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Arimura S, Wong MKS, Inoue R, Kawano M, Shimoyama K, Fujimori C, Tokunaga K, Takagi W, Hyodo S. Functional characterization of follicle-stimulating hormone and luteinizing hormone receptors in cloudy catshark, Scyliorhinus torazame. Gen Comp Endocrinol 2024; 354:114542. [PMID: 38685391 DOI: 10.1016/j.ygcen.2024.114542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The follicle-stimulating hormone receptor (FSHR) and luteinizing hormone receptor (LHR) in cloudy catshark were cloned, and recombinant FSHR and LHR were expressed for characterization. Ventral lobe extract (VLE) from the pituitary contains homologous FSH and LH, and it stimulated the cAMP signaling of FSHR and LHR dose-dependently. Two transcript variants of LHR (LHR-L with exon 10 and LHR-S without) were identified, and LHR-S was the dominant form with higher basal cAMP activity without VLE stimulation. Among various developmental stages of follicles, FSHR expression was mainly associated with the pre-vitellogenic and early white follicles. When follicles were recruited into vitellogenesis, the expression of FSHR decreased while of LHR was upregulated reciprocally, suggesting that LHR may also be responsible for the control of vitellogenesis in chondrichthyans. The expression of LHR-L was upregulated among maturing follicles before ovulation, indicating LHR-L could have a specific role in receiving the LH surge signal for final maturation. Plasma LH-like activity was transiently increased prior to the progesterone (P4)-surge and testosterone-drop at the beginning of P4-phase, supporting a pituitary control of follicle-maturation via LH signaling in chondrichthyans. The expression of follicular LHR was downregulated during the P4-phase when LH-like activity was high, indicating that the LH-dependent downregulation of LHR is conserved in chondrichthyans as it is in other vertebrate lineages. (213 words).
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Affiliation(s)
- Shogo Arimura
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Marty Kwok Shing Wong
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Ryotaro Inoue
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Mai Kawano
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Koya Shimoyama
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Chika Fujimori
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | - Kotaro Tokunaga
- Ibaraki Prefectural Oarai Aquarium, Oarai, Ibaraki 311-1301, Japan.
| | - Wataru Takagi
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Susumu Hyodo
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
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Sales-Oliveira VC, Dos Santos RZ, Goes CAG, Calegari RM, Garrido-Ramos MA, Altmanová M, Ezaz T, Liehr T, Porto-Foresti F, Utsunomia R, Cioffi MB. Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia). BMC Biol 2024; 22:47. [PMID: 38413947 PMCID: PMC10900743 DOI: 10.1186/s12915-024-01847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time. RESULTS Alligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement. CONCLUSIONS Alligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.
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Affiliation(s)
- Vanessa C Sales-Oliveira
- Departamento de Genética E Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | - Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
| | | | | | - Marcelo B Cioffi
- Departamento de Genética E Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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3
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Sales-Oliveira V, Altmanová M, Gvoždík V, Kretschmer R, Ezaz T, Liehr T, Padutsch N, Badjedjea G, Utsunomia R, Tanomtong A, Cioffi M. Cross-species chromosome painting and repetitive DNA mapping illuminate the karyotype evolution in true crocodiles (Crocodylidae). Chromosoma 2023; 132:289-303. [PMID: 37493806 DOI: 10.1007/s00412-023-00806-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/23/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Crocodilians have maintained very similar karyotype structures and diploid chromosome numbers for around 100 million years, with only minor variations in collinearity. Why this karyotype structure has largely stayed unaltered for so long is unclear. In this study, we analyzed the karyotypes of six species belonging to the genera Crocodylus and Osteolaemus (Crocodylidae, true crocodiles), among which the Congolian endemic O. osborni was included and investigated. We utilized various techniques (differential staining, fluorescence in situ hybridization with repetitive DNA and rDNA probes, whole chromosome painting, and comparative genomic hybridization) to better understand how crocodile chromosomes evolved. We studied representatives of three of the four main diploid chromosome numbers found in crocodiles (2n = 30/32/38). Our data provided new information about the species studied, including the identification of four major chromosomal rearrangements that occurred during the karyotype diversification process in crocodiles. These changes led to the current diploid chromosome numbers of 2n = 30 (fusion) and 2n = 38 (fissions), derived from the ancestral state of 2n = 32. The conserved cytogenetic tendency in crocodilians, where extant species keep near-ancestral state, contrasts with the more dynamic karyotype evolution seen in other major reptile groups.
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Affiliation(s)
- Vanessa Sales-Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand
| | - Marcelo Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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Doody JS, Burghardt G, Dinets V. The Evolution of Sociality and the Polyvagal Theory. Biol Psychol 2023; 180:108569. [PMID: 37094735 DOI: 10.1016/j.biopsycho.2023.108569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
The polyvagal theory (PT), offered by Porges (2021), proposes that the autonomic nervous system (ANS) was repurposed in mammals, via a "second vagal nerve", to suppress defensive strategies and support the expression of sociality. Three critical assumptions of this theory are that (1) the transition of the ANS was associated with the evolution of 'social' mammals from 'asocial' reptiles; (2) the transition enabled mammals, unlike their reptilian ancestors, to derive a biological benefit from social interactions; and (3) the transition forces a less parsimonious explanation (convergence) for the evolution of social behavior in birds and mammals, since birds evolved from a reptilian lineage. Two recently published reviews, however, provided compelling evidence that the social-asocial dichotomy is overly simplistic, neglects the diversity of vertebrate social systems, impedes our understanding of the evolution of social behavior, and perpetuates the erroneous belief that one group-non-avian reptiles-is incapable of complex social behavior. In the worst case, if PT depends upon a transition from 'asocial reptiles' to 'social mammals,' then the ability of PT to explain the evolution of the mammalian ANS is highly questionable. A great number of social behaviors occur in both reptiles and mammals. In the best case, PT has misused the terms 'social' and 'asocial'. Even here, however, the theory would still need to identify a particular suite of behaviors found in mammals and not reptiles that could be associated with, or explain, the transition of the ANS, and then replace the 'asocial' and 'social' labels with more specific descriptors.
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Affiliation(s)
- J Sean Doody
- Department of Integrative Biology, University of South Florida - St. Petersburg Campus, 140 7(th) Ave. South, St. Petersburg, Florida 33701, USA
| | - Gordon Burghardt
- Department of Psychology, University of Tennessee, 1404 Circle Drive, Knoxville, TN 37996; Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996
| | - Vladimir Dinets
- Department of Psychology, University of Tennessee, 1404 Circle Drive, Knoxville, TN 37996
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5
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Opazo JC, Vandewege MW, Hoffmann FG, Zavala K, Meléndez C, Luchsinger C, Cavieres VA, Vargas-Chacoff L, Morera FJ, Burgos PV, Tapia-Rojas C, Mardones GA. How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member. Mol Biol Evol 2023; 40:6993039. [PMID: 36656997 PMCID: PMC9897032 DOI: 10.1093/molbev/msad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.
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Affiliation(s)
| | - Michael W Vandewege
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Catalina Meléndez
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Charlotte Luchsinger
- Department of Physiology, School of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Viviana A Cavieres
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Luis Vargas-Chacoff
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, Universidad Austral de Chile, Valdivia, Chile
| | - Francisco J Morera
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Applied Biochemistry Laboratory, Facultad de Ciencias Veterinarias, Instituto de Farmacología y Morfofisiología, Universidad Austral de Chile, Valdivia, Chile
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Cheril Tapia-Rojas
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
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6
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Tokita M, Sato H. Creating morphological diversity in reptilian temporal skull region: A review of potential developmental mechanisms. Evol Dev 2023; 25:15-31. [PMID: 36250751 DOI: 10.1111/ede.12419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 01/13/2023]
Abstract
Reptilian skull morphology is highly diverse and broadly categorized into three categories based on the number and position of the temporal fenestrations: anapsid, synapsid, and diapsid. According to recent phylogenetic analysis, temporal fenestrations evolved twice independently in amniotes, once in Synapsida and once in Diapsida. Although functional aspects underlying the evolution of tetrapod temporal fenestrations have been well investigated, few studies have investigated the developmental mechanisms responsible for differences in the pattern of temporal skull region. To determine what these mechanisms might be, we first examined how the five temporal bones develop by comparing embryonic cranial osteogenesis between representative extant reptilian species. The pattern of temporal skull region may depend on differences in temporal bone growth rate and growth direction during ontogeny. Next, we compared the histogenesis patterns and the expression of two key osteogenic genes, Runx2 and Msx2, in the temporal region of the representative reptilian embryos. Our comparative analyses suggest that the embryonic histological condition of the domain where temporal fenestrations would form predicts temporal skull morphology in adults and regulatory modifications of Runx2 and Msx2 expression in osteogenic mesenchymal precursor cells are likely involved in generating morphological diversity in the temporal skull region of reptiles.
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Affiliation(s)
- Masayoshi Tokita
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Hiromu Sato
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
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7
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Oliveira VCS, Altmanová M, Viana PF, Ezaz T, Bertollo LAC, Ráb P, Liehr T, Al-Rikabi A, Feldberg E, Hatanaka T, Scholz S, Meurer A, de Bello Cioffi M. Revisiting the Karyotypes of Alligators and Caimans (Crocodylia, Alligatoridae) after a Half-Century Delay: Bridging the Gap in the Chromosomal Evolution of Reptiles. Cells 2021; 10:cells10061397. [PMID: 34198806 PMCID: PMC8228166 DOI: 10.3390/cells10061397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/16/2022] Open
Abstract
Although crocodilians have attracted enormous attention in other research fields, from the cytogenetic point of view, this group remains understudied. Here, we analyzed the karyotypes of eight species formally described from the Alligatoridae family using differential staining, fluorescence in situ hybridization with rDNA and repetitive motifs as a probe, whole chromosome painting (WCP), and comparative genome hybridization. All Caimaninae species have a diploid chromosome number (2n) 42 and karyotypes dominated by acrocentric chromosomes, in contrast to both species of Alligatorinae, which have 2n = 32 and karyotypes that are predominantly metacentric, suggesting fusion/fission rearrangements. Our WCP results supported this scenario by revealing the homeology of the largest metacentric pair present in both Alligator spp. with two smaller pairs of acrocentrics in Caimaninae species. The clusters of 18S rDNA were found on one chromosome pair in all species, except for Paleosuchus spp., which possessed three chromosome pairs bearing these sites. Similarly, comparative genomic hybridization demonstrated an advanced stage of sequence divergence among the caiman genomes, with Paleosuchus standing out as the most divergent. Thus, although Alligatoridae exhibited rather low species diversity and some level of karyotype stasis, their genomic content indicates that they are not as conserved as previously thought. These new data deepen the discussion of cytotaxonomy in this family.
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Affiliation(s)
- Vanessa C. S. Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil; (V.C.S.O.); (L.A.C.B.); (T.H.); (M.d.B.C.)
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic;
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic;
| | - Patrik F. Viana
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69083-000, Brazil; (P.F.V.); (E.F.)
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617, Australia;
| | - Luiz A. C. Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil; (V.C.S.O.); (L.A.C.B.); (T.H.); (M.d.B.C.)
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic;
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
- Correspondence: ; Tel.: +49-36-41-939-68-50; Fax: +49-3641-93-96-852
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69083-000, Brazil; (P.F.V.); (E.F.)
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil; (V.C.S.O.); (L.A.C.B.); (T.H.); (M.d.B.C.)
| | | | | | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil; (V.C.S.O.); (L.A.C.B.); (T.H.); (M.d.B.C.)
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8
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Mahbub M, Wahab Z, Reaz R, Rahman MS, Bayzid MS. wQFM: Highly Accurate Genome-scale Species Tree Estimation from Weighted Quartets. Bioinformatics 2021; 37:3734-3743. [PMID: 34086858 DOI: 10.1093/bioinformatics/btab428] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging. RESULTS We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL. AVAILABILITY wQFM is available in open source form at https://github.com/Mahim1997/wQFM-2020. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mahim Mahbub
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Zahin Wahab
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Rezwana Reaz
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - M Saifur Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
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9
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Starck JM, Stewart JR, Blackburn DG. Phylogeny and evolutionary history of the amniote egg. J Morphol 2021; 282:1080-1122. [PMID: 33991358 DOI: 10.1002/jmor.21380] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 01/02/2023]
Abstract
We review morphological features of the amniote egg and embryos in a comparative phylogenetic framework, including all major clades of extant vertebrates. We discuss 40 characters that are relevant for an analysis of the evolutionary history of the vertebrate egg. Special attention is given to the morphology of the cellular yolk sac, the eggshell, and extraembryonic membranes. Many features that are typically assigned to amniotes, such as a large yolk sac, delayed egg deposition, and terrestrial reproduction have evolved independently and convergently in numerous clades of vertebrates. We use phylogenetic character mapping and ancestral character state reconstruction as tools to recognize sequence, order, and patterns of morphological evolution and deduce a hypothesis of the evolutionary history of the amniote egg. Besides amnion and chorioallantois, amniotes ancestrally possess copulatory organs (secondarily reduced in most birds), internal fertilization, and delayed deposition of eggs that contain an embryo in the primitive streak or early somite stage. Except for the amnion, chorioallantois, and amniote type of eggshell, these features evolved convergently in almost all major clades of aquatic vertebrates possibly in response to selective factors such as egg predation, hostile environmental conditions for egg development, or to adjust hatching of young to favorable season. A functionally important feature of the amnion membrane is its myogenic contractility that moves the (early) embryo and prevents adhering of the growing embryo to extraembryonic materials. This function of the amnion membrane and the liquid-filled amnion cavity may have evolved under the requirements of delayed deposition of eggs that contain developing embryos. The chorioallantois is a temporary embryonic exchange organ that supports embryonic development. A possible evolutionary scenario is that the amniote egg presents an exaptation that paved the evolutionary pathway for reproduction on land. As shown by numerous examples from anamniotes, reproduction on land has occurred multiple times among vertebrates-the amniote egg presenting one "solution" that enabled the conquest of land for reproduction.
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Affiliation(s)
- J Matthias Starck
- Department of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - James R Stewart
- Department of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee, USA
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10
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Lyson TR, Bever GS. Origin and Evolution of the Turtle Body Plan. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-024746] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin of turtles and their uniquely shelled body plan is one of the longest standing problems in vertebrate biology. The unfulfilled need for a hypothesis that both explains the derived nature of turtle anatomy and resolves their unclear phylogenetic position among reptiles largely reflects the absence of a transitional fossil record. Recent discoveries have dramatically improved this situation, providing an integrated, time-calibrated model of the morphological, developmental, and ecological transformations responsible for the modern turtle body plan. This evolutionary trajectory was initiated in the Permian (>260 million years ago) when a turtle ancestor with a diapsid skull evolved a novel mechanism for lung ventilation. This key innovation permitted the torso to become apomorphically stiff, most likely as an adaption for digging and a fossorial ecology. The construction of the modern turtle body plan then proceeded over the next 100 million years following a largely stepwise model of osteological innovation.
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Affiliation(s)
- Tyler R. Lyson
- Department of Earth Sciences, Denver Museum of Nature & Science, Denver, Colorado 80205, USA
| | - Gabriel S. Bever
- Department of Earth Sciences, Denver Museum of Nature & Science, Denver, Colorado 80205, USA
- Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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11
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Blackburn DG. Functional morphology, diversity, and evolution of yolk processing specializations in embryonic reptiles and birds. J Morphol 2020; 282:995-1014. [PMID: 32960458 DOI: 10.1002/jmor.21267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022]
Abstract
Evolution of the terrestrial, amniotic egg of vertebrates required new mechanisms by which yolk material could be processed for embryonic use. Recent studies on each of the major extant reptile groups have revealed elaborate morphological specializations for yolk processing, features that differ dramatically from those of birds. In the avian pattern, liquid yolk is housed in a yolk sac whose endodermal lining absorbs and digests yolk material and sends resultant nutrients into the blood circulation. In snakes, lizards, turtles, and crocodilians, as documented herein, the yolk sac becomes invaded by endodermal cells that proliferate and phagocytose yolk material. Blood vessels then invade, and the endodermal cells become arranged around them, forming elongated "spaghetti-like" strands that fill the yolk sac cavity. This pattern provides an effective means by which yolk material is cellularized, digested, and transported by vitelline vessels to the developing embryo. Phylogenetically, the (non-avian) "reptilian" pattern was ancestral for sauropsids and was modified or replaced in ancestors to birds. This review postulates that evolution of the "avian" pattern involved increased reliance on extracellular digestion of yolk, allowing embryonic development to occur more rapidly than in typical reptiles. Comparative studies of yolk processing that draw on morphological, biochemical, molecular approaches are needed to explain how and why the "reptilian" pattern was replaced in birds or their archosaurian ancestors.
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Affiliation(s)
- Daniel G Blackburn
- Department of Biology, Electron Microscopy Center, Trinity College, Hartford, Connecticut, USA
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12
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Lõrincz D, Kálmán M. Distribution of GFAP in Squamata: Extended Immunonegative Areas, Astrocytes, High Diversity, and Their Bearing on Evolution. Front Neuroanat 2020; 14:49. [PMID: 32922269 PMCID: PMC7457009 DOI: 10.3389/fnana.2020.00049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/13/2020] [Indexed: 11/27/2022] Open
Abstract
Squamata is one of the richest and most diverse extant groups. The present study investigates the glial fibrillary acidic protein (GFAP)-immunopositive elements of five lizard and three snake species; each represents a different family. The study continues our former studies on bird, turtle, and caiman brains. Although several studies have been published on lizards, they usually only investigated one species. Almost no data are available on snakes. The animals were transcardially perfused. Immunoperoxidase reactions were performed with a mouse monoclonal anti-GFAP (Novocastra). The original radial ependymoglia is enmeshed by secondary, non-radial processes almost beyond recognition in several brain areas like in other reptiles. Astrocytes occur but only as complementary elements like in caiman but unlike in turtles, where astrocytes are absent. In most species, extended areas are free of GFAP—a meaningful difference from other reptiles. The predominance of astrocytes and the presence of areas free of GFAP immunopositivity are characteristic of birds and mammals; therefore, they must be apomorphic features of Squamata, which appeared independently from the evolution of avian glia. However, these features show a high diversity; in some lizards, they are even absent. There was no principal difference between the glial structures of snakes and lizards. In conclusion, the glial structure of Squamata seems to be the most apomorphic one among reptiles. The high diversity suggests that its evolution is still intense. The comparison of identical brain areas with different GFAP contents in different species may promote understanding the role of GFAP in neuronal networks. Our findings are in accordance with the supposal based on our previous studies that the GFAP-free areas expand during evolution.
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Affiliation(s)
- Dávid Lõrincz
- Faculty of Veterinary Science, University of Veterinary Medicine, Budapest, Hungary
| | - Mihály Kálmán
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
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13
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Hampl M, Dumkova J, Kavkova M, Dosedelova H, Bryjova A, Zahradnicek O, Pyszko M, Macholan M, Zikmund T, Kaiser J, Buchtova M. Polarized Sonic Hedgehog Protein Localization and a Shift in the Expression of Region-Specific Molecules Is Associated With the Secondary Palate Development in the Veiled Chameleon. Front Cell Dev Biol 2020; 8:572. [PMID: 32850780 PMCID: PMC7399257 DOI: 10.3389/fcell.2020.00572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/15/2020] [Indexed: 12/27/2022] Open
Abstract
Secondary palate development is characterized by the formation of two palatal shelves on the maxillary prominences, which fuse in the midline in mammalian embryos. However, in reptilian species, such as turtles, crocodilians, and lizards, the palatal shelves of the secondary palate develop to a variable extent and morphology. While in most Squamates, the palate is widely open, crocodilians develop a fully closed secondary palate. Here, we analyzed developmental processes that underlie secondary palate formation in chameleons, where large palatal shelves extend horizontally toward the midline. The growth of the palatal shelves continued during post-hatching stages and closure of the secondary palate can be observed in several adult animals. The massive proliferation of a multilayered oral epithelium and mesenchymal cells in the dorsal part of the palatal shelves underlined the initiation of their horizontal outgrowth, and was decreased later in development. The polarized cellular localization of primary cilia and Sonic hedgehog protein was associated with horizontal growth of the palatal shelves. Moreover, the development of large palatal shelves, supported by the pterygoid and palatine bones, was coupled with the shift in Meox2, Msx1, and Pax9 gene expression along the rostro-caudal axis. In conclusion, our results revealed distinctive developmental processes that contribute to the expansion and closure of the secondary palate in chameleons and highlighted divergences in palate formation across amniote species.
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Affiliation(s)
- Marek Hampl
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jana Dumkova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Michaela Kavkova
- Laboratory of Computed Tomography, Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Hana Dosedelova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | - Anna Bryjova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Oldrich Zahradnicek
- Department of Developmental Biology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia.,Department of Radiation Dosimetry, Nuclear Physics Institute, Czech Academy of Sciences, Prague, Czechia
| | - Martin Pyszko
- Department of Anatomy, Histology, and Embryology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia
| | - Milos Macholan
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | - Tomas Zikmund
- Laboratory of Computed Tomography, Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Jozef Kaiser
- Laboratory of Computed Tomography, Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Marcela Buchtova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
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14
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Islam M, Sarker K, Das T, Reaz R, Bayzid MS. STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency. BMC Genomics 2020; 21:136. [PMID: 32039704 PMCID: PMC7011378 DOI: 10.1186/s12864-020-6519-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Background Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated due to the presence of gene tree incongruence resulting from incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent process. Maximum likelihood and Bayesian MCMC methods can potentially result in accurate trees, but they do not scale well to large datasets. Results We present STELAR (Species Tree Estimation by maximizing tripLet AgReement), a new fast and highly accurate statistically consistent coalescent-based method for estimating species trees from a collection of gene trees. We formalized the constrained triplet consensus (CTC) problem and showed that the solution to the CTC problem is a statistically consistent estimate of the species tree under the multi-species coalescent (MSC) model. STELAR is an efficient dynamic programming based solution to the CTC problem which is highly accurate and scalable. We evaluated the accuracy of STELAR in comparison with SuperTriplets, which is an alternate fast and highly accurate triplet-based supertree method, and with MP-EST and ASTRAL – two of the most popular and accurate coalescent-based methods. Experimental results suggest that STELAR matches the accuracy of ASTRAL and improves on MP-EST and SuperTriplets. Conclusions Theoretical and empirical results (on both simulated and real biological datasets) suggest that STELAR is a valuable technique for species tree estimation from gene tree distributions.
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Affiliation(s)
- Mazharul Islam
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1205, Bangladesh
| | - Kowshika Sarker
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1205, Bangladesh
| | - Trisha Das
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1205, Bangladesh
| | - Rezwana Reaz
- Department of Computer Science, The University of Texas at Austin, Texas, 78712, USA
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1205, Bangladesh.
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15
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Ultrastructural analysis of the yolk processing pattern in embryonic pond slider turtles (Trachemys scripta: Emydidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:187-197. [DOI: 10.1002/jez.b.22894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/19/2019] [Accepted: 06/27/2019] [Indexed: 01/19/2023]
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16
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Blackburn DG, Lestz L, Barnes MS, Powers KG. How do embryonic turtles process yolk? Evidence from the Snapping Turtle, Chelydra serpentina (Chelydridae). CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Compared with amphibians, oviparous reptiles and birds lay large eggs that contain abundant yolk. Because the yolk is extracellular, it must be taken up by cells of the yolk sac and metabolized so that products of yolk digestion can be transported to the embryo to fuel development. In birds, the yolk is processed by cells that line the inside of the yolk sac. A very different developmental pattern recently has been demonstrated in lizards and snakes in which the yolk sac cavity is converted to a compact mass of blood vessels lined by endodermal cells. In this study, we used scanning electron microscopy to determine which of these developmental patterns (if either) occurs in a representative chelonian, the North American Snapping Turtle (Chelydra serpentina (Linnaeus, 1758)). Our observations reveal that yolk-filled endodermal cells progressively fill the yolk sac cavity. These cells become organized around anastomosing blood vessels, forming elongated strands that are morphologically well suited for yolk digestion and vascular transport of nutrients. This developmental pattern shares features with that of squamates, but it differs markedly from that of birds. These observations indicate that mechanisms of yolk processing in lizards and snakes have an evolutionary history that pre-dates the squamate clade.
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Affiliation(s)
- Daniel G. Blackburn
- Department of Biology, and Electron Microscopy Center, Trinity College, Hartford, CT 06106, USA
- Department of Biology, and Electron Microscopy Center, Trinity College, Hartford, CT 06106, USA
| | - Luisa Lestz
- Department of Biology, and Electron Microscopy Center, Trinity College, Hartford, CT 06106, USA
- Department of Biology, and Electron Microscopy Center, Trinity College, Hartford, CT 06106, USA
| | - Madeline S. Barnes
- Department of Biology, and Electron Microscopy Center, Trinity College, Hartford, CT 06106, USA
- Department of Biology, and Electron Microscopy Center, Trinity College, Hartford, CT 06106, USA
| | - Kathryn G. Powers
- Department of Biology, and Electron Microscopy Center, Trinity College, Hartford, CT 06106, USA
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17
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Asymmetric paralog evolution between the "cryptic" gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4. Sci Rep 2019; 9:3136. [PMID: 30816280 PMCID: PMC6395752 DOI: 10.1038/s41598-019-40055-1] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 02/07/2019] [Indexed: 12/05/2022] Open
Abstract
The vertebrate gene repertoire is characterized by “cryptic” genes whose identification has been hampered by their absence from the genomes of well-studied species. One example is the Bmp16 gene, a paralog of the developmental key genes Bmp2 and -4. We focus on the Bmp2/4/16 group of genes to study the evolutionary dynamics following gen(om)e duplications with special emphasis on the poorly studied Bmp16 gene. We reveal the presence of Bmp16 in chondrichthyans in addition to previously reported teleost fishes and reptiles. Using comprehensive, vertebrate-wide gene sampling, our phylogenetic analysis complemented with synteny analyses suggests that Bmp2, -4 and -16 are remnants of a gene quartet that originated during the two rounds of whole-genome duplication (2R-WGD) early in vertebrate evolution. We confirm that Bmp16 genes were lost independently in at least three lineages (mammals, archelosaurs and amphibians) and report that they have elevated rates of sequence evolution. This finding agrees with their more “flexible” deployment during development; while Bmp16 has limited embryonic expression domains in the cloudy catshark, it is broadly expressed in the green anole lizard. Our study illustrates the dynamics of gene family evolution by integrating insights from sequence diversification, gene repertoire changes, and shuffling of expression domains.
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18
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Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol 2019; 131:80-92. [DOI: 10.1016/j.ympev.2018.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
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19
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Holthaus KB, Eckhart L, Dalla Valle L, Alibardi L. Review: Evolution and diversification of corneous beta‐proteins, the characteristic epidermal proteins of reptiles and birds. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 330:438-453. [DOI: 10.1002/jez.b.22840] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/28/2018] [Accepted: 12/23/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Karin Brigit Holthaus
- Department of DermatologyMedical University of ViennaWien Austria
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA)University of BolognaBologna Italy
| | - Leopold Eckhart
- Department of DermatologyMedical University of ViennaWien Austria
| | | | - Lorenzo Alibardi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA)University of BolognaBologna Italy
- Comparative Histolab PadovaPadova Italy
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20
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Fleischle CV, Wintrich T, Sander PM. Quantitative histological models suggest endothermy in plesiosaurs. PeerJ 2018; 6:e4955. [PMID: 29892509 PMCID: PMC5994164 DOI: 10.7717/peerj.4955] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/18/2018] [Indexed: 11/20/2022] Open
Abstract
Background Plesiosaurs are marine reptiles that arose in the Late Triassic and survived to the Late Cretaceous. They have a unique and uniform bauplan and are known for their very long neck and hydrofoil-like flippers. Plesiosaurs are among the most successful vertebrate clades in Earth’s history. Based on bone mass decrease and cosmopolitan distribution, both of which affect lifestyle, indications of parental care, and oxygen isotope analyses, evidence for endothermy in plesiosaurs has accumulated. Recent bone histological investigations also provide evidence of fast growth and elevated metabolic rates. However, quantitative estimations of metabolic rates and bone growth rates in plesiosaurs have not been attempted before. Methods Phylogenetic eigenvector maps is a method for estimating trait values from a predictor variable while taking into account phylogenetic relationships. As predictor variable, this study employs vascular density, measured in bone histological sections of fossil eosauropterygians and extant comparative taxa. We quantified vascular density as primary osteon density, thus, the proportion of vascular area (including lamellar infillings of primary osteons) to total bone area. Our response variables are bone growth rate (expressed as local bone apposition rate) and resting metabolic rate (RMR). Results Our models reveal bone growth rates and RMRs for plesiosaurs that are in the range of birds, suggesting that plesiosaurs were endotherm. Even for basal eosauropterygians we estimate values in the range of mammals or higher. Discussion Our models are influenced by the availability of comparative data, which are lacking for large marine amniotes, potentially skewing our results. However, our statistically robust inference of fast growth and fast metabolism is in accordance with other evidence for plesiosaurian endothermy. Endothermy may explain the success of plesiosaurs consisting in their survival of the end-Triassic extinction event and their global radiation and dispersal.
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Affiliation(s)
- Corinna V Fleischle
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Tanja Wintrich
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - P Martin Sander
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.,Dinosaur Institute, Natural History Museum of Los Angeles County, Los Angeles, USA
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21
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Moldovan MA, Gelfand MS. Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. Front Microbiol 2018; 9:428. [PMID: 29593678 PMCID: PMC5857598 DOI: 10.3389/fmicb.2018.00428] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/23/2018] [Indexed: 11/13/2022] Open
Abstract
The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria Prochlorococcus marinus should be divided into two species. As a control we have confirmed the paraphyletic origin of Yersinia pseudotuberculosis (with embedded, monophyletic Y. pestis) and Burkholderia pseudomallei (with B. mallei). We also demonstrate that by our definition and in accordance with recent studies Escherichia coli and Shigella spp. are one species.
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Affiliation(s)
- Mikhail A. Moldovan
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (RAS), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail S. Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (RAS), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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22
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Phylogeny mandalas for illustrating the Tree of Life. Mol Phylogenet Evol 2017; 117:168-178. [DOI: 10.1016/j.ympev.2016.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/12/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
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23
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Valentin-Kahan A, García-Tejedor GB, Robello C, Trujillo-Cenóz O, Russo RE, Alvarez-Valin F. Gene Expression Profiling in the Injured Spinal Cord of Trachemys scripta elegans: An Amniote with Self-Repair Capabilities. Front Mol Neurosci 2017; 10:17. [PMID: 28223917 PMCID: PMC5293771 DOI: 10.3389/fnmol.2017.00017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/12/2017] [Indexed: 12/19/2022] Open
Abstract
Slider turtles are the only known amniotes with self-repair mechanisms of the spinal cord that lead to substantial functional recovery. Their strategic phylogenetic position makes them a relevant model to investigate the peculiar genetic programs that allow anatomical reconnection in some vertebrate groups but are absent in others. Here, we analyze the gene expression profile of the response to spinal cord injury (SCI) in the turtle Trachemys scripta elegans. We found that this response comprises more than 1000 genes affecting diverse functions: reaction to ischemic insult, extracellular matrix re-organization, cell proliferation and death, immune response, and inflammation. Genes related to synapses and cholesterol biosynthesis are down-regulated. The analysis of the evolutionary distribution of these genes shows that almost all are present in most vertebrates. Additionally, we failed to find genes that were exclusive of regenerating taxa. The comparison of expression patterns among species shows that the response to SCI in the turtle is more similar to that of mice and non-regenerative Xenopus than to Xenopus during its regenerative stage. This observation, along with the lack of conserved “regeneration genes” and the current accepted phylogenetic placement of turtles (sister group of crocodilians and birds), indicates that the ability of spinal cord self-repair of turtles does not represent the retention of an ancestral vertebrate character. Instead, our results suggest that turtles developed this capability from a non-regenerative ancestor (i.e., a lineage specific innovation) that was achieved by re-organizing gene expression patterns on an essentially non-regenerative genetic background. Among the genes activated by SCI exclusively in turtles, those related to anoxia tolerance, extracellular matrix remodeling, and axonal regrowth are good candidates to underlie functional recovery.
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Affiliation(s)
- Adrián Valentin-Kahan
- Department of Cellular and Molecular Neurophysiology, Instituto de Investigaciones Biológicas Clemente Estable Montevideo, Uruguay
| | - Gabriela B García-Tejedor
- Department of Cellular and Molecular Neurophysiology, Instituto de Investigaciones Biológicas Clemente Estable Montevideo, Uruguay
| | - Carlos Robello
- Molecular Biology Unit, Institut Pasteur de MontevideoMontevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la RepublicaMontevideo, Uruguay
| | - Omar Trujillo-Cenóz
- Department of Cellular and Molecular Neurophysiology, Instituto de Investigaciones Biológicas Clemente Estable Montevideo, Uruguay
| | - Raúl E Russo
- Department of Cellular and Molecular Neurophysiology, Instituto de Investigaciones Biológicas Clemente Estable Montevideo, Uruguay
| | - Fernando Alvarez-Valin
- Sección Biomatemática, Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
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24
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Schott RK, Panesar B, Card DC, Preston M, Castoe TA, Chang BS. Targeted Capture of Complete Coding Regions across Divergent Species. Genome Biol Evol 2017; 9:398-414. [PMID: 28137744 PMCID: PMC5381602 DOI: 10.1093/gbe/evx005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2017] [Indexed: 02/06/2023] Open
Abstract
Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here, we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.
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Affiliation(s)
- Ryan K. Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Bhawandeep Panesar
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
| | - Daren C. Card
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Matthew Preston
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Belinda S.W. Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
- Centre for the Analysis of Genomes and Function, University of Toronto, Canada
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Development of the turtle plastron, the order-defining skeletal structure. Proc Natl Acad Sci U S A 2016; 113:5317-22. [PMID: 27114549 DOI: 10.1073/pnas.1600958113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The dorsal and ventral aspects of the turtle shell, the carapace and the plastron, are developmentally different entities. The carapace contains axial endochondral skeletal elements and exoskeletal dermal bones. The exoskeletal plastron is found in all extant and extinct species of crown turtles found to date and is synaptomorphic of the order Testudines. However, paleontological reconstructed transition forms lack a fully developed carapace and show a progression of bony elements ancestral to the plastron. To understand the evolutionary development of the plastron, it is essential to know how it has formed. Here we studied the molecular development and patterning of plastron bones in a cryptodire turtle Trachemys scripta We show that plastron development begins at developmental stage 15 when osteochondrogenic mesenchyme forms condensates for each plastron bone at the lateral edges of the ventral mesenchyme. These condensations commit to an osteogenic identity and suppress chondrogenesis. Their development overlaps with that of sternal cartilage development in chicks and mice. Thus, we suggest that in turtles, the sternal morphogenesis is prevented in the ventral mesenchyme by the concomitant induction of osteogenesis and the suppression of chondrogenesis. The osteogenic subroutines later direct the growth and patterning of plastron bones in an autonomous manner. The initiation of plastron bone development coincides with that of carapacial ridge formation, suggesting that the development of dorsal and ventral shells are coordinated from the start and that adopting an osteogenesis-inducing and chondrogenesis-suppressing cell fate in the ventral mesenchyme has permitted turtles to develop their order-specific ventral morphology.
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26
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Legendre LJ, Guénard G, Botha-Brink J, Cubo J. Palaeohistological Evidence for Ancestral High Metabolic Rate in Archosaurs. Syst Biol 2016; 65:989-996. [PMID: 27073251 DOI: 10.1093/sysbio/syw033] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 11/13/2022] Open
Abstract
Metabolic heat production in archosaurs has played an important role in their evolutionary radiation during the Mesozoic, and their ancestral metabolic condition has long been a matter of debate in systematics and palaeontology. The study of fossil bone histology provides crucial information on bone growth rate, which has been used to indirectly investigate the evolution of thermometabolism in archosaurs. However, no quantitative estimation of metabolic rate has ever been performed on fossils using bone histological features. Moreover, to date, no inference model has included phylogenetic information in the form of predictive variables. Here we performed statistical predictive modeling using the new method of phylogenetic eigenvector maps on a set of bone histological features for a sample of extant and extinct vertebrates, to estimate metabolic rates of fossil archosauromorphs. This modeling procedure serves as a case study for eigenvector-based predictive modeling in a phylogenetic context, as well as an investigation of the poorly known evolutionary patterns of metabolic rate in archosaurs. Our results show that Mesozoic theropod dinosaurs exhibit metabolic rates very close to those found in modern birds, that archosaurs share a higher ancestral metabolic rate than that of extant ectotherms, and that this derived high metabolic rate was acquired at a much more inclusive level of the phylogenetic tree, among non-archosaurian archosauromorphs. These results also highlight the difficulties of assigning a given heat production strategy (i.e., endothermy, ectothermy) to an estimated metabolic rate value, and confirm findings of previous studies that the definition of the endotherm/ectotherm dichotomy may be ambiguous.
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Affiliation(s)
- Lucas J Legendre
- Institut des Sciences de la Terre de Paris (ISTeP), Sorbonne Universités - Université Pierre et Marie Curie , 4 Place Jussieu, F-75005 Paris, France;
| | - Guillaume Guénard
- Département de sciences biologiques, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Jennifer Botha-Brink
- Karoo Palaeontology, National Museum, Bloemfontein 9300, South Africa; and.,Department of Zoology and Entomology, University of the Free State, Bloemfontein 9300, South Africa
| | - Jorge Cubo
- Institut des Sciences de la Terre de Paris (ISTeP), Sorbonne Universités - Université Pierre et Marie Curie , 4 Place Jussieu, F-75005 Paris, France
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27
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Kugler R, Marschang RE, Ihász K, Lengyel G, Jakab F, Bányai K, Farkas SL. Whole genome characterization of a chelonian orthoreovirus strain identifies significant genetic diversity and may classify reptile orthoreoviruses into distinct species. Virus Res 2016; 215:94-8. [DOI: 10.1016/j.virusres.2016.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 10/22/2022]
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28
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Kuraku S, Feiner N, Keeley SD, Hara Y. Incorporating tree-thinking and evolutionary time scale into developmental biology. Dev Growth Differ 2016; 58:131-42. [PMID: 26818824 DOI: 10.1111/dgd.12258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 01/11/2023]
Abstract
Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples.
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Affiliation(s)
- Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | | | - Sean D Keeley
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | - Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
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29
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Yamagishi G, Yoshida A, Kobayashi A, Park MK. Molecular characterization of insulin from squamate reptiles reveals sequence diversity and possible adaptive evolution. Gen Comp Endocrinol 2016; 225:197-211. [PMID: 26344944 DOI: 10.1016/j.ygcen.2015.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/27/2015] [Accepted: 08/29/2015] [Indexed: 01/19/2023]
Abstract
The Squamata are the most adaptive and prosperous group among ectothermic amniotes, reptiles, due to their species-richness and geographically wide habitat. Although the molecular mechanisms underlying their prosperity remain largely unknown, unique features have been reported from hormones that regulate energy metabolism. Insulin, a central anabolic hormone, is one such hormone, as its roles and effectiveness in regulation of blood glucose levels remain to be examined in squamates. In the present study, cDNAs coding for insulin were isolated from multiple species that represent various groups of squamates. The deduced amino acid sequences showed a high degree of divergence, with four lineages showing obviously higher number of amino acid substitutions than most of vertebrates, from teleosts to mammals. Among 18 sites presented to comprise the two receptor binding surfaces (one with 12 sites and the other with 6 sites), substitutions were observed in 13 sites. Among them was the substitution of HisB10, which results in the loss of the ability to hexamerize. Furthermore, three of these substitutions were reported to increase mitogenicity in human analogues. These substitutions were also reported from insulin of hystricomorph rodents and agnathan fishes, whose mitogenic potency have been shown to be increased. The estimated value of the non-synonymous-to-synonymous substitution ratio (ω) for the Squamata clade was larger than those of the other reptiles and aves. Even higher values were estimated for several lineages among squamates. These results, together with the regulatory mechanisms of digestion and nutrient assimilation in squamates, suggested a possible adaptive process through the molecular evolution of squamate INS. Further studies on the roles of insulin, in relation to the physiological and ecological traits of squamate species, will provide an insight into the molecular mechanisms that have led to the adaptivity and prosperity of squamates.
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Affiliation(s)
- Genki Yamagishi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Ayaka Yoshida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Aya Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Min Kyun Park
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.
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30
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Abramyan J, Richman JM. Recent insights into the morphological diversity in the amniote primary and secondary palates. Dev Dyn 2015; 244:1457-68. [PMID: 26293818 PMCID: PMC4715671 DOI: 10.1002/dvdy.24338] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 02/06/2023] Open
Abstract
The assembly of the upper jaw is a pivotal moment in the embryonic development of amniotes. The upper jaw forms from the fusion of the maxillary, medial nasal, and lateral nasal prominences, resulting in an intact upper lip/beak and nasal cavities; together called the primary palate. This process of fusion requires a balance of proper facial prominence shape and positioning to avoid craniofacial clefting, whilst still accommodating the vast phenotypic diversity of adult amniotes. As such, variation in craniofacial ontogeny is not tolerated beyond certain bounds. For clarity, we discuss primary palatogenesis of amniotes into in two categories, according to whether the nasal and oral cavities remain connected throughout ontogeny or not. The transient separation of these cavities occurs in mammals and crocodilians, while remaining connected in birds, turtles and squamates. In the latter group, the craniofacial prominences fuse around a persistent choanal groove that connects the nasal and oral cavities. Subsequently, all lineages except for turtles, develop a secondary palate that ultimately completely or partially separates oral and nasal cavities. Here, we review the shared, early developmental events and highlight the points at which development diverges in both primary and secondary palate formation.
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Affiliation(s)
- John Abramyan
- Faculty of Dentistry, Life Sciences Institute, University of British Columbia, Vancouver BC, CANADA
| | - Joy Marion Richman
- Faculty of Dentistry, Life Sciences Institute, University of British Columbia, Vancouver BC, CANADA
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31
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Holthaus KB, Strasser B, Sipos W, Schmidt HA, Mlitz V, Sukseree S, Weissenbacher A, Tschachler E, Alibardi L, Eckhart L. Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell. Mol Biol Evol 2015; 33:726-37. [PMID: 26601937 PMCID: PMC4760078 DOI: 10.1093/molbev/msv265] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation.
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Affiliation(s)
- Karin Brigit Holthaus
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Bettina Strasser
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Sipos
- Clinical Department for Farm Animals and Herd Management, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Veronika Mlitz
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Supawadee Sukseree
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Lorenzo Alibardi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
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32
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Bierman HS, Carr CE. Sound localization in the alligator. Hear Res 2015; 329:11-20. [PMID: 26048335 DOI: 10.1016/j.heares.2015.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/12/2015] [Accepted: 05/24/2015] [Indexed: 10/23/2022]
Abstract
In early tetrapods, it is assumed that the tympana were acoustically coupled through the pharynx and therefore inherently directional, acting as pressure difference receivers. The later closure of the middle ear cavity in turtles, archosaurs, and mammals is a derived condition, and would have changed the ear by decoupling the tympana. Isolation of the middle ears would then have led to selection for structural and neural strategies to compute sound source localization in both archosaurs and mammalian ancestors. In the archosaurs (birds and crocodilians) the presence of air spaces in the skull provided connections between the ears that have been exploited to improve directional hearing, while neural circuits mediating sound localization are well developed. In this review, we will focus primarily on directional hearing in crocodilians, where vocalization and sound localization are thought to be ecologically important, and indicate important issues still awaiting resolution.
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Affiliation(s)
- Hilary S Bierman
- Center for Comparative and Evolutionary Biology of Hearing, Department of Biology, University of Maryland College Park, College Park, Maryland 20742, USA.
| | - Catherine E Carr
- Center for Comparative and Evolutionary Biology of Hearing, Department of Biology, University of Maryland College Park, College Park, Maryland 20742, USA.
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33
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Joyce WG. The origin of turtles: a paleontological perspective. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:181-93. [PMID: 25712176 DOI: 10.1002/jez.b.22609] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/27/2014] [Indexed: 11/10/2022]
Abstract
The origin of turtles and their unusual body plan has fascinated scientists for the last two centuries. Over the course of the last decades, a broad sample of molecular analyses have favored a sister group relationship of turtles with archosaurs, but recent studies reveal that this signal may be the result of systematic biases affecting molecular approaches, in particular sampling, non-randomly distributed rate heterogeneity among taxa, and the use of concatenated data sets. Morphological studies, by contrast, disfavor archosaurian relationships for turtles, but the proposed alternative topologies are poorly supported as well. The recently revived paleontological hypothesis that the Middle Permian Eunotosaurus africanus is an intermediate stem turtle is now robustly supported by numerous characters that were previously thought to be unique to turtles and that are now shown to have originated over the course of tens of millions of years unrelated to the origin of the turtle shell. Although E. africanus does not solve the placement of turtles within Amniota, it successfully extends the stem lineage of turtles to the Permian and helps resolve some questions associated with the origin of turtles, in particular the non-composite origin of the shell, the slow origin of the shell, and the terrestrial setting for the origin of turtles.
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Affiliation(s)
- Walter G Joyce
- Department of Geoscience, University of Fribourg, Fribourg, Switzerland
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34
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Abstract
Motivation With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree estimation is difficult in the presence of gene tree discordance, which is often due to incomplete lineage sorting (ILS), modelled by the multi-species coalescent. Several highly accurate coalescent-based species tree estimation methods have been developed over the last decade, including MP-EST. However, the running time for MP-EST increases rapidly as the number of species grows. Results We present divide-and-conquer techniques that improve the scalability of MP-EST so that it can run efficiently on large datasets. Surprisingly, this technique also improves the accuracy of species trees estimated by MP-EST, as our study shows on a collection of simulated and biological datasets.
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35
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Mirarab S, Bayzid MS, Warnow T. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. Syst Biol 2014; 65:366-80. [PMID: 25164915 DOI: 10.1093/sysbio/syu063] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/18/2014] [Indexed: 12/13/2022] Open
Abstract
Species tree estimation is complicated by processes, such as gene duplication and loss and incomplete lineage sorting (ILS), that cause discordance between gene trees and the species tree. Furthermore, while concatenation, a traditional approach to tree estimation, has excellent performance under many conditions, the expectation is that the best accuracy will be obtained through the use of species tree estimation methods that are specifically designed to address gene tree discordance. In this article, we report on a study to evaluate MP-EST-one of the most popular species tree estimation methods designed to address ILS-as well as concatenation under maximum likelihood, the greedy consensus, and two supertree methods (Matrix Representation with Parsimony and Matrix Representation with Likelihood). Our study shows that several factors impact the absolute and relative accuracy of methods, including the number of gene trees, the accuracy of the estimated gene trees, and the amount of ILS. Concatenation can be more accurate than the best summary methods in some cases (mostly when the gene trees have poor phylogenetic signal or when the level of ILS is low), but summary methods are generally more accurate than concatenation when there are an adequate number of sufficiently accurate gene trees. Our study suggests that coalescent-based species tree methods may be key to estimating highly accurate species trees from multiple loci.
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Affiliation(s)
- Siavash Mirarab
- Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA; and
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA; and
| | - Tandy Warnow
- Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA; and Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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36
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Field DJ, Gauthier JA, King BL, Pisani D, Lyson TR, Peterson KJ. Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles. Evol Dev 2014; 16:189-96. [PMID: 24798503 PMCID: PMC4215941 DOI: 10.1111/ede.12081] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding the phylogenetic position of crown turtles (Testudines) among amniotes has been a source of particular contention. Recent morphological analyses suggest that turtles are sister to all other reptiles, whereas the vast majority of gene sequence analyses support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodilians). Previously, a study using microRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this hypothesis with an expanded miRNA presence/absence dataset, and employ more rigorous criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister-relationship; instead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs. We further test this result by analyzing a super-alignment of precursor miRNA sequences for every miRNA inferred to have been present in the most recent common ancestor of tetrapods. This analysis yields a topology that is fully congruent with our presence/absence analysis; our results are therefore in accordance with most gene sequence studies, providing strong, consilient molecular evidence from diverse independent datasets regarding the phylogenetic position of turtles.
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Affiliation(s)
- Daniel J. Field
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Benjamin L. King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Queen’s Road, Bristol BS8 1RJ, United Kingdom and School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, United Kingdom
| | - Tyler R. Lyson
- Smithsonian National Museum of Natural History, 10 Street and Constitution Avenue, Washington, DC 20013, USA
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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37
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Feiner N, Meyer A, Kuraku S. Evolution of the vertebrate Pax4/6 class of genes with focus on its novel member, the Pax10 gene. Genome Biol Evol 2014; 6:1635-51. [PMID: 24951566 PMCID: PMC4122933 DOI: 10.1093/gbe/evu135] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The members of the paired box (Pax) family regulate key developmental pathways in many metazoans as tissue-specific transcription factors. Vertebrate genomes typically possess nine Pax genes (Pax1-9), which are derived from four proto-Pax genes in the vertebrate ancestor that were later expanded through the so-called two-round (2R) whole-genome duplication. A recent study proposed that pax6a genes of a subset of teleost fishes (namely, acanthopterygians) are remnants of a paralog generated in the 2R genome duplication, to be renamed pax6.3, and reported one more group of vertebrate Pax genes (Pax6.2), most closely related to the Pax4/6 class. We propose to designate this new member Pax10 instead and reconstruct the evolutionary history of the Pax4/6/10 class with solid phylogenetic evidence. Our synteny analysis showed that Pax4, -6, and -10 originated in the 2R genome duplications early in vertebrate evolution. The phylogenetic analyses of relationships between teleost pax6a and other Pax4, -6, and -10 genes, however, do not support the proposed hypothesis of an ancient origin of the acanthopterygian pax6a genes in the 2R genome duplication. Instead, we confirmed the traditional scenario that the acanthopterygian pax6a is derived from the more recent teleost-specific genome duplication. Notably, Pax6 is present in all vertebrates surveyed to date, whereas Pax4 and -10 were lost multiple times in independent vertebrate lineages, likely because of their restricted expression patterns: Among Pax6-positive domains, Pax10 has retained expression in the adult retina alone, which we documented through in situ hybridization and quantitative reverse transcription polymerase chain reaction experiments on zebrafish, Xenopus, and anole lizard.
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Affiliation(s)
- Nathalie Feiner
- Department of Biology, University of Konstanz, GermanyInternational Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, GermanyPresent address: Department of Zoology, University of Oxford, United Kingdom
| | - Axel Meyer
- Department of Biology, University of Konstanz, GermanyInternational Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Germany
| | - Shigehiro Kuraku
- Department of Biology, University of Konstanz, GermanyInternational Max-Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, GermanyPresent address: Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, Chuo-ku, Kobe, Hyogo, Japan
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38
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Antimicrobial peptides in reptiles. Pharmaceuticals (Basel) 2014; 7:723-53. [PMID: 24918867 PMCID: PMC4078517 DOI: 10.3390/ph7060723] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 12/17/2022] Open
Abstract
Reptiles are among the oldest known amniotes and are highly diverse in their morphology and ecological niches. These animals have an evolutionarily ancient innate-immune system that is of great interest to scientists trying to identify new and useful antimicrobial peptides. Significant work in the last decade in the fields of biochemistry, proteomics and genomics has begun to reveal the complexity of reptilian antimicrobial peptides. Here, the current knowledge about antimicrobial peptides in reptiles is reviewed, with specific examples in each of the four orders: Testudines (turtles and tortosises), Sphenodontia (tuataras), Squamata (snakes and lizards), and Crocodilia (crocodilans). Examples are presented of the major classes of antimicrobial peptides expressed by reptiles including defensins, cathelicidins, liver-expressed peptides (hepcidin and LEAP-2), lysozyme, crotamine, and others. Some of these peptides have been identified and tested for their antibacterial or antiviral activity; others are only predicted as possible genes from genomic sequencing. Bioinformatic analysis of the reptile genomes is presented, revealing many predicted candidate antimicrobial peptides genes across this diverse class. The study of how these ancient creatures use antimicrobial peptides within their innate immune systems may reveal new understandings of our mammalian innate immune system and may also provide new and powerful antimicrobial peptides as scaffolds for potential therapeutic development.
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Hirasawa T, Pascual-Anaya J, Kamezaki N, Taniguchi M, Mine K, Kuratani S. The evolutionary origin of the turtle shell and its dependence on the axial arrest of the embryonic rib cage. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:194-207. [PMID: 24898540 DOI: 10.1002/jez.b.22579] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/25/2014] [Accepted: 05/07/2014] [Indexed: 12/22/2022]
Abstract
Turtles are characterized by their possession of a shell with dorsal and ventral moieties: the carapace and the plastron, respectively. In this review, we try to provide answers to the question of the evolutionary origin of the carapace, by revising morphological, developmental, and paleontological comparative analyses. The turtle carapace is formed through modification of the thoracic ribs and vertebrae, which undergo extensive ossification to form a solid bony structure. Except for peripheral dermal elements, there are no signs of exoskeletal components ontogenetically added to the costal and neural bones, and thus the carapace is predominantly of endoskeletal nature. Due to the axial arrest of turtle rib growth, the axial part of the embryo expands laterally and the shoulder girdle becomes encapsulated in the rib cage, together with the inward folding of the lateral body wall in the late phase of embryogenesis. Along the line of this folding develops a ridge called the carapacial ridge (CR), a turtle-specific embryonic structure. The CR functions in the marginal growth of the carapacial primordium, in which Wnt signaling pathway might play a crucial role. Both paleontological and genomic evidence suggest that the axial arrest is the first step toward acquisition of the turtle body plan, which is estimated to have taken place after the divergence of a clade including turtles from archosaurs. The developmental relationship between the CR and the axial arrest remains a central issue to be solved in future.
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Affiliation(s)
- Tatsuya Hirasawa
- Laboratory for Evolutionary Morphology, RIKEN Center for Developmental Biology, Kobe, Japan
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Zayas-Santiago A, Agte S, Rivera Y, Benedikt J, Ulbricht E, Karl A, Dávila J, Savvinov A, Kucheryavykh Y, Inyushin M, Cubano LA, Pannicke T, Veh RW, Francke M, Verkhratsky A, Eaton MJ, Reichenbach A, Skatchkov SN. Unidirectional photoreceptor-to-Müller glia coupling and unique K+ channel expression in Caiman retina. PLoS One 2014; 9:e97155. [PMID: 24831221 PMCID: PMC4022631 DOI: 10.1371/journal.pone.0097155] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/15/2014] [Indexed: 02/07/2023] Open
Abstract
Background Müller cells, the principal glial cells of the vertebrate retina, are fundamental for the maintenance and function of neuronal cells. In most vertebrates, including humans, Müller cells abundantly express Kir4.1 inwardly rectifying potassium channels responsible for hyperpolarized membrane potential and for various vital functions such as potassium buffering and glutamate clearance; inter-species differences in Kir4.1 expression were, however, observed. Localization and function of potassium channels in Müller cells from the retina of crocodiles remain, hitherto, unknown. Methods We studied retinae of the Spectacled caiman (Caiman crocodilus fuscus), endowed with both diurnal and nocturnal vision, by (i) immunohistochemistry, (ii) whole-cell voltage-clamp, and (iii) fluorescent dye tracing to investigate K+ channel distribution and glia-to-neuron communications. Results Immunohistochemistry revealed that caiman Müller cells, similarly to other vertebrates, express vimentin, GFAP, S100β, and glutamine synthetase. In contrast, Kir4.1 channel protein was not found in Müller cells but was localized in photoreceptor cells. Instead, 2P-domain TASK-1 channels were expressed in Müller cells. Electrophysiological properties of enzymatically dissociated Müller cells without photoreceptors and isolated Müller cells with adhering photoreceptors were significantly different. This suggests ion coupling between Müller cells and photoreceptors in the caiman retina. Sulforhodamine-B injected into cones permeated to adhering Müller cells thus revealing a uni-directional dye coupling. Conclusion Our data indicate that caiman Müller glial cells are unique among vertebrates studied so far by predominantly expressing TASK-1 rather than Kir4.1 K+ channels and by bi-directional ion and uni-directional dye coupling to photoreceptor cells. This coupling may play an important role in specific glia-neuron signaling pathways and in a new type of K+ buffering.
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Affiliation(s)
- Astrid Zayas-Santiago
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
| | - Silke Agte
- Paul Flechsig Institute of Brain Research, Faculty of Medicine, University of Leipzig, Leipzig, Germany
- Division of Soft Matter Physics, Department of Physics, University of Leipzig, Leipzig, Germany
| | - Yomarie Rivera
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
| | - Jan Benedikt
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
| | - Elke Ulbricht
- Paul Flechsig Institute of Brain Research, Faculty of Medicine, University of Leipzig, Leipzig, Germany
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Anett Karl
- Paul Flechsig Institute of Brain Research, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - José Dávila
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
| | - Alexey Savvinov
- Department of Physical Sciences, Universidad de Puerto Rico, Recinto de Río Piedras, Río Piedras, Puerto Rico, United States of America
| | - Yuriy Kucheryavykh
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
| | - Mikhail Inyushin
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
| | - Luis A. Cubano
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
| | - Thomas Pannicke
- Paul Flechsig Institute of Brain Research, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | | | - Mike Francke
- Paul Flechsig Institute of Brain Research, Faculty of Medicine, University of Leipzig, Leipzig, Germany
- Translational Centre for Regenerative Medicine (TRM) University of Leipzig, Leipzig, Germany
| | - Alexei Verkhratsky
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Misty J. Eaton
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
| | - Andreas Reichenbach
- Paul Flechsig Institute of Brain Research, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Serguei N. Skatchkov
- Departments of Pathology, Biochemistry and Physiology, Universidad Central Del Caribe, Bayamón, Puerto Rico, United States of America
- * E-mail:
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Suzuki IK, Hirata T. A common developmental plan for neocortical gene-expressing neurons in the pallium of the domestic chicken Gallus gallus domesticus and the Chinese softshell turtle Pelodiscus sinensis. Front Neuroanat 2014; 8:20. [PMID: 24778607 PMCID: PMC3985024 DOI: 10.3389/fnana.2014.00020] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/20/2014] [Indexed: 11/13/2022] Open
Abstract
The six-layered neocortex is a unique characteristic of mammals and likely provides the neural basis of their sophisticated cognitive abilities. Although all mammalian species share the layered structure of the neocortex, the sauropsids exhibit an entirely different cytoarchitecture of the corresponding pallial region. Our previous gene expression study revealed that the chicken pallium possesses neural subtypes that express orthologs of layer-specific genes of the mammalian neocortex. To understand the evolutionary steps leading toward animal group-specific neuronal arrangements in the pallium in the course of amniote diversification, we examined expression patterns of the same orthologs and a few additional genes in the pallial development of the Chinese softshell turtle Pelodiscus sinensis, and compared these patterns to those of the chicken. Our analyses highlighted similarities in neuronal arrangements between the two species; the mammalian layer 5 marker orthologs are expressed in the medial domain and the layer 2/3 marker orthologs are expressed in the lateral domain in the pallia of both species. We hypothesize that the mediolateral arrangement of the neocortical layer-specific gene-expressing neurons originated in their common ancestor and is conserved among all sauropsid groups, whereas the neuronal arrangement within the pallium could have highly diversified independently in the mammalian lineage.
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Affiliation(s)
- Ikuo K Suzuki
- Division of Brain Function, National Institute of Genetics, Graduate University for Advanced Studies (Sokendai) Mishima, Japan ; Institute of Interdisciplinary Research in Human and Molecular Biology, Université Libre de Bruxelles Brussels, Belgium
| | - Tatsumi Hirata
- Division of Brain Function, National Institute of Genetics, Graduate University for Advanced Studies (Sokendai) Mishima, Japan
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Abstract
The turtle body plan, with its solid shell, deviates radically from those of other tetrapods. The dorsal part of the turtle shell, or the carapace, consists mainly of costal and neural bony plates, which are continuous with the underlying thoracic ribs and vertebrae, respectively. Because of their superficial position, the evolutionary origins of these costo-neural elements have long remained elusive. Here we show, through comparative morphological and embryological analyses, that the major part of the carapace is derived purely from endoskeletal ribs. We examine turtle embryos and find that the costal and neural plates develop not within the dermis, but within deeper connective tissue where the rib and intercostal muscle anlagen develop. We also examine the fossils of an outgroup of turtles to confirm that the structure equivalent to the turtle carapace developed independently of the true osteoderm. Our results highlight the hitherto unravelled evolutionary course of the turtle shell. The evolutionary origins of the costal and neural bony plates of the turtle shell have long remained elusive. Here the authors show, through comparative morphological and embryological analyses, that the most of the carapace is derived from endoskeletal ribs.
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Abramyan J, Leung KJM, Richman JM. Divergent palate morphology in turtles and birds correlates with differences in proliferation and BMP2 expression during embryonic development. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:73-85. [PMID: 24323766 DOI: 10.1002/jez.b.22547] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 10/08/2013] [Accepted: 10/14/2013] [Indexed: 12/20/2022]
Abstract
During embryonic development, amniotes typically form outgrowths from the medial sides of the maxillary prominences called palatal shelves or palatine processes. In mammals the shelves fuse in the midline and form a bony hard palate that completely separates the nasal and oral cavities. In birds and lizards, palatine processes develop but remain unfused, leaving a natural cleft. Adult turtles do not possess palatine processes and unlike other amniotes, the internal nares open into the oral cavity. Here we investigate craniofacial ontogeny in the turtle, Emydura subglobosa to determine whether vestigial palatine processes develop and subsequently regress, or whether development fails entirely. We found that the primary palate in turtles develops similarly to other amniotes, but secondary palate ontogeny diverges. Using histology, cellular dynamics and in situ hybridization we found no evidence of palatine process development at any time during ontogeny of the face in the turtle. Furthermore, detailed comparisons with chicken embryos (the model organism most closely related to turtles from a molecular phylogeny perspective), we identified differences in proliferation and gene expression patterns that correlate with the differences in palate morphology. We propose that, in turtles, palatine process outgrowth is never initiated due to a lack of mesenchymal bone morphogenetic protein 2 (BMP2) expression in the maxillary mesenchyme, which in turn fails to induce the relatively higher cellular proliferation required for medial tissue outgrowth. It is likely that these differences between turtles and birds arose after the divergence of the lineage leading to modern turtles.
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Affiliation(s)
- John Abramyan
- Faculty of Dentistry, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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Lu B, Yang W, Dai Q, Fu J. Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles. PLoS One 2013; 8:e79348. [PMID: 24278129 PMCID: PMC3836853 DOI: 10.1371/journal.pone.0079348] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Weizhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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Jensen B, Moorman AFM, Wang T. Structure and function of the hearts of lizards and snakes. Biol Rev Camb Philos Soc 2013; 89:302-36. [DOI: 10.1111/brv.12056] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 06/26/2013] [Accepted: 07/30/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Bjarke Jensen
- Department of Bioscience, Zoophysiology; Aarhus University; Aarhus C 8000 Denmark
- Department of Anatomy, Embryology & Physiology, Academic Medical Center; University of Amsterdam; Amsterdam 1105 The Netherlands
| | - Antoon F. M. Moorman
- Department of Anatomy, Embryology & Physiology, Academic Medical Center; University of Amsterdam; Amsterdam 1105 The Netherlands
| | - Tobias Wang
- Department of Bioscience, Zoophysiology; Aarhus University; Aarhus C 8000 Denmark
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Werner J, Griebeler EM. New insights into non-avian dinosaur reproduction and their evolutionary and ecological implications: linking fossil evidence to allometries of extant close relatives. PLoS One 2013; 8:e72862. [PMID: 23991160 PMCID: PMC3749170 DOI: 10.1371/journal.pone.0072862] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/15/2013] [Indexed: 11/23/2022] Open
Abstract
It has been hypothesized that a high reproductive output contributes to the unique gigantism in large dinosaur taxa. In order to infer more information on dinosaur reproduction, we established allometries between body mass and different reproductive traits (egg mass, clutch mass, annual clutch mass) for extant phylogenetic brackets (birds, crocodiles and tortoises) of extinct non-avian dinosaurs. Allometries were applied to nine non-avian dinosaur taxa (theropods, hadrosaurs, and sauropodomorphs) for which fossil estimates on relevant traits are currently available. We found that the reproductive traits of most dinosaurs conformed to similar-sized or scaled-up extant reptiles or birds. The reproductive traits of theropods, which are considered more bird-like, were indeed consistent with birds, while the traits of sauropodomorphs conformed better to reptiles. Reproductive traits of hadrosaurs corresponded to both reptiles and birds. Excluding Massospondyluscarinatus, all dinosaurs studied had an intermediary egg to body mass relationship to reptiles and birds. In contrast, dinosaur clutch masses fitted with either the masses predicted from allometries of birds (theropods) or to the masses of reptiles (all other taxa). Theropods studied had probably one clutch per year. For sauropodomorphs and hadrosaurs, more than one clutch per year was predicted. Contrary to current hypotheses, large dinosaurs did not have exceptionally high annual egg numbers (AEN). Independent of the extant model, the estimated dinosaur AEN did not exceed 850 eggs (75,000 kg sauropod) for any of the taxa studied. This estimated maximum is probably an overestimation due to unrealistic assumptions. According to most AEN estimations, the dinosaurs studied laid less than 200 eggs per year. Only some AEN estimates obtained for medium to large sized sauropods were higher (200-400 eggs). Our results provide new (testable) hypotheses, especially for reproductive traits that are insufficiently documented or lacking from the fossil record. This contributes to the understanding of their evolution.
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Affiliation(s)
- Jan Werner
- Department of Ecology, Zoological Institute, University of Mainz, Mainz, Germany.
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Tokita M, Chaeychomsri W, Siruntawineti J. Skeletal gene expression in the temporal region of the reptilian embryos: implications for the evolution of reptilian skull morphology. SPRINGERPLUS 2013; 2:336. [PMID: 24711977 PMCID: PMC3970585 DOI: 10.1186/2193-1801-2-336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Abstract
Reptiles have achieved highly diverse morphological and physiological traits that allow them to exploit various ecological niches and resources. Morphology of the temporal region of the reptilian skull is highly diverse and historically it has been treated as an important character for classifying reptiles and has helped us understand the ecology and physiology of each species. However, the developmental mechanism that generates diversity of reptilian skull morphology is poorly understood. We reveal a potential developmental basis that generates morphological diversity in the temporal region of the reptilian skull by performing a comparative analysis of gene expression in the embryos of reptile species with different skull morphology. By investigating genes known to regulate early osteoblast development, we find dorsoventrally broadened unique expression of the early osteoblast marker, Runx2, in the temporal region of the head of turtle embryos that do not form temporal fenestrae. We also observe that Msx2 is also uniquely expressed in the mesenchymal cells distributed at the temporal region of the head of turtle embryos. Furthermore, through comparison of gene expression pattern in the embryos of turtle, crocodile, and snake species, we find a possible correlation between the spatial patterns of Runx2 and Msx2 expression in cranial mesenchymal cells and skull morphology of each reptilian lineage. Regulatory modifications of Runx2 and Msx2 expression in osteogenic mesenchymal precursor cells are likely involved in generating morphological diversity in the temporal region of the reptilian skull.
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Affiliation(s)
- Masayoshi Tokita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tenno-dai 1-1-1, Tsukuba, Ibaraki, 305-8572 Japan ; Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138 USA
| | - Win Chaeychomsri
- Department of Zoology, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900 Thailand
| | - Jindawan Siruntawineti
- Department of Zoology, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900 Thailand
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Kálmán M, Somiya H, Lazarevic L, Milosevic I, Ari C, Majorossy K. Absence of post-lesion reactive gliosis in elasmobranchs and turtles and its bearing on the evolution of astroglia. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:351-67. [DOI: 10.1002/jez.b.22505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 01/15/2013] [Accepted: 03/19/2013] [Indexed: 12/14/2022]
Affiliation(s)
- M. Kálmán
- Department of Anatomy; Semmelweis University; Budapest; Hungary
| | - Hiro Somiya
- Graduate School of Bioagricultural Sciences; Nagoya University; Nagoya; Japan
| | | | | | - Csilla Ari
- Department of Anatomy; Semmelweis University; Budapest; Hungary
| | - K. Majorossy
- Department of Anatomy; Semmelweis University; Budapest; Hungary
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Rhinn M, Miyoshi K, Watanabe A, Kawaguchi M, Ito F, Kuratani S, Baker CV, Murakami Y, Rijli FM. Evolutionary divergence of trigeminal nerve somatotopy in amniotes. J Comp Neurol 2013; 521:1378-94. [DOI: 10.1002/cne.23236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 07/24/2012] [Accepted: 10/02/2012] [Indexed: 11/10/2022]
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Middle ear cavity morphology is consistent with an aquatic origin for testudines. PLoS One 2013; 8:e54086. [PMID: 23342082 PMCID: PMC3544720 DOI: 10.1371/journal.pone.0054086] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/10/2012] [Indexed: 12/05/2022] Open
Abstract
The position of testudines in vertebrate phylogeny is being re-evaluated. At present, testudine morphological and molecular data conflict when reconstructing phylogenetic relationships. Complicating matters, the ecological niche of stem testudines is ambiguous. To understand how turtles have evolved to hear in different environments, we examined middle ear morphology and scaling in most extant families, as well as some extinct species, using 3-dimensional reconstructions from micro magnetic resonance (MR) and submillimeter computed tomography (CT) scans. All families of testudines exhibited a similar shape of the bony structure of the middle ear cavity, with the tympanic disk located on the rostrolateral edge of the cavity. Sea Turtles have additional soft tissue that fills the middle ear cavity to varying degrees. When the middle ear cavity is modeled as an air-filled sphere of the same volume resonating in an underwater sound field, the calculated resonances for the volumes of the middle ear cavities largely fell within testudine hearing ranges. Although there were some differences in morphology, there were no statistically significant differences in the scaling of the volume of the bony middle ear cavity with head size among groups when categorized by phylogeny and ecology. Because the cavity is predicted to resonate underwater within the testudine hearing range, the data support the hypothesis of an aquatic origin for testudines, and function of the middle ear cavity in underwater sound detection.
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