1
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Zattara EE, Strelin MM. 5th Argentinean Meeting on Evolutionary Biology (RABE V): Report on the "Evo-Devo" Extended Symposium. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:335-341. [PMID: 38686706 DOI: 10.1002/jez.b.23252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Evolutionary developmental biology (Evo-Devo) is flourishing in Latin America, particularly Argentina, where researchers are leveraging this integrative field to unlock the secrets of the region's remarkable biodiversity. A recent symposium held at the 5th Argentinean Meeting on Evolutionary Biology (RABE V) showcased a vibrant Evo-Devo community and the diversity of its research endeavors. The symposium included 3 plenary talks, 3 short talks, and 12 posters, and spanned a range of organisms and approaches. Interestingly, the symposium highlighted a prevalence of "top-down" Evo-Devo studies in the region, where researchers first analyze existing diversity and then propose potential developmental mechanisms. This approach, driven in part by financial constraints and the region's historical focus on natural history, presents a unique opportunity to bridge disciplines like comparative biology, paleontology, and botany. The symposium's success underscores the vital role of Evo-Devo in Latin America, not only for advancing our understanding of evolution but also for providing valuable tools to conserve and manage the region's irreplaceable biodiversity. As Evo-Devo continues to grow in Latin America, fostering collaboration and knowledge exchange within the region and beyond will be crucial for realizing the full potential of this transformative field.
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Affiliation(s)
- Eduardo E Zattara
- INIBIOMA, Universidad Nacional del Comahue - CONICET, Bariloche, Rio Negro, Argentina
| | - Marina M Strelin
- INIBIOMA, Universidad Nacional del Comahue - CONICET, Bariloche, Rio Negro, Argentina
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2
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Bishop PJ, Pierce SE. The fossil record of appendicular muscle evolution in Synapsida on the line to mammals: Part II-Hindlimb. Anat Rec (Hoboken) 2024; 307:1826-1896. [PMID: 37727023 DOI: 10.1002/ar.25310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/15/2023] [Accepted: 08/08/2023] [Indexed: 09/21/2023]
Abstract
This paper is the second in a two-part series that charts the evolution of appendicular musculature along the mammalian stem lineage, drawing upon the exceptional fossil record of extinct synapsids. Here, attention is focused on muscles of the hindlimb. Although the hindlimb skeleton did not undergo as marked a transformation on the line to mammals as did the forelimb skeleton, the anatomy of extant tetrapods indicates that major changes to musculature have nonetheless occurred. To better understand these changes, this study surveyed the osteological evidence for muscular attachments in extinct mammalian and nonmammalian synapsids, two extinct amniote outgroups, and a large selection of extant mammals, saurians, and salamanders. Observations were integrated into an explicit phylogenetic framework, comprising 80 character-state complexes covering all muscles crossing the hip, knee, and ankle joints. These were coded for 33 operational taxonomic units spanning >330 Ma of tetrapod evolution, and ancestral state reconstruction was used to evaluate the sequence of muscular evolution along the stem lineage from Amniota to Theria. The evolutionary history of mammalian hindlimb musculature was complex, nonlinear, and protracted, with several instances of convergence and pulses of anatomical transformation that continued well into the crown group. Numerous traits typically regarded as characteristically "mammalian" have much greater antiquity than previously recognized, and for some traits, most synapsids are probably more reflective of the ancestral amniote condition than are extant saurians. More broadly, this study highlights the utility of the fossil record in interpreting the evolutionary appearance of distinctive anatomies.
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Affiliation(s)
- Peter J Bishop
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Geosciences Program, Queensland Museum, Brisbane, Queensland, Australia
| | - Stephanie E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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3
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Gouvêa DY, Brigandt I. Against unifying homology concepts: Redirecting the debate. J Morphol 2023; 284:e21599. [PMID: 37313763 DOI: 10.1002/jmor.21599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 04/29/2023] [Accepted: 05/06/2023] [Indexed: 06/15/2023]
Abstract
The term "homology" is persistently polysemous, defying the expectation that extensive scientific research should yield semantic stability. A common response has been to seek a unification of various prominent definitions. This paper proposes an alternative strategy, based on the insight that scientific concepts function as tools for research: When analyzing various conceptualizations of homology, we should preserve those distinguishing features that support particular research goals. We illustrate the fruitfulness of our strategy by application to two cases. First, we revisit Lankester's celebrated evolutionary reappraisal of homology and argue that his analysis has been distorted by assimilation to modern agendas. His "homogeny" does not mean the same thing as modern evolutionary "homology," and his "homoplasy" is no mere antonym. Instead, Lankester uses both new terms to pose a question that remains strikingly relevant-how do mechanistic and historical causes of morphological resemblance interact? Second, we examine the puzzle of avian digit homology, which exemplifies disciplinary differences in homology conceptualization and assessment. Recent progress has been fueled by the development of new tools within the relevant disciplines (paleontology and developmental biology) and especially by increasing interdisciplinary cooperation. Conceptual unification has played very little role in this work, which instead seeks concrete evolutionary scenarios that integrate all the available evidence. Together these cases indicate the complex relationship between concepts and other tools in homology research.
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Affiliation(s)
- Devin Y Gouvêa
- Department of Philosophy, College of the Holy Cross, Worcester, Massachusetts, USA
| | - Ingo Brigandt
- Department of Philosophy, University of Alberta, Edmonton, Canada
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4
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Egawa S, Griffin CT, Bishop PJ, Pintore R, Tsai HP, Botelho JF, Smith-Paredes D, Kuratani S, Norell MA, Nesbitt SJ, Hutchinson JR, Bhullar BAS. The dinosaurian femoral head experienced a morphogenetic shift from torsion to growth along the avian stem. Proc Biol Sci 2022; 289:20220740. [PMID: 36196539 PMCID: PMC9532989 DOI: 10.1098/rspb.2022.0740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Significant evolutionary shifts in locomotor behaviour often involve comparatively subtle anatomical transitions. For dinosaurian and avian evolution, medial overhang of the proximal femur has been central to discussions. However, there is an apparent conflict with regard to the evolutionary origin of the dinosaurian femoral head, with neontological and palaeontological data suggesting seemingly incongruent hypotheses. To reconcile this, we reconstructed the evolutionary history of morphogenesis of the proximal end of the femur from early archosaurs to crown birds. Embryological comparison of living archosaurs (crocodylians and birds) suggests the acquisition of the greater overhang of the femoral head in dinosaurs results from additional growth of the proximal end in the medial-ward direction. On the other hand, the fossil record suggests that this overhang was acquired by torsion of the proximal end, which projected in a more rostral direction ancestrally. We reconcile this apparent conflict by inferring that the medial overhang of the dinosaur femoral head was initially acquired by torsion, which was then superseded by mediad growth. Details of anatomical shifts in fossil forms support this hypothesis, and their biomechanical implications are congruent with the general consensus regarding broader morpho-functional evolution on the avian stem.
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Affiliation(s)
- Shiro Egawa
- Department of Earth & Planetary Sciences and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA.,Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,Department of Neurophysiology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Christopher T Griffin
- Department of Earth & Planetary Sciences and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Peter J Bishop
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms AL9 7TA, UK.,Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Geosciences Program, Queensland Museum, Brisbane, Australia
| | - Romain Pintore
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms AL9 7TA, UK.,Mécanismes adaptatifs et évolution (MECADEV)/UMR 7179, CNRS/Muséum National d'Histoire Naturelle, Paris, France
| | - Henry P Tsai
- Department of Biomedical Sciences, Missouri State University, Springfield, MO 65897, USA
| | - João F Botelho
- Department of Earth & Planetary Sciences and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA.,Department of Biology, Southern Connecticut State University, New Haven, CT 06515, USA.,Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniel Smith-Paredes
- Department of Earth & Planetary Sciences and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Mark A Norell
- Division of Vertebrate Paleontology, American Museum of Natural History, New York, NY, USA
| | | | - John R Hutchinson
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms AL9 7TA, UK
| | - Bhart-Anjan S Bhullar
- Department of Earth & Planetary Sciences and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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5
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Lev O, Edgecombe GD, Chipman AD. Serial Homology and Segment Identity in the Arthropod Head. Integr Org Biol 2022; 4:obac015. [PMID: 35620450 PMCID: PMC9128542 DOI: 10.1093/iob/obac015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The anterior-most unit of the crown-group arthropod body plan includes three segments, the pre-gnathal segments, that contain three neuromeres that together comprise the brain. Recent work on the development of this anterior region has shown that its three units exhibit many developmental differences to the more posterior segments, to the extent that they should not be considered serial homologs. Building on this revised understanding of the development of the pre-gnathal segments, we suggest a novel scenario for arthropod head evolution. We posit an expansion of an ancestral single-segmented head at the transition from Radiodonta to Deuteropoda in the arthropod stem group. The expanded head subdivided into three segmental units, each maintaining some of the structures of the ancestral head. This scenario is consistent with what we know of head evolution from the fossil record and helps reconcile some of the debates about early arthropod evolution.
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Affiliation(s)
- Oren Lev
- The Dept. of Ecology, Evolution & Behavior, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Ariel D Chipman
- The Dept. of Ecology, Evolution & Behavior, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem
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6
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Benito J, Chen A, Wilson LE, Bhullar BAS, Burnham D, Field DJ. Forty new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds. PeerJ 2022; 10:e13919. [PMID: 36545383 PMCID: PMC9762251 DOI: 10.7717/peerj.13919] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/28/2022] [Indexed: 12/23/2022] Open
Abstract
Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur-bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most complete morphological assessment of the postcranial skeleton of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds.
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Affiliation(s)
- Juan Benito
- Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, United Kingdom.,Department of Earth Sciences, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Albert Chen
- Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, United Kingdom.,Department of Earth Sciences, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Laura E Wilson
- Fort Hays State University, Sternberg Museum of Natural History and Department of Geosciences, Hays, Kansas, United States
| | - Bhart-Anjan S Bhullar
- Yale Peabody Museum of Natural History, New Haven, Conneticut, United States.,Department of Earth & Planetary Sciences, Yale University, New Haven, Conneticut, United States
| | - David Burnham
- University of Kansas, Biodiversity Institute and Natural History Museum, Lawrence, Kansas, United States
| | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom.,University Museum of Zoology, Cambridge, United Kingdom
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7
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Richardson MK. Theories, laws, and models in evo-devo. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:36-61. [PMID: 34570438 PMCID: PMC9292786 DOI: 10.1002/jez.b.23096] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/01/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary developmental biology (evo-devo) is the study of the evolution of developmental mechanisms. Here, I review some of the theories, models, and laws in evo-devo, past and present. Nineteenth-century evo-devo was dominated by recapitulation theory and archetypes. It also gave us germ layer theory, the vertebral theory of the skull, floral organs as modified leaves, and the "inverted invertebrate" theory, among others. Newer theories and models include the frameshift theory, the genetic toolkit for development, the ABC model of flower development, the developmental hourglass, the zootype, Urbilateria, and the hox code. Some of these new theories show the influence of archetypes and recapitulation. Interestingly, recent studies support the old "primordial leaf," "inverted invertebrate," and "segmented head" theories. Furthermore, von Baer's first three laws may now need to be rehabilitated, and the hourglass model modified, in view of what Abzhanov has pointed out about the maternal-zygotic transition. There are many supposed "laws" of evo-devo but I argue that these are merely generalizations about trends in particular lineages. I argue that the "body plan" is an archetype, and is often used in such a way that it lacks any scientific meaning. Looking to the future, one challenge for evo-devo will be to develop new theories and models to accommodate the wealth of new data from high-throughput sequencing, including single-cell sequencing. One step in this direction is the use of sophisticated in silico analyses, as in the "transcriptomic hourglass" models.
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8
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Dobreva MP, Camacho J, Abzhanov A. Time to synchronize our clocks: Connecting developmental mechanisms and evolutionary consequences of heterochrony. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:87-106. [PMID: 34826199 DOI: 10.1002/jez.b.23103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Heterochrony, defined as a change in the timing of developmental events altering the course of evolution, was first recognized by Ernst Haeckel in 1866. Haeckel's original definition was meant to explain the observed parallels between ontogeny and phylogeny, but the interpretation of his work became a source of controversy over time. Heterochrony took its modern meaning following the now classical work in the 1970-80s by Steven J. Gould, Pere Alberch, and co-workers. Predicted and described heterochronic scenarios emphasize the many ways in which developmental changes can influence evolution. However, while important examples of heterochrony detected with comparative morphological methods have multiplied, the more mechanistic understanding of this phenomenon lagged conspicuously behind. Considering the rapid progress in imaging and molecular tools available now for developmental biologists, this review aims to stress the need to take heterochrony research to the next level. It is time to synchronize the different levels of heterochrony research into a single analysis flow: from studies on organismal-level morphology to cells to molecules and genes, using complementary techniques. To illustrate how to achieve a more comprehensive understanding of phyletic morphological diversification associated with heterochrony, we discuss several recent case studies at various phylogenetic scales that combine morphological, cellular, and molecular analyses. Such a synergistic approach offers to more fully integrate phylogenetic and ontogenetic dimensions of the fascinating evolutionary phenomenon of heterochrony.
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Affiliation(s)
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Arkhat Abzhanov
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
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9
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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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10
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Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CJ, Vision TJ. A Logical Model of Homology for Comparative Biology. Syst Biol 2020; 69:345-362. [PMID: 31596473 PMCID: PMC7672696 DOI: 10.1093/sysbio/syz067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 01/09/2023] Open
Abstract
There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. [Homology; ontology; anatomy; morphology; evolution; knowledgebase; phenoscape.].
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Affiliation(s)
- Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA
| | - Wasila M Dahdul
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Todd J Vision
- Department of Biology and School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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11
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Havstad JC, Smith NA. Fossils with Feathers and Philosophy of Science. Syst Biol 2019; 68:840-851. [PMID: 30753719 PMCID: PMC6701454 DOI: 10.1093/sysbio/syz010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 01/14/2023] Open
Abstract
The last half century of paleornithological research has transformed the way that biologists perceive the evolutionary history of birds. This transformation has been driven, since 1969, by a series of exciting fossil discoveries combined with intense scientific debate over how best to interpret these discoveries. Ideally, as evidence accrues and results accumulate, interpretive scientific agreement forms. But this has not entirely happened in the debate over avian origins: the accumulation of scientific evidence and analyses has had some effect, but not a conclusive one, in terms of resolving the question of avian origins. Although the majority of biologists have come to accept that birds are dinosaurs, there is lingering and, in some quarters, strident opposition to this view. In order to both understand the ongoing disagreement about avian origins and generate a prediction about the future of the debate, here we use a revised model of scientific practice to assess the current and historical state of play surrounding the topic of bird evolutionary origins. Many scientists are familiar with the metascientific scholars Sir Karl Popper and Thomas Kuhn, and these are the primary figures that have been appealed to so far, in prior attempts to assess the dispute. But we demonstrate that a variation of Imre Lakatos's model of progressive versus degenerative research programmes provides a novel and productive assessment of the debate. We establish that a refurbished Lakatosian account both explains the intractability of the dispute and predicts a likely outcome for the debate about avian origins. In short, here, we offer a metascientific tool for rationally assessing competing theories-one that allows researchers involved in seemingly intractable scientific disputes to advance their debates.
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Affiliation(s)
- Joyce C Havstad
- Department of Philosophy, Oakland University, 146 Library Drive, Rochester, MI 48309, USA
| | - N Adam Smith
- Campbell Geology Museum, Clemson University, 140 Discovery Lane, Clemson SC 29634, USA
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12
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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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13
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Kawahata K, Cordeiro IR, Ueda S, Sheng G, Moriyama Y, Nishimori C, Yu R, Koizumi M, Okabe M, Tanaka M. Evolution of the avian digital pattern. Sci Rep 2019; 9:8560. [PMID: 31189916 PMCID: PMC6561939 DOI: 10.1038/s41598-019-44913-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/23/2019] [Indexed: 11/26/2022] Open
Abstract
Variation in digit number has occurred multiple times in the history of archosaur evolution. The five digits of dinosaur limbs were reduced to three in bird forelimbs, and were further reduced in the vestigial forelimbs of the emu. Regulation of digit number has been investigated previously by examining genes involved in anterior-posterior patterning in forelimb buds among emu (Dromaius novaehollandiae), chicken (Gallus gallus) and zebra finch (Taeniopygia guttata). It was described that the expression of posterior genes are conserved among these three birds, whereas expression of anterior genes Gli3 and Alx4 varied significantly. Here we re-examined the expression pattern of Gli3 and Alx4 in the forelimb of emu, chicken and zebra finch. We found that Gli3 is expressed in the anterior region, although its range varied among species, and that the expression pattern of Alx4 in forelimb buds is broadly conserved in a stage-specific manner. We also found that the dynamic expression pattern of the BMP antagonist Gremlin1 (Grem1) in limb buds, which is critical for autopodial expansion, was consistent with the digital pattern of emu, chicken and zebra finch. Furthermore, in emu, variation among individuals was observed in the width of Grem1 expression in forelimb buds, as well as in the adult skeletal pattern. Our results support the view that the signalling system that regulates the dynamic expression of Grem1 in the limb bud contributes substantially to variations in avian digital patterns.
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Affiliation(s)
- Kenta Kawahata
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | | | - Shogo Ueda
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Guojun Sheng
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,RIKEN Center for Developmental Biology, Kobe, Japan
| | - Yuuta Moriyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Department of Physics and Mathematics, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Chika Nishimori
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Reiko Yu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makoto Koizumi
- Laboratory Animal Facilities, The Jikei University School of Medicine, Tokyo, Japan
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, Tokyo, Japan
| | - Mikiko Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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14
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Coddington JA, Agnarsson I, Hamilton CA, Bond JE. Spiders did not repeatedly gain, but repeatedly lost, foraging webs. PeerJ 2019; 7:e6703. [PMID: 30976470 PMCID: PMC6451839 DOI: 10.7717/peerj.6703] [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: 11/12/2018] [Accepted: 02/21/2019] [Indexed: 11/20/2022] Open
Abstract
Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10-14 times, and that the orb web evolved at least three times. These findings in fact result from a particular phylogenetic character coding strategy, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e., not absent) web architectures. "Absence" of webs should be regarded as inapplicable data. To be analyzed properly by character optimization algorithms, it should be coded as "?" because these codes-or their equivalent-are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (misspellings cause some optimization algorithms to drop terminals, which affects taxon sampling and results), and mistakes in spider natural history. In sum, the method causes character optimization algorithms to produce counter-intuitive results, and does not distinguish absence from secondary loss. Proper treatment of missing entries and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ∼5-7 times, not gained 10-14 times. The orb web, specifically, may be homologous (originated only once) although lost 2-6 times.
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Affiliation(s)
- Jonathan A. Coddington
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA
| | - Ingi Agnarsson
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA
- Department of Biology, University of Vermont, Burlington, VT, United States of America
| | - Chris A. Hamilton
- Department of Entomology, Plant Pathology, & Nematology, University of Idaho, Moscow, ID, United States of America
| | - Jason E. Bond
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States of America
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15
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Dal Sasso C, Maganuco S, Cau A. The oldest ceratosaurian (Dinosauria: Theropoda), from the Lower Jurassic of Italy, sheds light on the evolution of the three-fingered hand of birds. PeerJ 2018; 6:e5976. [PMID: 30588396 PMCID: PMC6304160 DOI: 10.7717/peerj.5976] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/22/2018] [Indexed: 12/18/2022] Open
Abstract
The homology of the tridactyl hand of birds is a still debated subject, with both paleontological and developmental evidence used in support of alternative identity patterns in the avian fingers. With its simplified phalangeal morphology, the Late Jurassic ceratosaurian Limusaurus has been argued to support a II-III-IV digital identity in birds and a complex pattern of homeotic transformations in three-fingered (tetanuran) theropods. We report a new large-bodied theropod, Saltriovenator zanellai gen. et sp. nov., based on a partial skeleton from the marine Saltrio Formation (Sinemurian, lowermost Jurassic) of Lombardy (Northern Italy). Taphonomical analyses show bone bioerosion by marine invertebrates (first record for dinosaurian remains) and suggest a complex history for the carcass before being deposited on a well-oxygenated and well-illuminated sea bottom. Saltriovenator shows a mosaic of features seen in four-fingered theropods and in basal tetanurans. Phylogenetic analysis supports sister taxon relationships between the new Italian theropod and the younger Early Jurassic Berberosaurus from Morocco, in a lineage which is the basalmost of Ceratosauria. Compared to the atrophied hand of later members of Ceratosauria, Saltriovenator demonstrates that a fully functional hand, well-adapted for struggling and grasping, was primitively present in ceratosaurians. Ancestral state reconstruction along the avian stem supports 2-3-4-1-X and 2-3-4-0-X as the manual phalangeal formulae at the roots of Ceratosauria and Tetanurae, confirming the I-II-III pattern in the homology of the avian fingers. Accordingly, the peculiar hand of Limusaurus represents a derived condition restricted to late-diverging ceratosaurians and cannot help in elucidating the origin of the three-fingered condition of tetanurans. The evolution of the tridactyl hand of birds is explained by step-wise lateral simplification among non-tetanuran theropod dinosaurs, followed by a single primary axis shift from digit position 4 to 3 at the root of Tetanurae once the fourth finger was completely lost, which allowed independent losses of the vestigial fourth metacarpal among allosaurians, tyrannosauroids, and maniraptoromorphs. With an estimated body length of 7.5 m, Saltriovenator is the largest and most robust theropod from the Early Jurassic, pre-dating the occurrence in theropods of a body mass approaching 1,000 Kg by over 25 My. The radiation of larger and relatively stockier averostran theropods earlier than previously known may represent one of the factors that ignited the trend toward gigantism in Early Jurassic sauropods.
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Affiliation(s)
| | | | - Andrea Cau
- Museo Geologico "Giovanni Capellini", Bologna, Italy
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16
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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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17
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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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18
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Barta DE, Nesbitt SJ, Norell MA. The evolution of the manus of early theropod dinosaurs is characterized by high inter- and intraspecific variation. J Anat 2018; 232:80-104. [PMID: 29114853 PMCID: PMC5735062 DOI: 10.1111/joa.12719] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2017] [Indexed: 11/27/2022] Open
Abstract
The origin of the avian hand, with its reduced and fused carpals and digits, from the five-fingered hands and complex wrists of early dinosaurs represents one of the major transformations of manus morphology among tetrapods. Much attention has been directed to the later part of this transition, from four- to three-fingered taxa. However, earlier anatomical changes may have influenced these later modifications, possibly paving the way for a later frameshift in digit identities. We investigate the five- to four-fingered transition among early dinosaurs, along with changes in carpus morphology. New three-dimensional reconstructions from computed tomography data of the manus of the Triassic and Early Jurassic theropod dinosaurs Coelophysis bauri and Megapnosaurus rhodesiensis are described and compared intra- and interspecifically. Several novel findings emerge from these reconstructions and comparisons, including the first evidence of an ossified centrale and a free intermedium in some C. bauri specimens, as well as confirmation of the presence of a vestigial fifth metacarpal in this taxon. Additionally, a specimen of C. bauri and an unnamed coelophysoid from the Upper Triassic Hayden Quarry, New Mexico, are to our knowledge the only theropods (other than alvarezsaurs and birds) in which all of the distal carpals are completely fused together into a single unit. Several differences between the manus of C. bauri and M. rhodesiensis are also identified. We review the evolution of the archosauromorph manus more broadly in light of these new data, and caution against incorporating carpal characters in phylogenetic analyses of fine-scale relationships of Archosauromorpha, in light of the high degree of observed polymorphism in taxa for which large sample sizes are available, such as the theropod Coelophysis and the sauropodomorph Plateosaurus. We also find that the reduction of the carpus and ultimate loss of the fourth and fifth digits among early dinosaurs did not proceed in a neat, stepwise fashion, but was characterized by multiple losses and possible gains of carpals, metacarpals and phalanges. Taken together, the high degree of intra- and interspecific variability in the number and identities of carpals, and the state of reduction of the fourth and fifth digits suggest the presence of a 'zone of developmental variability' in early dinosaur manus evolution, from which novel avian-like morphologies eventually emerged and became channelized among later theropod clades.
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Affiliation(s)
- Daniel E. Barta
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Sterling J. Nesbitt
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of GeosciencesVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Mark A. Norell
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
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19
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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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20
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Fabrezi M, Goldberg J, Chuliver Pereyra M. Morphological Variation in Anuran Limbs: Constraints and Novelties. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:546-574. [DOI: 10.1002/jez.b.22753] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 03/27/2017] [Accepted: 05/04/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Marissa Fabrezi
- Instituto de Bio y Geociencias del NOA; IBIGEO (CONICET-UNSa); CCT-Salta Salta Argentina
| | - Javier Goldberg
- Instituto de Bio y Geociencias del NOA; IBIGEO (CONICET-UNSa); CCT-Salta Salta Argentina
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21
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Morinaga G, Bergmann PJ. Convergent body shapes have evolved via deterministic and historically contingent pathways in Lerista lizards. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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22
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Tickle C, Towers M. Sonic Hedgehog Signaling in Limb Development. Front Cell Dev Biol 2017; 5:14. [PMID: 28293554 PMCID: PMC5328949 DOI: 10.3389/fcell.2017.00014] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/08/2017] [Indexed: 02/04/2023] Open
Abstract
The gene encoding the secreted protein Sonic hedgehog (Shh) is expressed in the polarizing region (or zone of polarizing activity), a small group of mesenchyme cells at the posterior margin of the vertebrate limb bud. Detailed analyses have revealed that Shh has the properties of the long sought after polarizing region morphogen that specifies positional values across the antero-posterior axis (e.g., thumb to little finger axis) of the limb. Shh has also been shown to control the width of the limb bud by stimulating mesenchyme cell proliferation and by regulating the antero-posterior length of the apical ectodermal ridge, the signaling region required for limb bud outgrowth and the laying down of structures along the proximo-distal axis (e.g., shoulder to digits axis) of the limb. It has been shown that Shh signaling can specify antero-posterior positional values in limb buds in both a concentration- (paracrine) and time-dependent (autocrine) fashion. Currently there are several models for how Shh specifies positional values over time in the limb buds of chick and mouse embryos and how this is integrated with growth. Extensive work has elucidated downstream transcriptional targets of Shh signaling. Nevertheless, it remains unclear how antero-posterior positional values are encoded and then interpreted to give the particular structure appropriate to that position, for example, the type of digit. A distant cis-regulatory enhancer controls limb-bud-specific expression of Shh and the discovery of increasing numbers of interacting transcription factors indicate complex spatiotemporal regulation. Altered Shh signaling is implicated in clinical conditions with congenital limb defects and in the evolution of the morphological diversity of vertebrate limbs.
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Affiliation(s)
- Cheryll Tickle
- Department of Biology and Biochemistry, University of BathBath, UK
| | - Matthew Towers
- Department of Biomedical Science, The Bateson Centre, University of SheffieldWestern Bank, Sheffield, UK
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23
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Saxena A, Towers M, Cooper KL. The origins, scaling and loss of tetrapod digits. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0482. [PMID: 27994123 PMCID: PMC5182414 DOI: 10.1098/rstb.2015.0482] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/19/2022] Open
Abstract
Many of the great morphologists of the nineteenth century marvelled at similarities between the limbs of diverse species, and Charles Darwin noted these homologies as significant supporting evidence for descent with modification from a common ancestor. Sir Richard Owen also took great care to highlight each of the elements of the forelimb and hindlimb in a multitude of species with focused attention on the homology between the hoof of the horse and the middle digit of man. The ensuing decades brought about a convergence of palaeontology, experimental embryology and molecular biology to lend further support to the homologies of tetrapod limbs and their developmental origins. However, for all that we now understand about the conserved mechanisms of limb development and the development of gross morphological disturbances, little of what is presented in the experimental or medical literature reflects the remarkable diversity resulting from the 450 million year experiment of natural selection. An understanding of conserved and divergent limb morphologies in this new age of genomics and genome engineering promises to reveal more of the developmental potential residing in all limbs and to unravel the mechanisms of evolutionary variation in limb size and shape. In this review, we present the current state of our rapidly advancing understanding of the evolutionary origin of hands and feet and highlight what is known about the mechanisms that shape diverse limbs.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew Towers
- Bateson Centre, Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Kimberly L. Cooper
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,e-mail:
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24
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Anomalously high variation in postnatal development is ancestral for dinosaurs but lost in birds. Proc Natl Acad Sci U S A 2016; 113:14757-14762. [PMID: 27930315 DOI: 10.1073/pnas.1613813113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Compared with all other living reptiles, birds grow extremely fast and possess unusually low levels of intraspecific variation during postnatal development. It is now clear that birds inherited their high rates of growth from their dinosaurian ancestors, but the origin of the avian condition of low variation during development is poorly constrained. The most well-understood growth trajectories of later Mesozoic theropods (e.g., Tyrannosaurus, Allosaurus) show similarly low variation to birds, contrasting with higher variation in extant crocodylians. Here, we show that deep within Dinosauria, among the earliest-diverging dinosaurs, anomalously high intraspecific variation is widespread but then is lost in more derived theropods. This style of development is ancestral for dinosaurs and their closest relatives, and, surprisingly, this level of variation is far higher than in living crocodylians. Among early dinosaurs, this variation is widespread across Pangaea in the Triassic and Early Jurassic, and among early-diverging theropods (ceratosaurs), this variation is maintained for 165 million years to the end of the Cretaceous. Because the Late Triassic environment across Pangaea was volatile and heterogeneous, this variation may have contributed to the rise of dinosaurian dominance through the end of the Triassic Period.
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25
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Diogo R, Guinard G, Diaz RE. Dinosaurs, Chameleons, Humans, and Evo-Devo Path: Linking Étienne Geoffroy's Teratology, Waddington's Homeorhesis, Alberch's Logic of "Monsters," and Goldschmidt Hopeful "Monsters". JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:207-229. [PMID: 28422426 DOI: 10.1002/jez.b.22709] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/29/2016] [Accepted: 10/03/2016] [Indexed: 12/12/2022]
Abstract
Since the rise of evo-devo (evolutionary developmental biology) in the 1980s, few authors have attempted to combine the increasing knowledge obtained from the study of model organisms and human medicine with data from comparative anatomy and evolutionary biology in order to investigate the links between development, pathology, and macroevolution. Fortunately, this situation is slowly changing, with a renewed interest in evolutionary developmental pathology (evo-devo-path) in the past decades, as evidenced by the idea to publish this special, and very timely, issue on "Developmental Evolution in Biomedical Research." As all of us have recently been involved, independently, in works related in some way or another with evolution and developmental anomalies, we decided to join our different perspectives and backgrounds in the present contribution for this special issue. Specifically, we provide a brief historical account on the study of the links between evolution, development, and pathologies, followed by a review of the recent work done by each of us, and then by a general discussion on the broader developmental and macroevolutionary implications of our studies and works recently done by other authors. Our primary aims are to highlight the strength of studying developmental anomalies within an evolutionary framework to understand morphological diversity and disease by connecting the recent work done by us and others with the research done and broader ideas proposed by authors such as Étienne Geoffroy Saint-Hilaire, Waddington, Goldschmidt, Gould, and Per Alberch, among many others to pave the way for further and much needed work regarding abnormal development and macroevolution.
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Affiliation(s)
- Rui Diogo
- Department of Anatomy, College of Medicine, Howard University, Washington, District of Columbia
| | - Geoffrey Guinard
- UMR CNRS 5561, Biogéosciences, Université de Bourgogne, Dijon, France
| | - Raul E Diaz
- Department of Biology, La Sierra University, Riverside, California.,Natural History Museum of Los Angeles County, Los Angeles, California
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Moustakas-Verho JE, Cherepanov GO. The integumental appendages of the turtle shell: an evo-devo perspective. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 324:221-9. [PMID: 25877335 DOI: 10.1002/jez.b.22619] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/26/2015] [Indexed: 12/24/2022]
Abstract
The turtle shell is composed of dorsal armor (carapace) and ventral armor (plastron) covered by a keratinized epithelium. There are two epithelial appendages of the turtle shell: scutes (large epidermal shields separated by furrows and forming a unique mosaic) and tubercles (numerous small epidermal bumps located on the carapaces of some species). In our perspective, we take a synthetic, comparative approach to consider the homology and evolution of these integumental appendages. Scutes have been more intensively studied, as they are autapomorphic for turtles and can be diagnostic taxonomically. Their pattern of tessellation is stable phylogenetically, but labile in the individual. We discuss the history of developmental investigations of these structures and hypotheses of evolutionary and anomalous variation. In our estimation, the scutes of the turtle shell are an evolutionary novelty, whereas the tubercles found on the shells of some turtles are homologous to reptilian scales.
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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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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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Musser JM, Wagner GP. Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called "species signal". JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:588-604. [PMID: 26175303 DOI: 10.1002/jez.b.22636] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/29/2015] [Indexed: 01/01/2023]
Abstract
We elaborate a framework for investigating the evolutionary history of morphological characters. We argue that morphological character trees generated by phylogenetic analysis of transcriptomes provide a useful tool for identifying causal gene expression differences underlying the development and evolution of morphological characters. They also enable rigorous testing of different models of morphological character evolution and origination, including the hypothesis that characters originate via divergence of repeated ancestral characters. Finally, morphological character trees provide evidence that character transcriptomes undergo concerted evolution. We argue that concerted evolution of transcriptomes can explain the so-called "species signal" found in several recent comparative transcriptome studies. The species signal is the phenomenon that transcriptomes cluster by species rather than character type, even though the characters are older than the respective species. We suggest the species signal is a natural consequence of concerted gene expression evolution resulting from mutations that alter gene regulatory network interactions shared by the characters under comparison. Thus, character trees generated from transcriptomes allow us to investigate the variational independence, or individuation, of morphological characters at the level of genetic programs.
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Affiliation(s)
- Jacob M Musser
- Yale Systems Biology Institute, West Haven, Connecticut.,Yale Peabody Museum of Natural History, New Haven, Connecticut.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Günter P Wagner
- Yale Systems Biology Institute, West Haven, Connecticut.,Yale Peabody Museum of Natural History, New Haven, Connecticut.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut.,Department of Obstetrics Gynecology and Reproductive Sciences, Yale Medical School, New Haven, Connecticut.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan
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Cau A, Brougham T, Naish D. The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird? PeerJ 2015; 3:e1032. [PMID: 26157616 PMCID: PMC4476167 DOI: 10.7717/peerj.1032] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/27/2015] [Indexed: 11/20/2022] Open
Abstract
The exceptionally well-preserved Romanian dinosaur Balaur bondoc is the most complete theropod known to date from the Upper Cretaceous of Europe. Previous studies of this remarkable taxon have included its phylogenetic interpretation as an aberrant dromaeosaurid with velociraptorine affinities. However, Balaur displays a combination of both apparently plesiomorphic and derived bird-like characters. Here, we analyse those features in a phylogenetic revision and show how they challenge its referral to Dromaeosauridae. Our reanalysis of two distinct phylogenetic datasets focusing on basal paravian taxa supports the reinterpretation of Balaur as an avialan more crownward than Archaeopteryx but outside of Pygostylia, and as a flightless taxon within a paraphyletic assemblage of long-tailed birds. Our placement of Balaur within Avialae is not biased by character weighting. The placement among dromaeosaurids resulted in a suboptimal alternative that cannot be rejected based on the data to hand. Interpreted as a dromaeosaurid, Balaur has been assumed to be hypercarnivorous and predatory, exhibiting a peculiar morphology influenced by island endemism. However, a dromaeosaurid-like ecology is contradicted by several details of Balaur's morphology, including the loss of a third functional manual digit, the non-ginglymoid distal end of metatarsal II, and a non-falciform ungual on the second pedal digit that lacks a prominent flexor tubercle. Conversely, an omnivorous ecology is better supported by Balaur's morphology and is consistent with its phylogenetic placement within Avialae. Our reinterpretation of Balaur implies that a superficially dromaeosaurid-like taxon represents the enlarged, terrestrialised descendant of smaller and probably volant ancestors.
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Affiliation(s)
- Andrea Cau
- Earth, Life and Environmental Sciences Department, Alma Mater Studiorum, Bologna University, Italy
| | - Tom Brougham
- Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Darren Naish
- Ocean and Earth Science, University of Southampton, Southampton, UK
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Hirasawa T, Kuratani S. Evolution of the vertebrate skeleton: morphology, embryology, and development. ZOOLOGICAL LETTERS 2015; 1:2. [PMID: 26605047 PMCID: PMC4604106 DOI: 10.1186/s40851-014-0007-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/19/2014] [Indexed: 05/08/2023]
Abstract
Two major skeletal systems-the endoskeleton and exoskeleton-are recognized in vertebrate evolution. Here, we propose that these two systems are distinguished primarily by their relative positions, not by differences in embryonic histogenesis or cell lineage of origin. Comparative embryologic analyses have shown that both types of skeleton have changed their mode of histogenesis during evolution. Although exoskeletons were thought to arise exclusively from the neural crest, recent experiments in teleosts have shown that exoskeletons in the trunk are mesodermal in origin. The enameloid and dentine-coated postcranial exoskeleton seen in many vertebrates does not appear to represent an ancestral condition, as previously hypothesized, but rather a derived condition, in which the enameloid and dentine tissues became accreted to bones. Recent data from placoderm fossils are compatible with this scenario. In contrast, the skull contains neural crest-derived bones in its rostral part. Recent developmental studies suggest that the boundary between neural crest- and mesoderm-derived bones may not be consistent throughout evolution. Rather, the relative positions of bony elements may be conserved, and homologies of bony elements have been retained, with opportunistic changes in the mechanisms and cell lineages of development.
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Affiliation(s)
- Tatsuya Hirasawa
- Evolutionary Morphology Laboratory, RIKEN, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Shigeru Kuratani
- Evolutionary Morphology Laboratory, RIKEN, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047 Japan
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Gerson EM. The Interaction of Research Systems in the Evo-devo Juncture. BOSTON STUDIES IN THE PHILOSOPHY AND HISTORY OF SCIENCE 2015. [DOI: 10.1007/978-94-017-9412-1_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Xu X, Zhou Z, Dudley R, Mackem S, Chuong CM, Erickson GM, Varricchio DJ. An integrative approach to understanding bird origins. Science 2014; 346:1253293. [DOI: 10.1126/science.1253293] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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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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Introduction to Evolutionary Teratology, with an Application to the Forelimbs of Tyrannosauridae and Carnotaurinae (Dinosauria: Theropoda). Evol Biol 2014. [DOI: 10.1007/s11692-014-9296-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Botelho JF, Ossa-Fuentes L, Soto-Acuña S, Smith-Paredes D, Nuñez-León D, Salinas-Saavedra M, Ruiz-Flores M, Vargas AO. New developmental evidence clarifies the evolution of wrist bones in the dinosaur-bird transition. PLoS Biol 2014; 12:e1001957. [PMID: 25268520 PMCID: PMC4181957 DOI: 10.1371/journal.pbio.1001957] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/20/2014] [Indexed: 01/22/2023] Open
Abstract
From early dinosaurs with as many as nine wrist bones, modern birds evolved to develop only four ossifications. Their identity is uncertain, with different labels used in palaeontology and developmental biology. We examined embryos of several species and studied chicken embryos in detail through a new technique allowing whole-mount immunofluorescence of the embryonic cartilaginous skeleton. Beyond previous controversy, we establish that the proximal-anterior ossification develops from a composite radiale+intermedium cartilage, consistent with fusion of radiale and intermedium observed in some theropod dinosaurs. Despite previous claims that the development of the distal-anterior ossification does not support the dinosaur-bird link, we found its embryonic precursor shows two distinct regions of both collagen type II and collagen type IX expression, resembling the composite semilunate bone of bird-like dinosaurs (distal carpal 1+distal carpal 2). The distal-posterior ossification develops from a cartilage referred to as "element x," but its position corresponds to distal carpal 3. The proximal-posterior ossification is perhaps most controversial: It is labelled as the ulnare in palaeontology, but we confirm the embryonic ulnare is lost during development. Re-examination of the fossil evidence reveals the ulnare was actually absent in bird-like dinosaurs. We confirm the proximal-posterior bone is a pisiform in terms of embryonic position and its development as a sesamoid associated to a tendon. However, the pisiform is absent in bird-like dinosaurs, which are known from several articulated specimens. The combined data provide compelling evidence of a remarkable evolutionary reversal: A large, ossified pisiform re-evolved in the lineage leading to birds, after a period in which it was either absent, nonossified, or very small, consistently escaping fossil preservation. The bird wrist provides a modern example of how developmental and paleontological data illuminate each other. Based on all available data, we introduce a new nomenclature for bird wrist ossifications.
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Affiliation(s)
- João Francisco Botelho
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Luis Ossa-Fuentes
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sergio Soto-Acuña
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Daniel Smith-Paredes
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Daniel Nuñez-León
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Miguel Salinas-Saavedra
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena Ruiz-Flores
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Alexander O. Vargas
- Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Xu X, Han F, Zhao Q. Homologies and homeotic transformation of the theropod 'semilunate' carpal. Sci Rep 2014; 4:6042. [PMID: 25116378 PMCID: PMC4131224 DOI: 10.1038/srep06042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/02/2014] [Indexed: 11/20/2022] Open
Abstract
The homology of the 'semilunate' carpal, an important structure linking non-avian and avian dinosaurs, has been controversial. Here we describe the morphology of some theropod wrists, demonstrating that the 'semilunate' carpal is not formed by the same carpal elements in all theropods possessing this feature and that the involvement of the lateralmost distal carpal in forming the 'semilunate' carpal of birds is an inheritance from their non-avian theropod ancestors. Optimization of relevant morphological features indicates that these features evolved in an incremental way and the 'semilunate' structure underwent a lateral shift in position during theropod evolution, possibly as a result of selection for foldable wings in birds and their close theropod relatives. We propose that homeotic transformation was involved in the evolution of the 'semilunate' carpal. In combination with developmental data on avian wing digits, this suggests that homeosis played a significant role in theropod hand evolution in general.
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Affiliation(s)
- Xing Xu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology & Paleoanthropology, Chinese Academy of Sciences, 142 Xiwai Street, Beijing 100044
| | - Fenglu Han
- Faculty of Earth Sciences, China University of Geosciences, No. 388 Lumo Road, Wuhan 430074, People's Republic of China
| | - Qi Zhao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology & Paleoanthropology, Chinese Academy of Sciences, 142 Xiwai Street, Beijing 100044
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Salinas-Saavedra M, Gonzalez-Cabrera C, Ossa-Fuentes L, Botelho JF, Ruiz-Flores M, Vargas AO. New developmental evidence supports a homeotic frameshift of digit identity in the evolution of the bird wing. Front Zool 2014; 11:33. [PMID: 24725625 PMCID: PMC3986427 DOI: 10.1186/1742-9994-11-33] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/07/2014] [Indexed: 01/09/2023] Open
Abstract
Background The homology of the digits in the bird wing is a high-profile controversy in developmental and evolutionary biology. The embryonic position of the digits cartilages with respect to the primary axis (ulnare and ulna) corresponds to 2, 3, 4, but comparative-evolutionary morphology supports 1, 2, 3. A homeotic frameshift of digit identity in evolution could explain how cells in embryonic positions 2, 3, 4 began developing morphologies 1, 2, 3. Another alternative is that no re-patterning of cell fates occurred, and the primary axis shifted its position by some other mechanism. In the wing, only the anterior digit lacks expression of HoxD10 and HoxD12, resembling digit 1 of other limbs, as predicted by 1, 2, 3. However, upon loss of digit 1 in evolution, the most anterior digit 2 could have lost their expression, deceitfully resembling a digit 1. To test this notion, we observed HoxD10 and HoxD12 in a limb where digit 2 is the most anterior digit: The rabbit foot. We also explored whether early inhibition of Shh signalling in the embryonic wing bud induces an experimental homeotic frameshift, or an experimental axis shift. We tested these hypotheses using DiI injections to study the fate of cells in these experimental wings. Results We found strong transcription of HoxD10 and HoxD12 was present in the most anterior digit 2 of the rabbit foot. Thus, we found no evidence to question the use of HoxD expression as support for 1, 2, 3. When Shh signalling in early wing buds is inhibited, our fate maps demonstrate that an experimental homeotic frameshift is induced. Conclusion Along with comparative morphology, HoxD expression provides strong support for 1, 2, 3 identity of wing digits. As an explanation for the offset 2, 3, 4 embryological position, the homeotic frameshift hypothesis is consistent with known mechanisms of limb development, and further proven to be experimentally possible. In contrast, the underlying mechanisms and experimental plausibility of an axis shift remain unclear.
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Affiliation(s)
- Miguel Salinas-Saavedra
- Laboratorio de Ontogenia y Filogenia. Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Cristian Gonzalez-Cabrera
- Laboratorio de Ontogenia y Filogenia. Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Luis Ossa-Fuentes
- Laboratorio de Ontogenia y Filogenia. Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Joao F Botelho
- Laboratorio de Ontogenia y Filogenia. Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Macarena Ruiz-Flores
- Laboratorio de Ontogenia y Filogenia. Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Alexander O Vargas
- Laboratorio de Ontogenia y Filogenia. Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
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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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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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Reno PL, Horton WE, Lovejoy CO. Metapodial or phalanx? An evolutionary and developmental perspective on the homology of the first ray's proximal segment. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:276-85. [PMID: 23640850 DOI: 10.1002/jez.b.22506] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/29/2013] [Accepted: 04/01/2013] [Indexed: 12/30/2022]
Abstract
The first mammalian metapodial (MP1) has periodically been argued to actually be a phalanx, because the first ray has one less element than the four posterior rays, and because the MP1 growth plate is proximal like those of all phalanges, rather than distal as in metapodials 2-5. However, growth plates are formed at both ends in non-therian tetrapod metapodials, and phylogenetic analysis demonstrates that growth plate loss is a therian synapomorphy that postdates the establishment of the mammalian phalangeal formula. These data, along with results of developmental and morphological studies, suggest that the MP1 is not a phalanx. The singular, proximal growth plates in MPs 2-5 are likely to be an adaptation to dynamic erect quadrupedal gait which was characterized by conversion of the posterior metapodials into rigid struts with the carpus/tarsus. While the adaptive significance of the reversed ossification of MP1 is less clear, we present three functional/developmental hypotheses.
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Affiliation(s)
- Philip L Reno
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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Seki R, Kamiyama N, Tadokoro A, Nomura N, Tsuihiji T, Manabe M, Tamura K. Evolutionary and Developmental Aspects of Avian-Specific Traits in Limb Skeletal Pattern. Zoolog Sci 2012; 29:631-44. [DOI: 10.2108/zsj.29.631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Grieco TM, Rizk OT, Hlusko LJ. A MODULAR FRAMEWORK CHARACTERIZES MICRO- AND MACROEVOLUTION OF OLD WORLD MONKEY DENTITIONS. Evolution 2012; 67:241-59. [DOI: 10.1111/j.1558-5646.2012.01757.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Maxwell EE. Unraveling the influences of soft-tissue flipper development on skeletal variation using an extinct taxon. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 318:545-54. [PMID: 22744735 DOI: 10.1002/jez.b.22459] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 03/19/2012] [Accepted: 05/18/2012] [Indexed: 11/09/2022]
Abstract
Adaptation to an aquatic habitat results in dramatic changes in tetrapod limb morphology as limbs take on the roles of propulsion and steering and lose their weight-bearing function. Changes include enclosure of the limb in a soft-tissue flipper and proportional lengthening of the distal limb, often accomplished through the addition of skeletal elements (hyperphalangy). The flipper structure itself and changes to the developmental architecture permitting hyperphalangy are hypothesized to increase observed limb variation, based on a cetacean model. These hypotheses are examined in the ichthyosaurs Stenopterygius and Mixosaurus. Hyperphalangy combined with high levels of variation in phalangeal counts were observed in both genera. The amount of variation was not proportional to the number of phalanges in a digit, but was related to functional digit length. In addition, qualitative variants were catalogued in both genera. Polyphalangy, phalangeal fusion, and additional ossifications in the zeugopodial row were not observed in Mixosaurus, but were common in Stenopterygius, even though both genera exhibited a similar degree of hyperphalangy. These results suggest that while the flipper structure and processes resulting in hyperphalangy may increase observed variation in phalangeal counts, these factors are unlikely to be causing high levels of qualitative variation in ichthyosaurs. Patterns of variation in ichthyosaur limbs, and thus variability, are unique to species but can change over evolutionary time.
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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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Engeman JM, Mabee PM. Segmentation and fusion on the midline: basibranchial homologies in cypriniform fishes. J Morphol 2012; 273:725-36. [PMID: 22460806 DOI: 10.1002/jmor.20017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 12/17/2011] [Accepted: 02/05/2012] [Indexed: 11/09/2022]
Abstract
The development and homologies of the median elements of the ventral hyoid and branchial arches of Cypriniformes have been unclear. We compared the developmental morphology of this region across five species (Cycleptus elongatus, Luxilus zonatus, Danio rerio, Devario auropurpureus, and Cobitis striata), representing three of five major clades of cypriniforms. The development of basibranchial 1 is similar in catostomids and cyprinids, where a single, elongate, basihyal + anterior copula divides into separate elements. A gap develops between the posterior end of the basihyal cartilage and the anterior copula in catostomids but in cyprinids (Luxiluszonatus, Danio rerio, and Devarioauropurpureus) there is little separation and the basihyal and basibranchial 1 may grow close together or retain a cartilaginous connection (Danio rerio, several outgroups). In loaches and Gyrinocheilus, the gap posterior to the basihyal has been alternately interpreted as either the absence or posterior displacement of basibranchial 1. Uniquely among examined species, in Cobitis striata, the basihyal cartilage and anterior copula form as separate cartilages and remain distinct throughout development with a prominent gap between the basihyal and most anterior basibranchial, which we interpret as loss of basibranchial 1. In the posterior region associated with branchial arches 4 and 5, all examined species except Danio rerio, which has only a basibranchial 4 cartilage, have separate basibranchial 4 and 5 cartilages in early ontogeny. Basibranchials 4 and 5 remain separate in Cycleptus elongatus, Devario auropurpurea, and Cobitis striata, but fuse in Luxilus zonatus to form a posterior copula. The orientation of basibranchial 4 and 5 cartilages in Cobitis striata is similar to catostomids and cyprinids. The most posterior median element in the branchial arches, the post-ceratobranchial cartilage, generally forms as a separate cartilage in catostomids but in Cobitis striata is connected with basibranchial 5 cartilage from earliest appearance.
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Affiliation(s)
- Jeffrey M Engeman
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
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Finalism in Darwinian and Lamarckian Evolution: Lessons from Epigenetics and Developmental Biology. Evol Biol 2012. [DOI: 10.1007/s11692-012-9163-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Shockey BJ, Flynn JJ, Croft DA, Gans P, Wyss AR. New Leontiniid Notoungulata (Mammalia) from Chile and Argentina: Comparative Anatomy, Character Analysis, and Phylogenetic Hypotheses. AMERICAN MUSEUM NOVITATES 2012. [DOI: 10.1206/3737.2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
RNA-seq transcriptomics of digit primordia in the developing chick wing and leg has clarified a long-standing dispute between paleontologists and embryologists about evolutionary homology.
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Affiliation(s)
- Martin D Carkett
- Division of Developmental Biology, MRC National Institute of Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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