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Zheng D, Zou L, Zou J, Li Q, Lu S. Refining taxonomic identification of microalgae through molecular and genetic evolution: a case study of Prorocentrum lima and Prorocentrum arenarium. Microbiol Spectr 2024; 12:e0236723. [PMID: 38572997 PMCID: PMC11064606 DOI: 10.1128/spectrum.02367-23] [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: 06/06/2023] [Accepted: 02/08/2024] [Indexed: 04/05/2024] Open
Abstract
Species delimitation based on lineage definition has become increasingly popular. However, these methods have been limited, especially for species that lack genomic data and are morphologically similar. The trickiest part for the species identification is that the interspecific and intraspecific boundaries are vague. Taking Prorocentrum (Dinophyta) as an example, analysis of cell morphology, growth, and toxin synthesis in both species of P. lima and P. arenarium does not provide a reliable basis for species delineation. However, through phylogenetic and genetic distance analyses of their ITS and LSU sequences, establishment of evolutionary tree based on orthologous gene sequences, and combining the results of automatic barcode gap discovery and Poisson tree processes models, it was sustained that P. arenarium does not belong to the P. lima complex and should be considered as an independent species. Interspecies genetic evolution analysis revealed that P. lima and P. arenarium may contribute to evolutionary direction that favors combating reverse environmental factors. In P. lima, viral invasion may be one of the reasons for its large genome size. In the study, P. lima complex has been selected as an example to enhance the taxonomic identification of microalgae through molecular and genetic evolution, offering valuable insights into refining taxonomic identification and promoting microbial biodiversity research in other species.IMPORTANCEMicroalgae, especially the species known as Prorocentrum, have received significant attention due to their ability to trigger harmful algal blooms and produce toxins. However, the boundaries between species and within species are ambiguous. Clear and comprehensive species delineation indicates that Prorocentrum arenarium should be considered as an independent species, separate from the Prorocentrum lima complex. Improving the classification and identification of microalgae through molecular and genetic evolution will provide reference points for other cryptic species. Prorocentrum occupy multiple ecological niches in marine environments, and studying their evolutionary direction contributes to understanding their ecological adaptations and community succession.
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Affiliation(s)
- Danlin Zheng
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Ligong Zou
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Jian Zou
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Qun Li
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Songhui Lu
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
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2
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Zhu H, Xiong X, Liu B, Liu G. Lakes-scale pattern of eukaryotic phytoplankton diversity and assembly process shaped by electrical conductivity in central Qinghai-Tibet Plateau. FEMS Microbiol Ecol 2024; 100:fiad163. [PMID: 38100388 PMCID: PMC10791044 DOI: 10.1093/femsec/fiad163] [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: 10/09/2023] [Revised: 11/15/2023] [Accepted: 12/13/2023] [Indexed: 12/17/2023] Open
Abstract
Phytoplankton are the main primary producers in aquatic ecosystems and play an important role in food web and geochemical cycles. Its diversity, community structure, and assembly process are influenced by several factors. Alpine lake ecosystems are relatively weak and extremely sensitive to global climate change. However, the impact of climate change on phytoplankton in Qinghai-Tibet Plateau lakes and their responses are still unclear. In this study, we analyzed the diversity, environmental drivers, and assembly process of phytoplankton community in the central QTP lakes. The phytoplankton of these lakes can be primarily distinguished into freshwater and brackish types, with significant differences in species diversity and community dissimilarity. Both shared nearly same key environmental factors that significantly affecting phytoplankton such as EC, and brackish lakes were also positively correlative with TN. Stochastic process was predominant in phytoplankton assembly. Additionally, freshwater and brackish lakes were dominated by dispersal limitation and heterogeneous selection respectively. Alpine lakes had significant EC thresholds, and their diversity and assembly processes changed significantly around the thresholds. The present findings have important implications for understanding and predicting the response of lake phytoplankton communities to climate change and for making decisions to protect the ecological resources of alpine lakes.
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Affiliation(s)
- Huan Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiong Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Benwen Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guoxiang Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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3
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Boedeker C, Wynne MJ, Zuccarello GC. Hidden diversity in high-latitude Southern Hemisphere environments: Reinstatement of the genus Rama and description of Vandenhoekia gen. nov. (Cladophoraceae, Ulvophyceae, Chlorophyta), two highly variable genera. JOURNAL OF PHYCOLOGY 2023; 59:1284-1298. [PMID: 37795849 DOI: 10.1111/jpy.13394] [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: 05/02/2023] [Revised: 08/15/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023]
Abstract
The continental coasts and remote islands in the high-latitude Southern Hemisphere, including the subantarctic region, are characterized by many endemic species, high abundance of taxa, and intermediate levels of biodiversity. The macroalgal flora of these locations has received relatively little attention. Filamentous green algae are prolific in the intertidal of southern islands, but the taxonomy, distribution, and evolutionary history of these taxa are yet to be fully explored, mostly due to the difficulty of access to some of these locations. In this study, we examined specimens of the order Cladophorales from various locations in the high-latitude Southern Hemisphere including the subantarctic (the Auckland Islands, Bounty Islands, Campbell Island, Macquarie Island, and Kerguelen Islands), as well as mainland New Zealand, the Chatham Islands, Chile, and Tasmania. The analyses of the rDNA sequences of the samples revealed the existence of two new clades in a phylogeny of the Cladophoraceae. One of these clades is described as the novel genus Vandenhoekia gen. nov., which contains three species that are branched or unbranched. The amended genus Rama is reinstated to accommodate the other clade, and contains four species, including the Northern Hemisphere "Cladophora rupestris." In Rama both branched and unbranched morphologies are found. It is remarkable that gross morphology is not a predictor for generic affiliations in these algae. This study illustrates that much can still be learned about diversity in the Cladophorales and highlights the importance of new collections, especially in novel locations.
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Affiliation(s)
- Christian Boedeker
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Michael J Wynne
- Department of Ecology and Evolutionary Biology and Herbarium, University of Michigan, Ann Arbor, Michigan, USA
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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4
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Meinita MDN, Harwanto D, Choi JS. A concise review of the bioactivity and pharmacological properties of the genus Codium (Bryopsidales, Chlorophyta). JOURNAL OF APPLIED PHYCOLOGY 2022; 34:2827-2845. [PMID: 36259048 PMCID: PMC9559154 DOI: 10.1007/s10811-022-02842-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
The genus Codium is one of the most important genera of marine green macroalgae. Its distribution is widespread worldwide and it has a high degree of diversity in species and characteristics. This genus plays an important ecological role in marine ecosystems as it is a primary producer. However, some species in the genus Codium are invasive species and may disturb the functioning of the ecosystem. Economically, Codium has promising potential as a source of diverse nutritional and pharmacological compounds. Codium is edible, has a high nutrient value, and is rich in bioactive compounds. Hence, some species of Codium have been consumed as food and used as herbal medicines in some Asian countries. In recent decades, studies of the bioactivity and pharmacological properties of the genus Codium have attracted the attention of scientists. This review aims to identify gaps in studies analyzing Codium that have been conducted in the past three decades by assessing published research articles on its bioactivity and pharmacological properties. Compounds obtained from Codium have demonstrated significant biological activities, such as immunostimulatory, anticoagulant, anticancer, anti-inflammatory, antioxidant, antiviral, antibacterial, antifungal, antitumor, anti-angiogenic, osteoprotective, and anti-obesity activities. This review provides information that can be used as a future guideline for sustainably utilizing the genus Codium.
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Affiliation(s)
- Maria Dyah Nur Meinita
- Seafood Research Center, Industry Academy Cooperation Foundation (IACF), Silla University, 606, Advanced Seafood Processing Complex, Wonyang-ro, Amnam-dong, Seo-gu, Busan, 49277 Korea
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, 53123 Indonesia
- Center for Maritime Bioscience Studies, Jenderal Soedirman University, Purwokerto, 53123 Indonesia
| | - Dicky Harwanto
- Seafood Research Center, Industry Academy Cooperation Foundation (IACF), Silla University, 606, Advanced Seafood Processing Complex, Wonyang-ro, Amnam-dong, Seo-gu, Busan, 49277 Korea
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, 50275 Indonesia
| | - Jae-Suk Choi
- Seafood Research Center, Industry Academy Cooperation Foundation (IACF), Silla University, 606, Advanced Seafood Processing Complex, Wonyang-ro, Amnam-dong, Seo-gu, Busan, 49277 Korea
- Department of Seafood Science and Technology, The Institute of Marine Industry, Gyeongsang National University, 38 Cheondaegukchi-gil, Tongyeong-si, 53064 Gyeongsangnam-do Korea
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Tonicelli GA, Croce ME, Díaz-Tapia P, Fredericq S, Freshwater DW, Gauna MC, Parodi ER, Verbruggen H, Hommersand MH. Meridionella gen. nov., a New Genus of Cystocloniaceae (Gigartinales, Rhodophyta) from the Southern Hemisphere, Including M. obtusangula comb. nov. and M. antarctica sp. nov. JOURNAL OF PHYCOLOGY 2021; 57:797-816. [PMID: 33450046 DOI: 10.1111/jpy.13127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 06/12/2023]
Abstract
The classification of Cystoclonium obtusangulum has been questioned since the species was first described by Hooker and Harvey as Gracilaria? obtusangula. The objective of this study was to provide the first comprehensive taxonomic analysis of Cystoclonium obtusangulum, based on DNA sequences coupled with morphological observations made on syntype specimens and new collections. Sequence divergences of rbcL, UPA, and COI-5P, and maximum-likelihood phylogenies for rbcL and 18S demonstrated that specimens identified as Cystoclonium obtusangulum represent a clade of two distinct species that are distantly related to the generitype Cystoclonium purpureum. A new genus, Meridionella gen. nov., is proposed for this clade. The two species placed in this new genus were morphologically indistinguishable cryptic species, but have disjunct distributions, with Meridionella obtusangula comb. nov. found from temperate to cold coasts of South America and the Falkland Islands and Meridionella antarctica sp. nov., occurring in Antarctic waters. Vegetative and reproductive characters of Meridionella gen. nov. are described, and implications of our results for the biogeography of the family Cystocloniaceae are discussed.
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Affiliation(s)
- Gina A Tonicelli
- Instituto Argentino de Oceanografía, CONICET-UNS, Camino La carrindanga km 7.5, Bahía Blanca, 8000, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, Bahía Blanca, 8000, Argentina
| | - Maria Emilia Croce
- Instituto Argentino de Oceanografía, CONICET-UNS, Camino La carrindanga km 7.5, Bahía Blanca, 8000, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, Bahía Blanca, 8000, Argentina
| | - Pilar Díaz-Tapia
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071, A Coruña, Spain
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de A Coruña, Apdo, 130, 15080, A Coruña, Spain
| | - Suzanne Fredericq
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
| | - David Wilson Freshwater
- Center for Marine Science, University of North Carolina at Wilmington, 5600 Marvin Moss Lane, Wilmington, North Carolina, 28409, USA
| | - Maria Cecilia Gauna
- Instituto Argentino de Oceanografía, CONICET-UNS, Camino La carrindanga km 7.5, Bahía Blanca, 8000, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, Bahía Blanca, 8000, Argentina
| | - Elisa R Parodi
- Instituto Argentino de Oceanografía, CONICET-UNS, Camino La carrindanga km 7.5, Bahía Blanca, 8000, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, Bahía Blanca, 8000, Argentina
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Max H Hommersand
- Department of Biology, University of North Carolina at Chapel Hill, Coker Hall, Chapel Hill, North Carolina, 27599-3280, USA
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Zhu H, Sun H, Zhao Z, Liu X, Liu B, Hu Z, Leliaert F, Liu G. Chlorocladiella gen. nov. (Pithophoraceae, Cladophorales, Chlorophyta), Including Four New Species From Various Freshwater Habitats in China. JOURNAL OF PHYCOLOGY 2020; 56:895-907. [PMID: 32180225 DOI: 10.1111/jpy.12991] [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: 06/11/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Samples of Pithophoraceae, collected in diverse freshwater and damp terrestrial habitats from tropical and subtropical China, were characterized morphologically and ultrastructurally, and their phylogenetic position was determined based on nuclear ribosomal DNA sequences. Our phylogenetic analysis resolved a novel lineage of Pithophoraceae, sister to Aegagropilopsis. Based on our phylogenetic results, morphological observations and comparative rDNA ITS2 secondary structure analysis, we propose Chlorocladiella gen. nov., characterized by a well-developed system of prostrate filaments, and describe four new species, C. cochlea sp. nov., C. erecta sp. nov., C. medogensis sp. nov., and C. pisformis sp. nov. Two species were found growing on damp soil, which is an unusual habitat for cladophoralean green algae, indicating that the diversity of Cladophorales in terrestrial habitats may be greater than currently recognized.
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Affiliation(s)
- Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Hui Sun
- Qingdao Branch of Shandong Water Diversion Project Operation and Maintenance Center, Qingdao, 266100, China
| | - Zhijuan Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning, 530001, China
| | - Xudong Liu
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Frederik Leliaert
- Meise Botanic Garden, Meise, 1860, Belgium
- Biology Department, Ghent University, 9000, Ghent, Belgium
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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Rindi F, Pasella MM, Lee MFE, Verbruggen H. Phylogeography of the mediterranean green seaweed Halimeda tuna (Ulvophyceae, Chlorophyta). JOURNAL OF PHYCOLOGY 2020; 56:1109-1113. [PMID: 32315445 DOI: 10.1111/jpy.13006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Populations of many Mediterranean marine species show a strong phylogeographic structure, but the knowledge available for native seaweeds is limited. We investigated the genetic diversity of the green alga Halimeda tuna based on two plastid markers (tufA gene and a newly developed amplicon spanning five ribosomal protein genes and intergenic spacers, the rpl2-rpl14 region). The tufA sequences showed that Mediterranean H. tuna represents a single, well-defined species. The rpl2-rpl14 results highlighted a genetic separation between western and eastern Mediterranean populations; specimens collected from widely scattered locations in the Adriatic/Ionian region shared a haplotype unique to this region, and formed a group separated from all western Mediterranean regions. Specimens from Sardinia also formed a unique haplotype. Within the western Mediterranean basin, a gradual shift in the frequency of haplotypes was apparent along a West-East gradient. Our results represent the first clear evidence of an East-West genetic cleavage in a native Mediterranean macroalga and offer an interesting perspective for further research into fine-scale seaweed population structure in the NW Mediterranean Sea.
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Affiliation(s)
- Fabio Rindi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, Ancona, 60131, Italy
| | - Marisa M Pasella
- School of BioSciences, University of Melbourne, Victoria, 3010, Australia
| | - Ming-Fen E Lee
- School of BioSciences, University of Melbourne, Victoria, 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Victoria, 3010, Australia
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Díaz-Tapia P, Ly M, Verbruggen H. Extensive cryptic diversity in the widely distributed Polysiphonia scopulorum (Rhodomelaceae, Rhodophyta): Molecular species delimitation and morphometric analyses. Mol Phylogenet Evol 2020; 152:106909. [PMID: 32702527 DOI: 10.1016/j.ympev.2020.106909] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 10/23/2022]
Abstract
Our knowledge of seaweed diversity and biogeography still largely relies on information derived from morphological identifications, but the use of molecular tools is revealing that cryptic diversity is common among algae. Polysiphonia scopulorum is a turf-forming red alga widely reported in tropical and temperate coasts worldwide. The only study based on material collected from its Australian type locality and the Iberian Peninsula indicates that it is a species complex, but the extent of cryptic diversity across its geographical range is not known. To investigate the species diversity in P. scopulorum, the geographical distribution of species-level lineages and their morphological characterization, we collected 135 specimens from Australia, South Africa and southern Europe. Two gene datasets (cox1 and rbcL) were used to delimit species using three methods (GMYC, PTP, ABGD), leading to a consensus result that our collections of the P. scopulorum complex comprise 12 species. Five of these species were resolved in a highly supported clade, while the other seven species were related to other taxonomically accepted species or in unresolved parts of the tree. Morphometric and statistical analysis of a set of ten quantitative characters showed that there are no clear morphological correlates of species boundaries, demonstrating true cryptic diversity in the P. scopulorum complex. Distribution patterns of the 12 species were variable, ranging from species only known from a single site to species with a wide distribution spanning three continents. Our study indicates that a significant level of undiscovered cryptic diversity is likely to be found in algal turfs, a type of seaweed community formed by small entangled species.
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Affiliation(s)
- Pilar Díaz-Tapia
- School of BioSciences, University of Melbourne, Victoria 3010, Australia; Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071 A Coruña, Spain; Instituto Español de Oceanografía (IEO), Centro Oceanográfico de A Coruña, Aptdo. 130, 15080 A Coruña, Spain.
| | - Monica Ly
- School of BioSciences, University of Melbourne, Victoria 3010, Australia.
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Victoria 3010, Australia.
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Gomes FP, Maggs CA, Barros-Barreto MBB. Integrative approach reveals four new cryptic species in the genus Gayliella (Ceramiaceae, Rhodophyta) 1. JOURNAL OF PHYCOLOGY 2020; 56:437-457. [PMID: 31876951 DOI: 10.1111/jpy.12961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
The filamentous red algal genus Gayliella, typified by G. flaccida, was segregated from Ceramium for a group of epiphytic species on the basis of morphological data and molecular phylogenetic analyses. However, while the genus was well investigated in some geographical areas, the treatment of the Brazilian taxa "Ceramium flaccidum" and "C. dawsonii" was incomplete and they were not transferred to Gayliella due to the problematic status of the specific epithets. Brazilian "C. flaccidum" did not fit within the circumscription of Gayliella flaccida; Brazilian "C. dawsonii" was positioned in three distinct lineages, none of which corresponded to known Gayliella species. Since the establishment of Gayliella, there has been no re-evaluation of Brazilian species, so this study revises the genus in Brazil using molecular and morphological data. Brazilian "C. flaccidum", "C. dawsonii", and other Brazilian collections were investigated by an integrative approach using phylogenetic analysis, genetic divergence, two species delimitation methods using three molecular markers (rbcL, cox1, and partial LSU), and comparative morphological and quantitative analyses. This molecular-assisted alpha taxonomy (MAAT) analysis placed Brazilian samples in five distinct well-supported lineages. For these, we propose a new combination, Gayliella dawsonii comb. nov. (lineage 2), based on analysis of type specimens and molecular data obtained from specimens collected near the type locality, and four new species: Gayliella ardissonei sp. nov. ("Ceramium flaccidum" from Brazil), G. iemanja sp. nov. ("C. dawsonii" lineage 3), G. tamoiensis sp. nov., and G. jolyana sp. nov. ("C. dawsonii" lineage 1).
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Affiliation(s)
- Fernanda P Gomes
- Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão, 20940-040, Rio de Janeiro, Brazil
| | - Christine A Maggs
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5AJ, UK
| | - Maria Beatriz B Barros-Barreto
- Laboratório Integrado de Ficologia, Universidade Federal do Rio de Janeiro, Rua Professor Rodolpho P. Rocco 211, bloco A, 21941-902, Rio de Janeiro, Brazil
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Vitales D, Aragay J, Garnatje T, Gómez Garreta A, Rull Lluch J. Phylogeography of Dictyota fasciola and Dictyota mediterranea (Dictyotales, Phaeophyceae): unexpected patterns on the Atlantic-Mediterranean marine transition and taxonomic implications. PeerJ 2019; 7:e6916. [PMID: 31143543 PMCID: PMC6526009 DOI: 10.7717/peerj.6916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/06/2019] [Indexed: 12/25/2022] Open
Abstract
The Atlantic-Mediterranean marine transition is a fascinating biogeographic region, but still very poorly studied from the point of view of seaweed phylogeography. Dictyota fasciola and D. mediterranea (Dictyotales, Phaeophyceae) are two currently recognized sister species that share a large part of their distribution along the Mediterranean Sea and the Atlantic Ocean, representing a unique study model to understand the diversification processes experienced by macroalgae during and after Messinian at this marine region. In this study, we sampled 102 individuals of D. fasciola and D. mediterranea from 32 localities along their distribution range and sequenced the mitochondrial cox1 and the chloroplast rbcL-rbcS DNA regions for all the samples. Our data do not support the occurrence of two sister species but a morphologically variable and highly genetic diverse species or a complex of species. Most of the observed genetic diversity corresponds to the Mediterranean populations, whereas the Atlantic ones are much more homogeneous. The early-diverged lineages inferred from both mtDNA and cpDNA phylogenetic reconstructions were constituted by samples from the Mediterranean Sea. Together, these results suggest that the Mediterranean Sea acted as a refugium for the D. fasciola–D. mediterranea lineage during the geologic and climatic changes occurred on the region since the Miocene, subsequently dispersing to the Atlantic Ocean.
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Affiliation(s)
- Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
| | - Joana Aragay
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain.,Laboratori de Botànica, Facultat de Farmàcia i Ciències de l'Alimentació & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
| | - Amelia Gómez Garreta
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l'Alimentació & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Jordi Rull Lluch
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l'Alimentació & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
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11
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Pezzolesi L, Peña V, Le Gall L, Gabrielson PW, Kaleb S, Hughey JR, Rodondi G, Hernandez-Kantun JJ, Falace A, Basso D, Cerrano C, Rindi F. Mediterranean Lithophyllum stictiforme (Corallinales, Rhodophyta) is a genetically diverse species complex: implications for species circumscription, biogeography and conservation of coralligenous habitats. JOURNAL OF PHYCOLOGY 2019; 55:473-492. [PMID: 30657167 DOI: 10.1111/jpy.12837] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
Lithophyllum species in the Mediterranean Sea function as algal bioconstructors, contributing to the formation of biogenic habitats such as coralligenous concretions. In such habitats, thalli of Lithophyllum, consisting of crusts or lamellae with entire or lobed margins, have been variously referred to as either one species, L. stictiforme, or two species, L. stictiforme and L. cabiochiae, in the recent literature. We investigated species diversity and phylogenetic relationships in these algae by sequencing three markers (psbA and rbcL genes, cox2,3 spacer), in conjunction with methods for algorithmic delimitation of species (ABGD and GMYC). Mediterranean subtidal Lithophyllum belong to a well-supported lineage, hereby called the L. stictiforme complex, which also includes two species described from the Atlantic, L. lobatum and L. searlesii. Our results indicate that the L. stictiforme complex consists of at least 13 species. Among the Mediterranean species, some are widely distributed and span most of the western and central Mediterranean, whereas others appear to be restricted to specific localities. These patterns are interpreted as possibly resulting from allopatric speciation events that took place during the Messinian Salinity Crisis and subsequent glacial periods. A partial rbcL sequence from the lectotype of L. stictiforme unambiguously indicates that this name applies to the most common subtidal Lithophyllum in the central Mediterranean. We agree with recent treatments that considered L. cabiochiae and L. stictiforme conspecific. The diversity of Lithophyllum in Mediterranean coralligenous habitats has been substantially underestimated, and future work on these and other Mediterranean corallines should use identifications based on DNA sequences.
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Affiliation(s)
- Laura Pezzolesi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Via Sant'Alberto 163, 48123, Ravenna, Italy
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Viviana Peña
- Grupo BioCost, Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A, Coruña, Spain
| | - Line Le Gall
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 39, 75005, Paris, France
| | - Paul W Gabrielson
- Department of Biology and Herbarium, University of North Carolina, Coker Hall CB 3280, Chapel Hill, North Carolina, 27599-3280, USA
| | - Sara Kaleb
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Jeffery R Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, 411 Central Avenue, Salinas, California, 93901, USA
| | - Graziella Rodondi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Jazmin J Hernandez-Kantun
- Botany Department, National Museum of Natural History, Smithsonian Institution, MRC 166 PO Box 37012, Washington District of Columbia, USA
| | - Annalisa Falace
- Dipartimento di Scienze della Vita, Università di Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Daniela Basso
- Dipartimento di Scienze dell'Ambiente e della Terra, Università degli Studi di Milano-Bicocca, Piazza della Scienza 4, 20126, Milan, Italy
- CoNISMa, ULR Milano-Bicocca, Milan, Italy
| | - Carlo Cerrano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Fabio Rindi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
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12
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Díaz-Tapia P, Maggs CA, Macaya EC, Verbruggen H. Widely distributed red algae often represent hidden introductions, complexes of cryptic species or species with strong phylogeographic structure. JOURNAL OF PHYCOLOGY 2018; 54:829-839. [PMID: 30137690 DOI: 10.1111/jpy.12778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
Despite studies suggesting that most seaweeds are poor dispersers, many red algal species are reported to have circumglobal distributions. Such distributions have mostly been based on morphological identifications, but molecular data have revealed a range of issues with morphologically defined species boundaries. Consequently, the real distribution of such reportedly circumglobal species must be questioned. In this study, we analyzed molecular data sets (rbcL gene) of nine species in the Rhodomelaceae for which samples were available from widely spaced geographical locations. Three overall patterns were identified: (i) species showing strong phylogeographic structure (i.e., phylogenetic similarity correlates with geographical provenance), often to the point that populations from different locations could be considered as different species (Lophosiphonia obscura, Ophidocladus simpliciusculus, Polysiphonia villum, and Xiphosiphonia pinnulata); (ii) species with a broad distribution that is explained, in part, by putative human-mediated transport (Symphyocladia dendroidea and Polysiphonia devoniensis); and (iii) non-monophyletic complexes of cryptic species, most with a more restricted distribution than previously thought (Herposiphonia tenella, Symphyocladia dendroidea, and the Xiphosiphonia pennata complex that includes the species Xiphosiphonia pinnulata and Symphyocladia spinifera). This study shows that widely distributed species are the exception in marine red algae, unless they have been spread by humans.
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Affiliation(s)
- Pilar Díaz-Tapia
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071, A Coruña, Spain
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Christine A Maggs
- Portaferry Marine Laboratory, Queen's University Belfast, Belfast, BT22 1PF, UK
| | - Erasmo C Macaya
- Laboratorio de Estudios Algales (ALGALAB), Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Millennium Nucleus Ecology and Sustainable Management of Oceanic Island (ESMOI), Larrondo, 1281, Coquimbo, Chile
- Centro FONDAP de Investigaciones en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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Pinseel E, Kulichová J, Scharfen V, Urbánková P, Van de Vijver B, Vyverman W. Extensive Cryptic Diversity in the Terrestrial Diatom Pinnularia borealis (Bacillariophyceae). Protist 2018; 170:121-140. [PMID: 30954839 DOI: 10.1016/j.protis.2018.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/29/2018] [Accepted: 10/02/2018] [Indexed: 01/01/2023]
Abstract
With the increasing application of molecular techniques for diatom species discovery and identification, it is important both from a taxonomic as well as an ecological and applied perspective, to understand in which groups morphological species delimitation is congruent with molecular approaches, or needs reconsideration. Moreover, such studies can improve our understanding of morphological trait evolution in this important group of microalgae. In this study, we used morphometric analysis on light microscopy (LM) micrographs in SHERPA, detailed scanning electron microscopy (SEM), and cytological observations in LM to examine 70 clones belonging to eight distinct molecular lineages of the cosmopolitan terrestrial diatom Pinnularia borealis. Due to high within-lineage variation, no conclusive morphological separation in LM nor SEM could be detected. Morphological stasis due to the "low-morphology" problem or stabilizing selection, as well as parallel/convergent evolution, phenotypic plasticity and structural inheritance are discussed as potential drivers for the observations. Altogether, P. borealis is truly cryptic, in contrast to the majority of other diatom species complexes which turned out to be pseudo-cryptic following detailed morphological analysis.
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Affiliation(s)
- Eveline Pinseel
- Protistology & Aquatic Ecology (PAE), Department of Biology, Faculty of Science, Ghent University, Krijgslaan 281-S8, B-9000 Ghent, Belgium; Research Department, Botanic Garden Meise, Nieuwelaan 38, B-1860 Meise, Belgium; Ecosystem Management Research Group (ECOBE), Department of Biology, Faculty of Science, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Antwerp, Belgium.
| | - Jana Kulichová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague 2, Czech Republic
| | - Vojtěch Scharfen
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague 2, Czech Republic
| | - Pavla Urbánková
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague 2, Czech Republic
| | - Bart Van de Vijver
- Research Department, Botanic Garden Meise, Nieuwelaan 38, B-1860 Meise, Belgium; Ecosystem Management Research Group (ECOBE), Department of Biology, Faculty of Science, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Antwerp, Belgium
| | - Wim Vyverman
- Protistology & Aquatic Ecology (PAE), Department of Biology, Faculty of Science, Ghent University, Krijgslaan 281-S8, B-9000 Ghent, Belgium
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Cabral Oliveira M. Reclassification of the Rhodomelaceae using High Throughput Sequencing: application of big data to algal systematics. JOURNAL OF PHYCOLOGY 2017; 53:917-919. [PMID: 29044565 DOI: 10.1111/jpy.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Mariana Cabral Oliveira
- Botany Department, Institute of Biosciences, University of São Paulo, R. Matão, 277, São Paulo, SP, 05508-090, Brazil
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Boedeker C, O'Kelly CJ, West JA, Hanyuda T, Neale A, Wakana I, Wilcox MD, Karsten U, Zuccarello GC. Molecular phylogeny and taxonomic revision of the genus Wittrockiella (Pithophoraceae, Cladophorales), including the descriptions of W. australis sp. nov. and W. zosterae sp. nov. JOURNAL OF PHYCOLOGY 2017; 53:522-540. [PMID: 28295311 DOI: 10.1111/jpy.12530] [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: 09/05/2016] [Accepted: 12/04/2016] [Indexed: 06/06/2023]
Abstract
Wittrockiella is a small genus of filamentous green algae that occurs in habitats with reduced or fluctuating salinities. Many aspects of the basic biology of these algae are still unknown and the phylogenetic relationships within the genus have not been fully explored. We provide a phylogeny based on three ribosomal markers (ITS, LSU, and SSU rDNA) of the genus, including broad intraspecific sampling for W. lyallii and W. salina, recommendations for the use of existing names are made, and highlight aspects of their physiology and life cycle. Molecular data indicate that there are five species of Wittrockiella. Two new species, W. australis and W. zosterae, are described, both are endophytes. Although W. lyallii and W. salina can be identified morphologically, there are no diagnostic morphological characters to distinguish between W. amphibia, W. australis, and W. zosterae. A range of low molecular weight carbohydrates were analyzed but proved to not be taxonomically informative. The distribution range of W. salina is extended to the Northern Hemisphere as this species has been found in brackish lakes in Japan. Furthermore, it is shown that there are no grounds to recognize W. salina var. kraftii, which was described as an endemic variety from a freshwater habitat on Lord Howe Island, Australia. Culture experiments indicate that W. australis has a preference for growth in lower salinities over full seawater. For W. amphibia and W. zosterae, sexual reproduction is documented, and the split of these species is possibly attributable to polyploidization.
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Affiliation(s)
- Christian Boedeker
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Charles J O'Kelly
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, 98250, USA
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Vic, 3010, Australia
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Rokkodai, Nadaku, Kobe, 657-8501, Japan
| | - Adele Neale
- School of Biosciences 2, University of Melbourne, Parkville, Vic, 3010, Australia
| | - Isamu Wakana
- Lake Akan Eco-Museum Center, Akano-onsen 1-1-1, Akan, Hokkaido, 085-0467, Japan
| | - Mike D Wilcox
- Botany Department, Auckland Museum, Private Bag 92018, Auckland, 1142, New Zealand
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology & Phycology, University of Rostock, D-18059, Rostock, Germany
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
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Merényi Z, Varga T, Hubai AG, Pitlik P, Erős Á, Trappe JM, Bratek Z. Challenges in the delimitation of morphologically similar species: a case study of Tuber brumale agg. (Ascomycota, Pezizales). Mycol Prog 2017. [DOI: 10.1007/s11557-017-1296-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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17
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Weber XA, Edgar GJ, Banks SC, Waters JM, Fraser CI. A morphological and phylogenetic investigation into divergence among sympatric Australian southern bull kelps (Durvillaea potatorum and D. amatheiae sp. nov.). Mol Phylogenet Evol 2017; 107:630-643. [PMID: 28017856 DOI: 10.1016/j.ympev.2016.12.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 12/11/2016] [Accepted: 12/20/2016] [Indexed: 11/19/2022]
Abstract
Genetic analyses can reveal a wealth of hitherto undiscovered cryptic biodiversity. For co-occurring and morphologically similar species, the combination of molecular, ecological and morphological analyses provides an excellent opportunity for understanding some of the processes that can lead to divergence and speciation. The Australian endemic brown macroalga Durvillaea potatorum (Phaeophyceae) was examined with a combination of genetic and morphological approaches to confirm the presence of two separate species and to infer the processes that led to their divergence. A total of 331 individuals from 11 sites around coastal Tasmania were collected and measured in situ for a range of morphological and ecological characteristics. Tissue samples were also collected for each individual to allow genetic analyses using mitochondrial (COI) and nuclear (28S) markers. Genetic analyses confirmed the presence of two deeply divergent clades. The significant morphological differentiation, despite high levels of intra-lineage variability, further supported their recognition as distinct species. We describe a new species, D. amatheiae sp. nov., which is characterised by a narrower and proportionately shorter stipe, shorter total length, and higher number of stipitate lateral blades and branches than D. potatorum (sensu stricto). The occurrence of both species in sympatry along Tasmania's eastern and western coasts, as well as their contrasting patterns of haplotype diversity, supports a hypothesis of geographical isolation, allopatric speciation and subsequent secondary contact in response to sea level and ocean current change throughout the Pleistocene glaciation cycles. This research contributes to resolving the phylogenetic relationships, taxonomy and evolution of the ecologically keystone kelp genus Durvillaea.
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Affiliation(s)
- Xénia A Weber
- Fenner School of Environment and Society, Australian National University, Building 141, Linnaeus Way, Acton ACT 2601, Australia.
| | - Graham J Edgar
- Institute for Marine and Antarctic Studies, University of Tasmania, GPO Box 252-49, Hobart, Tasmania 7001, Australia
| | - Sam C Banks
- Fenner School of Environment and Society, Australian National University, Building 141, Linnaeus Way, Acton ACT 2601, Australia
| | - Jonathan M Waters
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Fenner School of Environment and Society, Australian National University, Building 141, Linnaeus Way, Acton ACT 2601, Australia
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From Alaska to Antarctica: Species boundaries and genetic diversity of Prasiola (Trebouxiophyceae), a foliose chlorophyte associated with the bipolar lichen-forming fungus Mastodia tessellata. Mol Phylogenet Evol 2017; 107:117-131. [DOI: 10.1016/j.ympev.2016.10.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/11/2016] [Accepted: 10/17/2016] [Indexed: 01/09/2023]
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Rindi F, Verbruggen H. Taxonomic Reshuffling of the Cladophoraceae. JOURNAL OF PHYCOLOGY 2016; 52:901-904. [PMID: 27976384 DOI: 10.1111/jpy.12459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Fabio Rindi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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Boedeker C, Leliaert F, Zuccarello GC. Molecular phylogeny of the Cladophoraceae (Cladophorales, Ulvophyceae), with the resurrection of Acrocladus Nägeli and Willeella Børgesen, and the description of Lurbica gen. nov. and Pseudorhizoclonium gen. nov. JOURNAL OF PHYCOLOGY 2016; 52:905-928. [PMID: 27535014 DOI: 10.1111/jpy.12457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/06/2016] [Indexed: 05/24/2023]
Abstract
The taxonomy of the Cladophoraceae, a large family of filamentous green algae, has been problematic for a long time due to morphological simplicity, parallel evolution, phenotypic plasticity, and unknown distribution ranges. Partial large subunit (LSU) rDNA sequences were generated for 362 isolates, and the analyses of a concatenated dataset consisting of unique LSU and small subunit (SSU) rDNA sequences of 95 specimens greatly clarified the phylogeny of the Cladophoraceae. The phylogenetic reconstructions showed that the three currently accepted genera Chaetomorpha, Cladophora, and Rhizoclonium are polyphyletic. The backbone of the phylogeny is robust and the relationships of the main lineages were inferred with high support, only the phylogenetic position of both Chaetomorpha melagonium and Cladophora rupestris could not be inferred unambiguously. There have been at least three independent switches between branched and unbranched morphologies within the Cladophoraceae. Freshwater environments have been colonized twice independently, namely by the freshwater Cladophora species as well as by several lineages of the Rhizoclonium riparium clade. In an effort to establish monophyletic genera, the genera Acrocladus and Willeella are resurrected and two new genera are described: Pseudorhizoclonium and Lurbica.
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Affiliation(s)
- Christian Boedeker
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, 6140, New Zealand
| | - Frederik Leliaert
- Phycology Research Group, Biology Department, Ghent University, Krijgslaan 281 S8, 9000, Ghent, Belgium
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, 6140, New Zealand
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Marcelino VR, Verbruggen H. Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae. Sci Rep 2016; 6:31508. [PMID: 27545322 PMCID: PMC4992875 DOI: 10.1038/srep31508] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/21/2016] [Indexed: 02/06/2023] Open
Abstract
Bacteria, fungi and green algae are common inhabitants of coral skeletons. Their diversity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the biodiversity. We used a cost-effective protocol and a combination of markers (tufA, 16S rDNA, 18S rDNA and 23S rDNA) to characterize the microbiome of 132 coral skeleton samples. We identified a wide range of prokaryotic and eukaryotic organisms, many never reported in corals before. We additionally investigated the phylogenetic diversity of the green algae—the most abundant eukaryotic member of this community, for which previous literature recognizes only a handful of endolithic species. We found more than 120 taxonomic units (near species level), including six family-level lineages mostly new to science. The results suggest that the existence of lineages with an endolithic lifestyle predates the existence of modern scleractinian corals by ca. 250my, and that this particular niche was independently invaded by over 20 lineages in green algae evolution. These results highlight the potential of the multi-marker approach to assist in species discovery and, when combined with a phylogenetic framework, clarify the evolutionary origins of host-microbiota associations.
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Mattio L, Zubia M, Maneveldt G, Anderson R, Bolton J, de Gaillande C, De Clerck O, Payri C. Marine flora of the Iles Eparses (Scattered Islands): A longitudinal transect through the Mozambique Channel. ACTA OECOLOGICA 2016. [DOI: 10.1016/j.actao.2015.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity. Mol Phylogenet Evol 2015; 94:814-826. [PMID: 26484942 DOI: 10.1016/j.ympev.2015.09.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification.
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Hernandez-Kantun JJ, Rindi F, Adey WH, Heesch S, Peña V, Le Gall L, Gabrielson PW. Sequencing type material resolves the identity and distribution of the generitype Lithophyllum incrustans, and related European species L. hibernicum and L. bathyporum (Corallinales, Rhodophyta). JOURNAL OF PHYCOLOGY 2015; 51:791-807. [PMID: 26986797 DOI: 10.1111/jpy.12319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 05/07/2015] [Indexed: 06/05/2023]
Abstract
DNA sequences from type material in the nongeniculate coralline genus Lithophyllum were used to unambiguously link some European species names to field-collected specimens, thus providing a great advance over morpho-anatomical identifi-cation. In particular, sequence comparisons of rbcL, COI and psbA genes from field-collected specimens allowed the following conclusion: the generitype species, L. incrustans, occurs mostly as subtidal rhodoliths and crusts on both Atlantic and Mediterranean coasts, and not as the common, NE Atlantic, epilithic, intertidal crust reported in the literature. The heterotypic type material of L. hibernicum was narrowed to one rhodolith belonging in Lithophyllum. As well as occurring as a subtidal rhodolith, L. hibernicum is a common, epilithic and epizoic crust in the intertidal zone from Ireland south to Mediterranean France. A set of four features distinguished L. incrustans from L. hibernicum, including epithallial cell diameter, pore canal shape of sporangial conceptacles and sporangium height and diameter. An rbcL sequence of the lectotype of Lithophyllum bathyporum, which was recently proposed to accommodate Atlantic intertidal collections of L. incrustans, corresponded to a distinct taxon hitherto known only from Brittany as the subtidal, bisporangial, lectotype, but also occurs intertidally in Atlantic Spain. Specimens from Ireland and France morpho-anatomically identified as L. fasciculatum and a specimen from Cornwall likewise identified as L. duckerae were resolved as L. incrustans and L. hibernicum, respectively.
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Affiliation(s)
- Jazmin J Hernandez-Kantun
- Botany Department, National Museum of Natural History, Smithsonian Institution, MRC 166 PO Box 37012, Washington, District of Columbia, USA
- Irish Seaweed Research Group, Ryan Institute, National University of Ireland, University Road, Galway, Ireland
| | - Fabio Rindi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, Ancona, 60131, Italy
| | - Walter H Adey
- Botany Department, National Museum of Natural History, Smithsonian Institution, MRC 166 PO Box 37012, Washington, District of Columbia, USA
| | - Svenja Heesch
- Irish Seaweed Research Group, Ryan Institute, National University of Ireland, University Road, Galway, Ireland
| | - Viviana Peña
- BIOCOST Research Group, Departamento de Bioloxía Animal, Bioloxía Vexetal e Ecoloxía, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, A Coruña, 15071, Spain
- Equipe Exploration, Espèces et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 ISYEB CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle (MNHN), Sorbonne Universités, 57 rue Cuvier CP 39, Paris, 75005, France
- Phycology Research Group, Ghent University, Krijgslaan 281, Building S8, Ghent, 9000, Belgium
| | - Line Le Gall
- Equipe Exploration, Espèces et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 ISYEB CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle (MNHN), Sorbonne Universités, 57 rue Cuvier CP 39, Paris, 75005, France
| | - Paul W Gabrielson
- Department of Biology and Herbarium, University of North Carolina, Chapel Hill, Coker Hall CB 3280, Chapel Hill, North Carolina, 27599-3280, USA
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Robuchon M, Valero M, Gey D, Le Gall L. How does molecular-assisted identification affect our estimation of α, β and γ biodiversity? An example from understory red seaweeds (Rhodophyta) of Laminaria kelp forests in Brittany, France. Genetica 2015; 143:207-23. [PMID: 25351554 DOI: 10.1007/s10709-014-9796-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022]
Abstract
Using two distinct identification methods, one based on morphological characters only and the other combining morphological and molecular characters (integrative identification method), we investigated the differences in the biodiversity patterns of red seaweed communities associated with kelp forests at various spatial scales: the regional diversity of Brittany, France (γ-diversity), the local diversity at different Breton sites (α-diversity) and the differentiation in species diversity and abundances among those sites (β-diversity). To characterise α and β diversities, we conducted an initial survey in winter 2011 at 20 sites belonging to four different sub-regions, with specimens collected from six quadrats of 0.10 m(2) at each site, three in the tidal zone dominated by Laminaria digitata and three in the zone dominated by Laminaria hyperborea. To further characterise the regional diversity, we carried out another survey combining several sampling methods (quadrats and visual census) in different seasons (winter, spring and summer) and different years (2011 and 2012). In all, we collected 1990 specimens that were assigned to 76 taxa with the identification method based on morphological characters and 139 taxa using the integrative method. For γ and α diversity, the use of molecular characters revealed several cases of cryptic diversity and both increased the number of identified taxa and improved their taxonomic resolution. However, the addition of molecular characters for specimen identification only slightly affected estimates of β-diversity.
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Affiliation(s)
- Marine Robuchon
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS, EPHE, MNHN, UPMC, Equipe Exploration, Espèces, Evolution, Muséum National d'Histoire Naturelle, Case Postale N° 39, 57 rue Cuvier, 75231, Cedex 05 Paris, France,
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26
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Sadowska-Deś AD, Dal Grande F, Lumbsch HT, Beck A, Otte J, Hur JS, Kim JA, Schmitt I. Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia. Mol Phylogenet Evol 2014; 76:202-10. [PMID: 24685499 DOI: 10.1016/j.ympev.2014.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/04/2014] [Accepted: 03/17/2014] [Indexed: 02/05/2023]
Abstract
The accurate assessment of species boundaries in symbiotic systems is a prerequisite for the study of speciation, co-evolution and selectivity. Many studies have shown the high genetic diversity of green algae from the genus Trebouxia, the most common photobiont of lichen-forming fungi. However, the phylogenetic relationships, and the amount of cryptic diversity of these algae are still poorly understood, and an adequate species concept for trebouxiophycean algae is still missing. In this study we used a multifaceted approach based on coalescence (GMYC, STEM) and phylogenetic relationships to assess species boundaries in the trebouxioid photobionts of the lichen-forming fungus Lasallia pustulata. We further investigated whether putative species of Trebouxia found in L. pustulata are shared with other lichen-forming fungi. We found that L. pustulata is associated with at least five species of Trebouxia and most of them are shared with other lichen-forming fungi, showing different patterns of species-to-species and species-to-community interactions. We also show that one of the putative Trebouxia species is found exclusively in association with L. pustulata and is restricted to thalli from localities with Mediterranean microclimate. We suggest that the species delimitation method presented in this study is a promising tool to address species boundaries within the heterogeneous genus Trebouxia.
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Affiliation(s)
- Anna D Sadowska-Deś
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany.
| | - Francesco Dal Grande
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany
| | - H Thorsten Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Andreas Beck
- Department of Lichenology and Bryology, Botanische Staatssammlung München, Menzinger Straße 67, D-80638 München, Germany; GeoBio-Center, Ludwig-Maximilians Universität München, Richard-Wagner-Str. 10, D-80333 München, Germany
| | - Jürgen Otte
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, South Korea
| | - Jung A Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, South Korea
| | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany.
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