1
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Puttick MN, O'Reilly JE, Oakley D, Tanner AR, Fleming JF, Clark J, Holloway L, Lozano-Fernandez J, Parry LA, Tarver JE, Pisani D, Donoghue PCJ. Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al.. Proc Biol Sci 2019; 284:rspb.2017.1636. [PMID: 29021176 DOI: 10.1098/rspb.2017.1636] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/11/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Mark N Puttick
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.,Department of Life Sciences, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK
| | - Joseph E O'Reilly
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Derek Oakley
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Alistair R Tanner
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James F Fleming
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James Clark
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Lucy Holloway
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jesus Lozano-Fernandez
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Luke A Parry
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James E Tarver
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK .,School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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2
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Brommage R, Liu J, Vogel P, Mseeh F, Thompson AY, Potter DG, Shadoan MK, Hansen GM, Jeter-Jones S, Cui J, Bright D, Bardenhagen JP, Doree DD, Movérare-Skrtic S, Nilsson KH, Henning P, Lerner UH, Ohlsson C, Sands AT, Tarver JE, Powell DR, Zambrowicz B, Liu Q. NOTUM inhibition increases endocortical bone formation and bone strength. Bone Res 2019; 7:2. [PMID: 30622831 PMCID: PMC6323125 DOI: 10.1038/s41413-018-0038-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/21/2018] [Accepted: 10/15/2018] [Indexed: 12/16/2022] Open
Abstract
The disability, mortality and costs caused by non-vertebral osteoporotic fractures are enormous. Existing osteoporosis therapies are highly effective at reducing vertebral but not non-vertebral fractures. Cortical bone is a major determinant of non-vertebral bone strength. To identify novel osteoporosis drug targets, we phenotyped cortical bone of 3 366 viable mouse strains with global knockouts of druggable genes. Cortical bone thickness was substantially elevated in Notum−/− mice. NOTUM is a secreted WNT lipase and we observed high NOTUM expression in cortical bone and osteoblasts but not osteoclasts. Three orally active small molecules and a neutralizing antibody inhibiting NOTUM lipase activity were developed. They increased cortical bone thickness and strength at multiple skeletal sites in both gonadal intact and ovariectomized rodents by stimulating endocortical bone formation. Thus, inhibition of NOTUM activity is a potential novel anabolic therapy for strengthening cortical bone and preventing non-vertebral fractures. NOTUM is an enzyme that inactivates WNT proteins (which play a key role in early tissue development), and inhibiting NOTUM has been found to increase the formation of endocortical bone (within the cortex, the hard exterior of bone) and enhance bone strength. Existing therapies for osteoporosis (condition causing bone to become weak and brittle) are effective in reducing vertebral, but not non-vertebral, fractures. A team headed by Robert Brommage at Lexicon Pharmaceuticals, Texas aimed to identify novel osteoporosis drug targets in mice. Following inhibition of NOTUM activity, the authors observed increased cortical bone thickness and strength at multiple skeletal sites through stimulation of endocortical bone formation. The team concluded that inhibiting NOTUM activity has good potential as a new therapeutic strategy and could be beneficial in preventing non-vertebral osteoporotic fractures.
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Affiliation(s)
- Robert Brommage
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,3Present Address: Centre for Bone and Arthritis Research, University of Gothenburg, Gothenburg, Sweden
| | - Jeff Liu
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,4Present Address: Biogen, Cambridge, MA, USA
| | - Peter Vogel
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,5Present Address: St. Jude Children's Research Hospital, Memphis, TN USA
| | - Faika Mseeh
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,6Present Address: MD Anderson Cancer Center, Houston, TX USA
| | | | - David G Potter
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,Present Address: Bethyl Laboratories, Montgomery, TX USA
| | - Melanie K Shadoan
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,8Present Address: Merck, Rahway, NJ USA
| | - Gwenn M Hansen
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,Present Address: Nurix, San Francisco, CA USA
| | - Sabrina Jeter-Jones
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,6Present Address: MD Anderson Cancer Center, Houston, TX USA
| | - Jie Cui
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,Present Address: Wntrix, Houston, TX USA
| | - Dawn Bright
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA
| | - Jennifer P Bardenhagen
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,6Present Address: MD Anderson Cancer Center, Houston, TX USA
| | - Deon D Doree
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,11Present Address: PRA Health Sciences, Raleigh, NC USA
| | - Sofia Movérare-Skrtic
- 2Centre for Bone and Arthritis Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Karin H Nilsson
- 2Centre for Bone and Arthritis Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Petra Henning
- 2Centre for Bone and Arthritis Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ulf H Lerner
- 2Centre for Bone and Arthritis Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Claes Ohlsson
- 2Centre for Bone and Arthritis Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Arthur T Sands
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,Present Address: Nurix, San Francisco, CA USA
| | - James E Tarver
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,12Present Address: University of Pennsylvania, Philadelphia, PA USA
| | | | - Brian Zambrowicz
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,13Present Address: Regeneron Pharmaceuticals, Tarrytown, NY USA
| | - Qingyun Liu
- 1Lexicon Pharmaceuticals, The Woodlands, TX USA.,14Present Address: University of Texas, Houston, TX USA
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3
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Bråte J, Neumann RS, Fromm B, Haraldsen AAB, Tarver JE, Suga H, Donoghue PCJ, Peterson KJ, Ruiz-Trillo I, Grini PE, Shalchian-Tabrizi K. Unicellular Origin of the Animal MicroRNA Machinery. Curr Biol 2018; 28:3288-3295.e5. [PMID: 30318349 PMCID: PMC6206976 DOI: 10.1016/j.cub.2018.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/22/2018] [Accepted: 08/07/2018] [Indexed: 12/16/2022]
Abstract
The emergence of multicellular animals was associated with an increase in phenotypic complexity and with the acquisition of spatial cell differentiation and embryonic development. Paradoxically, this phenotypic transition was not paralleled by major changes in the underlying developmental toolkit and regulatory networks. In fact, most of these systems are ancient, established already in the unicellular ancestors of animals [1-5]. In contrast, the Microprocessor protein machinery, which is essential for microRNA (miRNA) biogenesis in animals, as well as the miRNA genes themselves produced by this Microprocessor, have not been identified outside of the animal kingdom [6]. Hence, the Microprocessor, with the key proteins Pasha and Drosha, is regarded as an animal innovation [7-9]. Here, we challenge this evolutionary scenario by investigating unicellular sister lineages of animals through genomic and transcriptomic analyses. We identify in Ichthyosporea both Drosha and Pasha (DGCR8 in vertebrates), indicating that the Microprocessor complex evolved long before the last common ancestor of animals, consistent with a pre-metazoan origin of most of the animal developmental gene elements. Through small RNA sequencing, we also discovered expressed bona fide miRNA genes in several species of the ichthyosporeans harboring the Microprocessor. A deep, pre-metazoan origin of the Microprocessor and miRNAs comply with a view that the origin of multicellular animals was not directly linked to the innovation of these key regulatory components.
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Affiliation(s)
- Jon Bråte
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Ralf S Neumann
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Arthur A B Haraldsen
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - James E Tarver
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Nanatsuka 562, Shobara, Hiroshima 727-0023, Japan
| | | | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain
| | - Paul E Grini
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Kamran Shalchian-Tabrizi
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway.
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4
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Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ. Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. Genome Biol Evol 2018; 10:1457-1470. [PMID: 29788279 PMCID: PMC6007596 DOI: 10.1093/gbe/evy096] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Richard S Taylor
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Mark N Puttick
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Graeme T Lloyd
- School of Earth and Environment, University of Leeds, United Kingdom
| | - Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Bettina E Schirrmeister
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Philip C J Donoghue
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
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5
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Puttick MN, O'Reilly JE, Tanner AR, Fleming JF, Clark J, Holloway L, Lozano-Fernandez J, Parry LA, Tarver JE, Pisani D, Donoghue PCJ. Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data. Proc Biol Sci 2018; 284:rspb.2016.2290. [PMID: 28077778 PMCID: PMC5247500 DOI: 10.1098/rspb.2016.2290] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/05/2016] [Indexed: 11/12/2022] Open
Abstract
Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.
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Affiliation(s)
- Mark N Puttick
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.,Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Joseph E O'Reilly
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Alastair R Tanner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James F Fleming
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James Clark
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Lucy Holloway
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jesus Lozano-Fernandez
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.,School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Luke A Parry
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James E Tarver
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK .,School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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6
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O'Reilly JE, Puttick MN, Parry L, Tanner AR, Tarver JE, Fleming J, Pisani D, Donoghue PCJ. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data. Biol Lett 2017; 12:rsbl.2016.0081. [PMID: 27095266 PMCID: PMC4881353 DOI: 10.1098/rsbl.2016.0081] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/21/2016] [Indexed: 11/29/2022] Open
Abstract
Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphological data, we demonstrate that the Mk-model outperforms equal-weights parsimony in terms of topological accuracy, and implied-weights performs the most poorly. However, the Mk-model produces phylogenies that have less resolution than parsimony methods. This difference in the accuracy and precision of parsimony and Bayesian approaches to topology estimation needs to be considered when selecting a method for phylogeny reconstruction.
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Affiliation(s)
- Joseph E O'Reilly
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mark N Puttick
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Luke Parry
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Alastair R Tanner
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James E Tarver
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James Fleming
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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7
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Abstract
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a single species, the filamentous brown alga Ectocarpus sp. Here, we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families. Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.
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Affiliation(s)
- J. Mark Cock
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Fuli Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao National Laboratory for Marine Science and Technology, Lab for Marine Biology and Biotechnology, Qingdao, China
| | - Simon Bourdareau
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M. Coelho
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - James E. Tarver
- School of Earth Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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8
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9
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Tarver JE, Pabba PK, Barbosa J, Han Q, Gardyan MW, Brommage R, Thompson AY, Schmidt JM, Wilson AG, He W, Lombardo VK, Carson KG. Stimulation of cortical bone formation with thienopyrimidine based inhibitors of Notum Pectinacetylesterase. Bioorg Med Chem Lett 2016; 26:1525-1528. [DOI: 10.1016/j.bmcl.2016.02.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 02/06/2016] [Accepted: 02/09/2016] [Indexed: 12/30/2022]
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10
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Han Q, Pabba PK, Barbosa J, Mabon R, Healy JP, Gardyan MW, Terranova KM, Brommage R, Thompson AY, Schmidt JM, Wilson AG, Xu X, Tarver JE, Carson KG. 4H-Thieno[3,2-c]chromene based inhibitors of Notum Pectinacetylesterase. Bioorg Med Chem Lett 2016; 26:1184-7. [DOI: 10.1016/j.bmcl.2016.01.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 11/25/2022]
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11
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Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biol Evol 2016; 8:330-44. [PMID: 26733575 PMCID: PMC4779606 DOI: 10.1093/gbe/evv261] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157-170 Ma, crown Placentalia diverged 86-100 Ma, and crown Atlantogenata diverged 84-97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.
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Affiliation(s)
- James E Tarver
- Department of Biology, The National University of Ireland, Maynooth, Ireland School of Earth Sciences, University of Bristol, United Kingdom
| | - Mario Dos Reis
- Department of Genetics, Evolution and Environment, University College London, United Kingdom School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Siavash Mirarab
- Department of Computer Science, University of Texas at Austin Department of Electrical and Computer Engineering, University of California, San Diego
| | - Raymond J Moran
- Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Life Sciences, University of Leeds
| | - Sean Parker
- School of Earth Sciences, University of Bristol, United Kingdom
| | | | - Benjamin L King
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Life Sciences, University of Leeds
| | - Robert J Asher
- Museum of Zoology, University of Cambridge, United Kingdom
| | - Tandy Warnow
- Department of Computer Science, University of Texas at Austin Department of Electrical and Computer Engineering, University of California, San Diego Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, United Kingdom School of Biological Sciences, University of Bristol, United Kingdom
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12
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Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu Rev Genet 2015; 49:213-42. [PMID: 26473382 DOI: 10.1146/annurev-genet-120213-092023] [Citation(s) in RCA: 361] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database--MirGeneDB ( http://mirgenedb.org )--to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.
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Affiliation(s)
- Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research
| | - Tyler Billipp
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
| | - Liam E Peck
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | | | - James E Tarver
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland.,School of Earth Sciences, University of Bristol, BS8 1TQ Bristol, United Kingdom
| | - Benjamin L King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672
| | - James M Newcomb
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | - Lorenzo F Sempere
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research.,Department of Gastroenterological Surgery.,Institute of Clinical Medicine
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, N-0424 Oslo, Norway.,Department of Informatics, University of Oslo, Blindern, N-0318 Oslo, Norway
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
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Tarver JE, Cormier A, Pinzón N, Taylor RS, Carré W, Strittmatter M, Seitz H, Coelho SM, Cock JM. microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. Nucleic Acids Res 2015; 43:6384-98. [PMID: 26101255 PMCID: PMC4513859 DOI: 10.1093/nar/gkv578] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/19/2015] [Accepted: 05/21/2015] [Indexed: 01/02/2023] Open
Abstract
There is currently convincing evidence that microRNAs have evolved independently in at least six different eukaryotic lineages: animals, land plants, chlorophyte green algae, demosponges, slime molds and brown algae. MicroRNAs from different lineages are not homologous but some structural features are strongly conserved across the eukaryotic tree allowing the application of stringent criteria to identify novel microRNA loci. A large set of 63 microRNA families was identified in the brown alga Ectocarpus based on mapping of RNA-seq data and nine microRNAs were confirmed by northern blotting. The Ectocarpus microRNAs are highly diverse at the sequence level with few multi-gene families, and do not tend to occur in clusters but exhibit some highly conserved structural features such as the presence of a uracil at the first residue. No homologues of Ectocarpus microRNAs were found in other stramenopile genomes indicating that they emerged late in stramenopile evolution and are perhaps specific to the brown algae. The large number of microRNA loci in Ectocarpus is consistent with the developmental complexity of many brown algal species and supports a proposed link between the emergence and expansion of microRNA regulatory systems and the evolution of complex multicellularity.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK Genome Evolution Laboratory, Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland
| | - Alexandre Cormier
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Natalia Pinzón
- Institute of Human Genetics, UPR 1142, CNRS, 34396 Montpellier Cedex 5, France
| | - Richard S Taylor
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Wilfrid Carré
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Martina Strittmatter
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Hervé Seitz
- Institute of Human Genetics, UPR 1142, CNRS, 34396 Montpellier Cedex 5, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
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14
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Taylor RS, Tarver JE, Hiscock SJ, Donoghue PCJ. Evolutionary history of plant microRNAs. Trends Plant Sci 2014; 19:175-82. [PMID: 24405820 DOI: 10.1016/j.tplants.2013.11.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/18/2013] [Accepted: 11/28/2013] [Indexed: 05/11/2023]
Abstract
microRNAs (miRNAs) are short noncoding regulatory genes that perform important roles in plant development and physiology. With the increasing power of next generation sequencing technologies and the development of bioinformatic tools, there has been a dramatic increase in the number of studies surveying the miRNAomes of plant species, which has led to an explosion in the number of described miRNAs. Unfortunately, very many of these new discoveries have been incompletely annotated and thus fail to discriminate genuine miRNAs from small interfering RNAs (siRNAs), fragments of longer RNAs, and random sequence. We review the published repertoire of plant miRNAs, discriminating those that have been correctly annotated. We use these data to explore prevailing hypotheses on the tempo and mode of miRNA evolution within the plant kingdom.
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Affiliation(s)
- Richard S Taylor
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
| | - James E Tarver
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK; Genome Evolution Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Simon J Hiscock
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK.
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15
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Tarver JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM, King BL, Pisani D, Donoghue PCJ, Peterson KJ. miRNAs: small genes with big potential in metazoan phylogenetics. Mol Biol Evol 2013; 30:2369-82. [PMID: 23913097 DOI: 10.1093/molbev/mst133] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
microRNAs (miRNAs) are a key component of gene regulatory networks and have been implicated in the regulation of virtually every biological process found in multicellular eukaryotes. What makes them interesting from a phylogenetic perspective is the high conservation of primary sequence between taxa, their accrual in metazoan genomes through evolutionary time, and the rarity of secondary loss in most metazoan taxa. Despite these properties, the use of miRNAs as phylogenetic markers has not yet been discussed within a clear conceptual framework. Here we highlight five properties of miRNAs that underlie their utility in phylogenetics: 1) The processes of miRNA biogenesis enable the identification of novel miRNAs without prior knowledge of sequence; 2) The continuous addition of miRNA families to metazoan genomes through evolutionary time; 3) The low level of secondary gene loss in most metazoan taxa; 4) The low substitution rate in the mature miRNA sequence; and 5) The small probability of convergent evolution of two miRNAs. Phylogenetic analyses using both Bayesian and parsimony methods on a eumetazoan miRNA data set highlight the potential of miRNAs to become an invaluable new tool, especially when used as an additional line of evidence, to resolve previously intractable nodes within the tree of life.
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Affiliation(s)
- James E Tarver
- Department of Biological Sciences, Dartmouth College, Hanover, NH
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16
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Hill MS, Hill AL, Lopez J, Peterson KJ, Pomponi S, Diaz MC, Thacker RW, Adamska M, Boury-Esnault N, Cárdenas P, Chaves-Fonnegra A, Danka E, De Laine BO, Formica D, Hajdu E, Lobo-Hajdu G, Klontz S, Morrow CC, Patel J, Picton B, Pisani D, Pohlmann D, Redmond NE, Reed J, Richey S, Riesgo A, Rubin E, Russell Z, Rützler K, Sperling EA, di Stefano M, Tarver JE, Collins AG. Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes. PLoS One 2013; 8:e50437. [PMID: 23372644 PMCID: PMC3553142 DOI: 10.1371/journal.pone.0050437] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 10/22/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. METHODOLOGY/PRINCIPAL FINDINGS We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosa(p), Myxospongiae(p), Spongillida(p), Haploscleromorpha(p) (the marine haplosclerids) and Democlavia(p). We found conflicting results concerning the relationships of Keratosa(p) and Myxospongiae(p) to the remaining demosponges, but our results strongly supported a clade of Haploscleromorpha(p)+Spongillida(p)+Democlavia(p). In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillida(p)) are sister to Haploscleromorpha(p) rather than part of Democlavia(p). Within Keratosa(p), we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiae(p), Chondrosida and Verongida were monophyletic. A well-supported clade within Democlavia(p), Tetractinellida(p), composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlavia(p). Within Tetractinellida(p), we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. CONCLUSIONS/SIGNIFICANCE These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.
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Affiliation(s)
- Malcolm S. Hill
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - April L. Hill
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Jose Lopez
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Shirley Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Maria C. Diaz
- Museo Marino de Margarita, Boulevard de Boca Del Rio, Boca del Rio, Nueva Esparta, Venezuela
| | - Robert W. Thacker
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Maja Adamska
- Sars International Centre for Marine Molecular Biology, Thormøhlensgt, Bergen, Norway
| | - Nicole Boury-Esnault
- IMBE-UMR7263 CNRS, Université d'Aix-Marseille, Station marine d'Endoume, Marseille, France
| | - Paco Cárdenas
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Andia Chaves-Fonnegra
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Elizabeth Danka
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Bre-Onna De Laine
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Dawn Formica
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Eduardo Hajdu
- Departamento de Invertebrados, Museu Nacional/Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gisele Lobo-Hajdu
- Departamento de Genética, IBRAG, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sarah Klontz
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Christine C. Morrow
- School of Biological Sciences, MBC, Queen's University, Belfast, United Kingdom
| | - Jignasa Patel
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Bernard Picton
- National Museums Northern Ireland, Holywood, Northern Ireland, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, The University of Bristol, Bristol, United Kingdom
| | - Deborah Pohlmann
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Niamh E. Redmond
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - John Reed
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Stacy Richey
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Ana Riesgo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ewelina Rubin
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Zach Russell
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Klaus Rützler
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Erik A. Sperling
- Harvard University, Department of Earth and Planetary Science, Cambridge, Massachusetts, United States of America
| | - Michael di Stefano
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - James E. Tarver
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Allen G. Collins
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
- National Systematics Laboratory of NOAA's Fisheries Service, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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17
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Abstract
The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that miRNAs evolved convergently in animals and plants. We re-evaluate the evidence and find that none of the 73 plant and animal miRNAs described from protists meet the required criteria for miRNA annotation and, by implication, animals and plants did not acquire any of their respective miRNA genes from the crown ancestor of eukaryotes. Furthermore, of the 159 novel miRNAs previously identified among the seven species of unicellular protists examined, only 28 from the algae Ectocarpus and Chlamydomonas, meet the criteria for miRNA annotation. Therefore, at present only five groups of eukaryotes are known to possess miRNAs, indicating that miRNAs have evolved independently within eukaryotes through exaptation of their shared inherited RNAi machinery.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences, University of Bristol, Bristol, UK.
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18
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Parham JF, Donoghue PCJ, Bell CJ, Calway TD, Head JJ, Holroyd PA, Inoue JG, Irmis RB, Joyce WG, Ksepka DT, Patané JSL, Smith ND, Tarver JE, van Tuinen M, Yang Z, Angielczyk KD, Greenwood JM, Hipsley CA, Jacobs L, Makovicky PJ, Müller J, Smith KT, Theodor JM, Warnock RCM, Benton MJ. Best practices for justifying fossil calibrations. Syst Biol 2012; 61:346-59. [PMID: 22105867 PMCID: PMC3280042 DOI: 10.1093/sysbio/syr107] [Citation(s) in RCA: 378] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 09/22/2011] [Accepted: 11/14/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- James F Parham
- Alabama Museum of Natural History, University of Alabama, 427 6th Avenue, Smith Hall, Box 870340, Tuscaloosa, AL 35487, USA.
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19
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Tarver JE, Donoghue PCJ. The Trouble with Topology: Phylogenies without Fossils Provide a Revisionist Perspective of Evolutionary History in Topological Analyses of Diversity. Syst Biol 2011; 60:700-12. [DOI: 10.1093/sysbio/syr018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- James E. Tarver
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Philip C. J. Donoghue
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
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20
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Abstract
Mass media and popular science journals commonly report that new fossil discoveries have 'rewritten evolutionary history'. Is this merely journalistic hyperbole or is our sampling of systematic diversity so limited that attempts to derive evolutionary history from these datasets are premature? We use two exemplars-catarrhine primates (Old World monkeys and apes) and non-avian dinosaurs-to investigate how the maturity of datasets can be assessed. Both groups have been intensively studied over the past 200 years and so should represent pinnacles in our knowledge of vertebrate systematic diversity. We test the maturity of these datasets by assessing the completeness of their fossil records, their susceptibility to changes in macroevolutionary hypotheses and the balance of their phylogenies through study time. Catarrhines have shown prolonged stability, with discoveries of new species being evenly distributed across the phylogeny, and thus have had little impact on our understanding of their fossil record, diversification and evolution. The reverse is true for dinosaurs, where the addition of new species has been non-random and, consequentially, their fossil record, tree shape and our understanding of their diversification is rapidly changing. The conclusions derived from these analyses are relevant more generally: the maturity of systematic datasets can and should be assessed before they are exploited to derive grand macroevolutionary hypotheses.
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Affiliation(s)
- J E Tarver
- Department of Earth Sciences, University of Bristol, , Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK.
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21
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Jessop TC, Tarver JE, Carlsen M, Xu A, Healy JP, Heim-Riether A, Fu Q, Taylor JA, Augeri DJ, Shen M, Stouch TR, Swanson RV, Tari LW, Hunter M, Hoffman I, Keyes PE, Yu XC, Miranda M, Liu Q, Swaffield JC, David Kimball S, Nouraldeen A, Wilson AG, Foushee AMD, Jhaver K, Finch R, Anderson S, Oravecz T, Carson KG. Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors. Bioorg Med Chem Lett 2009; 19:6784-7. [DOI: 10.1016/j.bmcl.2009.09.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 09/21/2009] [Accepted: 09/22/2009] [Indexed: 10/20/2022]
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Tarver JE, Jessop TC, Carlsen M, Augeri DJ, Fu Q, Healy JP, Heim-Riether A, Xu A, Taylor JA, Shen M, Keyes PE, David Kimball S, Yu XC, Miranda M, Liu Q, Swaffield JC, Nouraldeen A, Wilson AGE, Finch R, Jhaver K, Foushee AMD, Anderson S, Oravecz T, Carson KG. 5-Fluorocytosine derivatives as inhibitors of deoxycytidine kinase. Bioorg Med Chem Lett 2009; 19:6780-3. [PMID: 19836229 DOI: 10.1016/j.bmcl.2009.09.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 09/21/2009] [Accepted: 09/22/2009] [Indexed: 10/20/2022]
Abstract
A series of potent piperidine-linked cytosine derivatives were prepared as inhibitors of deoxycytidine kinase (dCK). Compound 9h was discovered to be a potent inhibitor of dCK and shows a good combination of cellular potency and pharmacokinetic parameters. Compound 9h blocks the incorporation of radiolabeled cytosine into mouse T-cells in vitro, as well as in vivo in mice following a T-cell challenge.
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Affiliation(s)
- James E Tarver
- Lexicon Pharmaceuticals, Princeton, NJ 08540, United States
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23
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Lloyd GT, Davis KE, Pisani D, Tarver JE, Ruta M, Sakamoto M, Hone DWE, Jennings R, Benton MJ. Dinosaurs and the Cretaceous Terrestrial Revolution. Proc Biol Sci 2008; 275:2483-90. [PMID: 18647715 PMCID: PMC2603200 DOI: 10.1098/rspb.2008.0715] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The observed diversity of dinosaurs reached its highest peak during the mid- and Late Cretaceous, the 50 Myr that preceded their extinction, and yet this explosion of dinosaur diversity may be explained largely by sampling bias. It has long been debated whether dinosaurs were part of the Cretaceous Terrestrial Revolution (KTR), from 125-80 Myr ago, when flowering plants, herbivorous and social insects, squamates, birds and mammals all underwent a rapid expansion. Although an apparent explosion of dinosaur diversity occurred in the mid-Cretaceous, coinciding with the emergence of new groups (e.g. neoceratopsians, ankylosaurid ankylosaurs, hadrosaurids and pachycephalosaurs), results from the first quantitative study of diversification applied to a new supertree of dinosaurs show that this apparent burst in dinosaurian diversity in the last 18 Myr of the Cretaceous is a sampling artefact. Indeed, major diversification shifts occurred largely in the first one-third of the group's history. Despite the appearance of new clades of medium to large herbivores and carnivores later in dinosaur history, these new originations do not correspond to significant diversification shifts. Instead, the overall geometry of the Cretaceous part of the dinosaur tree does not depart from the null hypothesis of an equal rates model of lineage branching. Furthermore, we conclude that dinosaurs did not experience a progressive decline at the end of the Cretaceous, nor was their evolution driven directly by the KTR.
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Affiliation(s)
- Graeme T Lloyd
- Department of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK.
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24
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Abstract
A noncoded amino acid of cyclomarin A (1) was synthesized in a racemic fashion. The method employs a six-membered ring template to control the relative stereochemistry and introduction of the functional groups. Ultimately, Pd-catalyzed fragmentation of the lactone provided gamma,delta-unsaturated and delta,epsilon-unsaturated alpha-amino acids. A Pd-catalyzed ring opening of a gamma-lactone is also reported.
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Affiliation(s)
- James E Tarver
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
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25
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Tarver JE, Pfizenmayer AJ, Joullié MM. Total syntheses of conformationally constrained didemnin B analogues. replacements of N,O-dimethyltyrosine with L-1,2,3,4-tetrahydroisoquinoline and L-1,2,3,4-tetrahydro-7-methoxyisoquinoline. J Org Chem 2001; 66:7575-87. [PMID: 11701008 DOI: 10.1021/jo0105991] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The design and synthesis of two conformationally constrained analogues of didemnin B are described. The [N,O-Me(2)Tyr(5)]residue of didemnin B was replaced with L-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic) and L-1,2,3,4-tetrahydro-7-methoxyisoquinoline-3-carboxylic acid (MeO-Tic), which mimic the N,O-dimethylated tyrosine while constraining the conformation of the molecule. Preliminary results indicate that the conformation of the [N,O-Me(2)Tyr(5)]residue closely matches the conformation imposed by the Tic replacement.
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Affiliation(s)
- J E Tarver
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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