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Zhao ZY, Wan J, Chen HW, Sun ZS, Tao YT, Tong Y, Zang Y, Choo YM, Wang P, Li YL, Jiang CX, Li J, Xiong J, Li J, Jin ZX, Hu JF. Major specialized natural products from the endangered plant Heptacodium miconioides, potential medicinal uses and insights into its longstanding unresolved systematic classification. PHYTOCHEMISTRY 2024; 228:114259. [PMID: 39186996 DOI: 10.1016/j.phytochem.2024.114259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/15/2024] [Accepted: 08/23/2024] [Indexed: 08/28/2024]
Abstract
A comprehensive phytochemical investigation of the flower buds and leaves/twigs of Heptacodium miconioides, a cultivated ornamental plant native to China and categorized as 'vulnerable', has led to the isolation of 45 structurally diverse compounds, which comprise 18 phenylpropanoids (1-4, 7-20), 11 pentacyclic triterpenoids (5, 6, 21-29), eight secoiridoid glycosides (30-37), three quinic acid derivatives (38-40), and a few miscellaneous components (41-45). Among them, (+)-α-intermedianol (1), (+)-holophyllol A (2), and (-)-pseudolarkaemin A (3) represent previously unreported enantiomeric lignans, while (+)-7'(R)-hydroxymatairesinol (4) is an undescribed naturally occurring lignan. Heptacoacids A (5) and B (6) are undescribed 24-nor-urs-28-oic acid derivatives. Their chemical structures were determined by 2D-NMR, supplemented by evidence from specific rotations and circular dichroism spectra. Given the uncertainty surrounding the systematic position of Heptacodium, integrative taxonomy (ITA), a method utilized to define contentious species, is applied. Chemotaxonomy, a vital aspect of ITA, becomes significant. By employing hierarchical clustering analysis (HCA) and syntenic pattern analysis methods, a taxonomic examination based on the major specialized natural products from the flower buds of H. miconioides and two other Caprifoliaceae plants (i.e., Lonicera japonica and Abelia × grandiflora) could offer enhanced understanding of the systematic placement of Heptacodium. Additionally, compounds 39 and 40 displayed remarkable inhibitory activities against ATP-citrate lyase (ACL), with IC50 values of 0.11 and 1.10 μM, respectively. In summary, the discovery of medical properties and refining systematic classification can establish a sturdy groundwork for conservation efforts aimed at mitigating species diversity loss while addressing human diseases.
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Affiliation(s)
- Ze-Yu Zhao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiang Wan
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Hao-Wei Chen
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhong-Shuai Sun
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Yu-Tian Tao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Yingpeng Tong
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yeun-Mun Choo
- Chemistry Department, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Pan Wang
- Traditional Chinese Medicine Industry Development and Promotion Center of Pan'an County & Dapanshan National Natural Reserve, Zhejiang, 322300, China
| | - Yue-Ling Li
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Chun-Xiao Jiang
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Junming Li
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ze-Xin Jin
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Jin-Feng Hu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; School of Pharmacy, Fudan University, Shanghai, 201203, China.
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Lukhtanov VA, Dantchenko AV. Cryptic Taxa Revealed through Combined Analysis of Chromosomes and DNA Barcodes: The Polyommatus ripartii Species Complex in Armenia and NW Iran. INSECTS 2024; 15:545. [PMID: 39057277 PMCID: PMC11277131 DOI: 10.3390/insects15070545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77-79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73-75), P. demavendi antonius, subsp. nov. (n = 71-73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29-34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Alexander V. Dantchenko
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
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3
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Grupstra CGB, Gómez-Corrales M, Fifer JE, Aichelman HE, Meyer-Kaiser KS, Prada C, Davies SW. Integrating cryptic diversity into coral evolution, symbiosis and conservation. Nat Ecol Evol 2024; 8:622-636. [PMID: 38351091 DOI: 10.1038/s41559-023-02319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/12/2023] [Indexed: 04/13/2024]
Abstract
Understanding how diversity evolves and is maintained is critical to predicting the future trajectories of ecosystems under climate change; however, our understanding of these processes is limited in marine systems. Corals, which engineer reef ecosystems, are critically threatened by climate change, and global efforts are underway to conserve and restore populations as attempts to mitigate ocean warming continue. Recently, sequencing efforts have uncovered widespread undescribed coral diversity, including 'cryptic lineages'-genetically distinct but morphologically similar coral taxa. Such cryptic lineages have been identified in at least 24 coral genera spanning the anthozoan phylogeny and across ocean basins. These cryptic lineages co-occur in many reef systems, but their distributions often differ among habitats. Research suggests that cryptic lineages are ecologically specialized and several examples demonstrate differences in thermal tolerance, highlighting the critical implications of this diversity for predicting coral responses to future warming. Here, we draw attention to recent discoveries, discuss how cryptic diversity affects the study of coral adaptation and acclimation to future environments, explore how it shapes symbiotic partnerships, and highlight challenges and opportunities for conservation and restoration efforts.
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Affiliation(s)
| | | | - James E Fifer
- Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA.
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4
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Morrissey D, Gordon JD, Saso E, Bilewitch JP, Taylor ML, Hayes V, McFadden CS, Quattrini AM, Allcock AL. Bamboozled! Resolving deep evolutionary nodes within the phylogeny of bamboo corals (Octocorallia: Scleralcyonacea: Keratoisididae). Mol Phylogenet Evol 2023; 188:107910. [PMID: 37640170 DOI: 10.1016/j.ympev.2023.107910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/22/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough signal to explore the relationships among groups. Using increased phylogenomic resolution generated from Ultraconserved Elements and exons (i.e. conserved elements), we aim to resolve deeper nodes within the family and investigate the relationships among those predefined groups. In total, 109 libraries of conserved elements were generated from individuals representing both the genetic and morphological diversity of our keratoisidids. In addition, the conserved element data of 12 individuals from previous studies were included. Our taxon sampling included 11 of the 12 keratoisidid groups. We present two phylogenies, constructed from a 75% (231 loci) and 50% (1729 loci) taxon occupancy matrix respectively, using both Maximum Likelihood and Multiple Species Coalescence methods. These trees were congruent at deep nodes. As expected, S1 keratoisidids were recovered as a well-supported sister clade to the rest of the bamboo corals. S1 corals do not share the same mitochondrial gene arrangement found in other members of Keratoisididae. All other bamboo corals were recovered within two major clades. Clade I comprises individuals assigned to alphanumeric groups B1, C1, D1&D2, F1, H1, I4, and J3 while Clade II contains representatives from A1, I1, and M1. By combining genomics with already published morphological data, we provide evidence that group H1 is not monophyletic, and that the division between other groups - D1 and D2, and A1 and M1 - needs to be reconsidered. Overall, there is a lack of robust morphological markers within Keratoisididae, but subtle characters such as sclerite microstructure and ornamentation seem to be shared within groups and warrant further investigation as taxonomically diagnostic characters.
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Affiliation(s)
- Declan Morrissey
- Ryan Institute & School of Natural Sciences, University of Galway, University Road, Galway, Ireland.
| | - Jessica D Gordon
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Emma Saso
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Jaret P Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA), 301 Evans Bay Parade, Wellington 6021, New Zealand
| | - Michelle L Taylor
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Vonda Hayes
- Department of Fisheries and Oceans, St. John's, Newfoundland and Labrador, Canada
| | - Catherine S McFadden
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711, USA
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - A Louise Allcock
- Ryan Institute & School of Natural Sciences, University of Galway, University Road, Galway, Ireland
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5
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Wootton LM, Forest F, Verboom GA. Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation. Syst Biol 2023; 72:753-766. [PMID: 37098166 DOI: 10.1093/sysbio/syad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/27/2023] Open
Abstract
Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study, we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single-nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus Ehrharta, whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of Ehrharta and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualizes multiple values of K. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the E. setacea and E. rehmannii complexes, with the E. ramosa complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).].
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Affiliation(s)
- Lara M Wootton
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, 7701, Rondebosch, South Africa
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, FR-38000 Grenoble, France
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - G Anthony Verboom
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, 7701, Rondebosch, South Africa
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6
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Crandall ED, Toczydlowski RH, Liggins L, Holmes AE, Ghoojaei M, Gaither MR, Wham BE, Pritt AL, Noble C, Anderson TJ, Barton RL, Berg JT, Beskid SG, Delgado A, Farrell E, Himmelsbach N, Queeno SR, Trinh T, Weyand C, Bentley A, Deck J, Riginos C, Bradburd GS, Toonen RJ. Importance of timely metadata curation to the global surveillance of genetic diversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14061. [PMID: 36704891 PMCID: PMC10751740 DOI: 10.1111/cobi.14061] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 01/07/2023] [Indexed: 05/18/2023]
Abstract
Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.
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Affiliation(s)
- Eric D Crandall
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rachel H Toczydlowski
- Ecology, Evolution, and Behavior Program, Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Ann E Holmes
- Department of Animal Science, University of California, Davis, Davis, California, USA
| | - Maryam Ghoojaei
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Michelle R Gaither
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Briana E Wham
- Department of Research Informatics and Publishing, The Pennsylvania State University Libraries, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrea L Pritt
- Madlyn L. Hanes Library, The Pennsylvania State University Libraries, Pennsylvania State University, Middletown, Pennsylvania, USA
| | - Cory Noble
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Tanner J Anderson
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Randi L Barton
- Department of Marine Science, California State University Monterey Bay, Seaside, California, USA
- Moss Landing Marine Laboratories, Moss Landing, California, USA
| | - Justin T Berg
- UOG Marine Laboratory, University of Guam, Mangilao, Guam
| | - Sofia G Beskid
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Alonso Delgado
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Emily Farrell
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Nan Himmelsbach
- Department of Natural Science, Hawai'i Pacific University, Honolulu, Hawaii, USA
| | - Samantha R Queeno
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Thienthanh Trinh
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Courtney Weyand
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Andrew Bentley
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
| | - John Deck
- Berkeley Natural History Museums, University of California, Berkeley, Berkeley, California, USA
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Gideon S Bradburd
- Ecology, Evolution, and Behavior Program, Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, Hawaii, USA
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7
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Gijsbers JC, Englebert N, Prata KE, Pichon M, Dinesen Z, Brunner R, Eyal G, González-Zapata FL, Kahng SE, Latijnhouwers KRW, Muir P, Radice VZ, Sánchez JA, Vermeij MJA, Hoegh-Guldberg O, Jacobs SJ, Bongaerts P. Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths. BMC Biol 2023; 21:147. [PMID: 37365558 DOI: 10.1186/s12915-023-01630-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. RESULTS Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods. CONCLUSIONS The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.
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Affiliation(s)
- J C Gijsbers
- California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - N Englebert
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - K E Prata
- California Academy of Sciences, San Francisco, CA, 94118, USA
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - M Pichon
- Biodiversity Section, Queensland Museum, Townsville, 4810, Australia
| | - Z Dinesen
- Centre for Biodiversity and Conservation Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - R Brunner
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - G Eyal
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD, 4072, Australia
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - F L González-Zapata
- Laboratorio de Biología Molecular Marina (BIOMMAR), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, 111711, Bogotá, Colombia
| | - S E Kahng
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, HI, 96822, USA
| | - K R W Latijnhouwers
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH, Amsterdam, The Netherlands
| | - P Muir
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - V Z Radice
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, USA
| | - J A Sánchez
- Laboratorio de Biología Molecular Marina (BIOMMAR), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, 111711, Bogotá, Colombia
| | - M J A Vermeij
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH, Amsterdam, The Netherlands
| | - O Hoegh-Guldberg
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - S J Jacobs
- California Academy of Sciences, San Francisco, CA, 94118, USA
| | - P Bongaerts
- California Academy of Sciences, San Francisco, CA, 94118, USA.
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia.
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao.
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8
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Quattrini AM, Snyder KE, Purow-Ruderman R, Seiblitz IGL, Hoang J, Floerke N, Ramos NI, Wirshing HH, Rodriguez E, McFadden CS. Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes. Sci Rep 2023; 13:7443. [PMID: 37156831 PMCID: PMC10167242 DOI: 10.1038/s41598-023-34059-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.
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Affiliation(s)
- Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA.
| | - Karen E Snyder
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | | | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, São Sebastião, 11612-109, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Johnson Hoang
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Natasha Floerke
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Nina I Ramos
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Herman H Wirshing
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Estefanía Rodriguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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9
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Li C, Xiao H, Zhang X, Lin H, Elmer KR, Zhao J. Deep genome-wide divergences among species in White Cloud Mountain minnow Tanichthys albonubes (Cypriniformes: Tanichthyidae) complex: Conservation and species management implications. Mol Phylogenet Evol 2023; 182:107734. [PMID: 36804428 DOI: 10.1016/j.ympev.2023.107734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Identifying cryptic species is important for the assessments of biodiversity. Further, untangling mechanisms underlying the origins of cryptic species can facilitate our understanding of evolutionary processes. Advancements in genomic approaches for non-model systems have offered unprecedented opportunities to investigate these areas. The White Cloud Mountain minnow (Tanichthys albonubes) is a popular freshwater pet fish worldwide but its wild populations in China are critically endangered. Recent research based on a few molecular markers suggested that this species in fact comprised seven cryptic species, of which six were previously unknown. Here, we tested six of these cryptic species and quantified genomic interspecific divergences between species in the T. albonubes complex by analyzing genome-wide restriction site-associated DNA sequencing (RADseq) data generated from 189 individuals sampled from seven populations (including an outgroup congeneric species, T. micagemmae). We found that six cryptic species previously suggested were well supported by RADseq data. The genetic diversity of each species in the T. albonubes complex was low compared with T. micagemmae and the contemporary effective population sizes (Ne) of each cryptic species were small. Phylogenetic analysis showed seven clades with high support values confirmed with Neighbor-Net trees. The pairwise divergences between species in T. albonubes complex were deep and the highly differentiated loci were evenly distributed across the genome. We proposed that the divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Our findings provide new insights into cryptic speciation and have important implications for conservation and species management of T. albonubes complex.
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Affiliation(s)
- Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Han Xiao
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Xiuxia Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China.
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10
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Yi H, Dong S, Yang L, Wang J, Kidner C, Kang M. Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns. Mol Phylogenet Evol 2023; 184:107801. [PMID: 37088242 DOI: 10.1016/j.ympev.2023.107801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023]
Abstract
Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.
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Affiliation(s)
- Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Shiying Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Catherine Kidner
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK; Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China.
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11
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Kessel GM, Alderslade P, Bilewitch JP, Schnabel KE, Gardner JPA. The use of integrative taxonomy in Octocorallia (Cnidaria: Anthozoa): a literature survey. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abstract
Octocorals are problematic in their systematics, and the extent of their biodiversity is poorly understood. Integrative taxonomy (the use of two or more lines of evidence for the delimitation and description of taxa) is seen as a promising way to produce more robust species hypotheses and achieve taxonomic progress in this group. However, many octocoral descriptions continue to rely on morphological evidence alone, and the prevalence of integrative methods is unclear. Here, a literature survey was conducted to gain an overview of historical description rates and to examine trends in the publication of integrative descriptions between the years 2000 and 2020. We find that recent description rates are among the highest in the history of octocoral taxonomy, and although increasing, integrative taxon descriptions remain in the minority overall. We also find that integrative taxonomy has been applied unevenly across octocoral groups and geographical regions. Description rates show no signs of slowing, and no ceiling of total species richness has yet come into view. Coupled with a continued overreliance on morphological variation, particularly at the species level, this suggests that we might be adding to the workload of taxa requiring future revision faster than such instances can be resolved.
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Affiliation(s)
- Gustav M Kessel
- School of Biological Sciences, Te Toki a Rata Building L2, Victoria University of Wellington , Gate 7 Kelburn Parade, Wellington 6012 , New Zealand
| | - Philip Alderslade
- CSIRO Oceans and Atmosphere , Castray Esplanade, Hobart, TAS 7000 , Australia
| | - Jaret P Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA) , 301 Evans Bay Parade, Wellington 6021 , New Zealand
| | - Kareen E Schnabel
- National Institute of Water & Atmospheric Research Ltd (NIWA) , 301 Evans Bay Parade, Wellington 6021 , New Zealand
| | - Jonathan P A Gardner
- School of Biological Sciences, Te Toki a Rata Building L2, Victoria University of Wellington , Gate 7 Kelburn Parade, Wellington 6012 , New Zealand
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12
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Wanghe K, Feng C, Tang Y, Qi D, Ahmad S, Nabi G, Li X, Wang G, Jian L, Liu S, Zhao K, Tian F. Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.933632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Accurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in Gymnocypris eckloni, a schizothoracine fish endemic to the Qinghai–Tibetan Plateau. The aim of this study is robustly identifying the phylogeny of G. eckloni in the Yellow River (YR) population and Qaidam basin (QB) population. The specific-locus amplified fragments sequencing (SLAF-seq) is employed with comprehensively sampling of schizothoracine fishes. In total, 350,181,802 clean reads and 5,114,096 SNPs are identified from SLAF-seq. Phylogenetic analysis recovers a non-monophyletic population of G. eckloni between YR and QB populations, representing an independent phylogenetic relationship between the two populations. Species delimitation analyses by SNAPPER and GMYC methods using the genome-wide SNP data confirm that their taxonomic statuses are separated. This study highlights the importance of further reconsidering clearer taxonomy, which would improve the genetic diversity conservation of Tibetan highland fishes.
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13
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Revealing the Coral Species Diversity in Xiamen Bay: Spatial Distribution of Genus Astrogorgia (Cnidaria, Alcyonacea, Plexauridae) and Newly Recorded Species. WATER 2022. [DOI: 10.3390/w14152417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Coral reefs provide a habitat for many marine organisms and support the safety, coastal protection, well-being, and food and economic security of hundreds of millions of people. The focus on coral species diversity cannot be overemphasized. One of them, Astrogorgia, contains many marine natural active substances, and has important scientific research value and application prospects. Most of the current research on the active substances of the genus Astrogorgia is based on unidentified species, and in-depth taxonomic studies are urgently needed. A total of 1185 samples were collected from 2014 to 2021 in the waters of Xiamen Bay. Herein, the morphological identification, electronic microscopy, and gene fragment sequencing methods were used for the taxonomic study. There are three species of Astrogorgia identified, including Astrogorgia lafoa, A. arborea, and A. dumbea. Among them, A. lafoa and A. arborea are newly recorded species in the waters of China. A. lafoa is distributed in Qingyu Island, A. arborea is distributed in Wuyu Island, and A. dumbea is widely distributed in Baiha Reef, Qingyu Island, Wuyu Island, and Xiaobai Island. In this paper, the geographical distribution and the habits of 18 species of Astrogorgia are summarized, and the evolution of family and genus classification of Astrogorgia is discussed. The results enrich the geographical distribution information and coral species diversity records of Astrogorgia in China.
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14
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Calado R, Mamede R, Cruz S, Leal MC. Updated Trends on the Biodiscovery of New Marine Natural Products from Invertebrates. Mar Drugs 2022; 20:md20060389. [PMID: 35736192 PMCID: PMC9228037 DOI: 10.3390/md20060389] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 01/27/2023] Open
Abstract
From 1990–2019, a total of 15,442 New Marine Natural Products from Invertebrates (NMNPIs) were reported. The 2010s saw the most prolific decade of biodiscovery, with 5630 NMNPIs recorded. The phyla that contributed most biomolecules were the Porifera (sponges) (47.2%, 2659 NMNPIs) and the Cnidaria (35.3%, 1989 NMNPIs). The prevalence of these two phyla as the main sources of NMNPIs became more pronounced in the 2010s. The tropical areas of the Pacific Ocean yielded more NMNPIs, most likely due to the remarkable biodiversity of coral reefs. The Indo-Burma biodiversity hotspot (BH) was the most relevant area for the biodiscovery of NMNPIs in the 2010s, accounting for nearly one-third (1819 NMNPIs) of the total and surpassing the top BH from the 1990s and the 2000s (the Sea of Japan and the Caribbean Islands, respectively). The Chinese exclusive economic zone (EEZ) alone contributed nearly one-quarter (24.7%) of all NMNPIs recorded during the 2010s, displacing Japan’s leading role from the 1990s and the 2000s. With the biodiscovery of these biomolecules steadily decreasing since 2012, it is uncertain whether this decline has been caused by lower bioprospecting efforts or the potential exhaustion of chemodiversity from traditional marine invertebrate sources.
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15
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Titus BM, Daly M. Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes? Heredity (Edinb) 2022; 128:338-351. [PMID: 35418670 PMCID: PMC9076904 DOI: 10.1038/s41437-022-00531-3] [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: 09/09/2020] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/08/2022] Open
Abstract
Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.
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Affiliation(s)
- Benjamin M Titus
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
- Dauphin Island Sea Lab, Dauphin Island, AL, USA.
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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16
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Hinojosa JC, Dapporto L, Pitteloud C, Koubínová D, Hernández-Roldán J, Vicente JC, Alvarez N, Vila R. Hybridization fuelled diversification in Spialia butterflies. Mol Ecol 2022; 31:2951-2967. [PMID: 35263484 PMCID: PMC9310813 DOI: 10.1111/mec.16426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/17/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022]
Abstract
The importance of hybridization and introgression is well documented in the evolution of plants but, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using double‐digest RADseq (ddRADseq), we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer probably occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes.
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Affiliation(s)
- Joan C Hinojosa
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Leonardo Dapporto
- ZEN lab, Biology Department, Università degli Studi di Firenze, 50019, Sesto Fiorentino, Italy
| | - Camille Pitteloud
- Geneva Natural History Museum, Route de Malagnou 1, 1208, Geneva, Switzerland
| | - Darina Koubínová
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Juan Hernández-Roldán
- Departamento de Biología, Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Calle Darwin 2, 28049, Madrid, Spain
| | - Juan Carlos Vicente
- Asociación Española para la Protección de las Mariposas y su Medio (ZERYNTHIA), Madrid, Spain
| | - Nadir Alvarez
- Geneva Natural History Museum, Route de Malagnou 1, 1208, Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Boulevard d'Ivoy 4, 1205, Geneva, Switzerland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
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17
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Meza‐Lázaro RN, Peña‐Carrillo KI, Poteaux C, Lorenzi MC, Wetterer JK, Zaldívar‐Riverón A. Genome and cuticular hydrocarbon-based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex. Ecol Evol 2022; 12:e8704. [PMID: 35342602 PMCID: PMC8928884 DOI: 10.1002/ece3.8704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/02/2022] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
Geographic separation that leads to the evolution of reproductive isolation between populations generally is considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due to phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence, and mitonuclear conflict. Here, we performed an integrative study based on two genome-wide techniques (3RAD and ultraconserved elements) coupled with cuticular hydrocarbon (CHC) and mitochondrial (mt) DNA sequence data, to assess the species limits within the Ectatomma ruidum species complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy (i.e., presence of multiple mtDNA variants in an individual) has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex: two widely distributed across the Neotropics, and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, CHC differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.
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Affiliation(s)
- Rubi N. Meza‐Lázaro
- Colección Nacional de InsectosInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Kenzy I. Peña‐Carrillo
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
- INIFAPCampo Experimental General TeránGeneral TeránMexico
| | - Chantal Poteaux
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
| | - Maria Cristina Lorenzi
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
| | - James K. Wetterer
- Harriet L. Wilkes Honors CollegeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alejandro Zaldívar‐Riverón
- Colección Nacional de InsectosInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
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18
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Prata KE, Riginos C, Gutenkunst RN, Latijnhouwers KRW, Sánchez JA, Englebert N, Hay KB, Bongaerts P. Deep connections: divergence histories with gene flow in mesophotic
Agaricia
corals. Mol Ecol 2022; 31:2511-2527. [PMID: 35152496 PMCID: PMC9303685 DOI: 10.1111/mec.16391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/01/2022]
Abstract
Largely understudied, mesophotic coral ecosystems lie below shallow reefs (at >30 m depth) and comprise ecologically distinct communities. Brooding reproductive modes appear to predominate among mesophotic‐specialist corals and may limit genetic connectivity among populations. Using reduced representation genomic sequencing, we assessed spatial population genetic structure at 50 m depth in an ecologically important mesophotic‐specialist species Agaricia grahamae, among locations in the Southern Caribbean. We also tested for hybridisation with the closely related (but depth‐generalist) species Agaricia lamarcki, within their sympatric depth zone (50 m). In contrast to our expectations, no spatial genetic structure was detected between the reefs of Curaçao and Bonaire (~40 km apart) within A. grahamae. However, cryptic taxa were discovered within both taxonomic species, with those in A. lamarcki (incompletely) partitioned by depth and those in A. grahamae occurring sympatrically (at the same depth). Hybrid analyses and demographic modelling identified contemporary and historical gene flow among cryptic taxa, both within and between A. grahamae and A. lamarcki. These results (1) indicate that spatial connectivity and subsequent replenishment may be possible between islands of moderate geographic distances for A. grahamae, an ecologically important mesophotic species, (2) that cryptic taxa occur in the mesophotic zone and environmental selection along shallow to mesophotic depth gradients may drive divergence in depth‐generalists such as A. lamarcki, and (3) highlight that gene flow links taxa within this relativity diverse Caribbean genus.
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Affiliation(s)
- Katharine E. Prata
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
- California Academy of Sciences San Francisco CA USA
| | - Cynthia Riginos
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology University of Arizona Tuscon AZ USA
| | | | - Juan A. Sánchez
- Laboratorio de Biología Molecular Marina (BIOMMAR) Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
| | - Norbert Englebert
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
| | - Kyra B. Hay
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
| | - Pim Bongaerts
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
- California Academy of Sciences San Francisco CA USA
- Caribbean Research and Management of Biodiversity Foundation Willemstad, Curaçao
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19
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Cerri F, Saliu F, Maggioni D, Montano S, Seveso D, Lavorano S, Zoia L, Gosetti F, Lasagni M, Orlandi M, Taglialatela-Scafati O, Galli P. Cytotoxic Compounds from Alcyoniidae: An Overview of the Last 30 Years. Mar Drugs 2022; 20:134. [PMID: 35200663 PMCID: PMC8874409 DOI: 10.3390/md20020134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 11/30/2022] Open
Abstract
The octocoral family Alcyoniidae represents a rich source of bioactive substances with intriguing and unique structural features. This review aims to provide an updated overview of the compounds isolated from Alcyoniidae and displaying potential cytotoxic activity. In order to allow a better comparison among the bioactive compounds, we focused on molecules evaluated in vitro by using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, by far the most widely used method to analyze cell proliferation and viability. Specifically, we surveyed the last thirty years of research, finding 153 papers reporting on 344 compounds with proven cytotoxicity. The data were organized in tables to provide a ranking of the most active compounds, to be exploited for the selection of the most promising candidates for further screening and pre-clinical evaluation as anti-cancer agents. Specifically, we found that (22S,24S)-24-methyl-22,25-epoxyfurost-5-ene-3β,20β-diol (16), 3β,11-dihydroxy-24-methylene-9,11-secocholestan-5-en-9-one (23), (24S)-ergostane-3β,5α,6β,25 tetraol (146), sinulerectadione (227), sinulerectol C (229), and cladieunicellin I (277) exhibited stronger cytotoxicity than their respective positive control and that their mechanism of action has not yet been further investigated.
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Affiliation(s)
- Federico Cerri
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milano, Italy;
| | - Francesco Saliu
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | - Davide Maggioni
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- MaRHE Centre (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll 12030, Maldives
| | - Simone Montano
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- MaRHE Centre (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll 12030, Maldives
| | - Davide Seveso
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- MaRHE Centre (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll 12030, Maldives
| | - Silvia Lavorano
- Costa Edutainment SpA—Acquario di Genova, Area Porto Antico, Ponte Spinola, 16128 Genoa, Italy;
| | - Luca Zoia
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | - Fabio Gosetti
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | - Marina Lasagni
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | - Marco Orlandi
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | | | - Paolo Galli
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- MaRHE Centre (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll 12030, Maldives
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20
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Mitogenomics reveals low variation within a trigeneric complex of black corals from the North Pacific Ocean. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-021-00537-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Singhal S, Derryberry GE, Bravo GA, Derryberry EP, Brumfield RT, Harvey MG. The dynamics of introgression across an avian radiation. Evol Lett 2021; 5:568-581. [PMID: 34917397 PMCID: PMC8645201 DOI: 10.1002/evl3.256] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/11/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023] Open
Abstract
Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.
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Affiliation(s)
- Sonal Singhal
- Department of Biology California State University, Dominguez Hills Carson California 90747
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138.,Museum of Comparative Zoology Harvard University Cambridge Massachusetts 02138
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Robb T Brumfield
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana 70803.,Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael G Harvey
- Department of Biological Sciences The University of Texas at El Paso El Paso Texas 79968.,Biodiversity Collections The University of Texas at El Paso El Paso Texas 79968
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22
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Hayes JM, Abdul-Rahman NH, Gerdes MJ, Musah RA. Coral Genus Differentiation Based on Direct Analysis in Real Time-High Resolution Mass Spectrometry-Derived Chemical Fingerprints. Anal Chem 2021; 93:15306-15314. [PMID: 34761917 DOI: 10.1021/acs.analchem.1c02519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coral reefs are one of the most biologically diverse ecosystems, and the accurate identification of the species is essential for diversity assessment and conservation. Current genus determination approaches are time-consuming and resource-intensive and can be highly subjective. To explore the hypothesis that the small-molecule profiles of coral are genus-specific and can be used as a rapid tool to catalogue and distinguish between coral genera, the small-molecule chemical fingerprints of the species Acanthastrea echinata, Catalaphyllia jardinei, Duncanopsammia axifuga, Echinopora lamellosa, Euphyllia divisa, Euphyllia paraancora, Euphyllia paradivisa, Galaxea fascicularis, Herpolitha limax, Montipora confusa, Monitpora digitata, Montipora setosa, Pachyseris rugosa, Pavona cactus, Plerogyra sinuosa, Pocillopora acuta, Seriatopora hystrix, Sinularia dura, Turbinaria peltata, Turbinaria reniformis, Xenia elongata, and Xenia umbellata were generated using direct analysis in real time-high resolution mass spectrometry (DART-HRMS). It is demonstrated here that the mass spectrum-derived small-molecule profiles for coral of different genera are distinct. Multivariate statistical analysis processing of the DART-HRMS data enabled rapid genus-level differentiation based on the chemical composition of the coral. Coral samples were analyzed with no sample preparation required, making the approach rapid and efficient. The resulting spectra were subjected to kernel discriminant analysis (KDA), which furnished accurate genus differentiation of the coral. Leave-one-out cross-validation (LOOCV) was carried out to determine the classification accuracy of each model and confirm that this approach can be used for coral genus attribution with prediction accuracies ranging from 86.67 to 97.33%. The advantages and application of the statistical analysis to DART-HRMS-derived coral chemical signatures for genus-level differentiation are discussed.
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Affiliation(s)
- Jessica M Hayes
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Nana-Hawwa Abdul-Rahman
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Michael J Gerdes
- CapitalCorals Inc., 20 Colvin Avenue, Albany, New York 12206, United States
| | - Rabi A Musah
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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23
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Santos Rampasso A, O'Grady PM. Standardized terminology and visual atlas of the external morphology and terminalia for the genus Scaptomyza (Diptera: Drosophilidae). Fly (Austin) 2021; 16:37-61. [PMID: 34641736 PMCID: PMC8525988 DOI: 10.1080/19336934.2021.1969220] [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: 11/21/2022] Open
Abstract
The genus Scaptomyza is one of the two Drosophilidae genera with Hawaiian endemic species. This genus is an excellent model for biogeographic studies since it is distributed throughout the majority of continents, including continental islands, the Hawaiian Islands, and many other remote oceanic islands. This genus currently comprises 273 described species, 148 of which are endemic to the Hawaiian Islands. However, most descriptions were published before efforts to standardizing the morphological terminology across the Diptera were made in the 1980’s. Since research groups developed their own set of terminologies independently, without considering homologies, multiple terms have been used to refer to the same characters. This is especially true for the male terminalia, which have remarkable modifications within the family Drosophilidae. We reviewed the Scaptomyza literature, in addition to other studies across the Drosophilidae and Diptera, compiled the English synonyms, and provided a visual atlas of each body part, indicating how to recognize the morphological characters. The goal of the present study is to facilitate species identification and propose preferred terms to be adopted for future Scaptomyza descriptions.
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24
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Influence of temperature changes on symbiotic Symbiodiniaceae and bacterial communities’ structure: an experimental study on soft coral Sarcophyton trocheliophorum (Anthozoa: Alcyoniidae). JOURNAL OF TROPICAL ECOLOGY 2021. [DOI: 10.1017/s0266467421000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractIt is well concluded that microbial composition and diversity of coral species can be affected under temperature alterations. However, the interaction of environmental accumulation of corals and temperature stress on symbiotic Symbiodiniaceae and bacterial communities are rarely studied. In this study, two groups of soft coral Sarcophyton trocheliophorum were cultured under constant (26 °C) and inconstant (22 °C to 26 °C) temperature conditions for 30 days as control treatments. After that, water was cooled rapidly to decrease to 20 °C in 24 h. The results of diversity analysis showed that symbiotic Symbiodiniaceae and bacterial communities had a significant difference between the two accumulated groups. The principal coordinate analyses confirmed that symbiotic Symbiodiniaceae and bacterial communities of both control treatments were clustered into two groups. Our results evidenced that rapid cooling stress could not change symbiotic Symbiodiniaceae and bacterial communities’ composition. On the other hand, cooling stress could alter only bacterial communities in constant group. In conclusion, our study represents a clear relationship between environmental accumulation and the impact of short-term cooling stress in which microbial composition structure can be affected by early adaptation conditions.
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25
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Ramírez-Portilla C, Baird AH, Cowman PF, Quattrini AM, Harii S, Sinniger F, Flot JF. Solving the Coral Species Delimitation Conundrum. Syst Biol 2021; 71:461-475. [PMID: 34542634 DOI: 10.1093/sysbio/syab077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022] Open
Abstract
Distinguishing coral species is not only crucial for physiological, ecological and evolutionary studies, but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that inter-specific hybridization might be responsible for this apparent conundrum. Here, we used three lines of evidence - morphology, breeding trials and molecular approaches - to identify species boundaries in a group of ecologically important tabular Acropora corals. In contrast to previous studies, our morphological analyses yielded groups that were congruent with experimental crosses as well as with coalescent-based and allele sharing-based multilocus approaches to species delimitation. Our results suggest that species of the genus Acropora are reproductively isolated and independently evolving units that can be distinguished morphologically. These findings not only pave the way for a taxonomic revision of coral species, but also outline an approach that can provide a solid basis to address species delimitation and provide conservation support to a wide variety of keystone organisms.
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Affiliation(s)
- Catalina Ramírez-Portilla
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, B-1050, Belgium.,Systematics & Biodiversity, Justus-Liebig University, Giessen, D-35392, Germany
| | - Andrew H Baird
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Peter F Cowman
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - Saki Harii
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Frederic Sinniger
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, B-1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)2, Brussels, B-1050, Belgium
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26
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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27
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Grinblat M, Cooke I, Shlesinger T, Ben-Zvi O, Loya Y, Miller DJ, Cowman PF. Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals). Mol Phylogenet Evol 2021; 164:107265. [PMID: 34274488 DOI: 10.1016/j.ympev.2021.107265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/15/2022]
Abstract
While the escalating impacts of climate change and other anthropogenic pressures on coral reefs are well documented at the coral community level, studies of species-specific trends are less common, owing mostly to the difficulties and uncertainties in delineating coral species. It has also become clear that traditional coral taxonomy based largely on skeletal macromorphology has underestimated the diversity of many coral families. Here, we use targeted enrichment methods to sequence 2476 ultraconserved elements (UCEs) and exonic loci to investigate the relationship between populations of Fungia fungites from Okinawa, Japan, where this species reproduces by brooding (i.e., internal fertilization), and Papua New Guinea and Australia, where it reproduces by broadcast-spawning (i.e., external fertilization). Moreover, we analyzed the relationships between populations of additional fungiid species (Herpolitha limax and Ctenactis spp.) that reproduce only by broadcast-spawning. Our phylogenetic and species delimitation analyses reveal strong biogeographic structuring in both F. fungites and Herpolitha limax, consistent with cryptic speciation in Okinawa in both species and additionally for H. limax in the Red Sea. By combining UCE/exon data and mitochondrial sequences captured in off-target reads, we reinforce earlier findings that Ctenactis, a genus consisting of three nominal morphospecies, is not a natural group. Our results highlight the need for taxonomic and systematic re-evaluations of some species and genera within the family Fungiidae. This work demonstrates that sequence data generated by the application of targeted capture methods can provide objective criteria by which we can test phylogenetic hypotheses based on morphological and/or life history traits.
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Affiliation(s)
- Mila Grinblat
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Ira Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Tom Shlesinger
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL, USA
| | - Or Ben-Zvi
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel; The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Yossi Loya
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia; Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland, Australia.
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28
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Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans. Mol Phylogenet Evol 2021; 163:107233. [PMID: 34139346 DOI: 10.1016/j.ympev.2021.107233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Genome-level sequencing is the next step in understanding species-level relationships within Anthozoa (soft corals, anemones, stony corals, and their kin) as morphological and PCR-directed (single-locus) sequencing methods often fall short of differentiating species. The sea anemone genus Metridium is a common northern temperate sea anemone whose species are difficult to differentiate using morphology alone. Here we use Metridium as a case study to confirm the low level of information available in six loci for species differentiation commonly sequenced for Actiniaria and explore and compare the efficacy of ddRAD and sequence-capture methods in species-level systematics and biogeographic studies. We produce phylogenetic trees from concatenated datasets and perform DAPC and STRUCTURE analyses using SNP data. The six conventional loci are not able to consistently differentiate species within Metridium. The sequence-capture dataset resulted in high support and resolution for both current species and relationships between geographic areas. The ddRAD datasets displayed ambiguity among species, and support between major geographic groupings was not as high as the sequence-capture datasets. The level of resolution and support resulting from the sequence-capture data, combined with the ability to add additional individuals and expand beyond the genus Metridium over time, emphasizes the utility of sequence-capture methods for both systematics and future biogeographic studies within anthozoans. We discuss the strengths and weaknesses of the genomic approaches in light of our findings and suggest potential implications for the biogeography of Metridium based on our sampling.
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29
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Genetic Divergence and Polyphyly in the Octocoral Genus Swiftia [Cnidaria: Octocorallia], Including a Species Impacted by the DWH Oil Spill. DIVERSITY 2021. [DOI: 10.3390/d13040172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mesophotic coral ecosystems (MCEs) are recognized around the world as diverse and ecologically important habitats. In the northern Gulf of Mexico (GoMx), MCEs are rocky reefs with abundant black corals and octocorals, including the species Swiftia exserta. Surveys following the Deepwater Horizon (DWH) oil spill in 2010 revealed significant injury to these and other species, the restoration of which requires an in-depth understanding of the biology, ecology, and genetic diversity of each species. To support a larger population connectivity study of impacted octocorals in the GoMx, this study combined sequences of mtMutS and nuclear 28S rDNA to confirm the identity of Swiftia sea fans in the GoMx, compare these markers for different polyp colors in the GoMx and Atlantic, and examine the phylogeny of the genus. Two mtMutS haplotypes were identified, one seemingly endemic to the northern GoMx. Compared to other North Atlantic Swiftia, S. exserta, the type of the genus was found to be extremely divergent and distinct from the two other Swiftia at both loci, with strong evidence of polyphyly in the genus. This information refines our understanding of the geographical distribution of injured coral and highlights how little is known about MCEs. Substantial taxonomic revisions may be needed for several taxa injured by the DWH oil spill.
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30
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Terraneo TI, Benzoni F, Arrigoni R, Baird AH, Mariappan KG, Forsman ZH, Wooster MK, Bouwmeester J, Marshell A, Berumen ML. Phylogenomics of Porites from the Arabian Peninsula. Mol Phylogenet Evol 2021; 161:107173. [PMID: 33813021 DOI: 10.1016/j.ympev.2021.107173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia.
| | - Francesca Benzoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Roberto Arrigoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; European Commission, Joint Research Centre (JRC), Ispra, Italy; Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121 Napoli, Italy
| | - Andrew H Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Zac H Forsman
- Hawaii Institute of Marine Biology, Kaneohe 96744, HI, USA
| | - Michael K Wooster
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Michael L Berumen
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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31
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Arrigoni R, Huang D, Berumen ML, Budd AF, Montano S, Richards ZT, Terraneo TI, Benzoni F. Integrative systematics of the scleractinian coral genera
Caulastraea
,
Erythrastrea
and
Oulophyllia. ZOOL SCR 2021. [DOI: 10.1111/zsc.12481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms (BEOM) Stazione Zoologica Anton Dohrn Napoli Italy
| | - Danwei Huang
- Department of Biological Sciences and Tropical Marine Science Institute National University of Singapore Singapore Singapore
| | - Michael L. Berumen
- Reef Ecology Laboratory Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Ann F. Budd
- Department of Earth and Environmental Sciences University of Iowa Iowa City IA USA
| | - Simone Montano
- Department of Earth and Environmental Sciences (DISAT) University of Milano − Bicocca Milano Italy
- Marine Research and High Education Center Magoodhoo Island Faafu Atoll Maldives
| | - Zoe T. Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Aquatic Zoology Western Australian Museum Welshpool WA Australia
| | - Tullia I. Terraneo
- Habitat and Benthic Biodiversity Laboratory Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Francesca Benzoni
- Habitat and Benthic Biodiversity Laboratory Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal Saudi Arabia
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32
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Sikorskaya TV, Efimova KV, Imbs AB. Lipidomes of phylogenetically different symbiotic dinoflagellates of corals. PHYTOCHEMISTRY 2021; 181:112579. [PMID: 33166751 DOI: 10.1016/j.phytochem.2020.112579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
The structural base of all membranes of symbiotic dinoflagellates (SD) is composed of glycolipids and betaine lipids, whereas triacylglycerols (TG) constitute an energy reserve and are involved in biosynthesis of glycolipids. Since data on the SD lipidome and the host's influence on symbionts' lipidome are scanty, we analyzed and compared the lipidomes of SD isolated from the zoantharian Palythoa tuberculosa and the alcyonarian Sinularia heterospiculata. A sequencing of nuclear gene regions showed that both cnidarians hosted the dinoflagellates Cladocopium sp. (subclades C1 and C3), but the zoantharian also contained the dinoflagellates Durusdinium trenchii (clade D). The presence of the thermotolerant D. trenchii resulted in a higher unsaturation of mono- and digalactosyldiacylglycerols (MGDG and DGDG), but a lower unsaturation of sulfoquinovosyldiacylglycerol (SQDG). The same features were earlier described for same SD from a reef-building coral. Hence, the profile of glycolipid molecules, which form SD thylakoid membranes, seems to be species-specific and does not depend on the host's taxonomic position. In contrast, the betaine lipid molecular species profile of diacylglyceryl-3-O-carboxyhydroxymethylcholine (DGCC), which forms SD cell membranes, can be influenced by the host. The profiles of the TG molecular species from freshly isolated SD have been determined for the first time. These molecular species can be divided on the basis of the acyl group in sn-2 position. The TG with 16:0 acyl group in sn-2 position may enrich total TG of a cnidarian colony and originate from SD cytoplasm. In contrast, TG 18:3/18:4/18:3 may be biosynthetically related with DGDG and concentrated in SD plastoglobules. Our data may be useful for further investigations of natural and technogenic variations in microalgal lipids and symbiont-host interactions in marine ecosystems.
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Affiliation(s)
- Tatyana V Sikorskaya
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russian Federation.
| | - Kseniya V Efimova
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russian Federation; Laboratory of Ecology and Evolutionary Biology of Aquatic Organisms, Far Eastern Federal University, 690091, Vladivostok, Russian Federation
| | - Andrey B Imbs
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russian Federation
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Mendes CB, Norenburg JL, Andrade SCS. Species delimitation integrative approach reveals three new species in the Nemertopsis bivittata complex. INVERTEBR SYST 2021. [DOI: 10.1071/is20048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The presence of cryptic species is fairly frequent in many invertebrate groups and even more so among invertebrates with simple morphology, such as nemerteans. Consequently, the use of molecular methods for species delimitation has become a needed tool to complement morphological analyses to better recognise such species. Nemertopsis bivittata is one example of species with subtle morphological variation, but ample geographic distribution, being a good candidate for a species complex study. Here we applied two mitochondrial genes, and 2903 single nucleotide polymorphism (SNP) variants in addition to morphological characters to investigate the presence of cryptic species among specimens previously identified as N. bivittata along the Brazilian Coast. To do so, specimens were collected at 15 different sites in the north-east, south-east and southern regions. Three new species of Nemertopsis are described based on morphological and molecular analyses: Nemertopsis caete sp. nov., Nemertopsis pamelaroeae sp. nov. and Nemertopsis berthalutzae sp. nov. The species N. pamelaroeae and N. berthalutzae present broad distributions from north-east to south-east; N. caete, however, is restricted to the north-east coast. This is the first study to use this combined approach in nemerteans and shows the advantages of integrating genomic markers with classical taxonomy, and applying objective approaches to delimiting species as independently evolving entities.
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Núñez-Flores M, Gomez-Uchida D, López-González PJ. Molecular systematics of Thouarella (Octocorallia:Primnoidae) with the description of three new species from the Southern Ocean based on combined molecular and morphological evidence. INVERTEBR SYST 2021. [DOI: 10.1071/is20078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Thouarella Gray, 1870, is one of the most speciose genera among gorgonians of the family Primnoidae (Cnidaria:Octocorallia:Anthozoa), being remarkably diverse in the Antarctic and sub-Antarctic seafloor. However, their diversity in the Southern Ocean is likely underestimated. Phylogenetic analyses of mitochondrial and nuclear DNA markers were integrated with species delimitation approaches as well as morphological colonial and polyps features and skeletal SEM examinations to describe and illustrate three new species within Thouarella, from the Weddell Sea, Southern Ocean: T. amundseni sp. nov., T. dolichoespinosa sp. nov. and T. pseudoislai sp. nov. Our species delimitation results suggest, for the first time, the potential presence of Antarctic and sub-Antarctic cryptic species of primnoids, based on the likely presence of sibling species within T. undulata and T. crenelata. With the three new species here described, the global diversity of Thouarella has increased to 41 species, 15 of which are endemic to the Antarctic and sub-Antarctic waters. Consequently, our results provide new steps for uncovering the shelf benthonic macrofauna’s hidden diversity in the Southern Ocean. Finally, we recommend using an integrative taxonomic framework in this group of organisms and species delimitation approaches because the distinctions between some Thouarella species based only on a superficial examination of their macro- and micromorphological features is, in many cases, limited.
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Ermolenko EV, Imbs AB, Gloriozova TA, Poroikov VV, Sikorskaya TV, Dembitsky VM. Chemical Diversity of Soft Coral Steroids and Their Pharmacological Activities. Mar Drugs 2020; 18:E613. [PMID: 33276570 PMCID: PMC7761492 DOI: 10.3390/md18120613] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 02/07/2023] Open
Abstract
The review is devoted to the chemical diversity of steroids produced by soft corals and their determined and potential activities. There are about 200 steroids that belong to different types of steroids such as secosteroids, spirosteroids, epoxy- and peroxy-steroids, steroid glycosides, halogenated steroids, polyoxygenated steroids and steroids containing sulfur or nitrogen heteroatoms. Of greatest interest is the pharmacological activity of these steroids. More than 40 steroids exhibit antitumor and related activity with a confidence level of over 90 percent. A group of 32 steroids shows anti-hypercholesterolemic activity with over 90 percent confidence. Ten steroids exhibit anti-inflammatory activity and 20 steroids can be classified as respiratory analeptic drugs. Several steroids exhibit rather rare and very specific activities. Steroids exhibit anti-osteoporotic properties and can be used to treat osteoporosis, as well as have strong anti-eczemic and anti-psoriatic properties and antispasmodic properties. Thus, this review is probably the first and exclusive to present the known as well as the potential pharmacological activities of 200 marine steroids.
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Affiliation(s)
- Ekaterina V. Ermolenko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, 17 Palchevsky Str., 690041 Vladivostok, Russia; (E.V.E.); (A.B.I.); (T.V.S.)
| | - Andrey B. Imbs
- A.V. Zhirmunsky National Scientific Center of Marine Biology, 17 Palchevsky Str., 690041 Vladivostok, Russia; (E.V.E.); (A.B.I.); (T.V.S.)
| | - Tatyana A. Gloriozova
- Institute of Biomedical Chemistry, bldg. 8, 10 Pogodinskaya Str., 119121 Moscow, Russia; (T.A.G.); (V.V.P.)
| | - Vladimir V. Poroikov
- Institute of Biomedical Chemistry, bldg. 8, 10 Pogodinskaya Str., 119121 Moscow, Russia; (T.A.G.); (V.V.P.)
| | - Tatyana V. Sikorskaya
- A.V. Zhirmunsky National Scientific Center of Marine Biology, 17 Palchevsky Str., 690041 Vladivostok, Russia; (E.V.E.); (A.B.I.); (T.V.S.)
| | - Valery M. Dembitsky
- A.V. Zhirmunsky National Scientific Center of Marine Biology, 17 Palchevsky Str., 690041 Vladivostok, Russia; (E.V.E.); (A.B.I.); (T.V.S.)
- Centre for Applied Research, Innovation and Entrepreneurship, Lethbridge College, 3000 College Drive South, Lethbridge, AB T1K 1L6, Canada
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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O'Brien PA, Tan S, Yang C, Frade PR, Andreakis N, Smith HA, Miller DJ, Webster NS, Zhang G, Bourne DG. Diverse coral reef invertebrates exhibit patterns of phylosymbiosis. THE ISME JOURNAL 2020; 14:2211-2222. [PMID: 32444811 PMCID: PMC7608455 DOI: 10.1038/s41396-020-0671-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023]
Abstract
Microbiome assemblages of plants and animals often show a degree of correlation with host phylogeny; an eco-evolutionary pattern known as phylosymbiosis. Using 16S rRNA gene sequencing to profile the microbiome, paired with COI, 18S rRNA and ITS1 host phylogenies, phylosymbiosis was investigated in four groups of coral reef invertebrates (scleractinian corals, octocorals, sponges and ascidians). We tested three commonly used metrics to evaluate the extent of phylosymbiosis: (a) intraspecific versus interspecific microbiome variation, (b) topological comparisons between host phylogeny and hierarchical clustering (dendrogram) of host-associated microbial communities, and (c) correlation of host phylogenetic distance with microbial community dissimilarity. In all instances, intraspecific variation in microbiome composition was significantly lower than interspecific variation. Similarly, topological congruency between host phylogeny and the associated microbial dendrogram was more significant than would be expected by chance across all groups, except when using unweighted UniFrac distance (compared with weighted UniFrac and Bray-Curtis dissimilarity). Interestingly, all but the ascidians showed a significant positive correlation between host phylogenetic distance and associated microbial dissimilarity. Our findings provide new perspectives on the diverse nature of marine phylosymbioses and the complex roles of the microbiome in the evolution of marine invertebrates.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Chentao Yang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Pedro R Frade
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Hillary A Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David J Miller
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia.
- Australian Institute of Marine Science, Townsville, QLD, Australia.
- AIMS@JCU, Townsville, QLD, Australia.
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Bangs MR, Douglas MR, Chafin TK, Douglas ME. Gene flow and species delimitation in fishes of Western North America: Flannelmouth ( Catostomus latipinnis) and Bluehead sucker ( C. Pantosteus discobolus). Ecol Evol 2020; 10:6477-6493. [PMID: 32724527 PMCID: PMC7381754 DOI: 10.1002/ece3.6384] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction site-associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.
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Affiliation(s)
- Max R. Bangs
- Department of Biological SciencesFlorida State UniversityTallahasseeFLUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Tyler K. Chafin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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39
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Ip YCA, Tay YC, Gan SX, Ang HP, Tun K, Chou LM, Huang D, Meier R. From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach. Biodivers Data J 2019; 7:e46833. [PMID: 31866739 PMCID: PMC6917626 DOI: 10.3897/bdj.7.e46833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/21/2019] [Indexed: 12/27/2022] Open
Abstract
Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes ("biocodes"), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore's first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to "Biodiversity of Singapore" (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.
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Affiliation(s)
- Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Ywee Chieh Tay
- National University of Singapore, Singapore, SingaporeNational University of SingaporeSingaporeSingapore
- Temasek Life Sciences Laboratory, Singapore, SingaporeTemasek Life Sciences LaboratorySingaporeSingapore
| | - Su Xuan Gan
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Hui Ping Ang
- National Parks Board, Singapore, SingaporeNational Parks BoardSingaporeSingapore
| | - Karenne Tun
- National Parks Board, Singapore, SingaporeNational Parks BoardSingaporeSingapore
| | - Loke Ming Chou
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
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40
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Bogantes VE, Whelan NV, Webster K, Mahon AR, Halanych KM. Unrecognized diversity of a scale worm,Polyeunoa laevis(Annelida: Polynoidae), that feeds on soft coral. ZOOL SCR 2019. [DOI: 10.1111/zsc.12400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Viktoria E. Bogantes
- Department of Biological Sciences Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University Auburn AL USA
| | - Nathan V. Whelan
- Southeast Conservation Genetics Lab Warm Springs Fish Technology Center United States Fish and Wildlife Service Auburn AL USA
- School of Fisheries, Aquaculture, and Aquatic Sciences Auburn University Auburn AL USA
| | - Katelynn Webster
- Department of Biological Sciences Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University Auburn AL USA
| | - Andrew R. Mahon
- Department of Biology Central Michigan University Mount Pleasant MI USA
| | - Kenneth M. Halanych
- Department of Biological Sciences Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University Auburn AL USA
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Shimpi GG, Patel NP, Haldar S. Molecular species delimitation of reef-building coral genera, Porites and Turbinaria (Anthozoa: Scleractinia), from the intertidal fringing reefs of Gulf of Kutch, India reveals unrecognized diversity. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1677798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Gaurav G. Shimpi
- Marine Environment Group, Analytical and Environmental Science Division and Central Instrumentation Facility, CSIR-Central Salt and Marine Chemicals Research Institute (CSMCRI), Bhavnagar, Gujarat, 364002, India
- Bombay Natural History Society, Hornbill House, Dr. Salim Ali Chowk, Shahid Bhagat Singh Road, Mumbai, 400001, India
| | - Neha P. Patel
- Marine Environment Group, Analytical and Environmental Science Division and Central Instrumentation Facility, CSIR-Central Salt and Marine Chemicals Research Institute (CSMCRI), Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, Gujarat, 364 002, India
| | - Soumya Haldar
- Marine Environment Group, Analytical and Environmental Science Division and Central Instrumentation Facility, CSIR-Central Salt and Marine Chemicals Research Institute (CSMCRI), Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, Gujarat, 364 002, India
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42
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Chen Y, Dan YT, Lu H, Wang PZ, Asem A, Li W. The complete mitochondrial genome of Sinularia maxima Verseveldt, 1971 (Octocorallia: Alcyonacea) using next-generation sequencing. Mitochondrial DNA B Resour 2019; 4:3425-3426. [PMID: 33366023 PMCID: PMC7707301 DOI: 10.1080/23802359.2019.1674740] [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: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 11/24/2022] Open
Abstract
The mitochondrial genome of Sinularia maxima was completed using next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,730 bp in length. The gene arrangements include 14 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 1 tRNA (tRNA-Met). The base composition is 30.18% A, 16.47% C, 19.35% G, and 33.99% T, with an A + T content of 64.18%. With regard to the phylogenetic analysis, members of genus Sinularia were clustered in different clades.
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Affiliation(s)
- You Chen
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, China
| | - Ya-Ting Dan
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| | - Hao Lu
- College of Ocean, Hainan University, Haikou, China
| | - Pei-Zheng Wang
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, China
| | - Alireza Asem
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| | - Weidong Li
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
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