51
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Lamarca AP, Schrago CG. Fast speciations and slow genes: uncovering the root of living canids. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Despite ongoing efforts relying on computationally intensive tree-building methods and large datasets, the deeper phylogenetic relationships between living canid genera remain controversial. We demonstrate that this issue arises fundamentally from the uncertainty of root placement as a consequence of the short length of the branch connecting the major canid clades, which probably resulted from a fast radiation during the early diversification of extant Canidae. Using both nuclear and mitochondrial genes, we investigate the position of the canid root and its consistency by using three rooting methods. We find that mitochondrial genomes consistently retrieve a root node separating the tribe Canini from the remaining canids, whereas nuclear data mostly recover a root that places the Urocyon foxes as the sister lineage of living canids. We demonstrate that, to resolve the canid root, the nuclear segments sequenced so far are significantly less informative than mitochondrial genomes. We also propose that short intervals between speciations obscure the place of the true root, because methods are susceptible to stochastic error in the presence of short internal branches near the root.
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Affiliation(s)
- Alessandra P Lamarca
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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52
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53
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Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Warwick Vesztrocy A, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C. OMA standalone: orthology inference among public and custom genomes and transcriptomes. Genome Res 2019; 29:1152-1163. [PMID: 31235654 PMCID: PMC6633268 DOI: 10.1101/gr.243212.118] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/24/2019] [Indexed: 11/24/2022]
Abstract
Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0.
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Affiliation(s)
- Adrian M Altenhoff
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Jeremy Levy
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, United Kingdom.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Magdalena Zarowiecki
- Genomics England, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Bartłomiej Tomiczek
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom.,Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Alex Warwick Vesztrocy
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Daniel A Dalquen
- Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Steven Müller
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Natasha M Glover
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - David Dylus
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Department of Computer Science, University College London, London WC1E 6BT, United Kingdom
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54
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Abstract
A major problem in understanding animal evolution is where early branching phyla, especially sponges and comb jellies (sea gooseberries), sit in the tree of life. A new study seeks to overcome this problem by sampling more species and data cleansing.
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55
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Bradley D, Beltrao P. Evolution of protein kinase substrate recognition at the active site. PLoS Biol 2019; 17:e3000341. [PMID: 31233486 PMCID: PMC6611643 DOI: 10.1371/journal.pbio.3000341] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/05/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023] Open
Abstract
Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase-substrate motif. Kinases have been extensively duplicated throughout evolution, but little is known about when in time new target motifs have arisen. Here, we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity-determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but are not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired around the time of the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
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56
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Bornens M. [Cell polarity and the innovation of the primary cilium/centrosome organ in Metazoa]. Med Sci (Paris) 2019; 35:452-461. [PMID: 31115328 DOI: 10.1051/medsci/2019092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cell-autonomous polarity in Metazoans is inherited from ancestral unicellular organisms. We assume that permanent polarity in unicellular eukaryotes is required for cell motion and sensory reception and that the integration of these two activities corresponds to an evolutionary constrained cell function. While conserving the ancestral flagellum, Metazoans have co-opted a primary cilium/centrosome organ from it, ensuring similar functions, but in different cells, or in the same cell at different moments. We propose that the remodeling necessary to reach a new higher-level unit of selection in multi-cellular organisms, has been triggered by conflicts among individual cell polarities to reach an organismic polarity. We shall provisionally conclude that beyond critical consequences for embryo development, the conservation of cell-autonomous polarity in Metazoans has far reaching implications for the evolution of individuality.
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Affiliation(s)
- Michel Bornens
- Institut Curie, Université de recherche Paris-Sciences-et-Lettres, CNRS - UMR 144, 26, rue d'Ulm, 75248 Paris Cedex 05, France
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57
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Rahman IA, Thompson JR, Briggs DEG, Siveter DJ, Siveter DJ, Sutton MD. A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan. Proc Biol Sci 2019; 286:20182792. [PMID: 30966985 DOI: 10.1098/rspb.2018.2792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, Sollasina cthulhu, from the Silurian Herefordshire Lagerstätte, UK. Sollasina cthulhu belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical-optical tomography and computer reconstruction, we visualize the internal anatomy of S. cthulhu in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that Sollasina and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
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Affiliation(s)
- Imran A Rahman
- 1 Oxford University Museum of Natural History , Oxford OX1 3PW , UK
| | - Jeffrey R Thompson
- 2 Department of Earth Sciences, University of Southern California , Los Angeles, CA 90089-0740 , USA
| | - Derek E G Briggs
- 3 Department of Geology and Geophysics and Yale Peabody Museum of Natural History, Yale University , New Haven, CT 06520-8109 , USA
| | - David J Siveter
- 4 School of Geography, Geology and the Environment, University of Leicester , Leicester LE1 7RH , UK
| | - Derek J Siveter
- 1 Oxford University Museum of Natural History , Oxford OX1 3PW , UK.,5 Department of Earth Sciences, University of Oxford , South Parks Road, Oxford OX1 3AN , UK
| | - Mark D Sutton
- 6 Department of Earth Sciences and Engineering, Imperial College London , London SW7 2BP , UK
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58
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Affiliation(s)
- László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Hungarian Academy of Sciences, 6726 Szeged, Hungary.
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59
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Kratzer MC, England L, Apel D, Hassel M, Borchers A. Evolution of the Rho guanine nucleotide exchange factors Kalirin and Trio and their gene expression in Xenopus development. Gene Expr Patterns 2019; 32:18-27. [PMID: 30844509 DOI: 10.1016/j.gep.2019.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 01/23/2023]
Abstract
Guanine nucleotide exchange factors (GEFs) activate Rho GTPases by accelerating their GDP/GTP exchange. Trio and its paralog Kalirin (Kalrn) are unique members of the Rho-GEFs that harbor three catalytic domains: two functional GEF domains and a serine/threonine kinase domain. The N-terminal GEF domain activates Rac1 and RhoG GTPases, while the C-terminal GEF domain acts specifically on RhoA. Trio and Kalrn have an evolutionary conserved function in morphogenetic processes including neuronal development. De novo mutations in TRIO have lately been identified in patients with intellectual disability, suggesting that this protein family plays an important role in development and disease. Phylogenetic and domain analysis revealed that a Kalrn/Trio ancestor originated in Prebilateria and duplicated in Urbilateria to yield Kalrn and Trio. Only few taxa outside the vertebrates retained both of these highly conserved proteins. To obtain first insights into their redundant or distinct functions in a vertebrate model system, we show for the first time a detailed comparative analysis of trio and kalrn expression in Xenopus laevis development. The mRNAs are maternally transcribed and expression increases starting with neurula stages. Trio and kalrn are detected in mesoderm/somites and different neuronal populations in the neural plate/tube and later also in the brain. However, only trio is expressed in migrating neural crest cells, while kalrn expression is detected in the cranial nerves, suggesting distinct functions. Thus, our expression analysis provides a good basis for further functional studies.
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Affiliation(s)
- Marie-Claire Kratzer
- Philipps-Universität Marburg, Faculty of Biology, Molecular Embryology, Marburg, Germany; DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg, Germany
| | - Laura England
- Philipps-Universität Marburg, Faculty of Biology, Molecular Embryology, Marburg, Germany
| | - David Apel
- Philipps-Universität Marburg, Faculty of Biology, Morphology and Evolution of Invertebrates, Marburg, Germany; DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg, Germany
| | - Monika Hassel
- Philipps-Universität Marburg, Faculty of Biology, Morphology and Evolution of Invertebrates, Marburg, Germany; DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg, Germany
| | - Annette Borchers
- Philipps-Universität Marburg, Faculty of Biology, Molecular Embryology, Marburg, Germany; DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg, Germany.
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60
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Nielsen C. Was the ancestral panarthropod mouth ventral or terminal? ARTHROPOD STRUCTURE & DEVELOPMENT 2019; 49:152-154. [PMID: 30445117 DOI: 10.1016/j.asd.2018.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
It has recently been suggested that the panarthropod mouth was ancestrally terminal, based on the assumption that the ancestral tardigrade had a terminal mouth and on the observations of a terminal mouth in adults of some stem-group fossils. This is shown to be unlikely, and it is concluded that the ancestral panarthropod had a ventral mouth.
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Affiliation(s)
- Claus Nielsen
- Biosystematics, The Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark.
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61
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62
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Vinther J, Parry LA. Bilateral Jaw Elements in Amiskwia sagittiformis Bridge the Morphological Gap between Gnathiferans and Chaetognaths. Curr Biol 2019; 29:881-888.e1. [PMID: 30799238 DOI: 10.1016/j.cub.2019.01.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/28/2018] [Accepted: 01/21/2019] [Indexed: 01/10/2023]
Abstract
Amiskwia sagittiformis Walcott 1911 is an iconic soft-bodied taxon from the Burgess Shale [1-3]. It was originally interpreted as a chaetognath [1], but it was later interpreted as a pelagic nemertean [2] or considered of uncertain affinity [3]. Part of this ambiguity is due to direct comparisons with members of the crown groups of extant phyla [4] and a lack of clarity regarding the systematic position of chaetognaths, which would allow for assessing character polarity in the phylum with respect to outgroups. Here, we show that Amiskwia preserves a bilaterally arranged set of head structures visible in relief and high reflectivity. These structures are best interpreted as jaws situated within an expanded pharyngeal complex. Morphological studies have highlighted a likely homology between bilateral and chitinous jaw elements in gnathiferans and chaetognaths [5], which is congruent with a shared unique Hox gene that suggests a close relationship between Gnathifera and Chaetognatha [6]. Molecular phylogenetic studies have recently found gnathiferans to be a deep branch of Spiralia and Chaetognaths either a sister group to Spiralia [7] or forming a clade with gnathiferans [6, 8]. Our phylogenetic analyses render Gnathifera paraphyletic with respect to Chaetognatha, and we therefore suggest that Amiskwia is best interpreted as a stem chaetognath, but crown gnathiferan.
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Affiliation(s)
- Jakob Vinther
- 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; Department of Geology and Geophysics, Yale University, 210 Whitney Ave., New Haven, Connecticut 06511, USA
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63
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Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 2019; 35:518-522. [PMID: 29077904 PMCID: PMC5850222 DOI: 10.1093/molbev/msx281] [Citation(s) in RCA: 4290] [Impact Index Per Article: 858.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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Affiliation(s)
- Diep Thi Hoang
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
| | - Olga Chernomor
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Le Sy Vinh
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
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64
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Rico-Guevara A, Hurme KJ. Intrasexually selected weapons. Biol Rev Camb Philos Soc 2019; 94:60-101. [PMID: 29924496 DOI: 10.1111/brv.12436] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 05/14/2018] [Accepted: 05/18/2018] [Indexed: 01/24/2023]
Abstract
We propose a practical concept that distinguishes the particular kind of weaponry that has evolved to be used in combat between individuals of the same species and sex, which we term intrasexually selected weapons (ISWs). We present a treatise of ISWs in nature, aiming to understand their distinction and evolution from other secondary sex traits, including from 'sexually selected weapons', and from sexually dimorphic and monomorphic weaponry. We focus on the subset of secondary sex traits that are the result of same-sex combat, defined here as ISWs, provide not previously reported evolutionary patterns, and offer hypotheses to answer questions such as: why have only some species evolved weapons to fight for the opposite sex or breeding resources? We examined traits that seem to have evolved as ISWs in the entire animal phylogeny, restricting the classification of ISW to traits that are only present or enlarged in adults of one of the sexes, and are used as weapons during intrasexual fights. Because of the absence of behavioural data and, in many cases, lack of sexually discriminated series from juveniles to adults, we exclude the fossil record from this review. We merge morphological, ontogenetic, and behavioural information, and for the first time thoroughly review the tree of life to identify separate evolution of ISWs. We found that ISWs are only found in bilateral animals, appearing independently in nematodes, various groups of arthropods, and vertebrates. Our review sets a reference point to explore other taxa that we identify with potential ISWs for which behavioural or morphological studies are warranted. We establish that most ISWs come in pairs, are located in or near the head, are endo- or exoskeletal modifications, are overdeveloped structures compared with those found in females, are modified feeding structures and/or locomotor appendages, are most common in terrestrial taxa, are frequently used to guard females, territories, or both, and are also used in signalling displays to deter rivals and/or attract females. We also found that most taxa lack ISWs, that females of only a few species possess better-developed weapons than males, that the cases of independent evolution of ISWs are not evenly distributed across the phylogeny, and that animals possessing the most developed ISWs have non-hunting habits (e.g. herbivores) or are faunivores that prey on very small prey relative to their body size (e.g. insectivores). Bringing together perspectives from studies on a variety of taxa, we conceptualize that there are five ways in which a sexually dimorphic trait, apart from the primary sex traits, can be fixed: sexual selection, fecundity selection, parental role division, differential niche occupation between the sexes, and interference competition. We discuss these trends and the factors involved in the evolution of intrasexually selected weaponry in nature.
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Affiliation(s)
- Alejandro Rico-Guevara
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building, Berkeley, CA, 94720, U.S.A.,Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Unit 3043, Storrs, CT, 06269, U.S.A.,Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Código Postal 11001, Bogotá DC, Colombia
| | - Kristiina J Hurme
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building, Berkeley, CA, 94720, U.S.A.,Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Unit 3043, Storrs, CT, 06269, U.S.A
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65
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Rentzsch F, Juliano C, Galliot B. Modern genomic tools reveal the structural and cellular diversity of cnidarian nervous systems. Curr Opin Neurobiol 2019; 56:87-96. [PMID: 30654234 DOI: 10.1016/j.conb.2018.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022]
Abstract
Cnidarians shared a common ancestor with bilaterians more than 600 million years ago. This sister group relationship gives them an informative phylogenetic position for understanding the fascinating morphological and molecular cell type diversity of bilaterian nervous systems. Moreover, cnidarians display novel features such as endodermal neurogenesis and independently evolved centralizations, which provide a platform for understanding the evolution of nervous system innovations. In recent years, the application of modern genomic tools has significantly advanced our understanding of cnidarian nervous system structure and function. For example, transgenic reporter lines and gene knockdown experiments in several cnidarian species reveal a significant degree of conservation in the neurogenesis gene regulatory program, while single cell RNA sequencing projects are providing a much deeper understanding of cnidarian neural cell type diversity. At the level of neural function, the physiological properties of ion channels have been described and calcium imaging of the nervous system in whole animals has allowed for the identification of neural circuits underlying specific behaviours. Cnidarians have arrived in the modern era of molecular neurobiology and are primed to provide exciting new insights into the early evolution of nervous systems.
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Affiliation(s)
- Fabian Rentzsch
- Sars Centre for Marine Molecular Biology, Norway; Department for Biological Sciences, University of Bergen, Norway.
| | - Celina Juliano
- Department of Molecular and Cellular Biology, University of California Davis, CA 95616, United States.
| | - Brigitte Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Switzerland.
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66
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A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Curr Biol 2019; 29:312-318.e3. [PMID: 30639106 DOI: 10.1016/j.cub.2018.11.042] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/12/2018] [Accepted: 11/14/2018] [Indexed: 11/23/2022]
Abstract
Chaetognaths (arrow worms) are an enigmatic group of marine animals whose phylogenetic position remains elusive, in part because they display a mix of developmental and morphological characters associated with other groups [1, 2]. In particular, it remains unclear whether they are a sister group to protostomes [1, 2], one of the principal animal superclades, or whether they bear a closer relationship with some spiralian phyla [3, 4]. Addressing the phylogenetic position of chaetognaths and refining our understanding of relationships among spiralians are essential to fully comprehend character changes during bilaterian evolution [5]. To tackle these questions, we generated new transcriptomes for ten chaetognath species, compiling an extensive phylogenomic dataset that maximizes data occupancy and taxonomic representation. We employed inference methods that consider rate and compositional heterogeneity across taxa to avoid limitations of earlier analyses [6]. In this way, we greatly improved the resolution of the protostome tree of life. We find that chaetognaths cluster together with rotifers, gnathostomulids, and micrognathozoans within an expanded Gnathifera clade and that this clade is the sister group to other spiralians [7, 8]. Our analysis shows that several previously proposed groupings are likely due to systematic error, and we propose a revised organization of Lophotrochozoa with three main clades: Tetraneuralia (mollusks and entoprocts), Lophophorata (brachiopods, phoronids, and ectoprocts), and a third unnamed clade gathering annelids, nemerteans, and platyhelminthes. Consideration of classical morphological, developmental, and genomic characters in light of this topology indicates secondary loss as a fundamental trend in spiralian evolution.
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67
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Evolutionary distribution of deoxynucleoside 5-monophosphate N-glycosidase, DNPH1. Gene 2019; 683:1-11. [DOI: 10.1016/j.gene.2018.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/10/2018] [Accepted: 10/03/2018] [Indexed: 01/01/2023]
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68
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Formery L, Schubert M, Croce JC. Ambulacrarians and the Ancestry of Deuterostome Nervous Systems. Results Probl Cell Differ 2019; 68:31-59. [PMID: 31598852 DOI: 10.1007/978-3-030-23459-1_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The evolutionary origin and history of metazoan nervous systems has been at the heart of numerous scientific debates for well over a century. This has been a particularly difficult issue to resolve within the deuterostomes, chiefly due to the distinct neural architectures observed within this group of animals. Indeed, deuterosomes feature central nervous systems, apical organs, nerve cords, and basiepidermal nerve nets. Comparative analyses investigating the anatomy and molecular composition of deuterostome nervous systems have nonetheless succeeded in identifying a number of shared and derived features. These analyses have led to the elaboration of diverse theories about the origin and evolutionary history of deuterostome nervous systems. Here, we provide an overview of these distinct theories. Further, we argue that deciphering the adult nervous systems of representatives of all deuterostome phyla, including echinoderms, which have long been neglected in this type of surveys, will ultimately provide answers to the questions concerning the ancestry and evolution of deuterostome nervous systems.
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Affiliation(s)
- Laurent Formery
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Evolution of Intercellular Signaling in Development (EvoInSiDe) Team, Villefranche-sur-Mer, France
| | - Michael Schubert
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Evolution of Intercellular Signaling in Development (EvoInSiDe) Team, Villefranche-sur-Mer, France
| | - Jenifer C Croce
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Evolution of Intercellular Signaling in Development (EvoInSiDe) Team, Villefranche-sur-Mer, France.
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69
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Golubev A, Hanson AD, Gladyshev VN. A Tale of Two Concepts: Harmonizing the Free Radical and Antagonistic Pleiotropy Theories of Aging. Antioxid Redox Signal 2018; 29:1003-1017. [PMID: 28874059 PMCID: PMC6104246 DOI: 10.1089/ars.2017.7105] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/09/2017] [Accepted: 08/31/2017] [Indexed: 12/18/2022]
Abstract
SIGNIFICANCE The two foremost concepts of aging are the mechanistic free radical theory (FRT) of how we age and the evolutionary antagonistic pleiotropy theory (APT) of why we age. Both date from the late 1950s. The FRT holds that reactive oxygen species (ROS) are the principal contributors to the lifelong cumulative damage suffered by cells, whereas the APT is generally understood as positing that genes that are good for young organisms can take over a population even if they are bad for the old organisms. Recent Advances: Here, we provide a common ground for the two theories by showing how aging can result from the inherent chemical reactivity of many biomolecules, not just ROS, which imposes a fundamental constraint on biological evolution. Chemically reactive metabolites spontaneously modify slowly renewable macromolecules in a continuous way over time; the resulting buildup of damage wrought by the genes coding for enzymes that generate such small molecules eventually masquerades as late-acting pleiotropic effects. In aerobic organisms, ROS are major agents of this damage but they are far from alone. CRITICAL ISSUES Being related to two sides of the same phenomenon, these theories should be compatible. However, the interface between them is obscured by the FRT mistaking a subset of damaging processes for the whole, and the APT mistaking a cumulative quantitative process for a qualitative switch. FUTURE DIRECTIONS The manifestations of ROS-mediated cumulative chemical damage at the population level may include the often-observed negative correlation between fitness and the rate of its decline with increasing age, further linking FRT and APT. Antioxid. Redox Signal. 29, 1003-1017.
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Affiliation(s)
- Alexey Golubev
- Department of Carcinogenesis and Oncogerontology, Petrov Research Institute of Oncology, Saint Petersburg, Russia
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow Russia
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70
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Evolution of the bilaterian mouth and anus. Nat Ecol Evol 2018; 2:1358-1376. [PMID: 30135501 DOI: 10.1038/s41559-018-0641-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 06/26/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
It is widely held that the bilaterian tubular gut with mouth and anus evolved from a simple gut with one major gastric opening. However, there is no consensus on how this happened. Did the single gastric opening evolve into a mouth, with the anus forming elsewhere in the body (protostomy), or did it evolve into an anus, with the mouth forming elsewhere (deuterostomy), or did it evolve into both mouth and anus (amphistomy)? These questions are addressed by the comparison of developmental fates of the blastopore, the opening of the embryonic gut, in diverse animals that live today. Here we review comparative data on the identity and fate of blastoporal tissue, investigate how the formation of the through-gut relates to the major body axes, and discuss to what extent evolutionary scenarios are consistent with these data. Available evidence indicates that stem bilaterians had a slit-like gastric opening that was partially closed in subsequent evolution, leaving open the anus and most likely also the mouth, which would favour amphistomy. We discuss remaining difficulties, and outline directions for future research.
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71
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Grandchamp A, Monget P. Synchronous birth is a dominant pattern in receptor-ligand evolution. BMC Genomics 2018; 19:611. [PMID: 30107779 PMCID: PMC6092800 DOI: 10.1186/s12864-018-4977-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/31/2018] [Indexed: 12/11/2022] Open
Abstract
Background Interactions between proteins are key components in the chemical and physical processes of living organisms. Among these interactions, membrane receptors and their ligands are particularly important because they are at the interface between extracellular and intracellular environments. Many studies have investigated how binding partners have co-evolved in genomes during the evolution. However, little is known about the establishment of the interaction on a phylogenetic scale. In this study, we systematically studied the time of birth of genes encoding human membrane receptors and their ligands in the animal tree of life. We examined a total of 553 pairs of ligands/receptors, representing non-redundant interactions. Results We found that 41% of the receptors and their respective first ligands appeared in the same branch, representing 2.5-fold more than expected by chance, thus suggesting an evolutionary dynamic of interdependence and conservation between these partners. In contrast, 21% of the receptors appeared after their ligand, i.e. three-fold less often than expected by chance. Most surprisingly, 38% of the receptors appeared before their first ligand, as much as expected by chance. Conclusions According to these results, we propose that a selective pressure is exerted on ligands and receptors once they appear, that would remove molecules whose partner does not appear quickly. Electronic supplementary material The online version of this article (10.1186/s12864-018-4977-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Grandchamp
- PRC, UMR85, INRA, CNRS, IFCE, Université de Tours, F-37380, Nouzilly, France.
| | - Philippe Monget
- PRC, UMR85, INRA, CNRS, IFCE, Université de Tours, F-37380, Nouzilly, France.
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72
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Walters ET. Nociceptive Biology of Molluscs and Arthropods: Evolutionary Clues About Functions and Mechanisms Potentially Related to Pain. Front Physiol 2018; 9:1049. [PMID: 30123137 PMCID: PMC6085516 DOI: 10.3389/fphys.2018.01049] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/16/2018] [Indexed: 01/15/2023] Open
Abstract
Important insights into the selection pressures and core molecular modules contributing to the evolution of pain-related processes have come from studies of nociceptive systems in several molluscan and arthropod species. These phyla, and the chordates that include humans, last shared a common ancestor approximately 550 million years ago. Since then, animals in these phyla have continued to be subject to traumatic injury, often from predators, which has led to similar adaptive behaviors (e.g., withdrawal, escape, recuperative behavior) and physiological responses to injury in each group. Comparisons across these taxa provide clues about the contributions of convergent evolution and of conservation of ancient adaptive mechanisms to general nociceptive and pain-related functions. Primary nociceptors have been investigated extensively in a few molluscan and arthropod species, with studies of long-lasting nociceptive sensitization in the gastropod, Aplysia, and the insect, Drosophila, being especially fruitful. In Aplysia, nociceptive sensitization has been investigated as a model for aversive memory and for hyperalgesia. Neuromodulator-induced, activity-dependent, and axotomy-induced plasticity mechanisms have been defined in synapses, cell bodies, and axons of Aplysia primary nociceptors. Studies of nociceptive sensitization in Drosophila larvae have revealed numerous molecular contributors in primary nociceptors and interacting cells. Interestingly, molecular contributors examined thus far in Aplysia and Drosophila are largely different, but both sets overlap extensively with those in mammalian pain-related pathways. In contrast to results from Aplysia and Drosophila, nociceptive sensitization examined in moth larvae (Manduca) disclosed central hyperactivity but no obvious peripheral sensitization of nociceptive responses. Squid (Doryteuthis) show injury-induced sensitization manifested as behavioral hypersensitivity to tactile and especially visual stimuli, and as hypersensitivity and spontaneous activity in nociceptor terminals. Temporary blockade of nociceptor activity during injury subsequently increased mortality when injured squid were exposed to fish predators, providing the first demonstration in any animal of the adaptiveness of nociceptive sensitization. Immediate responses to noxious stimulation and nociceptive sensitization have also been examined behaviorally and physiologically in a snail (Helix), octopus (Adopus), crayfish (Astacus), hermit crab (Pagurus), and shore crab (Hemigrapsus). Molluscs and arthropods have systems that suppress nociceptive responses, but whether opioid systems play antinociceptive roles in these phyla is uncertain.
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Affiliation(s)
- Edgar T Walters
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
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73
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Bornens M. Cell polarity: having and making sense of direction-on the evolutionary significance of the primary cilium/centrosome organ in Metazoa. Open Biol 2018; 8:180052. [PMID: 30068565 PMCID: PMC6119866 DOI: 10.1098/rsob.180052] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
Cell-autonomous polarity in Metazoans is evolutionarily conserved. I assume that permanent polarity in unicellular eukaryotes is required for cell motion and sensory reception, integration of these two activities being an evolutionarily constrained function. Metazoans are unique in making cohesive multicellular organisms through complete cell divisions. They evolved a primary cilium/centrosome (PC/C) organ, ensuring similar functions to the basal body/flagellum of unicellular eukaryotes, but in different cells, or in the same cell at different moments. The possibility that this innovation contributed to the evolution of individuality, in being instrumental in the early specification of the germ line during development, is further discussed. Then, using the example of highly regenerative organisms like planarians, which have lost PC/C organ in dividing cells, I discuss the possibility that part of the remodelling necessary to reach a new higher-level unit of selection in multi-cellular organisms has been triggered by conflicts among individual cell polarities to reach an organismic polarity. Finally, I briefly consider organisms with a sensorimotor organ like the brain that requires exceedingly elongated polarized cells for its activity. I conclude that beyond critical consequences for embryo development, the conservation of cell-autonomous polarity in Metazoans had far-reaching implications for the evolution of individuality.
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Affiliation(s)
- Michel Bornens
- Institut Curie, PSL Research University, CNRS - UMR 144, 75005 Paris, France
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74
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Hernandez AM, Ryan JF. Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. PeerJ 2018; 6:e5067. [PMID: 29922518 PMCID: PMC6005172 DOI: 10.7717/peerj.5067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
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75
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López-Escardó D, Paps J, de Vargas C, Massana R, Ruiz-Trillo I, Del Campo J. Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. Sci Rep 2018; 8:9106. [PMID: 29904074 PMCID: PMC6002407 DOI: 10.1038/s41598-018-27509-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/05/2018] [Indexed: 11/08/2022] Open
Abstract
Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified, based on molecular data, a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected.
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Affiliation(s)
- David López-Escardó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Catalonia, Spain
| | - Jordi Paps
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Colomban de Vargas
- CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Catalonia, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Catalonia, Spain.
- Departament de Genètica, Microbiología i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Javier Del Campo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Catalonia, Spain.
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain.
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76
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Tohmonda T, Kamiya A, Ishiguro A, Iwaki T, Fujimi TJ, Hatayama M, Aruga J. Identification and Characterization of Novel Conserved Domains in Metazoan Zic Proteins. Mol Biol Evol 2018; 35:2205-2229. [DOI: 10.1093/molbev/msy122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Takahide Tohmonda
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akiko Kamiya
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akira Ishiguro
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Takashi Iwaki
- Meguro Parasitological Museum, Meguro-Ku, Tokyo, Japan
| | - Takahiko J Fujimi
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Minoru Hatayama
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
| | - Jun Aruga
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
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77
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Witteveen J. Typological thinking: Then and now. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:123-131. [PMID: 29578654 PMCID: PMC6001556 DOI: 10.1002/jez.b.22796] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 02/08/2018] [Accepted: 02/27/2018] [Indexed: 11/08/2022]
Abstract
A popular narrative about the history of modern biology has it that Ernst Mayr introduced the distinction between "typological thinking" and "population thinking" to mark a contrast between a metaphysically problematic and a promising foundation for (evolutionary) biology, respectively. This narrative sometimes continues with the observation that, since the late-20th century, typological concepts have been making a comeback in biology, primarily in the context of evolutionary developmental biology. It is hard to square this narrative with the historical and philosophical literature on the typology/population distinction from the last decade or so. The conclusion that emerges from this literature is that the very distinction between typological thinking and population thinking is a piece of mere rhetoric that was concocted and rehearsed for purely strategic, programmatic reasons. If this is right, it becomes hard to make sense of recent criticisms (and sometimes: espousals) of the purportedly typological underpinnings of certain contemporary research programs. In this article, I offer a way out of this apparent conflict. I show that we can make historical and philosophical sense of the continued accusations of typological thinking by looking beyond Mayr, to his contemporary and colleague George Gaylord Simpson. I show that before Mayr discussed the typology/population distinction as an issue in scientific metaphysics, Simpson introduced it to mark several contrasts in methodology and scientific practice. I argue that Simpson's insightful discussion offers useful resources for classifying and assessing contemporary attributions of typological thinking.
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Affiliation(s)
- Joeri Witteveen
- Descartes Centre for the History and Philosophy of the Sciences and the HumanitiesUtrecht UniversityUtrechtThe Netherlands
- Department of Science EducationSection for History and Philosophy of ScienceUniversity of CopenhagenCopenhagenDenmark
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78
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Nagy LG, Kovács GM, Krizsán K. Complex multicellularity in fungi: evolutionary convergence, single origin, or both? Biol Rev Camb Philos Soc 2018; 93:1778-1794. [DOI: 10.1111/brv.12418] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/23/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022]
Affiliation(s)
- László G. Nagy
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
| | - Gábor M. Kovács
- Department of Plant Anatomy; Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C; H-1117 Budapest Hungary
- Plant Protection Institute, Centre for Agricultural Research; Hungarian Academy of Sciences (MTA-ATK); PO Box 102, H-1525 Budapest Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
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79
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Wang HC, Minh BQ, Susko E, Roger AJ. Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation. Syst Biol 2018; 67:216-235. [PMID: 28950365 DOI: 10.1093/sysbio/syx068] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 08/02/2017] [Indexed: 11/14/2022] Open
Abstract
Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with $k$ classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately $k$/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.
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Affiliation(s)
- Huai-Chun Wang
- Department of Mathematics and Statistics, 6316 Coburg Road.,Department of Biochemistry and Molecular Biology, 5850 College Street, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Austria
| | - Edward Susko
- Department of Mathematics and Statistics, 6316 Coburg Road.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, 5850 College Street, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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80
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Abstract
The phylogenetic affinities of Xenacoelomorpha - the phylum comprising Xenoturbella bocki and acoelomorph worms - are debated. Two recent studies conclude they represent the earliest branching bilaterally symmetrical animals, but additional tests may be needed to confirm this notion.
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Affiliation(s)
- Maximilian J Telford
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
| | - Richard R Copley
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 181 chemin du Lazaret, 06230 Villefranche-sur-mer, France
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81
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Whelan NV, Halanych KM. Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses. Syst Biol 2018; 66:232-255. [PMID: 27633354 DOI: 10.1093/sysbio/syw084] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 09/04/2016] [Indexed: 11/14/2022] Open
Abstract
As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa, ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny, rather than rigorous testing with known trees via simulation. Moreover, CAT models have not been compared to other approaches for handling substitutional heterogeneity such as data partitioning with site-homogeneous substitution models. We simulated amino acid sequence datasets with substitutional heterogeneity on a variety of tree shapes including those susceptible to LBA. Data were analyzed with both CAT models and partitioning to explore model performance; in total over 670,000 CPU hours were used, of which over 97% was spent running analyses with CAT models. In many cases, all models recovered branching patterns that were identical to the known tree. However, CAT-F81 consistently performed worse than other models in inferring the correct branching patterns, and both CAT models often overestimated substitutional heterogeneity. Additionally, reanalysis of two empirical metazoan datasets supports the notion that CAT-F81 tends to recover less accurate trees than data partitioning and CAT-GTR. Given these results, we conclude that partitioning and CAT-GTR perform similarly in recovering accurate branching patterns. However, computation time can be orders of magnitude less for data partitioning, with commonly used implementations of CAT-GTR often failing to reach completion in a reasonable time frame (i.e., for Bayesian analyses to converge). Practices such as removing constant sites and parsimony uninformative characters, or using CAT-F81 when CAT-GTR is deemed too computationally expensive, cannot be logically justified. Given clear problems with CAT-F81, phylogenies previously inferred with this model should be reassessed. [Data partitioning; phylogenomics, simulation, site-heterogeneity, substitution models.].
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Affiliation(s)
- Nathan V Whelan
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
| | - Kenneth M Halanych
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
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82
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Feuda R, Dohrmann M, Pett W, Philippe H, Rota-Stabelli O, Lartillot N, Wörheide G, Pisani D. Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals. Curr Biol 2017; 27:3864-3870.e4. [DOI: 10.1016/j.cub.2017.11.008] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/19/2017] [Accepted: 11/02/2017] [Indexed: 10/18/2022]
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83
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Zhao F, Smith MR, Yin Z, Zeng H, Li G, Zhu M. Orthrozanclus elongata n. sp. and the significance of sclerite-covered taxa for early trochozoan evolution. Sci Rep 2017; 7:16232. [PMID: 29176685 PMCID: PMC5701144 DOI: 10.1038/s41598-017-16304-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/07/2017] [Indexed: 01/21/2023] Open
Abstract
Orthrozanclus is a shell-bearing, sclerite covered Cambrian organism of uncertain taxonomic affinity, seemingly representing an intermediate between its fellow problematica Wiwaxia and Halkieria. Attempts to group these slug-like taxa into a single ‘halwaxiid’ clade nevertheless present structural and evolutionary difficulties. Here we report a new species of Orthrozanclus from the early Cambrian Chengjiang Lagerstätte. The scleritome arrangement and constitution in this material corroborates the link between Orthrozanclus and Halkieria, but not with Wiwaxia — and calls into question its purported relationship with molluscs. Instead, the tripartite construction of the halkieriid scleritome finds a more compelling parallel in the camenellan tommotiids, relatives of the brachiopods and phoronids. Such a phylogenetic position would indicate the presence of a scleritome in the common ancestor of the three major trochozoan lineages, Mollusca, Annelida and Brachiozoa. On this view, the absence of fossil Ediacaran sclerites is evidence against any ‘Precambrian prelude’ to the explosive diversification of these phyla in the Cambrian, c. 540–530 million years ago.
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Affiliation(s)
- Fangchen Zhao
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing, 210008, China.
| | - Martin R Smith
- Department of Earth Sciences, Durham University, Durham, DH1 3LE, UK.
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing, 210008, China
| | - Han Zeng
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing, 210008, China.,College of Earth Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Guoxiang Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing, 210008, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing, 210008, China.,College of Earth Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
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84
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Brunet T, King N. The Origin of Animal Multicellularity and Cell Differentiation. Dev Cell 2017; 43:124-140. [PMID: 29065305 PMCID: PMC6089241 DOI: 10.1016/j.devcel.2017.09.016] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/31/2017] [Accepted: 09/19/2017] [Indexed: 12/14/2022]
Abstract
Over 600 million years ago, animals evolved from a unicellular or colonial organism whose cell(s) captured bacteria with a collar complex, a flagellum surrounded by a microvillar collar. Using principles from evolutionary cell biology, we reason that the transition to multicellularity required modification of pre-existing mechanisms for extracellular matrix synthesis and cytokinesis. We discuss two hypotheses for the origin of animal cell types: division of labor from ancient plurifunctional cells and conversion of temporally alternating phenotypes into spatially juxtaposed cell types. Mechanistic studies in diverse animals and their relatives promise to deepen our understanding of animal origins and cell biology.
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Affiliation(s)
- Thibaut Brunet
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Nicole King
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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85
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Abstract
The evolution of a nervous system as a control system of the body's functions is a key innovation of animals. Its fundamental units are neurons, highly specialized cells dedicated to fast cell-cell communication. Neurons pass signals to other neurons, muscle cells, or gland cells at specialized junctions, the synapses, where transmitters are released from vesicles in a Ca2+-dependent fashion to activate receptors in the membrane of the target cell. Reconstructing the origins of neuronal communication out of a more simple process remains a central challenge in biology. Recent genomic comparisons have revealed that all animals, including the nerveless poriferans and placozoans, share a basic set of genes for neuronal communication. This suggests that the first animal, the Urmetazoan, was already endowed with neurosecretory cells that probably started to connect into neuronal networks soon afterward. Here, we discuss scenarios for this pivotal transition in animal evolution.
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Affiliation(s)
- Frederique Varoqueaux
- Département des Neurosciences Fondamentales, Université de Lausanne, Lausanne, CH-1005 Switzerland; ,
| | - Dirk Fasshauer
- Département des Neurosciences Fondamentales, Université de Lausanne, Lausanne, CH-1005 Switzerland; ,
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86
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Alamo L, Pinto A, Sulbarán G, Mavárez J, Padrón R. Lessons from a tarantula: new insights into myosin interacting-heads motif evolution and its implications on disease. Biophys Rev 2017; 10:1465-1477. [PMID: 28871552 DOI: 10.1007/s12551-017-0292-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022] Open
Abstract
Tarantula's leg muscle thick filament is the ideal model for the study of the structure and function of skeletal muscle thick filaments. Its analysis has given rise to a series of structural and functional studies, leading, among other things, to the discovery of the myosin interacting-heads motif (IHM). Further electron microscopy (EM) studies have shown the presence of IHM in frozen-hydrated and negatively stained thick filaments of striated, cardiac, and smooth muscle of bilaterians, most showing the IHM parallel to the filament axis. EM studies on negatively stained heavy meromyosin of different species have shown the presence of IHM on sponges, animals that lack muscle, extending the presence of IHM to metazoans. The IHM evolved about 800 MY ago in the ancestor of Metazoa, and independently with functional differences in the lineage leading to the slime mold Dictyostelium discoideum (Mycetozoa). This motif conveys important functional advantages, such as Ca2+ regulation and ATP energy-saving mechanisms. Recent interest has focused on human IHM structure in order to understand the structural basis underlying various conditions and situations of scientific and medical interest: the hypertrophic and dilated cardiomyopathies, overfeeding control, aging and hormone deprival muscle weakness, drug design for schistosomiasis control, and conditioning exercise physiology for the training of power athletes.
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Affiliation(s)
- Lorenzo Alamo
- Centro de Biología Estructural "Humberto Fernández-Morán", Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 20632, Caracas, 1020A, Venezuela
| | - Antonio Pinto
- Centro de Biología Estructural "Humberto Fernández-Morán", Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 20632, Caracas, 1020A, Venezuela
| | - Guidenn Sulbarán
- Centro de Biología Estructural "Humberto Fernández-Morán", Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 20632, Caracas, 1020A, Venezuela.,Institut de Biologie Structurale (IBS), CEA-CNRS Université Grenoble Alpes, Grenoble, France
| | - Jesús Mavárez
- Laboratoire d'Ecologie Alpine, UMR 5553 CNRS-Université Grenoble Alpes, 2233 Rue de la Piscine, 38041, Grenoble, France
| | - Raúl Padrón
- Centro de Biología Estructural "Humberto Fernández-Morán", Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 20632, Caracas, 1020A, Venezuela.
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87
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Busengdal H, Rentzsch F. Unipotent progenitors contribute to the generation of sensory cell types in the nervous system of the cnidarian Nematostella vectensis. Dev Biol 2017; 431:59-68. [PMID: 28827097 DOI: 10.1016/j.ydbio.2017.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 08/08/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022]
Abstract
Nervous systems often consist of a large number of different types of neurons which are generated from neural stem and progenitor cells by a series of symmetric and asymmetric divisions. The origin and early evolution of these neural progenitor systems is not well understood. Here we use a cnidarian model organism, Nematostella vectensis, to gain insight into the generation of neural cell type diversity in a non-bilaterian animal. We identify NvFoxQ2d as a transcription factor that is expressed in a population of spatially restricted, proliferating ectodermal cells that are derived from NvSoxB(2)-expressing neural progenitor cells. Using a transgenic reporter line we show that the NvFoxQ2d cells undergo a terminal, symmetric division to generate a morphologically homogeneous population of putative sensory cells. The abundance of these cells, but not their proliferation status is affected by treatment with the γ-secretase inhibitor DAPT, suggesting regulation by Notch signalling. Our data suggest that intermediate progenitor cells and symmetric divisions contribute to the formation of the seemingly simple nervous system of a sea anemone.
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Affiliation(s)
- Henriette Busengdal
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway
| | - Fabian Rentzsch
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway.
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88
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Bahia J, Padula V, Schrödl M. Polycladida phylogeny and evolution: integrating evidence from 28S rDNA and morphology. ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-017-0327-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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89
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Liban TJ, Medina EM, Tripathi S, Sengupta S, Henry RW, Buchler NE, Rubin SM. Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family. Proc Natl Acad Sci U S A 2017; 114:4942-4947. [PMID: 28439018 PMCID: PMC5441720 DOI: 10.1073/pnas.1619170114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD-CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein-E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.
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Affiliation(s)
- Tyler J Liban
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Edgar M Medina
- Department of Biology, Duke University, Durham, NC 27708
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Satyaki Sengupta
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - R William Henry
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Nicolas E Buchler
- Department of Biology, Duke University, Durham, NC 27708
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064;
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90
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Griffith OW, Wagner GP. The placenta as a model for understanding the origin and evolution of vertebrate organs. Nat Ecol Evol 2017; 1:72. [DOI: 10.1038/s41559-017-0072] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/06/2017] [Indexed: 12/19/2022]
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91
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Cunningham JA, Liu AG, Bengtson S, Donoghue PCJ. The origin of animals: Can molecular clocks and the fossil record be reconciled? Bioessays 2016; 39:1-12. [PMID: 27918074 DOI: 10.1002/bies.201600120] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The evolutionary emergence of animals is one of the most significant episodes in the history of life, but its timing remains poorly constrained. Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed. Modern clock analyses do not predict the presence of the crown-representatives of most animal phyla in the Neoproterozoic. Furthermore, despite challenges provided by incomplete preservation, a paucity of phylogenetically informative characters, and uncertain expectations of the anatomy of early animals, a number of Neoproterozoic fossils can reasonably be interpreted as metazoans. A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identification in the fossil record. Critical assessment of both records may permit better resolution of the tempo and mode of early animal evolution.
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Affiliation(s)
- John A Cunningham
- School of Earth Sciences, University of Bristol, Bristol, UK.,Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexander G Liu
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Stefan Bengtson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm, Sweden
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92
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The Presence of a Functionally Tripartite Through-Gut in Ctenophora Has Implications for Metazoan Character Trait Evolution. Curr Biol 2016; 26:2814-2820. [DOI: 10.1016/j.cub.2016.08.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/04/2023]
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93
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Budd GE, Jackson ISC. Ecological innovations in the Cambrian and the origins of the crown group phyla. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150287. [PMID: 26598735 PMCID: PMC4685591 DOI: 10.1098/rstb.2015.0287] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Simulation studies of the early origins of the modern phyla in the fossil record, and the rapid diversification that led to them, show that these are inevitable outcomes of rapid and long-lasting radiations. Recent advances in Cambrian stratigraphy have revealed a more precise picture of the early bilaterian radiation taking place during the earliest Terreneuvian Series, although several ambiguities remain. The early period is dominated by various tubes and a moderately diverse trace fossil record, with the classical ‘Tommotian’ small shelly biota beginning to appear some millions of years after the base of the Cambrian at ca 541 Ma. The body fossil record of the earliest period contains a few representatives of known groups, but most of the record is of uncertain affinity. Early trace fossils can be assigned to ecdysozoans, but deuterostome and even spiralian trace and body fossils are less clearly represented. One way of explaining the relative lack of clear spiralian fossils until about 536 Ma is to assign the various lowest Cambrian tubes to various stem-group lophotrochozoans, with the implication that the groundplan of the lophotrochozoans included a U-shaped gut and a sessile habit. The implication of this view would be that the vagrant lifestyle of annelids, nemerteans and molluscs would be independently derived from such a sessile ancestor, with potentially important implications for the homology of their sensory and nervous systems.
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
| | - Illiam S C Jackson
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
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94
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Abstract
Understanding the evolution of early nervous systems is hazardous because we lack good criteria for determining homology between the systems of distant taxa; the timing of the evolutionary events is contested, and thus the relevant ecological and geological settings for them are also unclear. Here I argue that no simple approach will resolve the first issue, but that it remains likely that animals evolved relatively late, and that their nervous systems thus arose during the late Ediacaran, in a context provided by the changing planktonic and benthic environments of the time. The early trace fossil provides the most concrete evidence for early behavioural diversification, but it cannot simply be translated into increasing nervous system complexity: behavioural complexity does not map on a one-to-one basis onto nervous system complexity, both because of possible limitations to behaviour caused by the environment and because we know that even organisms without nervous systems are capable of relatively complex behaviour.
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
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95
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Abstract
An analysis of Hox genes reveals that the body of the adorably weird tardigrades is essentially a truncated front end. This illustrates that loss and simplification are a hallmark of the evolution of animal body plans.
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96
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Chou HC, Pruitt MM, Bastin BR, Schneider SQ. A transcriptional blueprint for a spiral-cleaving embryo. BMC Genomics 2016; 17:552. [PMID: 27496340 PMCID: PMC4974748 DOI: 10.1186/s12864-016-2860-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/29/2016] [Indexed: 01/29/2023] Open
Abstract
Background The spiral cleavage mode of early development is utilized in over one-third of all animal phyla and generates embryonic cells of different size, position, and fate through a conserved set of stereotypic and invariant asymmetric cell divisions. Despite the widespread use of spiral cleavage, regulatory and molecular features for any spiral-cleaving embryo are largely uncharted. To address this gap we use RNA-sequencing on the spiralian model Platynereis dumerilii to capture and quantify the first complete genome-wide transcriptional landscape of early spiral cleavage. Results RNA-sequencing datasets from seven stages in early Platynereis development, from the zygote to the protrochophore, are described here including the de novo assembly and annotation of ~17,200 Platynereis genes. Depth and quality of the RNA-sequencing datasets allow the identification of the temporal onset and level of transcription for each annotated gene, even if the expression is restricted to a single cell. Over 4000 transcripts are maternally contributed and cleared by the end of the early spiral cleavage phase. Small early waves of zygotic expression are followed by major waves of thousands of genes, demarcating the maternal to zygotic transition shortly after the completion of spiral cleavages in this annelid species. Conclusions Our comprehensive stage-specific transcriptional analysis of early embryonic stages in Platynereis elucidates the regulatory genome during early spiral embryogenesis and defines the maternal to zygotic transition in Platynereis embryos. This transcriptome assembly provides the first systems-level view of the transcriptional and regulatory landscape for a spiral-cleaving embryo. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2860-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hsien-Chao Chou
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.,Present Address: National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Margaret M Pruitt
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.,Present Address: Department of Pediatrics, University of Chicago, Chicago, IL, USA
| | - Benjamin R Bastin
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA
| | - Stephan Q Schneider
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.
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97
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Milutinović B, Kurtz J. Immune memory in invertebrates. Semin Immunol 2016; 28:328-42. [PMID: 27402055 DOI: 10.1016/j.smim.2016.05.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 12/21/2022]
Abstract
Evidence for innate immune memory (or 'priming') in invertebrates has been accumulating over the last years. We here provide an in-depth review of the current state of evidence for immune memory in invertebrates, and in particular take a phylogenetic viewpoint. Invertebrates are a very heterogeneous group of animals and accordingly, evidence for the phenomenon of immune memory as well as the hypothesized molecular underpinnings differ largely for the diverse invertebrate taxa. The majority of research currently focuses on Arthropods, while evidence from many other groups of invertebrates is fragmentary or even lacking. We here concentrate on immune memory that is induced by pathogenic challenges, but also extent our view to a non-pathogenic context, i.e. allograft rejection, which can also show forms of memory and can inform us about general principles of specific self-nonself recognition. We discuss definitions of immune memory and a number of relevant aspects such as the type of antigens used, the route of exposure, and the kinetics of reactions following priming.
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Affiliation(s)
- Barbara Milutinović
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany.
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98
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Leclère L, Bause M, Sinigaglia C, Steger J, Rentzsch F. Development of the aboral domain in Nematostella requires β-catenin and the opposing activities of Six3/6 and Frizzled5/8. Development 2016; 143:1766-77. [PMID: 26989171 PMCID: PMC4874479 DOI: 10.1242/dev.120931] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/08/2016] [Indexed: 01/25/2023]
Abstract
The development of the oral pole in cnidarians and the posterior pole in bilaterians is regulated by canonical Wnt signaling, whereas a set of transcription factors, including Six3/6 and FoxQ2, controls aboral development in cnidarians and anterior identity in bilaterians. However, it is poorly understood how these two patterning systems are initially set up in order to generate correct patterning along the primary body axis. Investigating the early steps of aboral pole formation in the sea anemone Nematostella vectensis, we found that, at blastula stage, oral genes are expressed before aboral genes and that Nvβ-catenin regulates both oral and aboral development. In the oral hemisphere, Nvβ-catenin specifies all subdomains except the oral-most, NvSnailA-expressing domain, which is expanded upon Nvβ-catenin knockdown. In addition, Nvβ-catenin establishes the aboral patterning system by promoting the expression of NvSix3/6 at the aboral pole and suppressing the Wnt receptor NvFrizzled5/8 at the oral pole. NvFrizzled5/8 expression thereby gets restricted to the aboral domain. At gastrula stage, NvSix3/6 and NvFrizzled5/8 are both expressed in the aboral domain, but they have opposing activities, with NvSix3/6 maintaining and NvFrizzled5/8 restricting the size of the aboral domain. At planula stage, NvFrizzled5/8 is required for patterning within the aboral domain and for regulating the size of the apical organ by modulation of a previously characterized FGF feedback loop. Our findings suggest conserved roles for Six3/6 and Frizzled5/8 in aboral/anterior development and reveal key functions for Nvβ-catenin in the patterning of the entire oral-aboral axis of Nematostella.
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Affiliation(s)
- Lucas Leclère
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, Bergen 5008, Norway Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 181 chemin du Lazaret, Villefranche-sur-mer 06230, France
| | - Markus Bause
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, Bergen 5008, Norway
| | - Chiara Sinigaglia
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, Bergen 5008, Norway
| | - Julia Steger
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, Bergen 5008, Norway
| | - Fabian Rentzsch
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, Bergen 5008, Norway
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99
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Rouse GW, Wilson NG, Carvajal JI, Vrijenhoek RC. New deep-sea species of Xenoturbella and the position of Xenacoelomorpha. Nature 2016; 530:94-7. [PMID: 26842060 DOI: 10.1038/nature16545] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022]
Abstract
The discovery of four new Xenoturbella species from deep waters of the eastern Pacific Ocean is reported here. The genus and two nominal species were described from the west coast of Sweden, but their taxonomic placement remains unstable. Limited evidence placed Xenoturbella with molluscs, but the tissues can be contaminated with prey. They were then considered deuterostomes. Further taxon sampling and analysis have grouped Xenoturbella with acoelomorphs (=Xenacoelomorpha) as sister to all other Bilateria (=Nephrozoa), or placed Xenacoelomorpha inside Deuterostomia with Ambulacraria (Hemichordata + Echinodermata). Here we describe four new species of Xenoturbella and reassess those hypotheses. A large species (>20 cm long) was found at cold-water hydrocarbon seeps at 2,890 m depth in Monterey Canyon and at 1,722 m in the Gulf of California (Mexico). A second large species (~10 cm long) also occurred at 1,722 m in the Gulf of California. The third large species (~15 cm long) was found at ~3,700 m depth near a newly discovered carbonate-hosted hydrothermal vent in the Gulf of California. Finally, a small species (~2.5 cm long), found near a whale carcass at 631 m depth in Monterey Submarine Canyon (California), resembles the two nominal species from Sweden. Analysis of whole mitochondrial genomes places the three larger species as a sister clade to the smaller Atlantic and Pacific species. Phylogenomic analyses of transcriptomic sequences support placement of Xenacoelomorpha as sister to Nephrozoa or Protostomia.
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Affiliation(s)
- Greg W Rouse
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92037, USA
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92037, USA.,Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia.,School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jose I Carvajal
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92037, USA
| | - Robert C Vrijenhoek
- Monterey Bay Aquarium and Research Institute, Moss Landing, California 95039, USA
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Nishihara H, Plazzi F, Passamonti M, Okada N. MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals. Genome Biol Evol 2016; 8:528-39. [PMID: 26872770 PMCID: PMC4824008 DOI: 10.1093/gbe/evw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, DeuSINEs, and Ceph-SINEs) have been reported so far, it is expected that new SINE superfamilies would be discovered by deep exploration of new SINEs in metazoan genomes. Here we describe 15 SINEs, among which 13 are novel, that have a similar 66-bp central region and therefore constitute a new SINE superfamily, MetaSINEs. MetaSINEs are distributed from fish to cnidarians, suggesting their common evolutionary origin at least 640 Ma. Because the 3′ tails of MetaSINEs are variable, these SINEs most likely survived by changing their partner long interspersed elements for retrotransposition during evolution. Furthermore, we examined the presence of members of other SINE superfamilies in bivalve genomes and characterized eight new SINEs belonging to the CORE-SINEs, V-SINEs, and DeuSINEs, in addition to the MetaSINEs. The broad distribution of bivalve SINEs suggests that at least three SINEs originated in the common ancestor of Bivalvia. Our comparative analysis of the central domains of the SINEs revealed that, in each superfamily, only a restricted region is shared among all of its members. Because the functions of the central domains of the SINE superfamilies remain unknown, such structural information of SINE superfamilies will be useful for future experimental and comparative analyses to reveal why they have been retained in metazoan genomes during evolution.
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Affiliation(s)
- Hidenori Nishihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-Ku, Yokohama, Kanagawa, Japan
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Norihiro Okada
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan Foundation for Advancement of International Science, Tsukuba, Japan
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