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Hjazi A, Jasim SA, Al-Dhalimy AMB, Bansal P, Kaur H, Qasim MT, Mohammed IH, Deorari M, Jawad MA, Zwamel AH. HOXA9 versus HOXB9; particular focus on their controversial role in tumor pathogenesis. J Appl Genet 2024; 65:473-492. [PMID: 38753266 DOI: 10.1007/s13353-024-00868-x] [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: 02/26/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 08/09/2024]
Abstract
The Homeobox (HOX) gene family is essential to regulating cellular processes because it maintains the exact coordination required for tissue homeostasis, cellular differentiation, and embryonic development. The most distinctive feature of this class of genes is the presence of the highly conserved DNA region known as the homeobox, which is essential for controlling their regulatory activities. Important players in the intricate process of genetic regulation are the HOX genes. Many diseases, especially in the area of cancer, are linked to their aberrant functioning. Due to their distinctive functions in biomedical research-particularly in the complex process of tumor advancement-HOXA9 and HOXB9 have drawn particular attention. HOXA9 and HOXB9 are more significant than what is usually connected with HOX genes since they have roles in the intricate field of cancer and beyond embryonic processes. The framework for a focused study of the different effects of HOXA9 and HOXB9 in the context of tumor biology is established in this study.
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Affiliation(s)
- Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | | | | | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-Be) University, Bengaluru, Karnataka, 560069, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh, 247341, India
- Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand, 831001, India
| | - Maytham T Qasim
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar, Nasiriyah, 64001, Iraq
| | - Israa Hussein Mohammed
- College of Nursing, National University of Science and Technology, Dhi Qar, Nasiriyah, Iraq
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Mohammed Abed Jawad
- Department of Medical Laboratories Technology, Al-Nisour University College, Baghdad, Iraq
| | - Ahmed Hussein Zwamel
- Medical Laboratory Technique College, The Islamic University, Najaf, Iraq
- Medical Laboratory Technique College, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- Medical Laboratory Technique College, The Islamic University of Babylon, Babylon, Iraq
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2
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White MA. Rapid evolution of body plans. Nat Ecol Evol 2024; 8:604-605. [PMID: 38378803 DOI: 10.1038/s41559-023-02141-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Affiliation(s)
- Michael A White
- Department of Genetics, University of Georgia, Athens, GA, USA.
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3
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Kingsley EP, Hager ER, Lassance JM, Turner KM, Harringmeyer OS, Kirby C, Neugeboren BI, Hoekstra HE. Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development. Nat Ecol Evol 2024; 8:791-805. [PMID: 38378804 PMCID: PMC11009118 DOI: 10.1038/s41559-024-02346-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Variation in the size and number of axial segments underlies much of the diversity in animal body plans. Here we investigate the evolutionary, genetic and developmental mechanisms driving tail-length differences between forest and prairie ecotypes of deer mice (Peromyscus maniculatus). We first show that long-tailed forest mice perform better in an arboreal locomotion assay, consistent with tails being important for balance during climbing. We then identify six genomic regions that contribute to differences in tail length, three of which associate with caudal vertebra length and the other three with vertebra number. For all six loci, the forest allele increases tail length, indicative of the cumulative effect of natural selection. Two of the genomic regions associated with variation in vertebra number contain Hox gene clusters. Of those, we find an allele-specific decrease in Hoxd13 expression in the embryonic tail bud of long-tailed forest mice, consistent with its role in axial elongation. Additionally, we find that forest embryos have more presomitic mesoderm than prairie embryos and that this correlates with an increase in the number of neuromesodermal progenitors, which are modulated by Hox13 paralogues. Together, these results suggest a role for Hoxd13 in the development of natural variation in adaptive morphology on a microevolutionary timescale.
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Affiliation(s)
- Evan P Kingsley
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Emily R Hager
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Jean-Marc Lassance
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- GIGA Institute, University of Liège, Liège, Belgium
| | - Kyle M Turner
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Centre for Teaching Support & Innovation, University of Toronto, Toronto, Ontario, Canada
| | - Olivia S Harringmeyer
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Christopher Kirby
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Beverly I Neugeboren
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Environmental Health and Safety, Harvard University, Cambridge, MA, USA
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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4
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Tingle JL, Garner KL, Astley HC. Functional diversity of snake locomotor behaviors: A review of the biological literature for bioinspiration. Ann N Y Acad Sci 2024; 1533:16-37. [PMID: 38367220 DOI: 10.1111/nyas.15109] [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] [Indexed: 02/19/2024]
Abstract
Organismal solutions to natural challenges can spark creative engineering applications. However, most engineers are not experts in organismal biology, creating a potential barrier to maximally effective bioinspired design. In this review, we aim to reduce that barrier with respect to a group of organisms that hold particular promise for a variety of applications: snakes. Representing >10% of tetrapod vertebrates, snakes inhabit nearly every imaginable terrestrial environment, moving with ease under many conditions that would thwart other animals. To do so, they employ over a dozen different types of locomotion (perhaps well over). Lacking limbs, they have evolved axial musculoskeletal features that enable their vast functional diversity, which can vary across species. Different species also have various skin features that provide numerous functional benefits, including frictional anisotropy or isotropy (as their locomotor habits demand), waterproofing, dirt shedding, antimicrobial properties, structural colors, and wear resistance. Snakes clearly have much to offer to the fields of robotics and materials science. We aim for this review to increase knowledge of snake functional diversity by facilitating access to the relevant literature.
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Affiliation(s)
| | - Kelsey L Garner
- Department of Biology, University of Akron, Akron, Ohio, USA
| | - Henry C Astley
- Department of Biology, University of Akron, Akron, Ohio, USA
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5
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Wang C, Zhao T, Liu X, Li T, He L, Wang Q, Wang L, Zhou L. CRISPR/Cas9-Mediated Mutagenesis of Antennapedia in Spodoptera frugiperda. INSECTS 2023; 15:16. [PMID: 38249022 PMCID: PMC10816051 DOI: 10.3390/insects15010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024]
Abstract
The homeotic gene Antennapedia (Antp) has been identified as playing a pivotal role in the morphogenesis of the thorax and wings across various insect species. Leveraging insights from previous studies, the functional characterization of Antp in S. frugiperda was undertaken using RT-qPCR and the CRISPR/Cas9 genome-editing system. Phylogenetic analyses indicate that Antp shares a high degree of sequence homology among Lepidoptera species. The expression profile of SfAntp was detected by RT-qPCR. The results showed that SfAntp was expressed in the whole growth cycle of S. frugiperda, the expression level was the highest in the egg stage, and the expression level was higher from 12 h to 48 h. Tissue-specific expression profiling demonstrated that SfAntp was most abundantly expressed in the thoracic segments and legs. To functionally disrupt SfAntp, two sgRNA sites were designed at the first exon of SfAntp and the gene was knocked out by CRISPR/Cas9 via microinjection. The results showed that the deletion of SfAntp produced a mutant phenotype of thoracic fusion, thoracic leg defect, leg-like protrusions between the head and thoracic segments and pupation deformity. In addition, deletion of SfAntp resulted in high embryo mortality. Through DNA sequencing, it was found that the target site of the SfAntp mutant had different degrees of frameshift mutations, indicating that the mutant phenotype was indeed caused by the knockout of SfAntp.
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Affiliation(s)
- Congke Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of New Pesticide Development and Application, Henan Agricultural University, Zhengzhou 450046, China
- Green Pesticide Creation Engineering Technology Research Center, Henan Agricultural University, Zhengzhou 450046, China
| | - Te Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of New Pesticide Development and Application, Henan Agricultural University, Zhengzhou 450046, China
- Green Pesticide Creation Engineering Technology Research Center, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaolong Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of New Pesticide Development and Application, Henan Agricultural University, Zhengzhou 450046, China
- Green Pesticide Creation Engineering Technology Research Center, Henan Agricultural University, Zhengzhou 450046, China
| | - Tianliang Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of New Pesticide Development and Application, Henan Agricultural University, Zhengzhou 450046, China
- Green Pesticide Creation Engineering Technology Research Center, Henan Agricultural University, Zhengzhou 450046, China
| | - Leiming He
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of New Pesticide Development and Application, Henan Agricultural University, Zhengzhou 450046, China
- Green Pesticide Creation Engineering Technology Research Center, Henan Agricultural University, Zhengzhou 450046, China
| | - Qinqin Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of New Pesticide Development and Application, Henan Agricultural University, Zhengzhou 450046, China
- Green Pesticide Creation Engineering Technology Research Center, Henan Agricultural University, Zhengzhou 450046, China
| | - Li Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of New Pesticide Development and Application, Henan Agricultural University, Zhengzhou 450046, China
- Green Pesticide Creation Engineering Technology Research Center, Henan Agricultural University, Zhengzhou 450046, China
| | - Lin Zhou
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of New Pesticide Development and Application, Henan Agricultural University, Zhengzhou 450046, China
- Green Pesticide Creation Engineering Technology Research Center, Henan Agricultural University, Zhengzhou 450046, China
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6
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Lozovska A, Korovesi AG, Duarte P, Casaca A, Assunção T, Mallo M. The control of transitions along the main body axis. Curr Top Dev Biol 2023; 159:272-308. [PMID: 38729678 DOI: 10.1016/bs.ctdb.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Although vertebrates display a large variety of forms and sizes, the mechanisms controlling the layout of the basic body plan are substantially conserved throughout the clade. Following gastrulation, head, trunk, and tail are sequentially generated through the continuous addition of tissue at the caudal embryonic end. Development of each of these major embryonic regions is regulated by a distinct genetic network. The transitions from head-to-trunk and from trunk-to-tail development thus involve major changes in regulatory mechanisms, requiring proper coordination to guarantee smooth progression of embryonic development. In this review, we will discuss the key cellular and embryological events associated with those transitions giving particular attention to their regulation, aiming to provide a cohesive outlook of this important component of vertebrate development.
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Affiliation(s)
| | | | - Patricia Duarte
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Ana Casaca
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Tereza Assunção
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Moises Mallo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal.
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7
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Gable SM, Mendez JM, Bushroe NA, Wilson A, Byars MI, Tollis M. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order. Genes (Basel) 2023; 14:1387. [PMID: 37510292 PMCID: PMC10379679 DOI: 10.3390/genes14071387] [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: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
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8
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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9
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Shaping Hox gene activity to generate morphological diversity across vertebrate phylogeny. Essays Biochem 2022; 66:717-726. [PMID: 35924372 DOI: 10.1042/ebc20220050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 02/07/2023]
Abstract
The importance of Hox genes for the development and evolution of the vertebrate axial skeleton and paired appendages has been recognized for already several decades. The steady growth of genomic sequence data from an increasing number of vertebrate species, together with the improvement of methods to analyze genomic structure and interactions, as well as to control gene activity in various species has refined our understanding of Hox gene activity in development and evolution. Here, I will review recent data addressing the influence of Hox regulatory processes in the evolution of the fins and the emergence of the tetrapod limb. In addition, I will discuss the involvement of posterior Hox genes in the control of vertebrate axial extension, focusing on an apparently divergent activity that Hox13 paralog group genes have on the regulation of tail bud development in mouse and zebrafish embryos.
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10
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Pereira AG, Grizante MB, Kohlsdorf T. What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda. Proc Biol Sci 2022; 289:20220841. [PMID: 35975445 PMCID: PMC9382212 DOI: 10.1098/rspb.2022.0841] [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: 05/01/2022] [Accepted: 07/25/2022] [Indexed: 12/14/2022] Open
Abstract
Developmental pathways encompass transcription factors and cis-regulatory elements that interact as transcription factor-regulatory element (TF-RE) units. Independent origins of similar phenotypes likely involve changes in different parts of these units, a hypothesis promisingly tested addressing the evolution of the rib-associated lumbar (RAL) morphotype that characterizes emblematic animals such as snakes and elephants. Previous investigation in these lineages identified a polymorphism in the Homology region 1 [H1] enhancer of the Myogenic factor-5 [Myf5], which interacts with HOX10 proteins to modulate rib development. Here we address the evolution of TF-RE units focusing on independent origins of RAL morphotypes. We compiled an extensive database for H1-Myf5 and HOX10 sequences with two goals: (i) evaluate if the enhancer polymorphism is present in amphibians exhibiting the RAL morphotype and (ii) test a hypothesis of enhanced evolutionary flexibility mediated by TF-RE units, according to which independent origins of the RAL morphotype might involve changes in either component of the interaction unit. We identified the H1-Myf5 polymorphism in lineages that diverged around 340 Ma, including Lissamphibia. Independent origins of the RAL morphotype in Tetrapoda involved sequence variation in either component of the TF-RE unit, confirming that different changes may similarly affect the phenotypic outcome of a given developmental pathway.
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Affiliation(s)
- Anieli G. Pereira
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mariana B. Grizante
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Dante Pazzanese Institute of Cardiology, Sao Paulo, Brazil
| | - Tiana Kohlsdorf
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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11
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MINCER ST, NIETHAMER TK, TENG T, BUSH JO, PERCIVAL CJ. Investigating the effects of compound paralogous EPHB receptor mutations on mouse facial development. Dev Dyn 2022; 251:1138-1155. [PMID: 35025117 PMCID: PMC9924224 DOI: 10.1002/dvdy.454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/09/2021] [Accepted: 12/21/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Variation in facial shape may arise from the combinatorial or overlapping actions of paralogous genes. Given its many members, and overlapping expression and functions, the EPH receptor family is a compelling candidate source of craniofacial morphological variation. We performed a detailed morphometric analysis of an allelic series of E14.5 Ephb1-3 receptor mutants to determine the effect of each paralogous receptor gene on craniofacial morphology. RESULTS We found that Ephb1, Ephb2, and Ephb3 genotypes significantly influenced facial shape, but Ephb1 effects were weaker than Ephb2 and Ephb3 effects. Ephb2-/- and Ephb3-/- mutations affected similar aspects of facial morphology, but Ephb3-/- mutants had additional facial shape effects. Craniofacial differences across the allelic series were largely consistent with predicted additive genetic effects. However, we identified a potentially important nonadditive effect where Ephb1 mutants displayed different morphologies depending on the combination of other Ephb paralogs present, where Ephb1+/- , Ephb1-/- , and Ephb1-/- ; Ephb3-/- mutants exhibited a consistent deviation from their predicted facial shapes. CONCLUSIONS This study provides a detailed assessment of the effects of Ephb receptor gene paralogs on E14.5 mouse facial morphology and demonstrates how the loss of specific receptors contributes to facial dysmorphology.
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Affiliation(s)
- Sarah T. MINCER
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Terren K. NIETHAMER
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, United States of America,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America,Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America,Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Teng TENG
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, United States of America,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America,Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America,Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Jeffrey O. BUSH
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, United States of America,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America,Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America,Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Christopher J. PERCIVAL
- Department of Anthropology, Stony Brook University, Stony Brook, New York, United States of America
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12
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Figueirido B, Serrano FJ, Pérez-Ramos A, Esteban JM, Ferrón HG, Martín-Serra A. Body-axis organization in tetrapods: a model-system to disentangle the developmental origins of convergent evolution in deep time. Biol Lett 2022; 18:20220047. [PMID: 35382583 PMCID: PMC8984341 DOI: 10.1098/rsbl.2022.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Convergent evolution is a central concept in evolutionary theory but the underlying mechanism has been largely debated since On the Origin of Species. Previous hypotheses predict that developmental constraints make some morphologies more likely to arise than others and natural selection discards those of the lowest fitness. However, the quantification of the role and strength of natural selection and developmental constraint in shaping convergent phenotypes on macroevolutionary timescales is challenging because the information regarding performance and development is not directly available. Accordingly, current knowledge of how embryonic development and natural selection drive phenotypic evolution in vertebrates has been extended from studies performed at short temporal scales. We propose here the organization of the tetrapod body-axis as a model system to investigate the developmental origins of convergent evolution over hundreds of millions of years. The quantification of the primary developmental mechanisms driving body-axis organization (i.e. somitogenesis, homeotic effects and differential growth) can be inferred from vertebral counts, and recent techniques of three-dimensional computational biomechanics have the necessary potential to reveal organismal performance even in fossil forms. The combination of both approaches offers a novel and robust methodological framework to test competing hypotheses on the functional and developmental drivers of phenotypic evolution and evolutionary convergence.
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Affiliation(s)
- Borja Figueirido
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, Spain
| | - Francisco J Serrano
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, Spain.,Dinosaur Institute, Natural History Museum of Los Angeles County; Exposition Boulevard, Los Angeles, CA 90007, USA
| | - Alejandro Pérez-Ramos
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, Spain
| | - Juan Miguel Esteban
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, Spain
| | - Humberto G Ferrón
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, 46980-Paterna, Valencia, Spain
| | - Alberto Martín-Serra
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, Spain
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13
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Rao WQ, Kalogeropoulos K, Allentoft ME, Gopalakrishnan S, Zhao WN, Workman CT, Knudsen C, Jiménez-Mena B, Seneci L, Mousavi-Derazmahalleh M, Jenkins TP, Rivera-de-Torre E, Liu SQ, Laustsen AH. The rise of genomics in snake venom research: recent advances and future perspectives. Gigascience 2022; 11:6562531. [PMID: 35365832 PMCID: PMC8975721 DOI: 10.1093/gigascience/giac024] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 12/12/2022] Open
Abstract
Snake venoms represent a danger to human health, but also a gold mine of bioactive proteins that can be harnessed for drug discovery purposes. The evolution of snakes and their venom has been studied for decades, particularly via traditional morphological and basic genetic methods alongside venom proteomics. However, while the field of genomics has matured rapidly over the past 2 decades, owing to the development of next-generation sequencing technologies, snake genomics remains in its infancy. Here, we provide an overview of the state of the art in snake genomics and discuss its potential implications for studying venom evolution and toxinology. On the basis of current knowledge, gene duplication and positive selection are key mechanisms in the neofunctionalization of snake venom proteins. This makes snake venoms important evolutionary drivers that explain the remarkable venom diversification and adaptive variation observed in these reptiles. Gene duplication and neofunctionalization have also generated a large number of repeat sequences in snake genomes that pose a significant challenge to DNA sequencing, resulting in the need for substantial computational resources and longer sequencing read length for high-quality genome assembly. Fortunately, owing to constantly improving sequencing technologies and computational tools, we are now able to explore the molecular mechanisms of snake venom evolution in unprecedented detail. Such novel insights have the potential to affect the design and development of antivenoms and possibly other drugs, as well as provide new fundamental knowledge on snake biology and evolution.
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Affiliation(s)
- Wei-Qiao Rao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark.,Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Konstantinos Kalogeropoulos
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, 6102, Bentley Perth, Australia.,Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350, Copenhagen, Denmark
| | - Wei-Ning Zhao
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Cecilie Knudsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Belén Jiménez-Mena
- DTU Aqua, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Lorenzo Seneci
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, 6102, Bentley Perth, Australia
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Si-Qi Liu
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
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14
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Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Rep 2022; 38:110280. [DOI: 10.1016/j.celrep.2021.110280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 01/02/2023] Open
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15
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hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proc Natl Acad Sci U S A 2021; 118:2114563118. [PMID: 34903669 PMCID: PMC8713815 DOI: 10.1073/pnas.2114563118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 01/11/2023] Open
Abstract
The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
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16
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Giraud G, Paul R, Duffraisse M, Khan S, Shashidhara LS, Merabet S. Developmental Robustness: The Haltere Case in Drosophila. Front Cell Dev Biol 2021; 9:713282. [PMID: 34368162 PMCID: PMC8343187 DOI: 10.3389/fcell.2021.713282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
Developmental processes have to be robust but also flexible enough to respond to genetic and environmental variations. Different mechanisms have been described to explain the apparent antagonistic nature of developmental robustness and plasticity. Here, we present a “self-sufficient” molecular model to explain the development of a particular flight organ that is under the control of the Hox gene Ultrabithorax (Ubx) in the fruit fly Drosophila melanogaster. Our model is based on a candidate RNAi screen and additional genetic analyses that all converge to an autonomous and cofactor-independent mode of action for Ubx. We postulate that this self-sufficient molecular mechanism is possible due to an unusually high expression level of the Hox protein. We propose that high dosage could constitute a so far poorly investigated molecular strategy for allowing Hox proteins to both innovate and stabilize new forms during evolution.
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Affiliation(s)
| | | | | | - Soumen Khan
- Indian Institute of Science Education and Research (IISER), Pune, India
| | - L S Shashidhara
- Indian Institute of Science Education and Research (IISER), Pune, India.,Ashoka University, Sonipat, India
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17
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Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution. Cells 2021; 10:cells10071707. [PMID: 34359877 PMCID: PMC8303610 DOI: 10.3390/cells10071707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.
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18
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Abstract
The axial skeleton of all vertebrates is composed of individual units known as vertebrae. Each vertebra has individual anatomical attributes, yet they can be classified in five different groups, namely cervical, thoracic, lumbar, sacral and caudal, according to shared characteristics and their association with specific body areas. Variations in vertebral number, size, morphological features and their distribution amongst the different regions of the vertebral column are a major source of the anatomical diversity observed among vertebrates. In this review I will discuss the impact of those variations on the anatomy of different vertebrate species and provide insights into the genetic origin of some remarkable morphological traits that often serve to classify phylogenetic branches or individual species, like the long trunks of snakes or the long necks of giraffes.
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19
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Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression. J Dev Biol 2021; 9:jdb9010006. [PMID: 33546292 PMCID: PMC7931043 DOI: 10.3390/jdb9010006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/23/2022] Open
Abstract
Knowledge of the diverse DNA binding specificities of transcription factors is important for understanding their specific regulatory functions in animal development and evolution. We have examined the genome-wide binding properties of the mouse HOXB1 protein in embryonic stem cells differentiated into neural fates. Unexpectedly, only a small number of HOXB1 bound regions (7%) correlate with binding of the known HOX cofactors PBX and MEIS. In contrast, 22% of the HOXB1 binding peaks display co-occupancy with the transcriptional repressor REST. Analyses revealed that co-binding of HOXB1 with PBX correlates with active histone marks and high levels of expression, while co-occupancy with REST correlates with repressive histone marks and repression of the target genes. Analysis of HOXB1 bound regions uncovered enrichment of a novel 15 base pair HOXB1 binding motif HB1RE (HOXB1 response element). In vitro template binding assays showed that HOXB1, PBX1, and MEIS can bind to this motif. In vivo, this motif is sufficient for direct expression of a reporter gene and over-expression of HOXB1 selectively represses this activity. Our analyses suggest that HOXB1 has evolved an association with REST in gene regulation and the novel HB1RE motif contributes to HOXB1 function in part through a repressive role in gene expression.
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20
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Etchegaray E, Naville M, Volff JN, Haftek-Terreau Z. Transposable element-derived sequences in vertebrate development. Mob DNA 2021; 12:1. [PMID: 33407840 PMCID: PMC7786948 DOI: 10.1186/s13100-020-00229-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
Transposable elements (TEs) are major components of all vertebrate genomes that can cause deleterious insertions and genomic instability. However, depending on the specific genomic context of their insertion site, TE sequences can sometimes get positively selected, leading to what are called "exaptation" events. TE sequence exaptation constitutes an important source of novelties for gene, genome and organism evolution, giving rise to new regulatory sequences, protein-coding exons/genes and non-coding RNAs, which can play various roles beneficial to the host. In this review, we focus on the development of vertebrates, which present many derived traits such as bones, adaptive immunity and a complex brain. We illustrate how TE-derived sequences have given rise to developmental innovations in vertebrates and how they thereby contributed to the evolutionary success of this lineage.
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Affiliation(s)
- Ema Etchegaray
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France.
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Zofia Haftek-Terreau
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
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21
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Simões TR, Vernygora O, Caldwell MW, Pierce SE. Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles. Nat Commun 2020; 11:3322. [PMID: 32620878 PMCID: PMC7335191 DOI: 10.1038/s41467-020-17190-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 06/17/2020] [Indexed: 11/18/2022] Open
Abstract
The origin of phenotypic diversity among higher clades is one of the most fundamental topics in evolutionary biology. However, due to methodological challenges, few studies have assessed rates of evolution and phenotypic disparity across broad scales of time to understand the evolutionary dynamics behind the origin and early evolution of new clades. Here, we provide a total-evidence dating approach to this problem in diapsid reptiles. We find major chronological gaps between periods of high evolutionary rates (phenotypic and molecular) and expansion in phenotypic disparity in reptile evolution. Importantly, many instances of accelerated phenotypic evolution are detected at the origin of major clades and body plans, but not concurrent with previously proposed periods of adaptive radiation. Furthermore, strongly heterogenic rates of evolution mark the acquisition of similarly adapted functional types, and the origin of snakes is marked by the highest rates of phenotypic evolution in diapsid history.
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Affiliation(s)
- Tiago R Simões
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
| | - Oksana Vernygora
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Michael W Caldwell
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephanie E Pierce
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
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22
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Scaal M. Development of the amniote ventrolateral body wall. Dev Dyn 2020; 250:39-59. [PMID: 32406962 DOI: 10.1002/dvdy.193] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
In vertebrates, the trunk consists of the musculoskeletal structures of the back and the ventrolateral body wall, which together enclose the internal organs of the circulatory, digestive, respiratory and urogenital systems. This review gives an overview on the development of the thoracic and abdominal wall during amniote embryogenesis. Specifically, I briefly summarize relevant historical concepts and the present knowledge on the early embryonic development of ribs, sternum, intercostal muscles and abdominal muscles with respect to anatomical bauplan, origin and specification of precursor cells, initial steps of pattern formation, and cellular and molecular regulation of morphogenesis.
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Affiliation(s)
- Martin Scaal
- Faculty of Medicine, Institute of Anatomy II, University of Cologne, Cologne, Germany
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23
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Mallo M. The vertebrate tail: a gene playground for evolution. Cell Mol Life Sci 2020; 77:1021-1030. [PMID: 31559446 PMCID: PMC11104866 DOI: 10.1007/s00018-019-03311-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 12/25/2022]
Abstract
The tail of all vertebrates, regardless of size and anatomical detail, derive from a post-anal extension of the embryo known as the tail bud. Formation, growth and differentiation of this structure are closely associated with the activity of a group of cells that derive from the axial progenitors that build the spinal cord and the muscle-skeletal case of the trunk. Gdf11 activity switches the development of these progenitors from a trunk to a tail bud mode by changing the regulatory network that controls their growth and differentiation potential. Recent work in the mouse indicates that the tail bud regulatory network relies on the interconnected activities of the Lin28/let-7 axis and the Hox13 genes. As this network is likely to be conserved in other mammals, it is possible that the final length and anatomical composition of the adult tail result from the balance between the progenitor-promoting and -repressing activities provided by those genes. This balance might also determine the functional characteristics of the adult tail. Particularly relevant is its regeneration potential, intimately linked to the spinal cord. In mammals, known for their complete inability to regenerate the tail, the spinal cord is removed from the embryonic tail at late stages of development through a Hox13-dependent mechanism. In contrast, the tail of salamanders and lizards keep a functional spinal cord that actively guides the tail's regeneration process. I will argue that the distinct molecular networks controlling tail bud development provided a collection of readily accessible gene networks that were co-opted and combined during evolution either to end the active life of those progenitors or to make them generate the wide diversity of tail shapes and sizes observed among vertebrates.
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Affiliation(s)
- Moisés Mallo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
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24
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Khosraviani N, Ostrowski LA, Mekhail K. Roles for Non-coding RNAs in Spatial Genome Organization. Front Cell Dev Biol 2019; 7:336. [PMID: 31921848 PMCID: PMC6930868 DOI: 10.3389/fcell.2019.00336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/29/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic loci are non-randomly arranged in the nucleus of the cell. This order, which is important to overall genome expression and stability, is maintained by a growing number of factors including the nuclear envelope, various genetic elements and dedicated protein complexes. Here, we review evidence supporting roles for non-coding RNAs (ncRNAs) in the regulation of spatial genome organization and its impact on gene expression and cell survival. Specifically, we discuss how ncRNAs from single-copy and repetitive DNA loci contribute to spatial genome organization by impacting perinuclear chromosome tethering, major nuclear compartments, chromatin looping, and various chromosomal structures. Overall, our analysis of the literature highlights central functions for ncRNAs and their transcription in the modulation of spatial genome organization with connections to human health and disease.
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Affiliation(s)
- Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lauren A. Ostrowski
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Canada Research Chairs Program, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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25
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Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization. Nat Commun 2019; 10:5560. [PMID: 31804475 PMCID: PMC6895188 DOI: 10.1038/s41467-019-13405-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/07/2019] [Indexed: 01/02/2023] Open
Abstract
Ecomorphological studies evaluating the impact of environmental and biological factors on the brain have so far focused on morphology or size measurements, and the ecological relevance of potential multi-level variations in brain architecture remains unclear in vertebrates. Here, we exploit the extraordinary ecomorphological diversity of squamates to assess brain phenotypic diversification with respect to locomotor specialization, by integrating single-cell distribution and transcriptomic data along with geometric morphometric, phylogenetic, and volumetric analysis of high-definition 3D models. We reveal significant changes in cerebellar shape and size as well as alternative spatial layouts of cortical neurons and dynamic gene expression that all correlate with locomotor behaviours. These findings show that locomotor mode is a strong predictor of cerebellar structure and pattern, suggesting that major behavioural transitions in squamates are evolutionarily correlated with mosaic brain changes. Furthermore, our study amplifies the concept of ‘cerebrotype’, initially proposed for vertebrate brain proportions, towards additional shape characters. The cerebellum is critical in sensory-motor control and is structurally diverse across vertebrates. Here, the authors investigate the evolutionary relationship between locomotory mode and cerebellum architecture across squamates by integrating study of gene expression, cell distribution, and 3D morphology.
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26
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Feiner N. Evolutionary lability in Hox cluster structure and gene expression in Anolis lizards. Evol Lett 2019; 3:474-484. [PMID: 31636940 PMCID: PMC6791295 DOI: 10.1002/evl3.131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/22/2019] [Accepted: 07/16/2019] [Indexed: 12/30/2022] Open
Abstract
Hox genes orchestrate development by patterning the embryonic axis. Vertebrate Hox genes are arranged in four compact clusters, and the spacing between genes is assumed to be crucial for their function. The genomes of squamate reptiles are unusually rich and variable in transposable elements (TEs), and it has been suggested that TE invasion is responsible for the Hox cluster expansion seen in snakes and lizards. Using de novo TE prediction on 17 genomes of lizards and snakes, I show that TE content of Hox clusters are generally 50% lower than genome‐wide TE levels. However, two distantly related lizards of the species‐rich genus Anolis have Hox clusters with a TE content that approaches genomic levels. The age distribution of TEs in Anolis lizards revealed that peaks of TE activity broadly coincide with speciation events. In accordance with theoretical models of Hox cluster regulation, I find that Anolis species with many TEs in their Hox clusters show aberrant Hox gene expression patterns, suggesting a functional link between TE accumulation and embryonic development. These results are consistent with the hypothesis that TEs play a role in developmental processes as well as in evolutionary diversifications.
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27
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da Silva RA, Fuhler GM, Janmaat VT, da C Fernandes CJ, da Silva Feltran G, Oliveira FA, Matos AA, Oliveira RC, Ferreira MR, Zambuzzi WF, Peppelenbosch MP. HOXA cluster gene expression during osteoblast differentiation involves epigenetic control. Bone 2019; 125:74-86. [PMID: 31054377 DOI: 10.1016/j.bone.2019.04.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/25/2019] [Accepted: 04/30/2019] [Indexed: 01/17/2023]
Abstract
The HOXA gene cluster is generally recognized as a pivotal mediator of positional identity in the skeletal system, expression of different orthologues conferring alternative locational phenotype of the vertebrate bone. Strikingly, however, the molecular mechanisms that regulate orthologue-specific expression of different HOXA cluster members in gestating osteoblasts remain largely obscure, but in analogy to the processes observed in acute lymphatic leukemia it is assumed that alternative methylation of HOXA promoter regions drives position specific expression patterns. In an effort to understand HOXA cluster gene expression in osteogenesis we characterize both expression and the epigenetic landscape of the HOXA gene cluster during in vitro osteoblast formation from mesenchymal precursors. We observe that osteoblast formation per se provokes strong upregulation of HOXA gene cluster expression, in particular of midcluster genes, and paradoxal downregulation of HOXA7 and HOXA10. These differences in expression appear related to promoter methylation. LnRNAs HOTAIR and HOTTIP, known to modulate HOXA expression, are also regulated by their promoter methylation processing, but do not correlate with HOXA cluster expression profile. We thus conclude that HOXA expression is profoundly regulated during osteoblast differentiation through canonical methylation-dependent mechanisms but not through the flanking lnRNAs.
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Affiliation(s)
- Rodrigo A da Silva
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil; Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Gwenny M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Vincent T Janmaat
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Célio Júnior da C Fernandes
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil
| | - Geórgia da Silva Feltran
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil
| | - Flávia Amadeu Oliveira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Adriana Arruda Matos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Rodrigo Cardoso Oliveira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Marcel Rodrigues Ferreira
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil
| | - Willian F Zambuzzi
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil.
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, the Netherlands.
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28
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Feiner N, Wood NJ. Lizards possess the most complete tetrapod Hox gene repertoire despite pervasive structural changes in Hox clusters. Evol Dev 2019; 21:218-228. [PMID: 31298799 DOI: 10.1111/ede.12300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/26/2019] [Accepted: 06/08/2019] [Indexed: 01/21/2023]
Abstract
Hox genes are a remarkable example of conservation in animal development and their nested expression along the head-to-tail axis orchestrates embryonic patterning. Early in vertebrate history, two duplications led to the emergence of four Hox clusters (A-D) and redundancy within paralog groups has been partially accommodated with gene losses. Here we conduct an inventory of squamate Hox genes using the genomes of 10 lizard and 7 snake species. Although the HoxC1 gene has been hypothesized to be lost in the amniote ancestor, we reveal that it is retained in lizards. In contrast, all snakes lack functional HoxC1 and -D12 genes. Varying levels of degradation suggest differences in the process of gene loss between the two genes. The vertebrate HoxC1 gene is prone to gene loss and its functional domains are more variable than those of other Hox1 genes. We describe for the first time the HoxC1 expression patterns in tetrapods. HoxC1 is broadly expressed during development in the diencephalon, the neural tube, dorsal root ganglia, and limb buds in two lizard species. Our study emphasizes the value of revisiting Hox gene repertoires by densely sampling taxonomic groups and its feasibility owing to growing sequence resources in evaluating gene repertoires across taxa.
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Affiliation(s)
- Nathalie Feiner
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Department of Biology, Lund University, Lund, Sweden
| | - Natalie J Wood
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Centre for Life's Origins and Evolution, Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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Reassessing the Role of Hox Genes during Vertebrate Development and Evolution. Trends Genet 2018; 34:209-217. [PMID: 29269261 DOI: 10.1016/j.tig.2017.11.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/21/2017] [Accepted: 11/29/2017] [Indexed: 12/13/2022]
Abstract
Since their discovery Hox genes have been at the core of the established models explaining the development and evolution of the vertebrate body plan as well as its paired appendages. Recent work brought new light to their role in the patterning processes along the main body axis. These studies show that Hox genes do not control the basic layout of the vertebrate body plan but carry out region-specific patterning instructions loaded on the derivatives of axial progenitors by Hox-independent processes. Furthermore, the finding that Hox clusters are embedded in functional chromatin domains, which critically impacts their expression, has significantly altered our understanding of the mechanisms of Hox gene regulation. This new conceptual framework has broadened our understanding of both limb development and the evolution of vertebrate paired appendages.
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Iwanishi S, Zaitsu S, Shibata H, Nitasaka E. An albino mutant of the Japanese rat snake (Elaphe climacophora) carries a nonsense mutation in the tyrosinase gene. Genes Genet Syst 2018; 93:163-167. [PMID: 30158334 DOI: 10.1266/ggs.18-00021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Japanese rat snake (Elaphe climacophora) is a common species in Japan and is widely distributed across the Japanese islands. An albino mutant of the Japanese rat snake ("pet trade" albino) has been bred and traded by hobbyists for around two decades because of its remarkable light-yellowish coloration with red eyes, attributable to a lack of melanin. Another albino Japanese rat snake mutant found in a natural population of the Japanese rat snake at high frequency in Iwakuni City, Yamaguchi Prefecture is known as "Iwakuni no Shirohebi". It has been conserved by the government as a natural monument. The Iwakuni albino also lacks melanin, having light-yellowish body coloration and red eyes. Albino mutants of several organisms have been studied, and mutation of the tyrosinase gene (TYR) is responsible for this phenotype. By determining the sequence of the TYR coding region of the pet trade albino, we identified a nonsense mutation in the second exon. Furthermore, RT-PCR revealed that TYR transcripts were not detected in this snake. These findings suggest that mutation of TYR is responsible for the albino phenotype of the pet trade line of the Japanese rat snake. However, the Iwakuni albino did not share this TYR mutation; thus, these two albino lines differ in their origins.
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Affiliation(s)
- Shuzo Iwanishi
- Graduate School of Systems Life Sciences, Kyushu University
| | - Shohei Zaitsu
- Graduate School of Systems Life Sciences, Kyushu University
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University
| | - Eiji Nitasaka
- Department of Biological Science, Faculty of Science, Kyushu University
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Yu F, Zhang Z, Chen L, Wang J, Shen Z. Spatial distribution characteristics of soil organic carbon in subtropical forests of mountain Lushan, China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2018; 190:545. [PMID: 30141063 DOI: 10.1007/s10661-018-6906-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 08/07/2018] [Indexed: 06/08/2023]
Abstract
The study on the spatial distribution of forest soil organic carbon (SOC) is of great significance for accurate assessment of carbon storage in forest ecosystems. In the present study, by taking eight kinds of forest soils of Mountain Lushan in the subtropical area as the research object, we studied the spatial distribution characteristics of SOC in this mountainous area. The results showed that the SOC content and SOC density (SOCD) of main forest types in the Mountain Lushan were lower than the national and the world average. The soil layer of Lushan forest was thinner, and the SOC and active SOC (ASOC) contents of different forest types and SOCDs are the highest in the surface soil. SOCD of the topsoil accounts for 32.64-54.03% of the total SOCD in the whole soil profile. Surface litter is an important source of SOC, and the different vegetation types are the important reason for the different spatial distribution of SOC in this area. Soil SOC contents in the high-altitude forest (bamboo forest, deciduous broadleaf forest, Pinus taiwanensis forest, evergreen-deciduous forest, and coniferous-broadleaved mixed forest) were higher than those in the low-altitude forest (evergreen broadleaf forest, shrub, and Pinus massoniana forest). However, the difference in SOC content exhibited at the altitude gradient is significantly lower than that in SOC in the soil profile. This indicates that both soil depth and elevation are the important factors that affected SOC distribution. However, the influence of soil depth on spatial distribution of SOC may be more complex than that of altitude. Vegetation types and soil properties are the main reasons for the large differences of reduction rate in the contents of SOC and ASOC.
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Affiliation(s)
- Fazhan Yu
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, No. 1 Daxue Road, Xuzhou, 221116, China
- School of Geography, Geomatics and Planning, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zhongqi Zhang
- School of Geography, Geomatics and Planning, Jiangsu Normal University, Xuzhou, 221116, China
| | - Longqian Chen
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, No. 1 Daxue Road, Xuzhou, 221116, China.
| | - Jinxin Wang
- School of Geography, Geomatics and Planning, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zhengping Shen
- School of Geography, Geomatics and Planning, Jiangsu Normal University, Xuzhou, 221116, China
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Computational analysis on the feasibility of transverse iliosacral screw fixation for different sacral segments. INTERNATIONAL ORTHOPAEDICS 2018; 43:1961-1967. [PMID: 30120558 DOI: 10.1007/s00264-018-4109-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
PURPOSE To evaluate the feasibility of transverse iliosacral (TIS) screw placement in different segments of the sacrum and measure the parameters of the unilateral iliosacral (IS) screw in the case that cannot be inserted the TIS screw. METHODS This study used 100 pelvic continuous computed tomography images. Mimics (Materialise Interactive Medical Image Control System) was used to reconstruct the three-dimensional pelvis model. All sacrums were divided into the normal group and dysmorphic group. Any difference in osseous fixation pathway (OFP) diameter in the first two segments between both groups was investigated. In dysmorphic sacrums, the optimal inserting angle and length of the unilateral S1 screw were measured. The number of foramen in every sacrum was recorded. RESULTS Thirty-two sacrums had sacral dysmorphism. The OFP diameter for the S2 TIS screw in the dysmorphic group was larger than that in the normal group (p = 0.02). Receiver operating characteristic curve analysis indicated the cutoff values as 20.55 mm and 15.18° for the S1 front edge height and S1S2 angle, respectively. In the dysmorphic case, the unilateral S1 IS screw should be inserted with a cephalad incline angle of 36.14 ± 5.97° and a ventrally incline angle of 37.33 ± 4.64°. S3 TIS screw placement rate was 53.1% in the dysmorphic group. CONCLUSIONS The most common cause of sacral dysmorphism is the fusion of the L5 to the true S1. In dysmorphic sacrums, the unilateral IS screw should be placed obliquely in the S1 segment, and the S2 segment usually has a sufficient OFP for the TIS screw. Using S3 TIS screw and two TIS screws in the first segment technique is not recommended because of a high risk.
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Smith FW, Cumming M, Goldstein B. Analyses of nervous system patterning genes in the tardigrade Hypsibius exemplaris illuminate the evolution of panarthropod brains. EvoDevo 2018; 9:19. [PMID: 30069303 PMCID: PMC6065069 DOI: 10.1186/s13227-018-0106-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Both euarthropods and vertebrates have tripartite brains. Several orthologous genes are expressed in similar regionalized patterns during brain development in both vertebrates and euarthropods. These similarities have been used to support direct homology of the tripartite brains of vertebrates and euarthropods. If the tripartite brains of vertebrates and euarthropods are homologous, then one would expect other taxa to share this structure. More generally, examination of other taxa can help in tracing the evolutionary history of brain structures. Tardigrades are an interesting lineage on which to test this hypothesis because they are closely related to euarthropods, and whether they have a tripartite brain or unipartite brain has recently been a focus of debate. RESULTS We tested this hypothesis by analyzing the expression patterns of six3, orthodenticle, pax6, unplugged, and pax2/5/8 during brain development in the tardigrade Hypsibius exemplaris-formerly misidentified as Hypsibius dujardini. These genes were expressed in a staggered anteroposterior order in H. exemplaris, similar to what has been reported for mice and flies. However, only six3, orthodenticle, and pax6 were expressed in the developing brain. Unplugged was expressed broadly throughout the trunk and posterior head, before the appearance of the nervous system. Pax2/5/8 was expressed in the developing central and peripheral nervous system in the trunk. CONCLUSION Our results buttress the conclusion of our previous study of Hox genes-that the brain of tardigrades is only homologous to the protocerebrum of euarthropods. They support a model based on fossil evidence that the last common ancestor of tardigrades and euarthropods possessed a unipartite brain. Our results are inconsistent with the hypothesis that the tripartite brain of euarthropods is directly homologous to the tripartite brain of vertebrates.
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Affiliation(s)
- Frank W. Smith
- Biology Department, University of North Florida, Jacksonville, FL USA
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Mandy Cumming
- Biology Department, University of North Florida, Jacksonville, FL USA
| | - Bob Goldstein
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
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Powell GL, Russell AP, Sutey J. Patterns of growth in the presacral vertebral column of the leopard gecko (Eublepharis macularius). J Morphol 2018; 279:1088-1103. [PMID: 29732599 DOI: 10.1002/jmor.20833] [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: 11/28/2017] [Revised: 03/06/2018] [Accepted: 04/08/2018] [Indexed: 11/10/2022]
Abstract
Postnatal growth patterns within the vertebral column may be informative about body proportions and regionalization. We measured femur length, lengths of all pre-sacral vertebrae, and lengths of intervertebral spaces, from radiographs of a series of 21 Eublepharis macularius, raised under standard conditions and covering most of the ontogenetic body size range. Vertebrae were grouped into cervical, sternal, and dorsal compartments, and lengths of adjacent pairs of vertebrae were summed before analysis. Femur length was included as an index of body size. Principal component analysis of the variance-covariance matrix of these data was used to investigate scaling among them. PC1 explained 94.19% of total variance, interpreted as the variance due to body size. PC1 differed significantly from the hypothetical isometric vector, indicating overall allometry. The atlas and axis vertebrae displayed strong negative allometry; the remainder of the vertebral pairs exhibited weak negative allometry, isometry or positive allometry. PC1 explained a markedly smaller amount of variance for the vertebral pairs of the cervical compartment than for the remainder of the vertebral pairs, with the exception of the final pair. The relative standard deviations of the eigenvalues from the PCAs of the three vertebral compartments indicated that the vertebrae of the cervical compartment were less strongly integrated by scaling than were the sternal or dorsal vertebrae, which did not differ greatly between themselves in their strong integration, suggesting that the growth of the cervical vertebrae is constrained by the mechanical requirements of the head. Regionalization of the remainder of the vertebral column is less clearly defined but may be associated with wave form propagation incident upon locomotion, and by locomotory changes occasioned by tail autotomy and regeneration. Femur length exhibits negative allometry relative to individual vertebral pairs and to vertebral column length, suggesting a change in locomotor requirements over the ontogenetic size range.
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Affiliation(s)
| | - Anthony P Russell
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Jennifer Sutey
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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Li K, Sun X, Chen M, Sun Y, Tian R, Wang Z, Xu S, Yang G. Evolutionary changes of Hox genes and relevant regulatory factors provide novel insights into mammalian morphological modifications. Integr Zool 2018; 13:21-35. [PMID: 28685945 PMCID: PMC5817400 DOI: 10.1111/1749-4877.12271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The diversity of body plans of mammals accelerates the innovation of lifestyles and the extensive adaptation to different habitats, including terrestrial, aerial and aquatic habitats. However, the genetic basis of those phenotypic modifications, which have occurred during mammalian evolution, remains poorly explored. In the present study, we synthetically surveyed the evolutionary pattern of Hox clusters that played a powerful role in the morphogenesis along the head–tail axis of animal embryos and the main regulatory factors (Mll, Bmi1 and E2f6) that control the expression of Hox genes. A deflected density of repetitive elements and lineage‐specific radical mutations of Mll have been determined in marine mammals with morphological changes, suggesting that evolutionary changes may alter Hox gene expression in these lineages, leading to the morphological modification of these lineages. Although no positive selection was detected at certain ancestor nodes of lineages, the increased ω values of Hox genes implied the relaxation of functional constraints of these genes during the mammalian evolutionary process. More importantly, 49 positively‐selected sites were identified in mammalian lineages with phenotypic modifications, indicating adaptive evolution acting on Hox genes and regulatory factors. In addition, 3 parallel amino acid substitutions in some Hox genes were examined in marine mammals, which might be responsible for their streamlined body.
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Affiliation(s)
- Kui Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaohui Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Meixiu Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yingying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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Ollonen J, Da Silva FO, Mahlow K, Di-Poï N. Skull Development, Ossification Pattern, and Adult Shape in the Emerging Lizard Model Organism Pogona vitticeps: A Comparative Analysis With Other Squamates. Front Physiol 2018; 9:278. [PMID: 29643813 PMCID: PMC5882870 DOI: 10.3389/fphys.2018.00278] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/08/2018] [Indexed: 12/02/2022] Open
Abstract
The rise of the Evo-Devo field and the development of multidisciplinary research tools at various levels of biological organization have led to a growing interest in researching for new non-model organisms. Squamates (lizards and snakes) are particularly important for understanding fundamental questions about the evolution of vertebrates because of their high diversity and evolutionary innovations and adaptations that portrait a striking body plan change that reached its extreme in snakes. Yet, little is known about the intricate connection between phenotype and genotype in squamates, partly due to limited developmental knowledge and incomplete characterization of embryonic development. Surprisingly, squamate models have received limited attention in comparative developmental studies, and only a few species examined so far can be considered as representative and appropriate model organism for mechanistic Evo-Devo studies. Fortunately, the agamid lizard Pogona vitticeps (central bearded dragon) is one of the most popular, domesticated reptile species with both a well-established history in captivity and key advantages for research, thus forming an ideal laboratory model system and justifying his recent use in reptile biology research. We first report here the complete post-oviposition embryonic development for P. vitticeps based on standardized staging systems and external morphological characters previously defined for squamates. Whereas the overall morphological development follows the general trends observed in other squamates, our comparisons indicate major differences in the developmental sequence of several tissues, including early craniofacial characters. Detailed analysis of both embryonic skull development and adult skull shape, using a comparative approach integrating CT-scans and gene expression studies in P. vitticeps as well as comparative embryology and 3D geometric morphometrics in a large dataset of lizards and snakes, highlights the extreme adult skull shape of P. vitticeps and further indicates that heterochrony has played a key role in the early development and ossification of squamate skull bones. Such detailed studies of embryonic character development, craniofacial patterning, and bone formation are essential for the establishment of well-selected squamate species as Evo-Devo model organisms. We expect that P. vitticeps will continue to emerge as a new attractive model organism for understanding developmental and molecular processes underlying tissue formation, morphology, and evolution.
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Affiliation(s)
- Joni Ollonen
- Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Filipe O. Da Silva
- Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristin Mahlow
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Nicolas Di-Poï
- Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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The ecological origins of snakes as revealed by skull evolution. Nat Commun 2018; 9:376. [PMID: 29371624 PMCID: PMC5785544 DOI: 10.1038/s41467-017-02788-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/28/2017] [Indexed: 12/11/2022] Open
Abstract
The ecological origin of snakes remains amongst the most controversial topics in evolution, with three competing hypotheses: fossorial; marine; or terrestrial. Here we use a geometric morphometric approach integrating ecological, phylogenetic, paleontological, and developmental data for building models of skull shape and size evolution and developmental rate changes in squamates. Our large-scale data reveal that whereas the most recent common ancestor of crown snakes had a small skull with a shape undeniably adapted for fossoriality, all snakes plus their sister group derive from a surface-terrestrial form with non-fossorial behavior, thus redirecting the debate toward an underexplored evolutionary scenario. Our comprehensive heterochrony analyses further indicate that snakes later evolved novel craniofacial specializations through global acceleration of skull development. These results highlight the importance of the interplay between natural selection and developmental processes in snake origin and diversification, leading first to invasion of a new habitat and then to subsequent ecological radiations.
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Feiner N. Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards. Proc Biol Sci 2017; 283:rspb.2016.1555. [PMID: 27733546 DOI: 10.1098/rspb.2016.1555] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/14/2016] [Indexed: 12/20/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region (Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis, TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards.
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Affiliation(s)
- Nathalie Feiner
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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39
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Leal F, Cohn MJ. Developmental, genetic, and genomic insights into the evolutionary loss of limbs in snakes. Genesis 2017; 56. [DOI: 10.1002/dvg.23077] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/29/2017] [Accepted: 10/06/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Francisca Leal
- Howard Hughes Medical Institute, UF Genetics Institute, University of Florida; Gainesville FL 32610
- Department of Biology; University of Florida; Gainesville FL 32610
| | - Martin J. Cohn
- Department of Biology; University of Florida; Gainesville FL 32610
- Department of Molecular Genetics and Microbiology; University of Florida; Gainesville FL 32610
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Darbellay F, Duboule D. Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci. Curr Top Dev Biol 2017; 116:299-314. [PMID: 26970625 DOI: 10.1016/bs.ctdb.2015.11.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hox gene clusters of jaw vertebrates display a tight genomic organization, which has no equivalent in any other bilateria genomes sequenced thus far. It was previously argued that such a topological consolidation toward a condensed, metagenic structure was due to the accumulation of long-range regulations flanking Hox loci, a phenomenon made possible by the successive genome duplications that occurred at the root of the vertebrate lineage, similar to gene neofunctionalization but applied to a coordinated multigenic system. Here, we propose that the emergence of such large vertebrate regulatory landscapes containing a range of global enhancers was greatly facilitated by the presence of topologically associating domains (TADs). These chromatin domains, mostly constitutive, may have been used as genomic niches where novel regulations could evolve due to both the preexistence of a structural backbone poised to integrate novel regulatory inputs, and a highly adaptive transcriptional readout. We propose a scenario for the coevolution of such TADs and the emergence of pleiotropy at ancestral vertebrate Hox loci.
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Affiliation(s)
- Fabrice Darbellay
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland
| | - Denis Duboule
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland; Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
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Powers KG, Blackburn DG. Morphological specializations of the yolk sac for yolk processing in embryonic corn snakes (Pantherophis guttatus: Colubridae). J Morphol 2017; 278:768-779. [DOI: 10.1002/jmor.20671] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/11/2017] [Accepted: 02/20/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Kathryn G. Powers
- Department of Biology, and Electron Microscopy Center; Trinity College; Hartford Connecticut 06106
| | - Daniel G. Blackburn
- Department of Biology, and Electron Microscopy Center; Trinity College; Hartford Connecticut 06106
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42
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Griffith OW, Wagner GP. The placenta as a model for understanding the origin and evolution of vertebrate organs. Nat Ecol Evol 2017; 1:72. [DOI: 10.1038/s41559-017-0072] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/06/2017] [Indexed: 12/19/2022]
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Abstract
Multiple technologies and software are now available facilitating the de novo sequencing and assembly of any vertebrate genome. Yet the quality of most available sequenced genomes is substantially poorer than that of the golden standard in the field: the human genome. Here, we present a step-by-step protocol for the successful sequencing and assembly of a high-quality snake genome that can be applied to any other reptilian or avian species. We combine the great sequencing depth and accuracy of short reads with the use of different insert size libraries for extended scaffolding followed by optical mapping. We show that this procedure improved the corn snake scaffold N50 from 3.7 kbp to 1.4 Mbp, currently making it one of the snake genomes with the longest scaffolds. Short guidelines are also given on the extraction of long DNA molecules from reptilian blood and the necessary modifications in DNA extraction protocols. This chapter is accompanied by a website ( www.reptilomics.org/stepbystep.html ), where we provide links to the suggested software, examples of input and output files, and running parameters.
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Affiliation(s)
- Asier Ullate-Agote
- Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Sciences III, 30, Quai Ernest-Ansermet, 1211, Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Yingguang Frank Chan
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany
| | - Athanasia C Tzika
- Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Sciences III, 30, Quai Ernest-Ansermet, 1211, Geneva, Switzerland.
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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Evolution of the Snake Venom Delivery System. EVOLUTION OF VENOMOUS ANIMALS AND THEIR TOXINS 2017. [DOI: 10.1007/978-94-007-6458-3_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Xu C, Grizante MB, Kusumi K. Somitogenesis and Axial Development in Reptiles. Methods Mol Biol 2017; 1650:335-353. [PMID: 28809033 DOI: 10.1007/978-1-4939-7216-6_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Among amniote vertebrates, reptiles display the greatest variation in axial skeleton morphology. Only recently have they been used in gene expression studies of somitogenesis , challenging previous assumptions about the segmentation clock and axial patterning. An increasing number of reptile genomes and transcriptomes are becoming available as next-generation sequencing becomes more affordable. Information regarding gene sequence and structure can be used to design and synthesize labeled riboprobes by in vitro transcription for gene expression analysis by in situ hybridization, thus, enabling the characterization of spatial and temporal expression patterns of genes involved in somitogenesis, a topic of great interest within evolutionary developmental studies of vertebrates.
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Affiliation(s)
- Cindy Xu
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Mariana B Grizante
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, Kato M, Garvin TH, Akiyama JA, Afzal V, Lopez-Rios J, Rubin EM, Dickel DE, Pennacchio LA, Visel A. Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell 2016; 167:633-642.e11. [PMID: 27768887 DOI: 10.1016/j.cell.2016.09.028] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/07/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.
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Affiliation(s)
- Evgeny Z Kvon
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Olga K Kamneva
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Uirá S Melo
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iros Barozzi
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marco Osterwalder
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brandon J Mannion
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Catherine S Pickle
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Elizabeth A Lee
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Lopez-Rios
- Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Edward M Rubin
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Diane E Dickel
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Len A Pennacchio
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
| | - Axel Visel
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA.
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Relationships between Numbers of Vertebrae, Scale Counts, and Body Size, with Implications for Taxonomy in Nightsnakes (Genus:Hypsiglena). J HERPETOL 2016. [DOI: 10.1670/15-066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Snake Genome Sequencing: Results and Future Prospects. Toxins (Basel) 2016; 8:toxins8120360. [PMID: 27916957 PMCID: PMC5198554 DOI: 10.3390/toxins8120360] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 11/23/2016] [Accepted: 11/25/2016] [Indexed: 12/16/2022] Open
Abstract
Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.
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Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper. Nat Commun 2016; 7:13107. [PMID: 27708285 PMCID: PMC5059746 DOI: 10.1038/ncomms13107] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 09/02/2016] [Indexed: 12/29/2022] Open
Abstract
Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. Snakes have many characteristics that distinguish them from their relatives. Here, Yin et al. sequence the genome of the five-pacer viper, Deinagkistrodon acutus, and use comparative genomic analyses to elucidate the evolution of transposable elements, developmental genes and sex chromosomes in snakes.
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Anderson G, Secor S. Differential growth of body segments explains ontogenetic shifts in organ position for the Diamondback Water Snake (Nerodia rhombifer). CAN J ZOOL 2016. [DOI: 10.1139/cjz-2015-0191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As snakes grow, their organs move anteriorly relative to body size. We explored a developmental explanation for the ontogenetic shift in the relative position of internal organs for snakes using the Diamondback Water Snake (Nerodia rhombifer (Hallowell, 1852)). With age, this water snake’s heart, liver, small intestine, and right kidney move anteriorly by 2.5–5.0 percentage points of snout–vent length. The number of precaudal vertebrae did not vary due to size or sex. The anterior edge of the heart, liver, small intestine, and right kidney were typically aligned within a span of 4–8 vertebrae that likewise did not differ as a function of size or sex. Snakes exhibited a positive relationship between the number of precaudal vertebrae and the vertebra number aligned with each organ. Total length, centrum length, centrum width, ball width, height, and mass of eight vertebrae sampled at consistent vertebral number revealed that vertebrae in the middle region of the body grow at a greater rate than vertebrae at the anterior or distal ends of the body. For N. rhombifer, the observed forward shift in relative organ positions is the product of regional differences in the growth of body segments. Predictably, these differences arise from a developmental program generated by the differential expression of Hox genes.
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Affiliation(s)
- G.E. Anderson
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35487-0344, USA
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35487-0344, USA
| | - S.M. Secor
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35487-0344, USA
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35487-0344, USA
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