systems Biology Institute, Yale University, West Haven, CT, 06516, USA.
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4
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Gold MEL, Norell MA, Budassi M, Vaska P, Schulz D. Rapid 18F-FDG Uptake in Brain of Awake, Behaving Rat and Anesthetized Chicken has Implications for Behavioral PET Studies in Species With High Metabolisms. Front Behav Neurosci 2018; 12:115. [PMID: 29922136 PMCID: PMC5996747 DOI: 10.3389/fnbeh.2018.00115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 05/18/2018] [Indexed: 11/30/2022] Open
Abstract
Brain-behavior studies using 18F-FDG PET aim to reveal brain regions that become active during behavior. In standard protocols, 18F-FDG is injected, the behavior is executed during 30–60 min of tracer uptake, and then the animal is anesthetized and scanned. Hence, the uptake of 18F-FDG is not itself observed and could, in fact, be complete in very little time. This has implications for behavioral studies because uptake is assumed to reflect concurrent behavior. Here, we utilized a new, miniature PET scanner termed RatCAP to measure uptake simultaneously with behavior. We employed a novel injection protocol in which we administered 18F-FDG (i.v.) four times over two 2 h to allow for repeated measurements and the correlation of changes in uptake and behavioral activity. Furthermore, using standard PET methods, we explored the effects of injection route on uptake time in chickens, a model for avians, for which PET studies are just beginning. We found that in the awake, behaving rat most of the 18F-FDG uptake occurred within minutes and overlapped to a large extent with 18F-FDG data taken from longer uptake periods. By contrast, behavior which occurred within minutes of the 18F-FDG infusion differed markedly from the behavior that occurred during later uptake periods. Accordingly, we found that changes in 18F-FDG uptake in the striatum, motor cortex and cerebellum relative to different reference regions significantly predicted changes in behavioral activity during the scan, if the time bins used for correlation were near the injection times of 18F-FDG. However, when morphine was also injected during the scan, which completely abolished behavioral activity for over 50 min, a large proportion of the variance in behavioral activity was also explained by the uptake data from the entire scan. In anesthetized chickens, tracer uptake was complete in about 80 min with s.c. injection, but 8 min with i.v. injection. In conclusion, uptake time needs to be taken into account to more accurately correlate PET and behavioral data in mammals and avians. Additionally, RatCAP together with multiple, successive injections of 18F-FDG may be useful to explore changes in uptake over time in relation to changes in behavior.
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Affiliation(s)
- Maria E L Gold
- Division of Paleontology, American Museum of Natural History, New York, NY, United States.,Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY, United States.,Department of Biology, Suffolk University, Boston, MA, United States
| | - Mark A Norell
- Division of Paleontology, American Museum of Natural History, New York, NY, United States
| | - Michael Budassi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, United States
| | - Paul Vaska
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, United States.,Department of Radiology, Stony Brook University, Stony Brook, NY, United States.,Biosciences Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Daniela Schulz
- Department of Psychology, Yeditepe University, Istanbul, Turkey
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5
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Kerney RR, Hanken J, Blackburn DC. Early limb patterning in the direct-developing salamander Plethodon cinereus revealed by sox9 and col2a1. Evol Dev 2018. [PMID: 29527799 DOI: 10.1111/ede.12250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Direct-developing amphibians form limbs during early embryonic stages, as opposed to the later, often postembryonic limb formation of metamorphosing species. Limb patterning is dramatically altered in direct-developing frogs, but little attention has been given to direct-developing salamanders. We use expression patterns of two genes, sox9 and col2a1, to assess skeletal patterning during embryonic limb development in the direct-developing salamander Plethodon cinereus. Limb patterning in P. cinereus partially resembles that described in other urodele species, with early formation of digit II and a generally anterior-to-posterior formation of preaxial digits. Unlike other salamanders described to date, differentiation of preaxial zeugopodial cartilages (radius/tibia) is not accelerated in relation to the postaxial cartilages, and there is no early differentiation of autopodial elements in relation to more proximal cartilages. Instead, digit II forms in continuity with the ulnar/fibular arch. This amniote-like connectivity to the first digit that forms may be a consequence of the embryonic formation of limbs in this direct-developing species. Additionally, and contrary to recent models of amphibian digit identity, there is no evidence of vestigial digits. This is the first account of gene expression in a plethodontid salamander and only the second published account of embryonic limb patterning in a direct-developing salamander species.
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Affiliation(s)
- Ryan R Kerney
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | - David C Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, Florida
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6
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Towers M. Evolution of antero-posterior patterning of the limb: Insights from the chick. Genesis 2018; 56:e23047. [PMID: 28734068 PMCID: PMC5811799 DOI: 10.1002/dvg.23047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/23/2017] [Accepted: 06/27/2017] [Indexed: 01/30/2023]
Abstract
The developing limbs of chicken embryos have served as pioneering models for understanding pattern formation for over a century. The ease with which chick wing and leg buds can be experimentally manipulated, while the embryo is still in the egg, has resulted in the discovery of important developmental organisers, and subsequently, the signals that they produce. Sonic hedgehog (Shh) is produced by mesenchyme cells of the polarizing region at the posterior margin of the limb bud and specifies positional values across the antero-posterior axis (the axis running from the thumb to the little finger). Detailed experimental embryology has revealed the fundamental parameters required to specify antero-posterior positional values in response to Shh signaling in chick wing and leg buds. In this review, the evolution of the avian wing and leg will be discussed in the broad context of tetrapod paleontology, and more specifically, ancestral theropod dinosaur paleontology. How the parameters that dictate antero-posterior patterning could have been modulated to produce the avian wing and leg digit patterns will be considered. Finally, broader speculations will be made regarding what the antero-posterior patterning of chick limbs can tell us about the evolution of other digit patterns, including those that were found in the limbs of the earliest tetrapods.
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Affiliation(s)
- Matthew Towers
- Department of Biomedical ScienceThe Bateson Centre, University of SheffieldWestern BankSheffieldS10 2TNUnited Kingdom
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7
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Farré M, Narayan J, Slavov GT, Damas J, Auvil L, Li C, Jarvis ED, Burt DW, Griffin DK, Larkin DM. Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles. Genome Biol Evol 2016; 8:2442-51. [PMID: 27401172 PMCID: PMC5010900 DOI: 10.1093/gbe/evw166] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and 5 outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm. We identified EBRs and HSBs in ancestral bird, archosaurian (bird, crocodile, and dinosaur), and reptile chromosomes. Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, including for example, avian-specific HSBs enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes were related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly on how chromosome rearrangements likely contributed to the formation of novel phenotypes.
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Affiliation(s)
- Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
| | - Jitendra Narayan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA, UK
| | - Gancho T Slavov
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
| | - Loretta Auvil
- Illinois Informatics Institute, University of Illinois, Urbana, IL 61801, USA
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Erich D Jarvis
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - David W Burt
- Department of Genomics and Genetics, the Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
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8
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The phantoms of a high-seven - or - why do our thumbs stick out? Front Zool 2015; 12:23. [PMID: 26379756 PMCID: PMC4570229 DOI: 10.1186/s12983-015-0117-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/05/2015] [Indexed: 11/30/2022] Open
Abstract
The earliest tetrapods had hands and feet with up to eight digits but this number was subsequently reduced during evolution. It was assumed that lineages with more than five digits no longer exist but investigations of clawed-frogs now indicate that they posses a rudimentary or atavistic sixth digit in their hindlimb. A recent reevaluation of the stem tetrapod Ichthyostega predicts that its seven digits evolved from two different types of ancestral fin radials, pre-axial and post-axial. In this context we now ask the question, should we consider a pre-axial origin of the thumb as reason for its unique genetic signature?
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9
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Guinard G. Limusaurus inextricabilis(Theropoda: Ceratosauria) gives a hand to evolutionary teratology: a complementary view on avian manual digits identities. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Tokita M. How the pterosaur got its wings. Biol Rev Camb Philos Soc 2014; 90:1163-78. [PMID: 25361444 DOI: 10.1111/brv.12150] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/10/2014] [Accepted: 10/01/2014] [Indexed: 12/19/2022]
Abstract
Throughout the evolutionary history of life, only three vertebrate lineages took to the air by acquiring a body plan suitable for powered flight: birds, bats, and pterosaurs. Because pterosaurs were the earliest vertebrate lineage capable of powered flight and included the largest volant animal in the history of the earth, understanding how they evolved their flight apparatus, the wing, is an important issue in evolutionary biology. Herein, I speculate on the potential basis of pterosaur wing evolution using recent advances in the developmental biology of flying and non-flying vertebrates. The most significant morphological features of pterosaur wings are: (i) a disproportionately elongated fourth finger, and (ii) a wing membrane called the brachiopatagium, which stretches from the posterior surface of the arm and elongated fourth finger to the anterior surface of the leg. At limb-forming stages of pterosaur embryos, the zone of polarizing activity (ZPA) cells, from which the fourth finger eventually differentiates, could up-regulate, restrict, and prolong expression of 5'-located Homeobox D (Hoxd) genes (e.g. Hoxd11, Hoxd12, and Hoxd13) around the ZPA through pterosaur-specific exploitation of sonic hedgehog (SHH) signalling. 5'Hoxd genes could then influence downstream bone morphogenetic protein (BMP) signalling to facilitate chondrocyte proliferation in long bones. Potential expression of Fgf10 and Tbx3 in the primordium of the brachiopatagium formed posterior to the forelimb bud might also facilitate elongation of the phalanges of the fourth finger. To establish the flight-adapted musculoskeletal morphology shared by all volant vertebrates, pterosaurs probably underwent regulatory changes in the expression of genes controlling forelimb and pectoral girdle musculoskeletal development (e.g. Tbx5), as well as certain changes in the mode of cell-cell interactions between muscular and connective tissues in the early phase of their evolution. Developmental data now accumulating for extant vertebrate taxa could be helpful in understanding the cellular and molecular mechanisms of body-plan evolution in extinct vertebrates as well as extant vertebrates with unique morphology whose embryonic materials are hard to obtain.
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Affiliation(s)
- Masayoshi Tokita
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, U.S.A
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11
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Nomura N, Yokoyama H, Tamura K. Altered developmental events in the anterior region of the chick forelimb give rise to avian-specific digit loss. Dev Dyn 2014; 243:741-52. [PMID: 24616028 DOI: 10.1002/dvdy.24117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 01/23/2014] [Accepted: 02/04/2014] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Avian forelimb (wing) contains only three digits, and the three-digit formation in the bird forelimb is one of the avian-specific limb characteristics that have been evolutionarily inherited from the common ancestral form in dinosaurs. Despite many studies on digit formation in the chick limb bud, the developmental mechanisms giving rise to the three-digit forelimb in birds have not been completely clarified. RESULTS To identify which cell populations of the early limb bud contribute to digit formation in the late limb bud, fate maps of the early fore- and hindlimb buds were prepared. Based on these fate maps, we found that the digit-forming region in the forelimb bud is narrower than that in the hindlimb bud, suggesting that some developmental mechanisms on the anterior-most region lead to a reduced number of digits in the forelimb. We also found temporal differences in the onset of appearance of the ANZ (anterior necrotic zone) as well as differences in the position of the anterior edge of the AER. CONCLUSIONS Forelimb-specific events in the anterior limb bud are possible developmental mechanisms that might generate the different cell fates in the fore- and hindlimb buds, regulating the number of digits in birds.
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Affiliation(s)
- Naoki Nomura
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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12
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Lopez-Real RE, Budge JJR, Marder TB, Whiting A, Hunt PN, Przyborski SA. Application of synthetic photostable retinoids induces novel limb and facial phenotypes during chick embryogenesis in vivo. J Anat 2013; 224:392-411. [PMID: 24303996 PMCID: PMC4098675 DOI: 10.1111/joa.12147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2013] [Indexed: 02/02/2023] Open
Abstract
We have recently developed a range of synthetic retinoid analogues which include the compounds EC23 and EC19. They are stable on exposure to light and are predicted to be resistant to the normal metabolic processes involved in the inactivation of retinoids in vivo. Based on the position of the terminal carboxylic acid groups in the compounds we suggest that EC23 is a structural analogue of all-trans retinoic acid (ATRA), and EC19 is an analogue of 13-cis retinoic acid. Their effects on the differentiation of pluripotent stem cells has been previously described in vitro and are consistent with this hypothesis. We present herein the first description of the effects of these molecules in vivo. Retinoids were applied to the anterior limb buds of chicken embryos in ovo via ion-exchange beads. We found that retinoid EC23 produces effects on the wing digits similar to ATRA, but does so at two orders of magnitude lower concentration. When larger quantities of EC23 are applied, a novel phenotype is obtained involving production of multiple digit 1s on the anterior limb. This corresponds to differential effects of ATRA and EC23 on sonic hedgehog (shh) expression in the developing limb bud. With EC23 application we also find digit 1 phenotypes similar to thumb duplications described in the clinical literature. EC23 and ATRA are shown to have effects on the entire proximal–distal axis of the limb, including hitherto undescribed effects on the scapula. This includes suppression of expression of the scapula marker Pax1. EC23 also produces effects similar to those of ATRA on the developing face, producing reductions of the upper beak at concentrations two orders of magnitude lower than ATRA. In contrast, EC19, which is structurally very similar to EC23, has novel, less severe effects on the face and rarely alters limb development. EC19 and ATRA are effective at similar concentrations. These results further demonstrate the ability of retinoids to influence embryonic development. Moreover, EC23 represents a useful new tool to investigate developmental processes and probe the mechanisms underlying congenital abnormalities in vertebrates including man.
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Affiliation(s)
- R E Lopez-Real
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
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13
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Capek D, Metscher BD, Müller GB. Thumbs down: a molecular-morphogenetic approach to avian digit homology. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:1-12. [PMID: 24323741 DOI: 10.1002/jez.b.22545] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 09/05/2013] [Accepted: 09/27/2013] [Indexed: 11/11/2022]
Abstract
Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain.
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Affiliation(s)
- Daniel Capek
- Department of Theoretical Biology, University of Vienna, Wien, Austria; Institute of Science and Technology, Klosterneuburg, Austria
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14
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Digit loss in archosaur evolution and the interplay between selection and constraints. Nature 2013; 500:445-8. [DOI: 10.1038/nature12336] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 05/24/2013] [Indexed: 11/08/2022]
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15
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Abstract
It is widely accepted that birds are a subgroup of dinosaurs, but there is an apparent conflict: modern birds have been thought to possess only the middle three fingers (digits II-III-IV) of an idealized five-digit tetrapod hand based on embryological data, but their Mesozoic tetanuran dinosaur ancestors are considered to have the first three digits (I-II-III) based on fossil evidence. How could such an evolutionary quirk arise? Various hypotheses have been proposed to resolve this paradox. Adding to the confusion, some recent developmental studies support a I-II-III designation for avian wing digits whereas some recent paleontological data are consistent with a II-III-IV identification of the Mesozoic tetanuran digits. A comprehensive analysis of both paleontological and developmental data suggests that the evolution of the avian wing digits may have been driven by homeotic transformations of digit identity, which are more likely to have occurred in a partial and piecemeal manner. Additionally, recent genetic studies in mouse models showing plausible mechanisms for central digit loss invite consideration of new alternative possibilities (I-II-IV or I-III-IV) for the homologies of avian wing digits. While much progress has been made, some advances point to the complexity of the problem and a final resolution to this ongoing debate demands additional work from both paleontological and developmental perspectives, which will surely yield new insights on mechanisms of evolutionary adaptation.
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Affiliation(s)
- Xing Xu
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology & Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044 China.
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16
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Sensiate LA, Sobreira DR, Da Veiga FC, Peterlini DJ, Pedrosa AV, Rirsch T, Joazeiro PP, Schubert FR, Collares-Buzato CB, Xavier-Neto J, Dietrich S, Alvares LE. Dact gene expression profiles suggest a role for this gene family in integrating Wnt and TGF-β signaling pathways during chicken limb development. Dev Dyn 2013; 243:428-39. [DOI: 10.1002/dvdy.23948] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 12/20/2012] [Accepted: 01/27/2013] [Indexed: 12/22/2022] Open
Affiliation(s)
| | - Débora R. Sobreira
- Department of Histology and Embryology; State University of Campinas UNICAMP; Campinas Brazil
- Institute of Biomedical and Biomolecular Science, University of Portsmouth; Portsmouth United Kingdom
| | | | | | | | - Thaís Rirsch
- Department of Histology and Embryology; State University of Campinas UNICAMP; Campinas Brazil
| | - Paulo Pinto Joazeiro
- Department of Histology and Embryology; State University of Campinas UNICAMP; Campinas Brazil
| | - Frank R. Schubert
- Institute of Biomedical and Biomolecular Science, University of Portsmouth; Portsmouth United Kingdom
| | | | | | - Susanne Dietrich
- Institute of Biomedical and Biomolecular Science, University of Portsmouth; Portsmouth United Kingdom
| | - Lúcia Elvira Alvares
- Department of Histology and Embryology; State University of Campinas UNICAMP; Campinas Brazil
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17
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Bickelmann C, Jiménez R, Richardson MK, Sánchez-Villagra MR. Humerus development in moles (Talpidae, Mammalia). ACTA ZOOL-STOCKHOLM 2013. [DOI: 10.1111/azo.12024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Constanze Bickelmann
- Paleontological Museum and Institute; University of Zurich; Karl-Schmid-Strasse 4 Zurich 8006 Switzerland
| | - Rafael Jiménez
- Departamento de Genética; Universidad de Granada; Avenida del Conocimiento Granada, Armilla 18100 Spain
| | - Michael K. Richardson
- Institute of Biology; University of Leiden; Sylviusweg 72 Leiden 2333 BE The Netherlands
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18
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Skeletal development in the fossorial gymnophthalmids Calyptommatus sinebrachiatus and Nothobachia ablephara. ZOOLOGY 2012; 115:289-301. [DOI: 10.1016/j.zool.2012.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 01/26/2012] [Accepted: 02/02/2012] [Indexed: 01/05/2023]
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Bickelmann C, Mitgutsch C, Richardson MK, Jiménez R, de Bakker MA, Sánchez-Villagra MR. Transcriptional heterochrony in talpid mole autopods. EvoDevo 2012; 3:16. [PMID: 22873211 PMCID: PMC3441920 DOI: 10.1186/2041-9139-3-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/04/2012] [Indexed: 11/24/2022] Open
Abstract
Background Talpid moles show many specializations in their adult skeleton linked to fossoriality, including enlarged hands when compared to the feet. Heterochrony in developmental mechanisms is hypothesized to account for morphological evolution in skeletal elements. Methods The temporal and spatial distribution of SOX9 expression, which is an early marker of chondrification, is analyzed in autopods of the fossorial Iberian mole Talpa occidentalis, as well as in shrew (Cryptotis parva) and mouse (Mus musculus) for comparison. Results and discussion SOX9 expression is advanced in the forelimb compared to the hind limb in the talpid mole. In contrast, in the shrew and the mouse, which do not show fossorial specializations in their autopods, it is synchronous. We provide evidence that transcriptional heterochrony affects the development of talpid autopods, an example of developmental penetrance. We discuss our data in the light of earlier reported pattern heterochrony and later morphological variation in talpid limbs. Conclusion Transcriptional heterochrony in SOX9 expression is found in talpid autopods, which is likely to account for pattern heterochrony in chondral limb development as well as size variation in adult fore- and hind limbs.
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Affiliation(s)
- Constanze Bickelmann
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, Zürich 8006, Switzerland.
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LARSSON HANSCE, WAGNER GÜNTERP. Testing Inferences in Developmental Evolution: The Forensic Evidence Principle. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 318:489-500. [DOI: 10.1002/jez.b.22458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 03/21/2012] [Accepted: 04/03/2012] [Indexed: 11/10/2022]
Affiliation(s)
| | - GÜNTER P. WAGNER
- Department of Ecology and Evolutionary Biology; Yale Systems Biology Institute; Yale University; New Haven; Connecticut
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21
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Mitgutsch C, Richardson MK, Jiménez R, Martin JE, Kondrashov P, de Bakker MAG, Sánchez-Villagra MR. Circumventing the polydactyly 'constraint': the mole's 'thumb'. Biol Lett 2012; 8:74-7. [PMID: 21752813 PMCID: PMC3259951 DOI: 10.1098/rsbl.2011.0494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/22/2011] [Indexed: 11/12/2022] Open
Abstract
Talpid moles across all northern continents exhibit a remarkably large, sickle-like radial sesamoid bone anterior to their five digits, always coupled with a smaller tibial sesamoid bone. A possible developmental mechanism behind this phenomenon was revealed using molecular markers during limb development in the Iberian mole (Talpa occidentalis) and a shrew (Cryptotis parva), as shrews represent the closest relatives of moles but do not show these conspicuous elements. The mole's radial sesamoid develops later than true digits, as shown by Sox9, and extends into the digit area, developing in relation to an Msx2-domain at the anterior border of the digital plate. Fgf8 expression, marking the apical ectodermal ridge, is comparable in both species. Developmental peculiarities facilitated the inclusion of the mole's radial sesamoid into the digit series; talpid moles circumvent the almost universal pentadactyly constraint by recruiting wrist sesamoids into their digital region using a novel developmental pathway and timing.
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Affiliation(s)
- Christian Mitgutsch
- Paläontologisches Institut und Museum, Universität Zürich, 8006 Zürich, Switzerland
| | | | - Rafael Jiménez
- Departamento de Genética, Universidad de Granada, 18100 Armilla, Granada, Spain
| | - José E. Martin
- Departamento de Parasitología y Biomedicina López-Neyra, CSIC, 18100 Armilla, Granada, Spain
| | - Peter Kondrashov
- A. T. Still University of Health Sciences, Kirksville College of Osteopathic Medicine, Kirksville, MO 63501, USA
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22
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Kerney R. Embryonic Staging Table for a Direct-Developing Salamander, Plethodon cinereus (Plethodontidae). Anat Rec (Hoboken) 2011; 294:1796-808. [DOI: 10.1002/ar.21480] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 08/02/2011] [Indexed: 11/10/2022]
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23
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Mitgutsch C, Wimmer C, Sánchez-Villagra MR, Hahnloser R, Schneider RA. Timing of ossification in duck, quail, and zebra finch: intraspecific variation, heterochronies, and life history evolution. Zoolog Sci 2011; 28:491-500. [PMID: 21728797 DOI: 10.2108/zsj.28.491] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Skeletogenic heterochronies have gained much attention in comparative developmental biology. The temporal appearance of mineralized individual bones in a species - the species ossification sequence - is an excellent marker in this kind of study. Several publications describe interspecific variation, but only very few detail intraspecific variation. In this study, we describe and analyze the temporal order of ossification of skeletal elements in the zebra finch, Taeniopygia guttata, the Japanese quail, Coturnix coturnix japonica, and the White Pekin duck, a domestic race of the mallard Anas platyrhynchos, and explore patterns of intraspecific variation in these events. The overall sequences were found to be conserved. In the duck, variability is present in the relative timing of ossification in the occipital, the basisphenoid and the otic regions of the skull and the phalanges in the postcranium. This variation appears generally in close temporal proximity. Comparison with previously published data shows differences in ossification sequence in the skull, the feet, and the pelvis in the duck, and especially the pelvis in the quail. This clearly documents variability among different breeds.
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Affiliation(s)
- Christian Mitgutsch
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, CH-8006 Zürich, Switzerland
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24
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Wang Z, Young RL, Xue H, Wagner GP. Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds. Nature 2011; 477:583-6. [DOI: 10.1038/nature10391] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 07/26/2011] [Indexed: 01/01/2023]
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25
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Towers M, Signolet J, Sherman A, Sang H, Tickle C. Insights into bird wing evolution and digit specification from polarizing region fate maps. Nat Commun 2011; 2:426. [DOI: 10.1038/ncomms1437] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/14/2011] [Indexed: 01/22/2023] Open
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26
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Bever GS, Gauthier JA, Wagner GP. Finding the frame shift: digit loss, developmental variability, and the origin of the avian hand. Evol Dev 2011; 13:269-79. [DOI: 10.1111/j.1525-142x.2011.00478.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Fisher M, Downie H, Welten MCM, Delgado I, Bain A, Planzer T, Sherman A, Sang H, Tickle C. Comparative analysis of 3D expression patterns of transcription factor genes and digit fate maps in the developing chick wing. PLoS One 2011; 6:e18661. [PMID: 21526123 PMCID: PMC3081307 DOI: 10.1371/journal.pone.0018661] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 03/08/2011] [Indexed: 11/23/2022] Open
Abstract
Hoxd13, Tbx2, Tbx3, Sall1 and Sall3 genes are candidates for encoding antero-posterior positional values in the developing chick wing and specifying digit identity. In order to build up a detailed profile of gene expression patterns in cell lineages that give rise to each of the digits over time, we compared 3 dimensional (3D) expression patterns of these genes during wing development and related them to digit fate maps. 3D gene expression data at stages 21, 24 and 27 spanning early bud to digital plate formation, captured from in situ hybridisation whole mounts using Optical Projection Tomography (OPT) were mapped to reference wing bud models. Grafts of wing bud tissue from GFP chicken embryos were used to fate map regions of the wing bud giving rise to each digit; 3D images of the grafts were captured using OPT and mapped on to the same models. Computational analysis of the combined computerised data revealed that Tbx2 and Tbx3 are expressed in digit 3 and 4 progenitors at all stages, consistent with encoding stable antero-posterior positional values established in the early bud; Hoxd13 and Sall1 expression is more dynamic, being associated with posterior digit 3 and 4 progenitors in the early bud but later becoming associated with anterior digit 2 progenitors in the digital plate. Sox9 expression in digit condensations lies within domains of digit progenitors defined by fate mapping; digit 3 condensations express Hoxd13 and Sall1, digit 4 condensations Hoxd13, Tbx3 and to a lesser extent Tbx2. Sall3 is only transiently expressed in digit 3 progenitors at stage 24 together with Sall1 and Hoxd13; then becomes excluded from the digital plate. These dynamic patterns of expression suggest that these genes may play different roles in digit identity either together or in combination at different stages including the digit condensation stage.
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Affiliation(s)
- Malcolm Fisher
- Division of Cell and Developmental Biology, University of Dundee, Dundee, Scotland, United Kingdom
| | - Helen Downie
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Monique C. M. Welten
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
- * E-mail:
| | - Irene Delgado
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Andrew Bain
- Division of Cell and Developmental Biology, University of Dundee, Dundee, Scotland, United Kingdom
| | - Thorsten Planzer
- Division of Cell and Developmental Biology, University of Dundee, Dundee, Scotland, United Kingdom
| | - Adrian Sherman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Helen Sang
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Cheryll Tickle
- Division of Cell and Developmental Biology, University of Dundee, Dundee, Scotland, United Kingdom
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
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28
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Young RL, Bever GS, Wang Z, Wagner GP. Identity of the avian wing digits: problems resolved and unsolved. Dev Dyn 2011; 240:1042-53. [PMID: 21412936 DOI: 10.1002/dvdy.22595] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2011] [Indexed: 01/01/2023] Open
Abstract
Controversy over bird wing digit identity has been a touchstone for various ideas in the phylogeny of birds, homology, and developmental evolution. This review summarizes the past 10 years of progress toward understanding avian digit identity. We conclude that the sum of evidence supports the Frame Shift Hypothesis, indicating that the avian wing digits have changed anatomical location. Briefly, the derivation of birds from theropod dinosaurs and the positional identities of the avian wing digits as 2, 3, and 4¹ are no longer in question. Additionally, increasing evidence indicates that the developmental programs for identity of the wing digits are of digits I, II, and III. Therefore, the attention moves from whether the digit identity frame shift occurred, to what the mechanisms of the frame shift were, and when in evolution it happened. There is considerable uncertainty about these issues and we identify exciting new research directions to resolve them.
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Affiliation(s)
- Rebecca L Young
- Yale Systems Biology Institute, Department of Ecology and Evolutionary Biology, Yale University, West Haven, Connecticut, USA.
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29
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Tamura K, Nomura N, Seki R, Yonei-Tamura S, Yokoyama H. Embryological Evidence Identifies Wing Digits in Birds as Digits 1, 2, and 3. Science 2011; 331:753-7. [DOI: 10.1126/science.1198229] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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30
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Vieira LG, Santos AL, Lima FC, Moura LR. Chondrogenesis of the limbs and mesopodial ossification ofPodocnemis expansaSchweigger, 1812 (Testudines: Podocnemidae). J Morphol 2011; 272:404-18. [DOI: 10.1002/jmor.10917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 09/03/2010] [Accepted: 09/25/2010] [Indexed: 11/06/2022]
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31
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Young RL, Wagner GP. Why ontogenetic homology criteria can be misleading: lessons from digit identity transformations. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316B:165-70. [DOI: 10.1002/jez.b.21396] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 11/29/2010] [Accepted: 12/04/2010] [Indexed: 01/16/2023]
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32
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Kerney R, Gross JB, Hanken J. Early cranial patterning in the direct-developing frog Eleutherodactylus coqui revealed through gene expression. Evol Dev 2010; 12:373-82. [PMID: 20618433 DOI: 10.1111/j.1525-142x.2010.00424.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetic and developmental alterations associated with the evolution of amphibian direct development remain largely unexplored. Specifically, little is known of the underlying expression of skeletal regulatory genes, which may reveal early modifications to cranial ontogeny in direct-developing species. We describe expression patterns of three key skeletal regulators (runx2, sox9, and bmp4) along with the cartilage-dominant collagen 2alpha1 gene (col2a1) during cranial development in the direct-developing anuran, Eleutherodactylus coqui. Expression patterns of these regulators reveal transient skeletogenic anlagen that correspond to larval cartilages, but which never fully form in E. coqui. Suprarostral anlagen in the frontonasal processes are detected through runx2, sox9, and bmp4 expression. Previous studies have described these cartilages as missing from Eleutherodactylus cranial ontogeny. These transcriptionally active suprarostral anlagen fuse to the more posterior cranial trabeculae before they are detectable with col2a1 staining or with the staining techniques used in earlier studies. Additionally, expression of sox9 fails to reveal an early anterior connection between the palatoquadrate and the neurocranium, which is detectable through sox9 staining in Xenopus laevis embryos (a metamorphosing species). Absence of this connection validates an instance of developmental repatterning, where the larval quadratocranial commissure cartilage is lost in E. coqui. Expression of runx2 reveals dermal-bone precursors several developmental stages before their detection with alizarin red. This early expression of runx2 correlates with the accelerated embryonic onset of bone formation characteristic of E. coqui and other direct-developing anurans, but which differs from the postembryonic bone formation of most metamorphosing species. Together these results provide an earlier depiction of cranial patterning in E. coqui by using earlier markers of skeletogenic cell differentiation. These data both validate and modify previously reported instances of larval recapitulation and developmental repatterning associated with the evolution of anuran direct development.
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Affiliation(s)
- Ryan Kerney
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, Canada B3H 4J1.
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33
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Kohlsdorf T, Lynch VJ, Rodrigues MT, Brandley MC, Wagner GP. DATA AND DATA INTERPRETATION IN THE STUDY OF LIMB EVOLUTION: A REPLY TO GALIS ET AL. ON THE REEVOLUTION OF DIGITS IN THE LIZARD GENUS BACHIA. Evolution 2010. [DOI: 10.1111/j.1558-5646.2010.01042.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Larsson HC, Heppleston AC, Elsey RM. Pentadactyl ground state of the manus of Alligator mississippiensis and insights into the evolution of digital reduction in Archosauria. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:571-9. [DOI: 10.1002/jez.b.21362] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 05/08/2010] [Accepted: 05/11/2010] [Indexed: 11/06/2022]
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35
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Delfino M, Sánchez-Villagra MR. A survey of the rock record of reptilian ontogeny. Semin Cell Dev Biol 2010; 21:432-40. [DOI: 10.1016/j.semcdb.2009.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 11/06/2009] [Indexed: 11/26/2022]
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36
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37
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Uejima A, Amano T, Nomura N, Noro M, Yasue T, Shiroishi T, Ohta K, Yokoyama H, Tamura K. Anterior shift in gene expression precedes anteriormost digit formation in amniote limbs. Dev Growth Differ 2010; 52:223-34. [DOI: 10.1111/j.1440-169x.2009.01161.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Young RL, Caputo V, Giovannotti M, Kohlsdorf T, Vargas AO, May GE, Wagner GP. Evolution of digit identity in the three-toed Italian skinkChalcides chalcides: a new case of digit identity frame shift. Evol Dev 2009; 11:647-58. [PMID: 19878286 DOI: 10.1111/j.1525-142x.2009.00372.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Rebecca L Young
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
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39
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A Jurassic ceratosaur from China helps clarify avian digital homologies. Nature 2009; 459:940-4. [PMID: 19536256 DOI: 10.1038/nature08124] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 04/29/2009] [Indexed: 11/09/2022]
Abstract
Theropods have traditionally been assumed to have lost manual digits from the lateral side inward, which differs from the bilateral reduction pattern seen in other tetrapod groups. This unusual reduction pattern is clearly present in basal theropods, and has also been inferred in non-avian tetanurans based on identification of their three digits as the medial ones of the hand (I-II-III). This contradicts the many developmental studies indicating II-III-IV identities for the three manual digits of the only extant tetanurans, the birds. Here we report a new basal ceratosaur from the Oxfordian stage of the Jurassic period of China (156-161 million years ago), representing the first known Asian ceratosaur and the only known beaked, herbivorous Jurassic theropod. Most significantly, this taxon possesses a strongly reduced manual digit I, documenting a complex pattern of digital reduction within the Theropoda. Comparisons among theropod hands show that the three manual digits of basal tetanurans are similar in many metacarpal features to digits II-III-IV, but in phalangeal features to digits I-II-III, of more basal theropods. Given II-III-IV identities in avians, the simplest interpretation is that these identities were shared by all tetanurans. The transition to tetanurans involved complex changes in the hand including a shift in digit identities, with ceratosaurs displaying an intermediate condition.
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40
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Vargas AO, Wagner GP. Frame-shifts of digit identity in bird evolution and Cyclopamine-treated wings. Evol Dev 2009; 11:163-9. [DOI: 10.1111/j.1525-142x.2009.00317.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Kundrát M. Primary chondrification foci in the wing basipodium ofStruthio cameluswith comments on interpretation of autopodial elements in Crocodilia and Aves. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312:30-41. [DOI: 10.1002/jez.b.21240] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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42
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Bastida MF, Ros MA. How do we get a perfect complement of digits? Curr Opin Genet Dev 2008; 18:374-80. [PMID: 18672062 DOI: 10.1016/j.gde.2008.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 06/13/2008] [Accepted: 06/17/2008] [Indexed: 12/26/2022]
Abstract
A crucial issue in limb development is how a correct set of precisely shaped digits forms in the digital plate. This process relies on patterning across the anterior-posterior axis of the limb bud, which is under the control of Sonic hedgehog emanating from the zone of polarizing activity. Recently, Sonic hedgehog function in the limb bud has been shown to have a dual character controlling both growth and patterning of the digital field. This finding has prompted the proposal of new models of how these two functions are achieved, and this will be discussed in this review.
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Affiliation(s)
- Ma Félix Bastida
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, C/ Herrera Oria s/n, E-39011 Santander, Spain
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In vitro whole-organ imaging: 4D quantification of growing mouse limb buds. Nat Methods 2008; 5:609-12. [DOI: 10.1038/nmeth.1219] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 05/13/2008] [Indexed: 11/08/2022]
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Ramírez MJ. Homology as a parsimony problem: a dynamic homology approach for morphological data. Cladistics 2007; 23:588-612. [PMID: 34905870 DOI: 10.1111/j.1096-0031.2007.00162.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The primary data used to reconstruct phylogenies comes organized in the conceptual grid of homology correspondences, and the construction of this theory-rich grid depends in part on knowledge of relationships. This situation is not satisfactory as a conceptual system, because the evidence is not clearly delimited from the results. I explore the testing of alternative hypotheses of morphological correspondences in a quantitative cladistic context. The varying homology assessments implied by classical criteria of homology (topological equivalence, or position and connections; composition of structures, or commonality in details of construction) can be expressed as regular characters in a cladistic analysis. Doing so provides adequate transformation costs for changes in schemas of correspondences. Correspondences imply evolutionary transformations, and multiple schemas of correspondences can be compared according to the evolutionary transformations that they imply. The method is used to test the correspondences in sclerites of the male copulatory organs of spiders of the subfamily Amaurobioidinae (Arachnida, Araneae, Anyphaenidae). The correspondences of three sclerites are tested, in a data set of 93 species having one, two or three sclerites, using a simultaneous analysis of all the morphological characters. Most parsimonious trees are identified together with the correspondences they imply. Once the correspondences are integrated in the phylogenetic analysis, it is easy to evaluate the robustness of trees or decay in optimality after changes in anatomical interpretations. A Bremer support for anatomical interpretations is proposed, calculated as the increase in tree length when the specific interpretation is not used.
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Zhou J, Meng J, Guo S, Gao B, Ma G, Zhu X, Hu J, Xiao Y, Lin C, Wang H, Ding L, Feng G, Guo X, He L. IHH and FGF8 coregulate elongation of digit primordia. Biochem Biophys Res Commun 2007; 363:513-8. [PMID: 17889828 DOI: 10.1016/j.bbrc.2007.08.198] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
Abstract
In the developing limb bud, digit pattern arises from anterior-posterior (A-P) positional information which is provided by the concentration gradient of SHH. However, the mechanisms of translating early asymmetry into morphological form are still unclear. Here, we examined the ability of IHH and FGF8 signaling to regulate digital chondrogenesis, by implanting protein-loaded beads in the interdigital space singly and in combination. We found that IHH protein induced an elongated digit and that FGF8 protein blocked the terminal phalange formation. Molecular marker analysis showed that IHH expanded Sox9 expression in mesenchymal cells possibly through up-regulated FGF8 expression. Application of both IHH and FGF8 protein induced a large terminal phalange. These results suggest that both enhanced IHH and FGF8 signaling are required for the development of additional cartilage element in limbs. IHH and FGF8 maybe play different roles and act synergistically to promote chondrogenesis during digit primordia elongation.
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Affiliation(s)
- Jian Zhou
- Bio-X Center, Shanghai Jiao Tong University, Shanghai, China
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Richardson MK, Crooijmans RPMA, Groenen MAM. Sequencing and genomic annotation of the chicken (Gallus gallus) Hox clusters, and mapping of evolutionarily conserved regions. Cytogenet Genome Res 2007; 117:110-9. [PMID: 17675851 DOI: 10.1159/000103171] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 09/29/2006] [Indexed: 11/19/2022] Open
Abstract
Hox genes encode transcription factors that are involved in the regulation of normal development and are mutated in some diseases and malformations. Chicken HOX genes have been extensively studied in the chick limb and other developmental models. To date while the chicken HOXA cluster has been completely sequenced many other chicken HOX genes are known only from partial mRNAs or unfinished genome assemblies. Furthermore, although a finished sequence of the HOXA cluster is available, the sequence has not yet been annotated. We have therefore manually annotated the available HOX sequences and improved the sequences by sequencing PCR fragments that bridge existing gaps in the genome sequences. These sequences complement the published sequences, including the currently incomplete WashUC Gallus_gallus-2.1 build, to give an improved coverage of the cluster. We used phylogenetic footprinting to map the genomic location of 398 Ultra Conserved Regions in the HOX complex 248 of which do not overlap with any known annotated coding exon. These included the hox-related microRNAs miR-10 and miR-196. The chicken HOX clusters appear to be broadly comparable to their human counterparts. A few human orthologues were not recovered from the chicken, presumably because of incomplete sequence.
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Affiliation(s)
- M K Richardson
- Department of Integrative Zoology, Institute of Biology, Leiden University, Leiden, The Netherlands
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Abstract
Digit formation is the last step in the skeletal patterning of developing limbs. This process involves important aspects such as determination of chondrogenic versus interdigital areas; growth of digital rays with periodic segmentation to form joints and thus phalanges, and finally tip formation. Traditionally it was believed that the properties of digital rays were fixed at earlier stages, but recently a surprising plasticity of digit primordia at the time of condensation has been demonstrated. This implies the presence of local interactions that are able to modulate the particular programs that make a given digit, but we don't fully understand how they operate. An involvement of signaling from the interdigital spaces and from the apical ectodermal ridge has been proposed. Another interesting question is the formation of the last limb structure, digit tips, which may involve a specific molecular and cellular program. Indeed, the expression of several developmentally important genes is restricted to digit tips at late stages of limb development. Understanding the molecular and cellular interactions that lead to digit morphogenesis has important implications not only in the context of embryonic development (for example, how early cues received by cells are translated into anatomy or what are the mechanisms that control the cease of activity of signaling regions) but also in terms of limb diversification during evolution.
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Affiliation(s)
- Jesús C Casanova
- Department of Immunology and Oncology, Centro Nacional de Biotecnología, CSIC, Darwin, 3, 28049 Madrid, Spain
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LIVEZEY BRADLEYC, ZUSI RICHARDL. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool J Linn Soc 2007; 149:1-95. [PMID: 18784798 PMCID: PMC2517308 DOI: 10.1111/j.1096-3642.2006.00293.x] [Citation(s) in RCA: 277] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.
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Affiliation(s)
- BRADLEY C LIVEZEY
- Section of Birds, Carnegie Museum of Natural History4400 Forbes Avenue, Pittsburgh, PA 15213-4080, USA
| | - RICHARD L ZUSI
- Division of Birds, National Museum of Natural HistoryWashington, DC 20013-7012, USA
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Abstract
We develop and demonstrate improved image-forming optics for optical projection tomography (OPT), with which the parallel integral throughout an object can be obtained. This method results in an improved resolution for OPT images, especially for the cross sections far from the optical axis of the image-forming optics. We find the optimal configuration used in our OPT system by use of a point spread function and simulation technique. The new method is validated by both numerical simulations and experimental results. The spatial resolution of the OPT system presented is approximately 40 microm.
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Affiliation(s)
- Yi Wang
- Department of Biomedical Engineering, Oregon Heath & Science University, Beaverton, OR 97006, USA
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Kohlsdorf T, Wagner GP. EVIDENCE FOR THE REVERSIBILITY OF DIGIT LOSS: A PHYLOGENETIC STUDY OF LIMB EVOLUTION IN BACHIA (GYMNOPHTHALMIDAE: SQUAMATA). Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb00533.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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