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Kobayashi G. Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA). PeerJ 2023; 11:e16446. [PMID: 38047014 PMCID: PMC10693233 DOI: 10.7717/peerj.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/21/2023] [Indexed: 12/05/2023] Open
Abstract
Background The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA. Methods The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank. Results and Discussion mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.
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Affiliation(s)
- Genki Kobayashi
- Research Center for Creative Partnerships, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
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2
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Zhong S, Ma X, Jiang Y, Qiao Y, Zhao L, Huang L, Huang G, Zhao Y, Liu Y, Chen X. The Draft Genome of Chinese Endemic Species Phascolosoma esculenta (Sipuncula, Phascolosomatidae) Reveals the Phylogenetic Position of Sipuncula. Front Genet 2022; 13:910344. [PMID: 35937983 PMCID: PMC9354978 DOI: 10.3389/fgene.2022.910344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shengping Zhong
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Yan Jiang
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Longyan Zhao
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Lianghua Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
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3
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de la Fuente M, Novo M. Understanding Diversity, Evolution, and Structure of Small Heat Shock Proteins in Annelida Through in Silico Analyses. Front Physiol 2022; 13:817272. [PMID: 35530508 PMCID: PMC9075518 DOI: 10.3389/fphys.2022.817272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/22/2022] [Indexed: 12/04/2022] Open
Abstract
Small heat shock proteins (sHsps) are oligomeric stress proteins characterized by an α-crystallin domain (ACD). These proteins are localized in different subcellular compartments and play critical roles in the stress physiology of tissues, organs, and whole multicellular eukaryotes. They are ubiquitous proteins found in all living organisms, from bacteria to mammals, but they have never been studied in annelids. Here, a data set of 23 species spanning the annelid tree of life, including mostly transcriptomes but also two genomes, was interrogated and 228 novel putative sHsps were identified and manually curated. The analysis revealed very high protein diversity and showed that a significant number of sHsps have a particular dimeric architecture consisting of two tandemly repeated ACDs. The phylogenetic analysis distinguished three main clusters, two of them containing both monomeric sHsps, and ACDs located downstream in the dimeric sHsps, and the other one comprising the upstream ACDs from those dimeric forms. Our results support an evolutionary history of these proteins based on duplication events prior to the Spiralia split. Monomeric sHsps 76) were further divided into five subclusters. Physicochemical properties, subcellular location predictions, and sequence conservation analyses provided insights into the differentiating elements of these putative functional groups. Strikingly, three of those subclusters included sHsps with features typical of metazoans, while the other two presented characteristics resembling non-metazoan proteins. This study provides a solid background for further research on the diversity, evolution, and function in the family of the sHsps. The characterized annelid sHsps are disclosed as essential for improving our understanding of this important family of proteins and their pleotropic functions. The features and the great diversity of annelid sHsps position them as potential powerful molecular biomarkers of environmental stress for acting as prognostic tool in a diverse range of environments.
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Affiliation(s)
- Mercedes de la Fuente
- Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), Las Rozas, Spain
- *Correspondence: Mercedes de la Fuente,
| | - Marta Novo
- Faculty of Biology, Biodiversity, Ecology and Evolution Department, Complutense University of Madrid, Madrid, Spain
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4
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Gunton LM, Kupriyanova EK, Alvestad T, Avery L, Blake JA, Biriukova O, Böggemann M, Borisova P, Budaeva N, Burghardt I, Capa M, Georgieva MN, Glasby CJ, Hsueh PW, Hutchings P, Jimi N, Kongsrud JA, Langeneck J, Meißner K, Murray A, Nikolic M, Paxton H, Ramos D, Schulze A, Sobczyk R, Watson C, Wiklund H, Wilson RS, Zhadan A, Zhang J. Annelids of the eastern Australian abyss collected by the 2017 RV 'Investigator' voyage. Zookeys 2021; 1020:1-198. [PMID: 33708002 PMCID: PMC7930015 DOI: 10.3897/zookeys.1020.57921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/01/2020] [Indexed: 01/18/2023] Open
Abstract
In Australia, the deep-water (bathyal and abyssal) benthic invertebrate fauna is poorly known in comparison with that of shallow (subtidal and shelf) habitats. Benthic fauna from the deep eastern Australian margin was sampled systematically for the first time during 2017 RV 'Investigator' voyage 'Sampling the Abyss'. Box core, Brenke sledge, and beam trawl samples were collected at one-degree intervals from Tasmania, 42°S, to southern Queensland, 24°S, from 900 to 4800 m depth. Annelids collected were identified by taxonomic experts on individual families around the world. A complete list of all identified species is presented, accompanied with brief morphological diagnoses, taxonomic remarks, and colour images. A total of more than 6000 annelid specimens consisting of 50 families (47 Polychaeta, one Echiura, two Sipuncula) and 214 species were recovered. Twenty-seven species were given valid names, 45 were assigned the qualifier cf., 87 the qualifier sp., and 55 species were considered new to science. Geographical ranges of 16 morphospecies extended along the eastern Australian margin to the Great Australian Bight, South Australia; however, these ranges need to be confirmed with genetic data. This work providing critical baseline biodiversity data on an important group of benthic invertebrates from a virtually unknown region of the world's ocean will act as a springboard for future taxonomic and biogeographic studies in the area.
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Affiliation(s)
| | - Elena K. Kupriyanova
- Australian Museum Research Institute, Sydney, Australia
- Macquarie University, Sydney, Australia
| | - Tom Alvestad
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | | | - James A. Blake
- Aquatic Research & Consulting, Duxbury, Massachusetts, USA
| | - Olga Biriukova
- Museum and Art Gallery of the Northern Territory, Darwin, Australia
| | | | - Polina Borisova
- P.P. Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya Budaeva
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
- P.P. Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | | | - Maria Capa
- Department of Biology, University of the Balearic Islands, Palma, Spain
| | | | | | - Pan-Wen Hsueh
- Department of Life Sciences, National Chung Hsing University, Taichung City, China
| | - Pat Hutchings
- Australian Museum Research Institute, Sydney, Australia
- Macquarie University, Sydney, Australia
| | - Naoto Jimi
- National Institute of Polar Research, Tachikawa, Tokyo, Japan
| | - Jon A. Kongsrud
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | | | - Karin Meißner
- Forschungsinstitut Senckenberg, DZMB, Hamburg, Germany
| | - Anna Murray
- Australian Museum Research Institute, Sydney, Australia
| | | | - Hannelore Paxton
- Australian Museum Research Institute, Sydney, Australia
- Macquarie University, Sydney, Australia
| | | | - Anja Schulze
- Texas A&M University at Galveston, Galveston, TX, USA
| | - Robert Sobczyk
- Department of Zoology of Invertebrates and Hydrobiology, University of Lodz, Lodz, Poland
| | - Charlotte Watson
- Museum and Art Gallery of the Northern Territory, Darwin, Australia
| | - Helena Wiklund
- Natural History Museum, London, UK
- Gothenburg Global Biodiversity Centre and University of Gothenburg, Gothenburg, Sweden
| | | | - Anna Zhadan
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Jinghuai Zhang
- South China Sea Environmental Monitoring Centre, State Oceanic Administration, Guangzhou, China
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Abstract
Sipuncula, long considered a separate phylum, are now commonly included in the Annelida based on phylogenomic analyses. The sipunculan body consists of an unsegmented trunk and a retractable introvert, usually with a set of tentacles at its anterior end. Unlike other annelids, they have no chaetae, but the introvert is often adorned with proteinaceous hooks that can be important taxonomic characters. Other external taxonomic characters include the tentacles (number, shape and arrangement), body papillae and, in some cases, hardened shields, as well as length ratios. Many species require dissection for correct identification to reveal internal characteristics, such as introvert retractor muscles, nephridia and contractile vessels. Here we summarize the state of the current knowledge of species diversity in sipunculans. We emphasize molecular studies, conducted over the past two decades, that have revealed multiple complexes of cryptic or pseudocryptic species. It has become obvious that diversity is significantly higher than the current taxonomic scheme accounts for, but formal species descriptions are lagging behind. Although the major branches in the sipunculan phylogeny have become increasingly consolidated, the internal relationships within most branches are still in flux.
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Zhong S, Huang L, Liu Y, Huang G, Chen X. The complete mitochondrial genome of Phascolosoma scolops (Sipuncula, Phascolosomatidae) from Beibu Bay. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1756954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Shengping Zhong
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Lianghua Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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7
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Analyzing drivers of speciation in the Southern Ocean using the sea spider species complex Colossendeis megalonyx as a test case. Polar Biol 2020. [DOI: 10.1007/s00300-020-02636-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractColossendeis megalonyx Hoek, 1881 has the broadest distribution of all sea spiders in the Southern Ocean. Previous studies have detected several evolutionarily young lineages within this taxon and interpreted them as a result of allopatric speciation in a few shelf refuges during glacial maxima. However, alternative scenarios such as ecological speciation in sympatry have rarely been considered or tested. Here, we generated the most extensive genomic and morphometric data set on the C. megalonyx species complex to (i) comprehensively describe species diversity, (ii) explore intraspecific connectivity between populations located around Antarctica, and (iii) systematically test for positive selection indicative of adaptive speciation. We successfully applied a target hybrid enrichment approach and recovered all 1607 genes targeted. Phylogenomic analysis was consistent with previous findings and, moreover, increased the resolution of branching within lineages. We found specimens of phylogenetically well-separated lineages occurring in sympatry to be genetically distinct from each other and gene flow between geographically separated populations of the same lineages to be restricted. Evidence for positive selection was found for four genes associated with structural and neuronal functions. Hence, there is an indication for positive selection in the C. megalonyx species complex, yet its specific contribution to the speciation process remains to be explored further. Finally, morphometric analyses revealed multiple significant differences between lineages, but a clear separation proved difficult. Our study highlights the relevance of positive selection as a potential driver for speciation in the Southern Ocean.
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8
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Zhong S, Huang L, Liu Y, Huang G, Chen X. The first complete mitochondrial genome of Siphonosoma from Siphonosoma cumanense (Sipuncula, Sipunculidae). Mitochondrial DNA B Resour 2020; 5:957-958. [PMID: 33366825 PMCID: PMC7748483 DOI: 10.1080/23802359.2020.1721364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Siphonosoma cumanense is economic important species in the fishery of southeast China. However, the current classification and the phylogeny of genus Siphonosoma had not been verified yet. Here, we report the complete mitochondrial genome sequence of S. Siphonosoma. The mitogenome has 15,917 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study was the first available complete mitogenomes of Siphonosoma and will provide useful genetic information for future phylogenetic and taxonomic classification of Sipuncula.
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Affiliation(s)
- Shengping Zhong
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China.,Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Lianghua Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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9
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Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing. Mol Phylogenet Evol 2020; 146:106737. [PMID: 31982455 DOI: 10.1016/j.ympev.2020.106737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 01/27/2023]
Abstract
Allium L. is one of the largest monocotyledonous genera with extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. The branch-site model (BSM) was conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flowers-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various stresses and stimuli (e.g. hypoxia, low temperature, aridity), DNA repair, metabolism, nutrient or energy intake, photosynthesis, and signal transduction. Our study revealed a clear interspecies relationship of Chinese endemics in Allium section Daghestanica and suggested that the discordance between morphological characters and molecular relationships might result from that the former are more susceptible to convergence compared with the latter. PSGs detected in our study may provide some insights into highland adaptation in Allium species.
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Gough HM, Allen JM, Toussaint EFA, Storer CG, Kawahara AY. Transcriptomics illuminate the phylogenetic backbone of tiger beetles. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz195] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Phylogenomics is progressing rapidly, allowing large strides forward into our understanding of the tree of life. In this study, we generated transcriptomes from ethanol-preserved specimens of 13 tiger beetle species (Coleoptera: Cicindelinae) and one Scaritinae outgroup. From these 14 transcriptomes and seven publicly available transcriptomes, we recovered an average of 2538 loci for phylogenetic analysis. We constructed an evolutionary tree of tiger beetles to examine deep-level relationships and examined the extent to which the composition of the dataset, missing data, gene tree inconsistency and codon position saturation impacted phylogenetic accuracy. Ethanol-preserved specimens yielded similar numbers of loci to specimens originally preserved in costly reagents, showcasing more flexibility in transcriptomics than anticipated. The number of loci and gene tree inconsistency had less impact on downstream results than third codon position saturation and missing data. Our results recovered tiger beetles as sister to Carabidae with strong support, confirming their taxonomic status as an independent family within Adephaga. Within tiger beetles, phylogenetic relationships were robust across all nodes. This new phylogenomic backbone represents a useful framework for future endeavours in tiger beetle systematics and serves as a starting point for the development of less costly target capture toolkits to expand the taxonomic breadth of the future tiger beetle tree of life.
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Affiliation(s)
- Harlan M Gough
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Julie M Allen
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | | | - Caroline G Storer
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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11
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Miller SW, Movsesyan A, Zhang S, Fernández R, Posakony JW. Evolutionary emergence of Hairless as a novel component of the Notch signaling pathway. eLife 2019; 8:48115. [PMID: 31545167 PMCID: PMC6777938 DOI: 10.7554/elife.48115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/23/2019] [Indexed: 11/30/2022] Open
Abstract
Suppressor of Hairless [Su(H)], the transcription factor at the end of the Notch pathway in Drosophila, utilizes the Hairless protein to recruit two co-repressors, Groucho (Gro) and C-terminal Binding Protein (CtBP), indirectly. Hairless is present only in the Pancrustacea, raising the question of how Su(H) in other protostomes gains repressive function. We show that Su(H) from a wide array of arthropods, molluscs, and annelids includes motifs that directly bind Gro and CtBP; thus, direct co-repressor recruitment is ancestral in the protostomes. How did Hairless come to replace this ancestral paradigm? Our discovery of a protein (S-CAP) in Myriapods and Chelicerates that contains a motif similar to the Su(H)-binding domain in Hairless has revealed a likely evolutionary connection between Hairless and Metastasis-associated (MTA) protein, a component of the NuRD complex. Sequence comparison and widely conserved microsynteny suggest that S-CAP and Hairless arose from a tandem duplication of an ancestral MTA gene.
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Affiliation(s)
- Steven W Miller
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Artem Movsesyan
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Sui Zhang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Center for Genomic Regulation, Barcelona, Spain
| | - James W Posakony
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States
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12
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Parks MB, Wickett NJ, Alverson AJ. Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta). Mol Biol Evol 2019; 35:80-93. [PMID: 29040712 PMCID: PMC5850769 DOI: 10.1093/molbev/msx268] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available.
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Affiliation(s)
- Matthew B Parks
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL
| | - Norman J Wickett
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR
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13
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Zhao Y, Zhang Q, Zhong S. The complete mitochondrial genome of Chinese endemic specie Phascolosoma esculenta (Sipuncula, Phascolosomatidae) from Beibu Bay. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1547169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yanfei Zhao
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Qin Zhang
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Shengping Zhong
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
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14
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Phylogeny and evolutionary history of Pinaceae updated by transcriptomic analysis. Mol Phylogenet Evol 2018; 129:106-116. [DOI: 10.1016/j.ympev.2018.08.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/21/2018] [Accepted: 08/20/2018] [Indexed: 11/19/2022]
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15
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Zhong S, Zhao Y, Zhang Q, Chen X. The complete mitochondrial genome of the cryptic species in peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) from Beibu Bay. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:484-485. [PMID: 33474213 PMCID: PMC7800096 DOI: 10.1080/23802359.2018.1463830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The peanut worm Sipunculus nudus is an economic important species in the fishery and aquaculture in Indo-West Pacific. However, it is a species complex consisting of cryptic species, which can be difficult to identify based on morphology. Here, we report the complete mitochondrial genome sequence of S. nudus from Beibu Bay. The mitogenome has 15,375 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs, and two ribosomal RNAs), and a putative control region. There were 5948 mutations sites between Chinese and French populations. This study adds a distinct mitogenome of S. nudus, and will provide useful genetic information for future genetic variation identification and genetic diversity evaluation of this economic valuable marine benthic invertebrate.
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Affiliation(s)
- Shengping Zhong
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Yanfei Zhao
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Qin Zhang
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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Dai W, Zou M, Yang L, Du K, Chen W, Shen Y, Mayden RL, He S. Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages. Sci Rep 2018; 8:205. [PMID: 29317769 PMCID: PMC5760653 DOI: 10.1038/s41598-017-18432-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022] Open
Abstract
The phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes. Based on a selection of 125 nuclear genes screened from single-gene maximum likelihood (ML) analyses and sequence bias testing, well-established relationships among Otocephala were reconstructed. We suggested that Gymnotiformes are more closely related to Characiformes than to Siluriformes and Characiformes are possibly paraphyletic. We also estimated that Otocephala originated in the Early-Late Jurassic, which postdates most previous estimations, and hypothesized scenarios of the early historical biogeographies of major otocephalan lineages.
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Affiliation(s)
- Wei Dai
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Ming Zou
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Beijing, 430070, People's Republic of China
| | - Liandong Yang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Kang Du
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Weitao Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Yanjun Shen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Richard L Mayden
- Department of Biology, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
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Lemer S, González VL, Bieler R, Giribet G. Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach. Proc Biol Sci 2017; 283:rspb.2016.0857. [PMID: 27358369 PMCID: PMC4936043 DOI: 10.1098/rspb.2016.0857] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/03/2016] [Indexed: 11/12/2022] Open
Abstract
Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix (Matrix 3: 51 genes, 90% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea.
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Affiliation(s)
- Sarah Lemer
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Vanessa L González
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Rüdiger Bieler
- Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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18
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Combosch DJ, Lemer S, Ward PD, Landman NH, Giribet G. Genomic signatures of evolution in Nautilus-An endangered living fossil. Mol Ecol 2017; 26:5923-5938. [PMID: 28872211 DOI: 10.1111/mec.14344] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 08/15/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022]
Abstract
Living fossils are survivors of previously more diverse lineages that originated millions of years ago and persisted with little morphological change. Therefore, living fossils are model organisms to study both long-term and ongoing adaptation and speciation processes. However, many aspects of living fossil evolution and their persistence in the modern world remain unclear. Here, we investigate three major aspects of the evolutionary history of living fossils: cryptic speciation, population genetics and effective population sizes, using members of the genera Nautilus and Allonautilus as classic examples of true living fossils. For this, we analysed genomewide ddRAD-Seq data for all six currently recognized nautiloid species throughout their distribution range. Our analyses identified three major allopatric Nautilus clades: a South Pacific clade, subdivided into three subclades with no signs of admixture between them; a Coral Sea clade, consisting of two genetically distinct populations with significant admixture; and a widespread Indo-Pacific clade, devoid of significant genetic substructure. Within these major clades, we detected five Nautilus groups, which likely correspond to five distinct species. With the exception of Nautilus macromphalus, all previously described species are at odds with genomewide data, testifying to the prevalence of cryptic species among living fossils. Detailed FST analyses further revealed significant genome-wide and locus-specific signatures of selection between species and differentiated populations, which is demonstrated here for the first time in a living fossil. Finally, approximate Bayesian computation (ABC) simulations suggest large effective population sizes, which may explain the low levels of population differentiation commonly observed in living fossils.
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Affiliation(s)
- David J Combosch
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Marine Laboratory, University of Guam, Mangilao, GU, USA
| | - Sarah Lemer
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Marine Laboratory, University of Guam, Mangilao, GU, USA
| | - Peter D Ward
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Neil H Landman
- Division of Paleontology, American Museum of Natural History, New York, NY, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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Schwentner M, Combosch DJ, Pakes Nelson J, Giribet G. A Phylogenomic Solution to the Origin of Insects by Resolving Crustacean-Hexapod Relationships. Curr Biol 2017; 27:1818-1824.e5. [DOI: 10.1016/j.cub.2017.05.040] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/10/2017] [Accepted: 05/10/2017] [Indexed: 12/11/2022]
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20
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Sung JM, Karagozlu MZ, Kim CB. Complete mitochondrial genome analysis of Phascolosoma sp. (Sipuncula, Phascolosomatida, Phascolosomatidea) from Micronesia. Mitochondrial DNA B Resour 2017; 2:264-265. [PMID: 33473793 PMCID: PMC7799974 DOI: 10.1080/23802359.2017.1325337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In this study a Sipuncula species Phascolosoma sp. was collected from seagrass area from Chuuk lagoon Micronesia and its complete mitochondrial genome analyzed. This is the second complete mitochondrial genome record from the genus after Phascolosoma esculenta. The total length of mitochondrial genome of the species is 16,571 bp, which is longer than P. esculenta record. Also, locations of tRNA-Gly and putative control region are different between two records. Furthermore, phylogenetic relationship of Phascolosoma sp. are investigated due to protein-coding genes of mitochondrial genome. Due to the lack of recorded data, P. esculenta has been observed is the closest species to Phascolosoma sp. and they are belonging to the monophyletic group.
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Affiliation(s)
- Jin-Mo Sung
- Department of Bioengineering, Sangmyung University, Seoul, Korea
| | | | - Chang-Bae Kim
- Department of Bioengineering, Sangmyung University, Seoul, Korea
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21
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Kerbl A, Fofanova EG, Mayorova TD, Voronezhskaya EE, Worsaae K. Comparison of neuromuscular development in two dinophilid species (Annelida) suggests progenetic origin of Dinophilus gyrociliatus. Front Zool 2016; 13:49. [PMID: 27833644 PMCID: PMC5101659 DOI: 10.1186/s12983-016-0181-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 10/20/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Several independent meiofaunal lineages are suggested to have originated through progenesis, however, morphological support for this heterochronous process is still lacking. Progenesis is defined as an arrest of somatic development (synchronously in various organ systems) due to early maturation, resulting in adults resembling larvae or juveniles of the ancestors. Accordingly, we established a detailed neuromuscular developmental atlas of two closely related Dinophilidae using immunohistochemistry and CLSM. This allows us to test for progenesis, questioning whether i) the adult smaller, dimorphic Dinophilus gyrociliatus resembles a younger developmental stage of the larger, monomorphic D. taeniatus and whether ii) dwarf males of D. gyrociliatus resemble an early developmental stage of D. gyrociliatus females. RESULTS Both species form longitudinal muscle bundles first, followed by circular muscles, creating a grid of body wall musculature, which is the densest in adult D. taeniatus, while the architecture in adult female D. gyrociliatus resembles that of prehatching D. taeniatus. Both species display a subepidermal ganglionated nervous system with an anterior dorsal brain and five longitudinal ventral nerve bundles with six sets of segmental commissures (associated with paired ganglia). Neural differentiation of D. taeniatus and female D. gyrociliatus commissures occurs before hatching: both species start out forming one transverse neurite bundle per segment, which are thereafter joined by additional thin bundles. Whereas D. gyrociliatus arrests its development at this stage, adult D. taeniatus condenses the thin commissures again into one thick commissural bundle per segment. Generally, D. taeniatus adults demonstrate a seemingly more organized (= segmental) pattern of serotonin-like and FMRFamide-like immunoreactive elements. The dwarf male of D. gyrociliatus displays a highly aberrant neuromuscular system, showing no close resemblance to any early developmental stage of female Dinophilus, although the onset of muscular development mirrors the early myogenesis in females. CONCLUSION The apparent synchronous arrest of nervous and muscular development in adult female D. gyrociliatus, resembling the prehatching stage of D. taeniatus, suggests that D. gyrociliatus have originated through progenesis. The synchrony in arrest of three organ systems, which show opposing reduction and addition of elements, presents one of the morphologically best-argued cases of progenesis within Spiralia.
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Affiliation(s)
- Alexandra Kerbl
- Marine Biological Section – Department of Biology, University of Copenhagen, Universitetsparken 4, 2100 Copenhagen, Denmark
| | - Elizaveta G. Fofanova
- Laboratory of Developmental Neurobiology, Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., Moscow, Russia
| | - Tatiana D. Mayorova
- Laboratory of Developmental Neurobiology, Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., Moscow, Russia
- Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, NIH, 49 Convent Dr., Bethesda, MD USA
| | - Elena E. Voronezhskaya
- Laboratory of Developmental Neurobiology, Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., Moscow, Russia
| | - Katrine Worsaae
- Marine Biological Section – Department of Biology, University of Copenhagen, Universitetsparken 4, 2100 Copenhagen, Denmark
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22
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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: 53] [Impact Index Per Article: 6.6] [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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23
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Zhang J, Gordon ERL, Forthman M, Hwang WS, Walden K, Swanson DR, Johnson KP, Meier R, Weirauch C. Evolution of the assassin's arms: insights from a phylogeny of combined transcriptomic and ribosomal DNA data (Heteroptera: Reduvioidea). Sci Rep 2016; 6:22177. [PMID: 26916580 PMCID: PMC4768186 DOI: 10.1038/srep22177] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 02/09/2016] [Indexed: 01/24/2023] Open
Abstract
Assassin bugs (Reduvioidea) are one of the most diverse (>7,000 spp.) lineages of predatory animals and have evolved an astounding diversity of raptorial leg modifications for handling prey. The evolution of these modifications is not well understood due to the lack of a robust phylogeny, especially at deeper nodes. We here utilize refined data from transcriptomes (370 loci) to stabilize the backbone phylogeny of Reduvioidea, revealing the position of major clades (e.g., the Chagas disease vectors Triatominae). Analyses combining transcriptomic and Sanger-sequencing datasets result in the first well-resolved phylogeny of Reduvioidea. Despite amounts of missing data, the transcriptomic loci resolve deeper nodes while the targeted ribosomal genes anchor taxa at shallower nodes, both with high support. This phylogeny reveals patterns of raptorial leg evolution across major leg types. Hairy attachment structures (fossula spongiosa), present in the ancestor of Reduvioidea, were lost multiple times within the clade. In contrast to prior hypotheses, this loss is not directly correlated with the evolution of alternative raptorial leg types. Our results suggest that prey type, predatory behavior, salivary toxicity, and morphological adaptations pose intricate and interrelated factors influencing the evolution of this diverse group of predators.
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Affiliation(s)
- Junxia Zhang
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Eric R. L. Gordon
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Michael Forthman
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Wei Song Hwang
- Lee Kong Chian Natural History Museum, Department of Biological Sciences, National University of Singapore, 117377, Singapore
| | - Kim Walden
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Daniel R. Swanson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Rudolf Meier
- Lee Kong Chian Natural History Museum, Department of Biological Sciences, National University of Singapore, 117377, Singapore
| | - Christiane Weirauch
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
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25
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Novo M, Fernández R, Andrade SCS, Marchán DF, Cunha L, Díaz Cosín DJ. Phylogenomic analyses of a Mediterranean earthworm family (Annelida: Hormogastridae). Mol Phylogenet Evol 2015; 94:473-478. [PMID: 26522608 DOI: 10.1016/j.ympev.2015.10.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 10/19/2015] [Accepted: 10/24/2015] [Indexed: 10/22/2022]
Abstract
Earthworm taxonomy and evolutionary biology remain a challenge because of their scarce distinct morphological characters of taxonomic value, the morphological convergence by adaptation to the uniformity of the soil where they inhabit, and their high plasticity when challenged with stressful or new environmental conditions. Here we present a phylogenomic study of the family Hormogastridae, representing also the first piece of work of this type within earthworms. We included seven transcriptomes of the group representing the main lineages as previously-described, analysed in a final matrix that includes twelve earthworms and eleven outgroups. While there is a high degree of gene conflict in the generated trees that obscure some of the internal relationships, the origin of the family is well resolved: the hormogastrid Hemigastrodrilus appears as the most ancestral group, followed by the ailoscolecid Ailoscolex, therefore rejecting the validity of the family Ailoscolecidae. Our results place the origin of hormogastrids in Southern France, as previously hypothesised.
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Affiliation(s)
- Marta Novo
- Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3AT, UK; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain.
| | - Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, IB-USP, São Paulo, CEP 05508-090, Brazil
| | - Daniel F Marchán
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain
| | - Luis Cunha
- Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3AT, UK
| | - Darío J Díaz Cosín
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain
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26
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New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0236-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Andrade SC, Novo M, Kawauchi GY, Worsaae K, Pleijel F, Giribet G, Rouse GW. Articulating “Archiannelids”: Phylogenomics and Annelid Relationships, with Emphasis on Meiofaunal Taxa. Mol Biol Evol 2015. [DOI: 10.1093/molbev/msv157] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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28
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Whelan NV, Kocot KM, Halanych KM. Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians. Integr Comp Biol 2015; 55:1084-95. [PMID: 25972566 DOI: 10.1093/icb/icv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite an explosion in the amount of sequence data, phylogenomics has failed to settle controversy regarding some critical nodes on the animal tree of life. Understanding relationships among Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera is essential for studying how complex traits such as neurons, muscles, and gastrulation have evolved. Recent studies have cast doubt on the historical viewpoint that sponges are sister to all other animal lineages with recent studies recovering ctenophores as sister. However, the ctenophore-sister hypothesis has been criticized as unrealistic and caused by systematic error. We review past phylogenomic studies and potential causes of systematic error in an effort to identify areas that can be improved in future studies. Increased sampling of taxa, less missing data, and a priori removal of sequences and taxa that may cause systematic error in phylogenomic inference will likely be the most fruitful areas of focus when assembling future datasets. Ultimately, we foresee metazoan relationships being resolved with higher support in the near future, and we caution against dismissing novel hypotheses merely because they conflict with historical viewpoints of animal evolution.
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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;
| | - Kevin M Kocot
- School of Biological Sciences, The University of Queensland, 325 Goddard Building, St Lucia, QLD 4101, Australia
| | - 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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29
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Giribet G. Morphology should not be forgotten in the era of genomics–a phylogenetic perspective. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.01.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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