1
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Safadi A, Lovell SC, Doig AJ. Essentiality, protein-protein interactions and evolutionary properties are key predictors for identifying cancer-associated genes using machine learning. Sci Rep 2024; 14:9199. [PMID: 38649399 PMCID: PMC11035574 DOI: 10.1038/s41598-023-44118-2] [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] [Received: 04/25/2023] [Accepted: 10/04/2023] [Indexed: 04/25/2024] Open
Abstract
The distinctive nature of cancer as a disease prompts an exploration of the special characteristics the genes implicated in cancer exhibit. The identification of cancer-associated genes and their characteristics is crucial to further our understanding of this disease and enhanced likelihood of therapeutic drug targets success. However, the rate at which cancer genes are being identified experimentally is slow. Applying predictive analysis techniques, through the building of accurate machine learning models, is potentially a useful approach in enhancing the identification rate of these genes and their characteristics. Here, we investigated gene essentiality scores and found that they tend to be higher for cancer-associated genes compared to other protein-coding human genes. We built a dataset of extended gene properties linked to essentiality and used it to train a machine-learning model; this model reached 89% accuracy and > 0.85 for the Area Under Curve (AUC). The model showed that essentiality, evolutionary-related properties, and properties arising from protein-protein interaction networks are particularly effective in predicting cancer-associated genes. We were able to use the model to identify potential candidate genes that have not been previously linked to cancer. Prioritising genes that score highly by our methods could aid scientists in their cancer genes research.
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Affiliation(s)
- Amro Safadi
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Simon C Lovell
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Andrew J Doig
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9BL, UK.
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2
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Rischer M, Guo H, Beemelmanns C. Signalling molecules inducing metamorphosis in marine organisms. Nat Prod Rep 2022; 39:1833-1855. [PMID: 35822257 DOI: 10.1039/d1np00073j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: findings from early 1980s until early 2022Microbial-derived cues of marine biofilms induce settlement and metamorphosis of marine organisms, a process responsible for the emergence of diverse flora and fauna in marine habitats. Although this phenomenon is known for more than 80 years, the research field has only recently gained much momentum. Here, we summarize the currently existing biochemical and microbial knowledge about microbial signalling molecules, con-specific signals, and synthetic compounds that induce or prevent recruitment, settlement, and metamorphosis in invertebrate larvae. We discuss the possible modes of action and conclude with perspectives for future research directions in the field of marine chemical ecology.
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Affiliation(s)
- Maja Rischer
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany.
| | - Huijuan Guo
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany.
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany. .,Biochemistry of Microbial Metabolism, Institute of Biochemistry, Leipzig University, Johannisallee 21-23, Leipzig 04103, Germany
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3
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Ferran JL, Irimia M, Puelles L. Is There a Prechordal Region and an Acroterminal Domain in Amphioxus? BRAIN, BEHAVIOR AND EVOLUTION 2022; 96:334-352. [PMID: 35034027 DOI: 10.1159/000521966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/03/2022] [Indexed: 12/16/2022]
Abstract
This essay re-examines the singular case of the supposedly unique rostrally elongated notochord described classically in amphioxus. We start from our previous observations in hpf 21 larvae [Albuixech-Crespo et al.: PLoS Biol. 2017;15(4):e2001573] indicating that the brain vesicle has rostrally a rather standard hypothalamic molecular configuration. This correlates with the notochord across a possible rostromedian acroterminal hypothalamic domain. The notochord shows some molecular differences that specifically characterize its pre-acroterminal extension beyond its normal rostral end under the mamillary region. We explored an alternative interpretation that the putative extension of this notochord actually represents a variant form of the prechordal plate in amphioxus, some of whose cells would adopt the notochordal typology, but would lack notochordal patterning properties, and might have some (but not all) prechordal ones instead. We survey in detail the classic and recent literature on gastrulation, prechordal plate, and notochord formation in amphioxus, compare the observed patterns with those of some other vertebrates of interest, and re-examine the literature on differential gene expression patterns in this rostralmost area of the head. We noted that previous literature failed to identify the amphioxus prechordal primordia at appropriate stages. Under this interpretation, a consistent picture can be drawn for cephalochordates, tunicates, and vertebrates. Moreover, there is little evidence for an intrinsic capacity of the early notochord to grow rostralwards (it normally elongates caudalwards). Altogether, we conclude that the hypothesis of a prechordal nature of the elongated amphioxus notochord is consistent with the evidence presented.
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Affiliation(s)
- José Luis Ferran
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute of Biomedical Research of Murcia - IMIB, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute of Biomedical Research of Murcia - IMIB, Virgen de la Arrixaca University Hospital, Murcia, Spain
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4
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Maria Costa-Paiva E, Mello B, Santos Bezerra B, Coates CJ, Halanych KM, Brown F, de Moraes Leme J, Trindade RIF. Molecular dating of the blood pigment hemocyanin provides new insight into the origin of animals. GEOBIOLOGY 2022; 20:333-345. [PMID: 34766436 DOI: 10.1111/gbi.12481] [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: 12/23/2020] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
The Neoproterozoic included changes in oceanic redox conditions, the configuration of continents and climate, extreme ice ages (Sturtian and Marinoan), and the rise of complex life forms. A much-debated topic in geobiology concerns the influence of atmospheric oxygenation on Earth and the origin and diversification of animal lineages, with the most widely popularized hypotheses relying on causal links between oxygen levels and the rise of animals. The vast majority of extant animals use aerobic metabolism for growth and homeostasis; hence, the binding and transportation of oxygen represent a vital physiological task. Considering the blood pigment hemocyanin (Hc) is present in sponges and ctenophores, and likely to be present in the common ancestor of animals, we investigated the evolution and date of Hc emergence using bioinformatics approaches on both transcriptomic and genomic data. Bayesian molecular dating suggested that the ancestral animal Hc gene arose approximately 881 Ma during the Tonian Period (1000-720 Ma), prior to the extreme glaciation events of the Cryogenian Period (720-635 Ma). This result is corroborated by a recently discovered fossil of a putative sponge ~890 Ma and modern molecular dating for the origin of metazoans of ~1,000-650 Ma (but does contradict previous inferences regarding the origin of Hc ~700-600 Ma). Our data reveal that crown-group animals already possessed hemocyanin-like blood pigments, which may have enhanced the oxygen-carrying capacity of these animals in hypoxic environments at that time or acted in the transport of hormones, detoxification of heavy metals, and immunity pathways.
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Affiliation(s)
- Elisa Maria Costa-Paiva
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
- Geophysics and Atmospheric Sciences, Institute of Astronomy, University of Sao Paulo, Sao Paulo, Brazil
| | - Beatriz Mello
- Genetics Department, Biology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Santos Bezerra
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Christopher J Coates
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea, UK
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Federico Brown
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Ricardo I F Trindade
- Geophysics and Atmospheric Sciences, Institute of Astronomy, University of Sao Paulo, Sao Paulo, Brazil
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5
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Resurrecting Golgi proteins to grasp Golgi ribbon formation and self-association under stress. Int J Biol Macromol 2022; 194:264-275. [PMID: 34861272 DOI: 10.1016/j.ijbiomac.2021.11.173] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022]
Abstract
The Golgi complex is an essential organelle of the eukaryotic exocytic pathway. A subfamily of Golgi matrix proteins, called GRASPs, is central in stress-induced unconventional secretion, Golgi dynamics during mitosis/apoptosis, and Golgi ribbon formation. The Golgi ribbon is vertebrate-specific and correlates with the appearance of two GRASP paralogues and two Golgins (GM130/Golgin45), which form specific GRASP-Golgin pairs. The molecular details of their appearance only in Metazoans are unknown. Moreover, despite new functionalities supported by GRASP paralogy, little is known about their structural and evolutionary differences. Here, we used ancestor sequence reconstruction and biophysical/biochemical approaches to assess the evolution of GRASPs structure/dynamics, fibrillation, and how they started anchoring their Golgin partners. Our data showed that a GRASP ancestor anchored Golgins before gorasp gene duplication in Metazoans. After gene duplication, variations within the GRASP binding pocket determined which paralogue would recruit which Golgin. These interactions are responsible for their specific Golgi location and Golgi ribbon appearance. We also suggest that GRASPs have a long-standing capacity to form supramolecular structures, affecting their participation in stress-induced processes.
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6
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Sommer NR, Ferraro KM. An interest‐based rights ethic for wildlife management and applications to behavioral training. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Nathalie R. Sommer
- Yale School of the Environment New Haven Connecticut USA
- Yale Law School: Law, Animal and Ethics Program New Haven Connecticut USA
| | - Kristy M. Ferraro
- Yale School of the Environment New Haven Connecticut USA
- Yale Law School: Law, Animal and Ethics Program New Haven Connecticut USA
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7
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Song X, Ruthensteiner B, Lyu M, Liu X, Wang J, Han J. Advanced Cambrian hydroid fossils (Cnidaria: Hydrozoa) extend the medusozoan evolutionary history. Proc Biol Sci 2021; 288:20202939. [PMID: 33529559 DOI: 10.1098/rspb.2020.2939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Primitive cnidarians are crucial for elucidating the early evolution of metazoan body plans and life histories in the late Neoproterozoic and Palaeozoic. The highest complexity of both evolutionary aspects within cnidarians is found in extant hydrozoans. Many colonial hydrozoans coated with chitinous exoskeletons have the potential to form fossils; however, only a few fossils possibly representing hydroids have been reported, which still require scrutiny. Here, we present an exceptionally well-preserved hydroid found in the Upper Cambrian Fengshan Formation in northern China. It was originally interpreted as a problematic graptolite with an uncertain systematic position. Based on three characteristic morphological traits shared with extant hydroids (with paired hydrothecae, regular hydrocaulus internodes and special intrathecal origin pattern of hydrocladium), we propose this fossil hydroid as a new genus, Palaeodiphasia gen. nov., affiliated with the advanced monophyletic hydrozoan clade Macrocolonia typically showing loss of the medusa stage. More Macrocolonia fossils reviewed here indicate that this life strategy of medusa loss has been achieved already as early as the Middle Devonian. The early stratigraphical appearance of such advanced hydroid contrasts with previous molecular hypotheses regarding the timing of medusozoan evolution, and may be indicative for understanding the Ediacaran cnidarian radiation.
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Affiliation(s)
- Xikun Song
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China
| | | | - Mingxin Lyu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Xi Liu
- Northwest University Museum, Northwest University, Xi'an 710069, People's Republic of China
| | - Jian Wang
- Xi'an Center of Geological Survey, China Geological Survey, Xi'an 710054, People's Republic of China
| | - Jian Han
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life and Environments, Department of Geology, Northwest University, Xi'an 710069, People's Republic of China
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8
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Schluttenhofer C. Origin and evolution of jasmonate signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110542. [PMID: 32771155 DOI: 10.1016/j.plantsci.2020.110542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 05/15/2023]
Abstract
Jasmonate (JA) signaling is a key mediator of plant development and defense which arose during plants transition from an aqueous to terrestrial environment. Elucidating the evolution of JA signaling is important for understanding plant development, defense, and production of specialized metabolites. The lineage of key protein domains characterizing JA signaling factors was traced to identify the origins of CORONITINE INSENSITIVE 1 (COI1), JASMONATE ZIM-DOMAIN (JAZ), NOVEL INTERACTOR OF JAZ, MYC2, TOPLESS, and MEDIATOR SUBUNIT 25. Charophytes do not possess genes encoding key JA signaling components, including COI1, JAZ, MYC2, and the JAZ-interacting bHLH factors, yet their orthologs are present in bryophytes. TIFY family genes were found in charophyta and chlorophya algae. JAZs evolved from ZIM genes of the TIFY family through changes to several key amino acids. Dating placed the origin of JA signaling 515 to 473 million years ago during the middle Cambrian to early Ordovician periods. This time is known for rapid biodiversification and mass extinction events. An increased predation from the diversifying and changing fauna may have driven evolution of JA signaling and plant defense.
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Affiliation(s)
- Craig Schluttenhofer
- Agriculture Research and Development Program, 1400 Brush Row Road, Wilberforce OH, 45384, USA.
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9
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Boulêtreau S, Carry L, Meyer E, Filloux D, Menchi O, Mataix V, Santoul F. High predation of native sea lamprey during spawning migration. Sci Rep 2020; 10:6122. [PMID: 32273527 PMCID: PMC7145853 DOI: 10.1038/s41598-020-62916-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/17/2020] [Indexed: 11/09/2022] Open
Abstract
Sea lamprey (Petromyzon marinus) is a unique jawless vertebrate among the most primitive of all living vertebrates. This migratory fish is endangered in much of its native area due to dams, overfishing, pollution, and habitat loss. An introduced predator, the European catfish (Silurus glanis), is now widespread in Western and Southern European freshwaters, adding a new threat for sea lamprey migrating into freshwater to spawn. Here, we use a new prototype predation tag coupled with RFID telemetry on 49 individuals from one of the largest sea lamprey European populations (Southwestern France) to quantify the risk of predation for adult sea lampreys during its spawning migration in rivers with large populations of European catfish. We found that at least 80% of tagged sea lampreys (39 among 49) were preyed upon within one month, and that 50% of the released lampreys were rapidly consumed on average 8 days after tagging. This very high predation rate suggests that the European catfish represents a supplementary serious threat of extirpation for the native sea lamprey population we studied. This threat is likely to happen throughout most of the native lamprey distribution area, as the European catfish is becoming established almost everywhere the sea lamprey is.
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Affiliation(s)
| | | | | | | | | | - Vincent Mataix
- EDF, Développement Durable, 4 rue Claude Marie Perroud, 31096, Toulouse, France
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10
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Wang J, Zhang L, Lian S, Qin Z, Zhu X, Dai X, Huang Z, Ke C, Zhou Z, Wei J, Liu P, Hu N, Zeng Q, Dong B, Dong Y, Kong D, Zhang Z, Liu S, Xia Y, Li Y, Zhao L, Xing Q, Huang X, Hu X, Bao Z, Wang S. Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae. Nat Ecol Evol 2020; 4:725-736. [PMID: 32203475 DOI: 10.1038/s41559-020-1138-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 02/06/2020] [Indexed: 12/16/2022]
Abstract
The transient larva-bearing biphasic life cycle is the hallmark of many metazoan phyla, but how metazoan larvae originated remains a major enigma in animal evolution. There are two hypotheses for larval origin. The 'larva-first' hypothesis suggests that the first metazoans were similar to extant larvae, with later evolution of the adult-added biphasic life cycle; the 'adult-first' hypothesis suggests that the first metazoans were adult forms, with the biphasic life cycle arising later via larval intercalation. Here, we investigate the evolutionary origin of primary larvae by conducting ontogenetic transcriptome profiling for Mollusca-the largest marine phylum characterized by a trochophore larval stage and highly variable adult forms. We reveal that trochophore larvae exhibit rapid transcriptome evolution with extraordinary incorporation of novel genes (potentially contributing to adult shell evolution), and that cell signalling/communication genes (for example, caveolin and innexin) are probably crucial for larval evolution. Transcriptome age analysis of eight metazoan species reveals the wide presence of young larval transcriptomes in both trochozoans and other major metazoan lineages, therefore arguing against the prevailing larva-first hypothesis. Our findings support an adult-first evolutionary scenario with a single metazoan larval intercalation, and suggest that the first appearance of proto-larva probably occurred after the divergence of direct-developing Ctenophora from a metazoan ancestor.
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Affiliation(s)
- Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shanshan Lian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenkui Qin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuan Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Dai
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Jiankai Wei
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Naina Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bo Dong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Dexu Kong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Sinuo Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Xia
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Liang Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,The Sars-Fang Centre, Ocean University of China, Qingdao, China.
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11
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The Cosmic Zoo: The (Near) Inevitability of the Evolution of Complex, Macroscopic Life. Life (Basel) 2016; 6:life6030025. [PMID: 27376334 PMCID: PMC5041001 DOI: 10.3390/life6030025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/17/2016] [Accepted: 06/22/2016] [Indexed: 12/31/2022] Open
Abstract
Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily. The conclusion for other worlds is that if the origin of life can occur rather easily, we should live in a cosmic zoo, as the innovations necessary to lead to complex life will occur with high probability given sufficient time and habitat. On the other hand, if the origin of life is rare, then we might live in a rather empty universe.
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12
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Abstract
Patterns of origination and evolution of early complex life on this planet are largely interpreted from the fossils of the Precambrian soft-bodied Ediacara Biota. These fossils occur globally and represent a diverse suite of organisms living in marine environments. Although these exceptionally preserved fossil assemblages are typically difficult to reconcile with modern phyla, examination of the morphology, ecology, and taphonomy of these taxa provides keys to their relationships with modern taxa. Within the more than 30 million y range of the Ediacara Biota, fossils of these multicellular organisms demonstrate the advent of mobility, heterotrophy by multicellular animals, skeletonization, sexual reproduction, and the assembly of complex ecosystems, all of which are attributes of modern animals. This approach to these fossils, without the constraint of attempting phylogenetic reconstructions, provides a mechanism for comparing these taxa with both living and extinct animals.
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13
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Chen H, Lin F, Xing K, He X. The reverse evolution from multicellularity to unicellularity during carcinogenesis. Nat Commun 2015; 6:6367. [PMID: 25751731 DOI: 10.1038/ncomms7367] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 01/22/2015] [Indexed: 12/21/2022] Open
Abstract
Theoretical reasoning suggests that cancer may result from a knockdown of the genetic constraints that evolved for the maintenance of metazoan multicellularity. By characterizing the whole-life history of a xenograft tumour, here we show that metastasis is driven by positive selection for general loss-of-function mutations on multicellularity-related genes. Expression analyses reveal mainly downregulation of multicellularity-related genes and an evolving expression profile towards that of embryonic stem cells, the cell type resembling unicellular life in its capacity of unlimited clonal proliferation. Also, the emergence of metazoan multicellularity ~600 Myr ago is accompanied by an elevated birth rate of cancer genes, and there are more loss-of-function tumour suppressors than activated oncogenes in a typical tumour. These data collectively suggest that cancer represents a loss-of-function-driven reverse evolution back to the unicellular 'ground state'. This cancer evolution model may account for inter-/intratumoural genetic heterogeneity, could explain distant-organ metastases and hold implications for cancer therapy.
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Affiliation(s)
- Han Chen
- Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China
| | - Fangqin Lin
- Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China
| | - Ke Xing
- 1] Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China [2] Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xionglei He
- 1] Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China [2] Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou 510275, China
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14
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Holland PWH. Did homeobox gene duplications contribute to the Cambrian explosion? ZOOLOGICAL LETTERS 2015; 1:1. [PMID: 26605046 PMCID: PMC4604119 DOI: 10.1186/s40851-014-0004-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/03/2014] [Indexed: 06/05/2023]
Abstract
The Cambrian explosion describes an apparently rapid increase in the diversity of bilaterian animals around 540-515 million years ago. Bilaterian animals explore the world in three-dimensions deploying forward-facing sense organs, a brain, and an anterior mouth; they possess muscle blocks enabling efficient crawling and burrowing in sediments, and they typically have an efficient 'through-gut' with separate mouth and anus to process bulk food and eject waste, even when burrowing in sediment. A variety of ecological, environmental, genetic, and developmental factors have been proposed as possible triggers and correlates of the Cambrian explosion, and it is likely that a combination of factors were involved. Here, I focus on a set of developmental genetic changes and propose these are part of the mix of permissive factors. I describe how ANTP-class homeobox genes, which encode transcription factors involved in body patterning, increased in number in the bilaterian stem lineage and earlier. These gene duplications generated a large array of ANTP class genes, including three distinct gene clusters called NK, Hox, and ParaHox. Comparative data supports the idea that NK genes were deployed primarily to pattern the bilaterian mesoderm, Hox genes coded position along the central nervous system, and ParaHox genes most likely originally specified the mouth, midgut, and anus of the newly evolved through-gut. It is proposed that diversification of ANTP class genes played a role in the Cambrian explosion by contributing to the patterning systems used to build animal bodies capable of high-energy directed locomotion, including active burrowing.
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Affiliation(s)
- Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
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Abstract
The first animals arose more than six hundred million years ago, yet they left little impression in the fossil record. Nonetheless, the cell biology and genome composition of the first animal, the Urmetazoan, can be reconstructed through the study of phylogenetically relevant living organisms. Comparisons among animals and their unicellular and colonial relatives reveal that the Urmetazoan likely possessed a layer of epithelium-like collar cells, preyed on bacteria, reproduced by sperm and egg, and developed through cell division, cell differentiation, and invagination. Although many genes involved in development, body patterning, immunity, and cell-type specification evolved in the animal stem lineage or after animal origins, several gene families critical for cell adhesion, signaling, and gene regulation predate the origin of animals. The ancestral functions of these and other genes may eventually be revealed through studies of gene and genome function in early-branching animals and their closest non-animal relatives.
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Affiliation(s)
- Daniel J Richter
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200; ,
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Riesgo A, Farrar N, Windsor PJ, Giribet G, Leys SP. The analysis of eight transcriptomes from all poriferan classes reveals surprising genetic complexity in sponges. Mol Biol Evol 2014; 31:1102-20. [PMID: 24497032 DOI: 10.1093/molbev/msu057] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Sponges (Porifera) are among the earliest evolving metazoans. Their filter-feeding body plan based on choanocyte chambers organized into a complex aquiferous system is so unique among metazoans that it either reflects an early divergence from other animals prior to the evolution of features such as muscles and nerves, or that sponges lost these characters. Analyses of the Amphimedon and Oscarella genomes support this view of uniqueness-many key metazoan genes are absent in these sponges-but whether this is generally true of other sponges remains unknown. We studied the transcriptomes of eight sponge species in four classes (Hexactinellida, Demospongiae, Homoscleromorpha, and Calcarea) specifically seeking genes and pathways considered to be involved in animal complexity. For reference, we also sought these genes in transcriptomes and genomes of three unicellular opisthokonts, two sponges (A. queenslandica and O. carmela), and two bilaterian taxa. Our analyses showed that all sponge classes share an unexpectedly large complement of genes with other metazoans. Interestingly, hexactinellid, calcareous, and homoscleromorph sponges share more genes with bilaterians than with nonbilaterian metazoans. We were surprised to find representatives of most molecules involved in cell-cell communication, signaling, complex epithelia, immune recognition, and germ-lineage/sex, with only a few, but potentially key, absences. A noteworthy finding was that some important genes were absent from all demosponges (transcriptomes and the Amphimedon genome), which might reflect divergence from main-stem lineages including hexactinellids, calcareous sponges, and homoscleromorphs. Our results suggest that genetic complexity arose early in evolution as shown by the presence of these genes in most of the animal lineages, which suggests sponges either possess cryptic physiological and morphological complexity and/or have lost ancestral cell types or physiological processes.
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Affiliation(s)
- Ana Riesgo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University
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MALLATT JON, HOLLAND NICHOLAS. Pikaia gracilensWalcott: Stem Chordate, or Already Specialized in the Cambrian? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:247-71. [DOI: 10.1002/jez.b.22500] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 03/11/2013] [Indexed: 12/25/2022]
Affiliation(s)
- JON MALLATT
- School of Biological Sciences; Washington State University; Pullman; Washington
| | - NICHOLAS HOLLAND
- Scripps Institution of Oceanography; University of California; San Diego, La Jolla; California
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Xiao S. Neoproterozoic Glaciations and the Fossil Record. THE EXTREME PROTEROZOIC: GEOLOGY, GEOCHEMISTRY, AND CLIMATE 2013. [DOI: 10.1029/146gm16] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Yuan X, Chen Z, Xiao S, Wan B, Guan C, Wang W, Zhou C, Hua H. The Lantian biota: A new window onto the origin and early evolution of multicellular organisms. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5483-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Rehm P, Borner J, Meusemann K, von Reumont BM, Simon S, Hadrys H, Misof B, Burmester T. Dating the arthropod tree based on large-scale transcriptome data. Mol Phylogenet Evol 2011; 61:880-7. [DOI: 10.1016/j.ympev.2011.09.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 09/01/2011] [Accepted: 09/05/2011] [Indexed: 01/15/2023]
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21
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The morphology and phylogenetic significance ofKerygmachela kierkegaardiBudd (Buen Formation, Lower Cambrian, N Greenland). ACTA ACUST UNITED AC 2011. [DOI: 10.1017/s0263593300002418] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSpecimens ofKerygmachela kierkegaardiBudd are described, from the Lower Cambrian Sirius Passet fauna of N Greenland. The cephalic region is characterised by a pair of stout unsegmented appendages each bearing long spinose processes, and an anterior mouth. The trunk shows alternating rows of tubercles and transverse annulations along the axis, to which are attached 11 pairs of gill-bearing lateral lobes and lobopodous limbs. The caudal region is small, and bears two long tail spines. There is some evidence for circular musculature arranged around the trunk and a dorsal, longitudinal sinus, and several details of the muscular pharynx have been preserved.The combination of characters found inKerygmachelaallows it to be allied with the lobopods, represented in the extant fauna by the onychophorans, tardigrades, and possibly the pentastomids, and in the Cambrian fossil record by a morphologically diverse set of taxa, some of which are not assignable to the extant groupings. It also shares important characters with the previously problematic Burgess Shale formsOpabinia regalisWalcott andAnomalocarisWhiteaves, and the Sirius Passet form Pambdelurion Budd. These taxa together form a paraphyletic group at the base of the clade of biramous arthropods. The position of the so-called ‘Uniramia’ remains unclear. It can be demonstrated from the reconstruction of the arthropod stem-group that full arthropod segmentation has a different derivation from that of the annelids. In line with other recent analyses, this suggests that the ‘Articulata’ of Cuvier should be dismantled, and the arthropods considered to be a group of protostomes which are phylogenetically distinct from the classic spiralians. Arthropod affinities may rather lie with the other moulting animals, in the so-called ‘Ecdysozoa’.
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Abstract
The reconstruction of ancestors is a central aim of comparative anatomy and evolutionary developmental biology, not least in attempts to understand the relationship between developmental and organismal evolution. Inferences based on living taxa can and should be tested against the fossil record, which provides an independent and direct view onto historical character combinations. Here, we consider the nature of the last common ancestor of living ecdysozoans through a detailed analysis of palaeoscolecids, an early and extinct group of introvert-bearing worms that have been proposed to be ancestral ecdysozoans. In a review of palaeoscolecid anatomy, including newly resolved details of the internal and external cuticle structure, we identify specific characters shared with various living nematoid and scalidophoran worms, but not with panarthropods. Considered within a formal cladistic context, these characters provide most overall support for a stem-priapulid affinity, meaning that palaeoscolecids are far-removed from the ecdysozoan ancestor. We conclude that previous interpretations in which palaeoscolecids occupy a deeper position in the ecdysozoan tree lack particular morphological support and rely instead on a paucity of preserved characters. This bears out a more general point that fossil taxa may appear plesiomorphic merely because they preserve only plesiomorphies, rather than the mélange of primitive and derived characters anticipated of organisms properly allocated to a position deep within animal phylogeny.
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Abstract
Cancers are rare because their evolution is actively restrained by a range of tumour suppressors. Of these p53 seems unusually crucial as either it or its attendant upstream or downstream pathways are inactivated in virtually all cancers. p53 is an evolutionarily ancient coordinator of metazoan stress responses. Its role in tumour suppression is likely to be a relatively recent adaptation, which is only necessary when large, long-lived organisms acquired the sufficient size and somatic regenerative capacity to necessitate specific mechanisms to reign in rogue proliferating cells. However, such evolutionary reappropriation of this venerable transcription factor entails compromises that restrict its efficacy as a tumour suppressor.
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Affiliation(s)
- Melissa R Junttila
- Department of Pathology and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco, 513 Parnassus Avenue, Room HSW-450A, UCSF Box 0502, San Francisco, California 94143-0502, USA
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Albert JS, Johnson DM, Knouft JH. Fossils provide better estimates of ancestral body size than do extant taxa in fishes. ACTA ZOOL-STOCKHOLM 2009. [DOI: 10.1111/j.1463-6395.2008.00364.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
SUMMARYOur understanding of the neurobiology of the Platyhelminthes has come in large part from free-living turbellarians. In addition to providing considerable information about the capabilities of the rudimentary nervous system present in all members of the phylum, turbellarians have provided the most definitive information about the variety of ion channels present in the membranes of neurones and muscle cells, and about the physiology and pharmacology of those channels. Furthermore, preparations of single, viable muscle cells have provided some of the most conclusive evidence about the variety of transmitters present, and the types of response they evoke. Here, we review what is known about the physiology and pharmacology of the turbellarian neuromuscular system. Particular attention is given to the triclad flatworm Bdelloura Candida, the best studied species in this respect, but other species are included where relevant.
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Müller WEG, Wang X, Schröder HC. Paleoclimate and Evolution: Emergence of Sponges During the Neoproterozoic. BIOSILICA IN EVOLUTION, MORPHOGENESIS, AND NANOBIOTECHNOLOGY 2009; 47:55-77. [DOI: 10.1007/978-3-540-88552-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Lartillot N, Philippe H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc Lond B Biol Sci 2008; 363:1463-72. [PMID: 18192187 DOI: 10.1098/rstb.2007.2236] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another one, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both genes and species, combined with a probabilistic method (maximum likelihood or Bayesian) using sophisticated models of sequence evolution, should alleviate these two major limitations. We applied this approach to a dataset of 94 genes and 79 species using CAT, a previously developed model accounting for site-specific amino acid replacement patterns. The resulting tree is in good agreement with current knowledge: the monophyly of most major groups (e.g. Chordata, Arthropoda, Lophotrochozoa, Ecdysozoa, Protostomia) was recovered with high support. Two results are surprising and are discussed in an evo-devo framework: the sister-group relationship of Platyhelminthes and Annelida to the exclusion of Mollusca, contradicting the Neotrochozoa hypothesis, and, with a lower statistical support, the paraphyly of Deuterostomia. These results, in particular the status of deuterostomes, need further confirmation, both through increased taxonomic sampling, and future improvements of probabilistic models.
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Affiliation(s)
- Nicolas Lartillot
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, CNRS-Université de Montpellier 2, 34392 Montpellier Cedex 5, France
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MORRIS SCONWAY. The cuticular structure of the 495-Myr-old type species of the fossil worm Palaeoscolex, P. piscatorum (?Priapulida). Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.1997.tb00136.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Fortey R, Briggs D, WILLS M. The Cambrian evolutionary ‘explosion’: decoupling cladogenesis from morphological disparity. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.1996.tb01693.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lamb TD, Collin SP, Pugh EN. Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nat Rev Neurosci 2007; 8:960-76. [PMID: 18026166 PMCID: PMC3143066 DOI: 10.1038/nrn2283] [Citation(s) in RCA: 327] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Charles Darwin appreciated the conceptual difficulty in accepting that an organ as wonderful as the vertebrate eye could have evolved through natural selection. He reasoned that if appropriate gradations could be found that were useful to the animal and were inherited, then the apparent difficulty would be overcome. Here, we review a wide range of findings that capture glimpses of the gradations that appear to have occurred during eye evolution, and provide a scenario for the unseen steps that have led to the emergence of the vertebrate eye.
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Affiliation(s)
- Trevor D Lamb
- Australian National University, Division of Neuroscience, The John Curtin School of Medical Research, Garran Road, The Australian National University, Canberra, Australian Capital Territory 2600, Australia.
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Elliott GRD, Leys SP. Coordinated contractions effectively expel water from the aquiferous system of a freshwater sponge. J Exp Biol 2007; 210:3736-48. [DOI: 10.1242/jeb.003392] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
SUMMARY
In response to mechanical stimuli the freshwater sponge Ephydatia muelleri (Demospongiae, Haplosclerida, Spongillidae) carries out a series of peristaltic-like contractions that is effective in expelling clumps of waste material from the aquiferous system. Rates of contraction depend on the region of tissue they are propagating through: 0.3–1 μm s–1 in the peripheral canals, 1–4 μm s–1 in central canals, and 6–122 μm s–1 in the osculum. Faster events include twitches of the entire sponge choanosome and contraction of the sheet-like apical pinacoderm that forms the outer surface of the animal. Contraction events are temporally and spatially coordinated. Constriction of the tip of the osculum leads to dilation of excurrent canals; fields of ostia in the apical pinacoderm close in unison just prior to contraction of the choanosome, apical pinacoderm and osculum. Relaxation returns the osculum, canals and the apical pinacoderm to their normal state, and three such coordinated `inflation–contraction'responses typically follow a single stimulus. Cells in the mesohyl arrest crawling as a wave of contraction passes, suggesting an extracellular signal may pass between cells. Bundles of actin filaments traverse endopinacocytes of the apical pinacoderm. Actin-dense plaques join actin bundles in adjacent pinacocytes to form continuous tracts spanning the whole sponge. The orchestrated and highly repeatable series of contractions illustrates that cellular sponges are capable of coordinated behavioural responses even in the absence of neurons and true muscle. Propagation of the events through the pinacocytes also illustrates the presence of a functional epithelium in cellular sponges. These results suggest that control over a hydrostatic skeleton evolved prior to the origin of nerves and true muscle.
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Affiliation(s)
- Glen R. D. Elliott
- Department of Biological Sciences, University of Alberta, Edmonton,Alberta T6G 2E9, Canada
| | - Sally P. Leys
- Department of Biological Sciences, University of Alberta, Edmonton,Alberta T6G 2E9, Canada
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Phylogenetic position of sponges in early metazoan evolution and bionic applications of siliceous sponge spicules. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11434-007-0402-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Cobbett A, Wilkinson M, Wills MA. Fossils Impact as Hard as Living Taxa in Parsimony Analyses of Morphology. Syst Biol 2007; 56:753-66. [PMID: 17886145 DOI: 10.1080/10635150701627296] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Systematists disagree whether data from fossils should be included in parsimony analyses. In a handful of well-documented cases, the addition of fossil data radically overturns a hypothesis of relationships based on extant taxa alone. Fossils can break up long branches and preserve character combinations closer in time to deep splitting events. However, fossils usually require more interpretation than extant taxa, introducing greater potential for spurious codings. Moreover, because fossils often have more "missing" codings, they are frequently accused of increasing numbers of MPTs, frustrating resolution and reducing support. Despite the controversy, remarkably little is known about the effects of fossils more generally. Here we provide the first systematic study, investigating empirically the behavior of fossil and extant taxa in 45 published morphological data sets. First-order jackknifing is used to determine the effects that each terminal has on inferred relationships, on the number of MPTs, and on CI' and RI as measures of homoplasy. Bootstrap leaf stabilities provide a proxy for the contribution of individual taxa to the branch support in the rest of the tree. There is no significant difference in the impact of fossil versus extant taxa on relationships, numbers of MPTs, and CI' or RI. However, adding individual fossil taxa is more likely to reduce the total branch support of the tree than adding extant taxa. This must be weighed against the superior taxon sampling afforded by including judiciously coded fossils, providing data from otherwise unsampled regions of the tree. We therefore recommend that investigators should include fossils, in the absence of compelling and case specific reasons for their exclusion.
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Affiliation(s)
- Andrea Cobbett
- Department of Biology and Biochemistry, The University of Bath, Claverton Down, Bath, UK
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González-Mariscal L, Lechuga S, Garay E. Role of tight junctions in cell proliferation and cancer. ACTA ACUST UNITED AC 2007; 42:1-57. [PMID: 17502225 DOI: 10.1016/j.proghi.2007.01.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The acquisition of a cancerous phenotype by epithelial cells involves the disruption of intercellular adhesions. The reorganization of the E-cadherin/beta-catenin complex in adherens junctions during cell transformation is widely recognized. Instead the implication of tight junctions (TJs) in this process is starting to be unraveled. The aim of this article is to review the role of TJ proteins in cell proliferation and cancer.
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Affiliation(s)
- Lorenza González-Mariscal
- Center for Research and Advanced Studies (Cinvestav), Department of Physiology, Biophysics and Neuroscience, Ave. Instituto Politécnico Nacional 2508, México, DF 07360, México.
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BUDD GRAHAME, JENSEN SÖREN. A critical reappraisal of the fossil record of the bilaterian phyla. Biol Rev Camb Philos Soc 2007. [DOI: 10.1111/j.1469-185x.1999.tb00046.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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JENNER RONALDA, SGHRAM FREDERICKR. The grand game of metazoan phylogeny: rules and strategies. Biol Rev Camb Philos Soc 2007. [DOI: 10.1111/j.1469-185x.1999.tb00183.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Müller F, Borycki AG. Sequence analyses to study the evolutionary history and cis-regulatory elements of Hedgehog genes. Methods Mol Biol 2007; 397:231-250. [PMID: 18025724 DOI: 10.1007/978-1-59745-516-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Sequence analysis and comparative genomics are powerful tools to gain knowledge on multiple aspects of gene and protein regulation and function. These have been widely used to understand the evolutionary history and the biochemistry of Hedgehog (Hh) proteins, and the molecular control of Hedgehog gene expression. Here, we report on some of the methods available to retrieve protein and genomic sequences. We describe how protein sequence comparison can produce information on the evolutionary history of Hh proteins. Moreover, we describe the use of genomic sequence analysis including phylogenetic footprinting and transcription factor-binding site search tools, techniques that allow for the characterization of cis-regulatory elements of developmental genes such as the Hedgehog genes.
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Abstract
One of the goals of the present Martian exploration is to search for evidence of extinct (or even extant) life. This could be redefined as a search for carbon. The carbon cycle (or, more properly, cycles) on Earth is a complex interaction among three reservoirs: the atmosphere; the hydrosphere; and the lithosphere. Superimposed on this is the biosphere, and its presence influences the fixing and release of carbon in these reservoirs over different time-scales. The overall carbon balance is kept at equilibrium on the surface by a combination of tectonic processes (which bury carbon), volcanism (which releases it) and biology (which mediates it). In contrast to Earth, Mars presently has no active tectonic system; neither does it possess a significant biosphere. However, these observations might not necessarily have held in the past. By looking at how Earth's carbon cycles have changed with time, as both the Earth's tectonic structure and a more sophisticated biology have evolved, and also by constructing a carbon cycle for Mars based on the carbon chemistry of Martian meteorites, we investigate whether or not there is evidence for a Martian biosphere.
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Affiliation(s)
- Monica M Grady
- Planetary and Space Sciences Research Institute, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK.
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Meldal BHM, Debenham NJ, De Ley P, De Ley IT, Vanfleteren JR, Vierstraete AR, Bert W, Borgonie G, Moens T, Tyler PA, Austen MC, Blaxter ML, Rogers AD, Lambshead PJD. An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa. Mol Phylogenet Evol 2006; 42:622-36. [PMID: 17084644 DOI: 10.1016/j.ympev.2006.08.025] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 06/26/2006] [Accepted: 08/31/2006] [Indexed: 10/24/2022]
Abstract
Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for >200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (f) Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling.
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Affiliation(s)
- Birgit H M Meldal
- School of Ocean and Earth Science, Southampton Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK.
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Xiao S, Shen B, Zhou C, Xie G, Yuan X. A uniquely preserved Ediacaran fossil with direct evidence for a quilted bodyplan. Proc Natl Acad Sci U S A 2005; 102:10227-32. [PMID: 16014417 PMCID: PMC1177372 DOI: 10.1073/pnas.0502176102] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 05/26/2005] [Indexed: 11/18/2022] Open
Abstract
Ediacara fossils are among the oldest known macroscopic and complex life forms. Their bodyplan, ecology, and phylogenetic affinities have been controversial. On the basis of taphonomic observations, Seilacher [Seilacher, A. (1989) Lethaia 22, 229-239] proposed that the core elements of the Ediacara biota, the vendobionts, were constructed with serially or fractally arranged quilts or tube-like units. However, anatomy of quilt walls has been rarely reported, because most Ediacara fossils are preserved as casts and molds in siliciclastic rocks with inadequate morphological resolution. Here, we report an Ediacara form, uniquely preserved in situ and in three dimensions with its organic walls cast by early diagenetic calcite, from bituminous limestone of the 551- to 542-mega-annum Dengying Formation of South China. Despite diagenetic tampering, serial sections show that the Dengying form consists of biserially arranged, tube-like quilts, each with two vertical side walls, a floor, a roof, and an open distal end. Three-dimensional morphological complexity of the Dengying form excludes a microbial interpretation but is broadly consistent with vendobionts. Unlike classic frondose vendobionts sensu Seilacher, however, the Dengying form probably lacked a smooth margin and had distally open quilts. It probably lived procumbently at or near the water-sediment interface and shows evidence for substrate utilization. Despite its uncertain phylogeny, ontogeny, and functional biology, the Dengying form adds to Ediacaran biodiversity, places key constraints on the ecology and extinction of Ediacara organisms, and points to the need to explore an alternative taphonomic window for Ediacara biology.
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Affiliation(s)
- Shuhai Xiao
- Department of Geosciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Cereijido M, Contreras RG, Shoshani L. Cell Adhesion, Polarity, and Epithelia in the Dawn of Metazoans. Physiol Rev 2004; 84:1229-62. [PMID: 15383651 DOI: 10.1152/physrev.00001.2004] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transporting epithelia posed formidable conundrums right from the moment that Du Bois Raymond discovered their asymmetric behavior, a century and a half ago. It took a century and a half to start unraveling the mechanisms of occluding junctions and polarity, but we now face another puzzle: lest its cells died in minutes, the first high metazoa (i.e., higher than a sponge) needed a transporting epithelium, but a transporting epithelium is an incredibly improbable combination of occluding junctions and cell polarity. How could these coincide in the same individual organism and within minutes? We review occluding junctions (tight and septate) as well as the polarized distribution of Na+-K+-ATPase both at the molecular and the cell level. Junctions and polarity depend on hosts of molecular species and cellular processes, which are briefly reviewed whenever they are suspected to have played a role in the dawn of epithelia and metazoan. We come to the conclusion that most of the molecules needed were already present in early protozoan and discuss a few plausible alternatives to solve the riddle described above.
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Affiliation(s)
- M Cereijido
- Center For Research and Advanced Studies, Dept. of Physiology, Biophysics, and Neurosciences, Avenida Instituto Politécnico Nacional 2508, Código Postal 07360, México D.F., Mexico.
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45
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Lundin K, Schander C. Epidermal ciliary ultrastructure of adult and larval sipunculids (Sipunculida). ACTA ZOOL-STOCKHOLM 2003. [DOI: 10.1046/j.1463-6395.2003.00136.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kusche K, Ruhberg H, Burmester T. A hemocyanin from the Onychophora and the emergence of respiratory proteins. Proc Natl Acad Sci U S A 2002; 99:10545-8. [PMID: 12149441 PMCID: PMC124969 DOI: 10.1073/pnas.152241199] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2002] [Indexed: 11/18/2022] Open
Abstract
The velvet worms (Onychophora) are considered living fossils and are closely related to the Euarthropoda. Onychophora possess a tracheal system for respiratory function, but oxygen-transport proteins have been considered unnecessary. Here, we show that the hemolymph of the Epiperipatus sp. (Onychophora: Peripatidae) contains an arthropod-type hemocyanin, demonstrating that such protein exists outside the Euarthropoda. Thus, the evolution of oxygen carriers preceded the divergence of the Onychophora and Euarthropoda and was most likely linked to the evolution of an efficient circulatory system in a low-oxygen environment. The cDNA of the Epiperipatus hemocyanin subunit comprises 2,287 bp and encodes for a protein of 641 aa (73.6 kDa). Phylogenetic analyses of the arthropod hemocyanin sequences show that the Onychophora form a robust sister-group of the Euarthropoda, whereas the monophyly of the Tracheata is not supported.
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Affiliation(s)
- Kristina Kusche
- Institute of Zoology, Johannes Gutenberg University Mainz, D-55099 Mainz, Germany
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Rodriguez-Trelles F, Tarrio R, Ayala FJ. A methodological bias toward overestimation of molecular evolutionary time scales. Proc Natl Acad Sci U S A 2002; 99:8112-5. [PMID: 12060757 PMCID: PMC123029 DOI: 10.1073/pnas.122231299] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2002] [Indexed: 11/18/2022] Open
Abstract
There is presently a conflict between fossil- and molecular-based evolutionary time scales. Molecular approaches for dating the branches of the tree of life frequently lead to substantially deeper times of divergence than those inferred by paleontologists. The discrepancy between molecular and fossil estimates persists despite the booming growth of sequence data sets, which increasingly feeds the interpretation that molecular estimates are older than stratigraphic dates because of deficiencies in the fossil record. Here we show that molecular time estimates suffer from a methodological handicap, namely that they are asymmetrically bounded random variables, constrained by a nonelastic boundary at the lower end, but not at the higher end of the distribution. This introduces a bias toward an overestimation of time since divergence, which becomes greater as the length of the molecular sequence and the rate of evolution decrease.
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Affiliation(s)
- Francisco Rodriguez-Trelles
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697-2525, USA.
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48
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Affiliation(s)
- Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595, USA.
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49
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Callaerts P, Lee PN, Hartmann B, Farfan C, Choy DWY, Ikeo K, Fischbach KF, Gehring WJ, de Couet HG. HOX genes in the sepiolid squid Euprymna scolopes: implications for the evolution of complex body plans. Proc Natl Acad Sci U S A 2002; 99:2088-93. [PMID: 11842209 PMCID: PMC122323 DOI: 10.1073/pnas.042683899] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2001] [Indexed: 11/18/2022] Open
Abstract
Molluscs display a rich diversity of body plans ranging from the wormlike appearance of aplacophorans to the complex body plan of the cephalopods with highly developed sensory organs, a complex central nervous system, and cognitive abilities unrivaled among the invertebrates. The aim of the current study is to define molecular parameters relevant to the developmental evolution of cephalopods by using the sepiolid squid Euprymna scolopes as a model system. Using PCR-based approaches, we identified one anterior, one paralog group 3, five central, and two posterior group Hox genes. The deduced homeodomain sequences of the E. scolopes Hox cluster genes are most similar to known annelid, brachiopod, and nemertean Hox gene homeodomain sequences. Our results are consistent with the presence of a single Hox gene cluster in cephalopods. Our data also corroborate the proposed existence of a differentiated Hox gene cluster in the last common ancestor of Bilaterians. Furthermore, our phylogenetic analysis and in particular the identification of Post-1 and Post-2 homologs support the Lophotrochozoan clade.
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Affiliation(s)
- Patrick Callaerts
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5513, USA
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Miller MF, Labandeira CC. Slow Crawl Across the Salinity Divide: Delayed Colonization of Freshwater Ecosystems by Invertebrates. ACTA ACUST UNITED AC 2002. [DOI: 10.1130/1052-5173(2002)012<0004:scatsd>2.0.co;2] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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