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Lee H, Lee KS, Hsu CH, Lee CW, Li CE, Wang JK, Tseng CC, Chen WJ, Horng CC, Ford CT, Kroh A, Bronstein O, Tanaka H, Oji T, Lin JP, Janies D. Phylogeny, ancestral ranges and reclassification of sand dollars. Sci Rep 2023; 13:10199. [PMID: 37353534 PMCID: PMC10290142 DOI: 10.1038/s41598-023-36848-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/11/2023] [Indexed: 06/25/2023] Open
Abstract
Classification of the Class Echinoidea is under significant revision in light of emerging molecular phylogenetic evidence. In particular, the sister-group relationships within the superorder Luminacea (Echinoidea: Irregularia) have been considerably updated. However, the placement of many families remains largely unresolved due to a series of incongruent evidence obtained from morphological, paleontological, and genetic data for the majority of extant representatives. In this study, we investigated the phylogenetic relationships of 25 taxa, belonging to eleven luminacean families. We proposed three new superfamilies: Astriclypeoidea, Mellitoidea, and Taiwanasteroidea (including Dendrasteridae, Taiwanasteridae, Scutellidae, and Echinarachniidae), instead of the currently recognized superfamily Scutelloidea Gray, 1825. In light of the new data obtained from ten additional species, the historical biogeography reconstructed shows that the tropical western Pacific and eastern Indian Oceans are the cradle for early sand dollar diversification. Hothouse conditions during the late Cretaceous and early Paleogene were coupled with diversification events of major clades of sand dollars. We also demonstrate that Taiwan fauna can play a key role in terms of understanding the major Cenozoic migration and dispersal events in the evolutionary history of Luminacea.
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Affiliation(s)
- Hsin Lee
- National Museum of Marine Biology and Aquarium, Pingtung, 944401, Taiwan
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, 10617, Taiwan
| | - Kwen-Shen Lee
- Biology Department, National Museum of Natural Science, Taichung, 40453, Taiwan
| | - Chia-Hsin Hsu
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Chen-Wei Lee
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Ching-En Li
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Jia-Kang Wang
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Chien-Chia Tseng
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei, 10617, Taiwan
| | - Ching-Chang Horng
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Colby T Ford
- Tuple LLC, 2413 Commonwealth Ave, Charlotte, NC, 28205, USA
- School of Data Science, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
| | - Andreas Kroh
- Department of Geology and Palaeontology, Natural History Museum Vienna, 1010, Vienna, Austria
| | - Omri Bronstein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
- Steinhardt Museum of Natural History, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Hayate Tanaka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, 113-0033, Japan
| | - Tatsuo Oji
- University Museum, Nagoya University, Furo-cho, Nagoya, 464-8601, Japan
| | - Jih-Pai Lin
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan.
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
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Abstract
AbstractEvolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats.
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Mongiardino Koch N. Exploring adaptive landscapes across deep time: A case study using echinoid body size. Evolution 2021; 75:1567-1581. [PMID: 33782962 DOI: 10.1111/evo.14219] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/30/2022]
Abstract
Adaptive landscapes are a common way of conceptualizing the phenotypic evolution of lineages across deep time. Although multiple approaches exist to implement this concept into operational models of trait evolution, inferring adaptive landscapes from comparative datasets remains challenging. Here, I explore the macroevolutionary dynamics of echinoid body size using data from over 5000 specimens and a phylogenetic framework incorporating a dense fossil sampling and spanning approximately 270 million years. Furthermore, I implement a novel approach of exploring alternative parameterizations of adaptive landscapes that succeeds in finding simpler, yet better-fitting models. Echinoid body size has been constrained to evolve within a single adaptive optimum for much of the clade's history. However, most of the morphological disparity of echinoids was generated by multiple regime shifts that drove the repeated evolution of miniaturized and gigantic forms. Events of body size innovation occurred predominantly in the Late Cretaceous and were followed by a drastic slowdown following the Cretaceous-Paleogene mass extinction. The discovery of these patterns is contingent upon directly sampling fossil taxa. The macroevolution of echinoid body size is therefore characterized by a late increase in disparity (likely linked to an expansion of ecospace), generated by active processes driving lineages toward extreme morphologies.
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Petsios E, Portell RW, Farrar L, Tennakoon S, Grun TB, Kowalewski M, Tyler CL. An asynchronous Mesozoic marine revolution: the Cenozoic intensification of predation on echinoids. Proc Biol Sci 2021; 288:20210400. [PMID: 33784862 PMCID: PMC8059962 DOI: 10.1098/rspb.2021.0400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Predation traces found on fossilized prey remains can be used to quantify the evolutionary history of biotic interactions. Fossil mollusc shells bearing these types of traces provided key evidence for the rise of predation during the Mesozoic marine revolution (MMR), an event thought to have reorganized global marine ecosystems. However, predation pressure on prey groups other than molluscs has not been explored adequately. Consequently, the ubiquity, tempo and synchronicity of the MMR cannot be thoroughly assessed. Here, we expand the evolutionary record of biotic interactions by compiling and analysing a new comprehensively collected database on drilling predation in Meso-Cenozoic echinoids. Trends in drilling frequency reveal an Eocene rise in drilling predation that postdated echinoid infaunalization and the rise in mollusc-targeted drilling (an iconic MMR event) by approximately 100 Myr. The temporal lag between echinoid infaunalization and the rise in drilling frequencies suggests that the Eocene upsurge in predation did not elicit a coevolutionary or escalatory response. This is consistent with rarity of fossil samples that record high frequency of drilling predation and scarcity of fossil prey recording failed predation events. These results suggest that predation intensification associated with the MMR was asynchronous across marine invertebrate taxa and represented a long and complex process that consisted of multiple uncoordinated steps probably with variable coevolutionary responses.
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Affiliation(s)
- Elizabeth Petsios
- Department of Geosciences, Baylor University, One Bear Place #97354, Waco, TX 76798-7354, USA
| | - Roger W Portell
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Lyndsey Farrar
- Department of Geology and Environmental Earth Science, Miami University, 250 S. Patterson Avenue, Oxford, OH 45056, USA
| | - Shamindri Tennakoon
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Tobias B Grun
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Michal Kowalewski
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Carrie L Tyler
- Department of Geology and Environmental Earth Science, Miami University, 250 S. Patterson Avenue, Oxford, OH 45056, USA
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Perricone V, Grun TB, Marmo F, Langella C, Candia Carnevali MD. Constructional design of echinoid endoskeleton: main structural components and their potential for biomimetic applications. BIOINSPIRATION & BIOMIMETICS 2020; 16:011001. [PMID: 32927446 DOI: 10.1088/1748-3190/abb86b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
The endoskeleton of echinoderms (Deuterostomia: Echinodermata) is of mesodermal origin and consists of cells, organic components, as well as an inorganic mineral matrix. The echinoderm skeleton forms a complex lattice-system, which represents a model structure for naturally inspired engineering in terms of construction, mechanical behaviour and functional design. The sea urchin (Echinodermata: Echinoidea) endoskeleton consists of three main structural components: test, dental apparatus and accessory appendages. Although, all parts of the echinoid skeleton consist of the same basic material, their microstructure displays a great potential in meeting several mechanical needs according to a direct and clear structure-function relationship. This versatility has allowed the echinoid skeleton to adapt to different activities such as structural support, defence, feeding, burrowing and cleaning. Although, constrained by energy and resource efficiency, many of the structures found in the echinoid skeleton are optimized in terms of functional performances. Therefore, these structures can be used as role models for bio-inspired solutions in various industrial sectors such as building constructions, robotics, biomedical and material engineering. The present review provides an overview of previous mechanical and biomimetic research on the echinoid endoskeleton, describing the current state of knowledge and providing a reference for future studies.
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Affiliation(s)
- Valentina Perricone
- Dept. of Engineering, University of Campania Luigi Vanvitelli, Aversa, Italy
| | - Tobias B Grun
- Dept. of Invertebrate Paleontology, University of Florida, Florida Museum, Gainesville, Florida, United States of America
| | - Francesco Marmo
- Dept. of Structures for Engineering and Architecture, University of Naples Federico II, Napoli, Italy
| | - Carla Langella
- Dept. of Architecture and Industrial Design, University of Campania Luigi Vanvitelli, Aversa, Italy
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Erwin DH. A conceptual framework of evolutionary novelty and innovation. Biol Rev Camb Philos Soc 2020; 96:1-15. [PMID: 32869437 DOI: 10.1111/brv.12643] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/31/2020] [Accepted: 08/12/2020] [Indexed: 12/20/2022]
Abstract
Since 1990 the recognition of deep homologies among metazoan developmental processes and the spread of more mechanistic approaches to developmental biology have led to a resurgence of interest in evolutionary novelty and innovation. Other evolutionary biologists have proposed central roles for behaviour and phenotypic plasticity in generating the conditions for the construction of novel morphologies, or invoked the accessibility of new regions of vast sequence spaces. These approaches contrast with more traditional emphasis on the exploitation of ecological opportunities as the primary source of novelty. This definitional cornucopia reflects differing stress placed on three attributes of novelties: their radical nature, the generation of new taxa, and ecological and evolutionary impact. Such different emphasis has led to conflating four distinct issues: the origin of novel attributes (genes, developmental processes, phenotypic characters), new functions, higher clades and the ecological impact of new structures and functions. Here I distinguish novelty (the origin of new characters, deep character transformations, or new combinations) from innovation, the ecological and evolutionary success of clades. Evidence from the fossil record of macroevolutionary lags between the origin of a novelty and its ecological success demonstrates that novelty may be decoupled from innovation, and only definitions of novelty based on radicality (rather than generativity or consequentiality) can be assessed without reference to the subsequent history of the clade to which a novelty belongs. These considerations suggest a conceptual framework for novelty and innovation, involving: (i) generation of the potential for novelty; (ii) the formation of novel attributes; (iii) refinement of novelties through adaptation; (iv) exploitation of novelties by a clade, which may coincide with a new round of ecological or environmental potentiation; followed by (v) the establishment of innovations through ecological processes. This framework recognizes that there is little empirical support for either the dominance of ecological opportunity, nor abrupt discontinuities (often caricatured as 'hopeful monsters'). This general framework may be extended to aspects of cultural and social innovation.
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Affiliation(s)
- Douglas H Erwin
- Department of Paleobiology, MRC-121 National Museum of Natural History, PO Box 37012, Washington, DC, 20013-7012, U.S.A.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, U.S.A
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Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12040164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.
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Souto C, Mooi R, Martins L, Menegola C, Marshall CR. Homoplasy and extinction: the phylogeny of cassidulid echinoids (Echinodermata). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abstract
Inclusion of fossils can be crucial to address evolutionary questions, because their unique morphology, often drastically modified in recent species, can improve phylogenetic resolution. We performed a cladistic analysis of 45 cassidulids with 98 characters, which resulted in 24 most parsimonious trees. The strict consensus recovers three major cassiduloid clades, and the monophyly of the family Cassidulidae is not supported. Ancillary analyses to determine the sensitivity of the phylogeny to missing data do not result in significantly different topologies. The taxonomic implications of these results, including the description of a new cassiduloid family and the evolution of some morphological features, are discussed. Cassiduloids (as defined here) most probably originated in the Early Cretaceous, and their evolutionary history has been dominated by high levels of homoplasy and a dearth of unique, novel traits. Despite their high diversity during the Palaeogene, there are only seven extant cassiduloid species, and three of these are relicts of lineages dating back to the Eocene. Future studies of the biology of these poorly known species, some of which brood their young, will yield further insights into the evolutionary history of this group.
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Affiliation(s)
- Camilla Souto
- Department of Integrative Biology and University of California Museum of Paleontology, University of California, Berkeley, CA, USA
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, USA
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Av. Barão de Jeremoabo s/n, Campus Universitário, Ondina, Salvador, BA, Brazil
| | - Rich Mooi
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, USA
| | - Luciana Martins
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Av. Barão de Jeremoabo s/n, Campus Universitário, Ondina, Salvador, BA, Brazil
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carla Menegola
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Av. Barão de Jeremoabo s/n, Campus Universitário, Ondina, Salvador, BA, Brazil
- Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Universidade Federal do Rio Grande do Sul, Campus Litoral Norte, Imbé, RS, Brazil
| | - Charles R Marshall
- Department of Integrative Biology and University of California Museum of Paleontology, University of California, Berkeley, CA, USA
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Mongiardino Koch N, Coppard SE, Lessios HA, Briggs DEG, Mooi R, Rouse GW. A phylogenomic resolution of the sea urchin tree of life. BMC Evol Biol 2018; 18:189. [PMID: 30545284 PMCID: PMC6293586 DOI: 10.1186/s12862-018-1300-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 11/19/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved. RESULTS We performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We show that phylogenetic signal for novel resolutions of these lineages is strong and distributed throughout the genome, and fail to recover systematic biases as drivers of our results. CONCLUSIONS Our investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.
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Affiliation(s)
| | - Simon E. Coppard
- Department of Biology, Hamilton College, Clinton, NY USA
- Smithsonian Tropical Research Institute, Balboa, Panama
| | | | - Derek E. G. Briggs
- Department of Geology and Geophysics, Yale University, New Haven, CT USA
- Peabody Museum of Natural History, Yale University, New Haven, CT USA
| | - Rich Mooi
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, CA USA
| | - Greg W. Rouse
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA USA
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Boivin S, Saucède T, Laffont R, Steimetz E, Neige P. Correction: Diversification rates indicate an early role of adaptive radiations at the origin of modern echinoid fauna. PLoS One 2018; 13:e0196375. [PMID: 29672645 PMCID: PMC5908174 DOI: 10.1371/journal.pone.0196375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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