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Colin L, Abed-Navandi D, Conde DA, Craggs J, da Silva R, Janse M, Källström B, Pearce-Kelly A, Yesson C. What's left in the tank? Identification of non-ascribed aquarium's coral collections with DNA barcodes as part of an integrated diagnostic approach. CONSERV GENET RESOUR 2022; 14:167-182. [PMID: 35035629 PMCID: PMC8750641 DOI: 10.1007/s12686-021-01250-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022]
Abstract
The unprecedented threats to coral reef ecosystems from global climate change require an urgent response from the aquarium community, which is becoming an increasingly vital coral conservation resource. Unfortunately, many hermatypic corals in aquaria are not identified to species level, which hinders assessment of their conservation significance. Traditional methods of species identification using morphology can be challenging, especially to non-taxonomists. DNA barcoding is an option for species identification of Scleractinian corals, especially when used in concert with morphology-based assessment. This study uses DNA barcodes to try to identify aquarium specimens of the diverse reef-forming genus Acropora from 127 samples. We identified to our best current knowledge, to species name 44% of the analysed samples and provided provisional identification for 80% of them (101/127, in the form of a list of species names with associate confidence values). We highlighted a sampling bias in public nucleotide sequences repertories (e.g. GenBank) towards more charismatic and more studied species, even inside a well-studied genus like Acropora. In addition, we showed a potential “single observer” effect with over a quarter of the reference sequences used for these identifications coming from the same study. We propose the use of barcoding and query matching as an additional tool for taxonomic experts and general aquarists, as an additional tool to increase their chances of making high confidence species-level identifications. We produce a standardised and easily repeatable methodology to increase the capacity of aquariums and other facilities to assess non-ascribed species, emphasising the value of integrating this approach with morphological identification optimising usage of authoritative identification guides and expert opinion.
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Affiliation(s)
- Luigi Colin
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY UK
| | - Daniel Abed-Navandi
- Haus des Meeres-Aqua Terra Zoo, Fritz Gruenbaum Platz 1, 1060 Vienna, Austria
| | - Dalia A Conde
- Interdisciplinary Centre on Population Dynamics (CPop), Biology Department, University of Southern Denmark, Syddansk Universitet, Campusvej 55, 5230 Odense, Denmark.,Conservation Science Alliance, Species360, 7900 International Drive, Suite 1040, Bloomington, MN 55425 USA
| | - Jamie Craggs
- Horniman Museum and Gardens, 100 London Road, Forest Hill, London, SE23 3PQ UK
| | - Rita da Silva
- Interdisciplinary Centre on Population Dynamics (CPop), Biology Department, University of Southern Denmark, Syddansk Universitet, Campusvej 55, 5230 Odense, Denmark
| | - Max Janse
- Royal Burgers' Zoo, Antoon van Hooffplein 1, 6816 SH Arnhem, the Netherlands
| | - Björn Källström
- Maritime Museum and Aquarium, Karl Johansgatan 1-3, 41459 Göteborg, Sweden
| | | | - Chris Yesson
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY UK
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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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Cowman PF, Quattrini AM, Bridge TC, Watkins-Colwell GJ, Fadli N, Grinblat M, Roberts TE, McFadden CS, Miller DJ, Baird AH. An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives. Mol Phylogenet Evol 2020; 153:106944. [DOI: 10.1016/j.ympev.2020.106944] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022]
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Niu W, Xiao J, Tian P, Yu S, Guo F, Wang J, Huang D. Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics. PeerJ 2020; 8:e8455. [PMID: 32002337 PMCID: PMC6984341 DOI: 10.7717/peerj.8455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 12/24/2019] [Indexed: 11/20/2022] Open
Abstract
Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.
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Affiliation(s)
- Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Shuangen Yu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Jianjia Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Dingyong Huang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
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Stampar SN, Broe MB, Macrander J, Reitzel AM, Brugler MR, Daly M. Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia. Sci Rep 2019; 9:6094. [PMID: 30988357 PMCID: PMC6465557 DOI: 10.1038/s41598-019-42621-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/04/2019] [Indexed: 01/10/2023] Open
Abstract
Sequences and structural attributes of mitochondrial genomes have played a critical role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia (“tube anemones”) remains one of the most enigmatic in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both Isarachnanthus nocturnus and Pachycerianthus magnus, the mitochondrial gene sequences could not be assembled into a single circular genome. Instead, our analyses suggest that both species have mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The inferred number of fragments and variation in gene order between species is much greater within Ceriantharia than among the lineages of Medusozoa. We identify origins of replication for each of the five putative chromosomes of the Isarachnanthus nocturnus mitogenome and for each of the eight putative chromosomes of the Pachycerianthus magnus mitogenome. At 80,923 bp, I. nocturnus now holds the record for the largest animal mitochondrial genome reported to date. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other Anthozoa. The presence of tRNAMet and tRNATrp in both ceriantharian mitogenomes supports a closer relationship between Ceriantharia and Hexacorallia than between Ceriantharia and any other cnidarian lineage, but phylogenetic analysis of the genes contained in the mitogenomes suggests that Ceriantharia is sister to a clade containing Octocorallia + Hexacorallia indicating a possible suppression of tRNATrp in Octocorallia.
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Affiliation(s)
- Sérgio N Stampar
- Departamento de Ciências Biológicas, Faculdade de Ciências e Letras, UNESP - Universidade Estadual Paulista, Assis, SP, Brazil.
| | - Michael B Broe
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jason Macrander
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Department of Biology, Florida Southern College, Lakeland, FL, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mercer R Brugler
- Biological Sciences Department, NYC College of Technology, City University of New York, 285 Jay Street, Brooklyn, New York, 11201, USA.,Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Brugler MR, González-Muñoz RE, Tessler M, Rodríguez E. An EPIC journey to locate single-copy nuclear markers in sea anemones. ZOOL SCR 2018. [DOI: 10.1111/zsc.12309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mercer R. Brugler
- Division of Invertebrate Zoology; American Museum of Natural History; New York New York
- Biological Sciences Department; NYC College of Technology (CUNY); Brooklyn New York
| | - Ricardo E. González-Muñoz
- Laboratorio de Biología de Cnidarios; Instituto de Investigaciones Marinas y Costeras (IIMyC); CONICET; Universidad Nacional de Mar del Plata; Mar del Plata Argentina
- Instituto de Ciencias del Mar y Limnología (ICMyL); Posgrado en Ciencias del Mar y Limnología (PCMyL); UNAM, Ciudad Universitaria; Ciudad de México México
| | - Michael Tessler
- Division of Invertebrate Zoology; American Museum of Natural History; New York New York
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology; American Museum of Natural History; New York New York
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Robert R, Rodrigues KF, Waheed Z, Kumar SV. Extensive sharing of mitochondrial COI and CYB haplotypes among reef-building staghorn corals (Acropora spp.) in Sabah, North Borneo. Mitochondrial DNA A DNA Mapp Seq Anal 2018. [PMID: 29521145 DOI: 10.1080/24701394.2018.1448080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts/Tv), synonymous-to-nonsynonymous rate ratio (dN/dS), and substitution patterns at the three codon positions. Despite the relatively high haplotype diversity (Hd), nucleotide diversity (π) of the haplotype datasets was low due to stringent purifying selection operating on the genes. Subsequently, we identified individual COI and CYB haplotypes that were each extensively shared across sympatrically and allopatrically distributed Indo-Pacific Acropora. These reciprocally common mtDNA types were suspected to be ancestral forms of the genes whereas other haplotypes have mostly evolved from autoapomorphic mutations which have not been fixed within the species even though they are selectively neutral. To our knowledge, this is the first report on DNA barcodes of Acropora species in North Borneo and this understanding will play an important role in the management and conservation of these important reef-building corals.
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Affiliation(s)
- Rolando Robert
- a Biotechnology Research Institute , Universiti Malaysia Sabah, Jalan UMS , Kota Kinabalu , Sabah , Malaysia
| | - Kenneth Francis Rodrigues
- a Biotechnology Research Institute , Universiti Malaysia Sabah, Jalan UMS , Kota Kinabalu , Sabah , Malaysia
| | - Zarinah Waheed
- b Endangered Marine Species Research Unit, Borneo Marine Research Institute , Universiti Malaysia Sabah, Jalan UMS , Kota Kinabalu , Sabah , Malaysia
| | - Subbiah Vijay Kumar
- a Biotechnology Research Institute , Universiti Malaysia Sabah, Jalan UMS , Kota Kinabalu , Sabah , Malaysia
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Soler-Hurtado MM, López-González PJ, Machordom A. Molecular phylogenetic relationships reveal contrasting evolutionary patterns in Gorgoniidae (Octocorallia) in the Eastern Pacific. Mol Phylogenet Evol 2017; 111:219-230. [PMID: 28344106 DOI: 10.1016/j.ympev.2017.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 03/15/2017] [Accepted: 03/19/2017] [Indexed: 10/19/2022]
Abstract
The description and delimitation of species in an evolutionary framework is essential for understanding patterns of biodiversity and distribution, and in the assessment of conservation strategies for natural resources. This study seeks to clarify the evolutionary history and genetic variation within and between closely related octocoral species that are fundamental to benthic marine ecosystems for harbouring a high diversity of associated fauna. For our study system, we focused on members of the Gorgoniidae family in the Eastern Pacific, particularly of the Ecuadorian littoral, a less studied marine ecosystem. According to our results, the diagnosis of the genus Pacifigorgia is here amended to include species previously considered in the genus Leptogorgia. The genera Leptogorgia and Eugorgia are included within a single clade, and neither are recovered as monophyletic. In this case, according to the priority rule of the International Code of Zoological Nomenclature (ICZN), our proposal is to include the species considered in these two genera in Leptogorgia. In addition, we found evidence of interesting speciation patterns: morphological differentiation with no apparent genetic differentiation (in Pacifigorgia), and inconsistencies between mitochondrial and nuclear data that suggest a hybridisation phenomenon (in Leptogorgia). In the first case, recent radiation, ancient hybridisation, sympatric speciation, and in the second, reticulate evolution may have contributed to the evolutionary history of the studied taxa. Therefore, incongruences observed between morphological and molecular evidences in these octocorals, and in corals in general, may reveal the types of events/patterns that have influenced their evolution.
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Affiliation(s)
- M M Soler-Hurtado
- Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain; Biodiversidad y Ecología de Invertebrados Marinos, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; Instituto Nacional de Biodiversidad, Museo Ecuatoriano de Ciencias Naturales, Rumipamba 341 y Av. Shyris, Quito, Ecuador.
| | - P J López-González
- Biodiversidad y Ecología de Invertebrados Marinos, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain
| | - A Machordom
- Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain
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Schuster A, Lopez JV, Becking LE, Kelly M, Pomponi SA, Wörheide G, Erpenbeck D, Cárdenas P. Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding. BMC Evol Biol 2017; 17:82. [PMID: 28320321 PMCID: PMC5360047 DOI: 10.1186/s12862-017-0928-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/28/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns. RESULTS For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated. CONCLUSION This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.
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Affiliation(s)
- Astrid Schuster
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
| | - Jose V. Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004 USA
| | - Leontine E. Becking
- Marine Animal Ecology, Wageningen University & Research Centre, P.O. Box 3700, AH, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Marine Zoology Department, PO Box 9517, 2300 RA, Leiden, The Netherlands
| | - Michelle Kelly
- National Centre for Aquatic Biodiversity and Biosecurity, National Institute of Water and Atmospheric Research, P.O. Box 109–695, Newmarket, Auckland, New Zealand
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute-Florida Atlantic University, 5600 U.S. 1 North, Ft Pierce, FL 34946 USA
| | - Gert Wörheide
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
- SNSB - Bavarian State Collections of Palaeontology and Geology, Richard-Wagner Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Paco Cárdenas
- Department of Medicinal Chemistry, Division of Pharmacognosy, BioMedical Center, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
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Pratlong M, Rancurel C, Pontarotti P, Aurelle D. Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree? ZOOL SCR 2016. [DOI: 10.1111/zsc.12208] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marine Pratlong
- Aix Marseille Univ; Univ Avignon; CNRS; IRD; IMBE; Marseille France
- Aix Marseille Univ; CNRS; Centrale Marseille, I2M, Equipe Evolution Biologique et Modélisation; Marseille France
| | - Corinne Rancurel
- INRA; University Nice Sophia Antipolis; CNRS; UMR 1355-7254 Institut Sophia Agrobiotech; Sophia Antipolis France
| | - Pierre Pontarotti
- Aix Marseille Univ; CNRS; Centrale Marseille, I2M, Equipe Evolution Biologique et Modélisation; Marseille France
| | - Didier Aurelle
- Aix Marseille Univ; Univ Avignon; CNRS; IRD; IMBE; Marseille France
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Addamo AM, Vertino A, Stolarski J, García-Jiménez R, Taviani M, Machordom A. Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia. BMC Evol Biol 2016; 16:108. [PMID: 27193263 PMCID: PMC4870751 DOI: 10.1186/s12862-016-0654-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 12/16/2022] Open
Abstract
Background In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary Desmophyllum dianthus and colonial Lophelia pertusa. Results In the mitochondrial control region, an astonishing 99.8 % of nucleotides between L. pertusa and D. dianthus were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of L. pertusa and D. dianthus showed genetic similarity is about 97 %. Our results also indicated that L. pertusa and D. dianthus show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits). Conclusions Molecularly and morphologically, the solitary Desmophyllum and the dendroid Lophelia appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name Desmophyllum (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0654-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Maria Addamo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Agostina Vertino
- Dipartimento di Scienze dell'Ambiente e del Territorio e di Scienze della Terra, Università di Milano Bicocca (UNIMIB), Piazza della Scienza 4, 20126, Milan, Italy.,Department of Geology Renard Centre of Marine Geology, Universiteit Ghent, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Jaroslaw Stolarski
- Polskiej Akademii Nauk, Instytut Paleobiologii, Twarda 51/55, PL-00-818, Warsaw, Poland
| | - Ricardo García-Jiménez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Marco Taviani
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine (ISMAR), Via Gobetti 101, 40129, Bologna, Italy.,Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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Samimi-Namin K, van Ofwegen LP. Overview of the genus Briareum (Cnidaria, Octocorallia, Briareidae) in the Indo-Pacific, with the description of a new species. Zookeys 2016:1-44. [PMID: 26877697 PMCID: PMC4740834 DOI: 10.3897/zookeys.557.6298] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/09/2015] [Indexed: 11/16/2022] Open
Abstract
The status of Indo-Pacific Briareum species (Cnidaria, Octocorallia, Briareidae) is reviewed by presenting their sclerite features and habitus descriptions. Following the re-examination of type material, museum specimens and newly collected specimens, a species identification key is provided. The species distributions are discussed and updated distribution ranges are depicted. Moreover, a new taxon, Briareumcylindrumsp. n. is described and depicted, whereas Briareumexcavatum (Nutting, 1911) is synonymised with Briareumstechei (Kükenthal, 1908). Briareumhamrum (Gohar, 1948) is recorded from the Persian Gulf and Oman Sea for the first time. Consequently, in total four Briareum species are recognized in the Indo-Pacific; Briareumhamrum from the western Indian Ocean, and Briareumcylindrumsp. n., Briareumstechei, and Briareumviolaceum from the central and eastern Indo-Pacific region.
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Affiliation(s)
- Kaveh Samimi-Namin
- Department of Marine Zoology, Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands
| | - Leen P van Ofwegen
- Department of Marine Zoology, Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands
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13
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Santodomingo N, Wallace CC, Johnson KG. Fossils reveal a high diversity of the staghorn coral generaAcroporaandIsopora(Scleractinia: Acroporidae) in the Neogene of Indonesia. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12295] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nadiezhda Santodomingo
- Department of Earth Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Naturalis Biodiversity Center; P.O. Box 9517 2300 RA Leiden the Netherlands
| | - Carden C. Wallace
- Museum of Tropical Queensland; 70-102 Flinders St. Townsville QLD 4810 Australia
| | - Kenneth G. Johnson
- Department of Earth Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
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14
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Rosser NL. Asynchronous spawning in sympatric populations of a hard coral reveals cryptic species and ancient genetic lineages. Mol Ecol 2015; 24:5006-19. [DOI: 10.1111/mec.13372] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Natalie L. Rosser
- School of Animal Biology (M092); University of Western Australia; Crawley WA 6009 Australia
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15
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Hill AE, Plyler ZE, Tiwari H, Patki A, Tully JP, McAtee CW, Moseley LA, Sorscher EJ. Longevity and plasticity of CFTR provide an argument for noncanonical SNP organization in hominid DNA. PLoS One 2014; 9:e109186. [PMID: 25350658 PMCID: PMC4211684 DOI: 10.1371/journal.pone.0109186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 09/09/2014] [Indexed: 12/03/2022] Open
Abstract
Like many other ancient genes, the cystic fibrosis transmembrane conductance regulator (CFTR) has survived for hundreds of millions of years. In this report, we consider whether such prodigious longevity of an individual gene – as opposed to an entire genome or species – should be considered surprising in the face of eons of relentless DNA replication errors, mutagenesis, and other causes of sequence polymorphism. The conventions that modern human SNP patterns result either from purifying selection or random (neutral) drift were not well supported, since extant models account rather poorly for the known plasticity and function (or the established SNP distributions) found in a multitude of genes such as CFTR. Instead, our analysis can be taken as a polemic indicating that SNPs in CFTR and many other mammalian genes may have been generated—and continue to accrue—in a fundamentally more organized manner than would otherwise have been expected. The resulting viewpoint contradicts earlier claims of ‘directional’ or ‘intelligent design-type’ SNP formation, and has important implications regarding the pace of DNA adaptation, the genesis of conserved non-coding DNA, and the extent to which eukaryotic SNP formation should be viewed as adaptive.
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Affiliation(s)
- Aubrey E. Hill
- Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zackery E. Plyler
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Hemant Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amit Patki
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joel P. Tully
- Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Christopher W. McAtee
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Leah A. Moseley
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Eric J. Sorscher
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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16
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Dornburg A, Townsend JP, Friedman M, Near TJ. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evol Biol 2014; 14:169. [PMID: 25103329 PMCID: PMC4236503 DOI: 10.1186/s12862-014-0169-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/21/2014] [Indexed: 11/24/2022] Open
Abstract
Background Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. Results We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. Conclusions Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.
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Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology, Yale University, New Haven 06520, Connecticut, USA.
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17
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Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, Johansen SD. Sea anemones possess dynamic mitogenome structures. Mol Phylogenet Evol 2014; 75:184-93. [DOI: 10.1016/j.ympev.2014.02.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/31/2014] [Accepted: 02/17/2014] [Indexed: 11/24/2022]
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McFadden CS, Reynolds AM, Janes MP. DNA barcoding of xeniid soft corals (Octocorallia: Alcyonacea: Xeniidae) from Indonesia: species richness and phylogenetic relationships. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.902866] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Fišer Pečnikar Ž, Buzan EV. 20 years since the introduction of DNA barcoding: from theory to application. J Appl Genet 2013; 55:43-52. [PMID: 24203863 DOI: 10.1007/s13353-013-0180-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 10/14/2013] [Accepted: 10/15/2013] [Indexed: 01/29/2023]
Abstract
Traditionally, taxonomic identification has relied upon morphological characters. In the last two decades, molecular tools based on DNA sequences of short standardised gene fragments, termed DNA barcodes, have been developed for species discrimination. The most common DNA barcode used in animals is a fragment of the cytochrome c oxidase (COI) mitochondrial gene, while for plants, two chloroplast gene fragments from the RuBisCo large subunit (rbcL) and maturase K (matK) genes are widely used. Information gathered from DNA barcodes can be used beyond taxonomic studies and will have far-reaching implications across many fields of biology, including ecology (rapid biodiversity assessment and food chain analysis), conservation biology (monitoring of protected species), biosecurity (early identification of invasive pest species), medicine (identification of medically important pathogens and their vectors) and pharmacology (identification of active compounds). However, it is important that the limitations of DNA barcoding are understood and techniques continually adapted and improved as this young science matures.
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Affiliation(s)
- Živa Fišer Pečnikar
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia,
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Brugler MR, Opresko DM, France SC. The evolutionary history of the order Antipatharia (Cnidaria: Anthozoa: Hexacorallia) as inferred from mitochondrial and nuclear DNA: implications for black coral taxonomy and systematics. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12060] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mercer R. Brugler
- Department of Biology; University of Louisiana at Lafayette; PO Box 42451 Lafayette LA USA
| | - Dennis M. Opresko
- Smithsonian Institution; National Museum of Natural History; Washington, DC USA
| | - Scott C. France
- Department of Biology; University of Louisiana at Lafayette; PO Box 42451 Lafayette LA USA
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21
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Richards ZT, Miller DJ, Wallace CC. Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation. Mol Phylogenet Evol 2013; 69:837-51. [PMID: 23850500 DOI: 10.1016/j.ympev.2013.06.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 06/18/2013] [Accepted: 06/27/2013] [Indexed: 10/26/2022]
Abstract
To better understand the underlying causes of rarity and extinction risk in Acropora (staghorn coral), we contrast the minimum divergence ages and nucleotide diversity of an array of species with different range sizes and levels of threat. Time-calibrated Bayesian analyses based upon concatenated nuclear and mitochondrial sequence data implied contemporary range size and vulnerability are linked to species age. However, contrary to previous hypotheses that suggest geographically restricted Acropora species evolved in the Plio-Pleistocene, the molecular phylogeny depicts some Indo-Australian species have greater antiquity, diverging in the Miocene. Species age is not related to range size as a simple positive linear function and interpreting the precise tempo of evolution in this genus is greatly complicated by morphological homoplasy and a sparse fossil record. Our phylogenetic reconstructions provide new examples of how morphology conceals cryptic evolutionary relationships in this keystone genus, and offers limited support for the species groupings currently used in Acropora systematics. We hypothesize that in addition to age, other mechanisms (such as a reticulate ancestry) delimit the contemporary range of some Acropora species, as evidenced by the complex patterns of allele sharing and paraphyly we uncover. Overall, both new and ancient evolutionary information may be lost if geographically restricted and threatened Acropora species are forced to extinction. In order to protect coral biodiversity and resolve the evolutionary history of staghorn coral, further analyses based on comprehensive and heterogeneous morphological and molecular data utilizing reticulate models of evolution are needed.
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Affiliation(s)
- Z T Richards
- Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia.
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22
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Morphological and genetic analyses of xeniid soft coral diversity (Octocorallia; Alcyonacea). ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0119-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Reyes-Bermudez A, Miller DJ, Sprungala S. The Neuronal Calcium Sensor protein Acrocalcin: a potential target of calmodulin regulation during development in the coral Acropora millepora. PLoS One 2012; 7:e51689. [PMID: 23284743 PMCID: PMC3524228 DOI: 10.1371/journal.pone.0051689] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 11/05/2012] [Indexed: 12/28/2022] Open
Abstract
To understand the calcium-mediated signalling pathways underlying settlement and metamorphosis in the Scleractinian coral Acropora millepora, a predicted protein set derived from larval cDNAs was scanned for the presence of EF-hand domains (Pfam Id: PF00036). This approach led to the identification of a canonical calmodulin (AmCaM) protein and an uncharacterised member of the Neuronal Calcium Sensor (NCS) family of proteins known here as Acrocalcin (AmAC). While AmCaM transcripts were present throughout development, AmAC transcripts were not detected prior to gastrulation, after which relatively constant mRNA levels were detected until metamorphosis and settlement. The AmAC protein contains an internal CaM-binding site and was shown to interact in vitro with AmCaM. These results are consistent with the idea that AmAC is a target of AmCaM in vivo, suggesting that this interaction may regulate calcium-dependent processes during the development of Acropora millepora.
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Affiliation(s)
- Alejandro Reyes-Bermudez
- ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - David J. Miller
- ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
| | - Susanne Sprungala
- ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- * E-mail:
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24
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Abstract
Invertebrates comprise approximately 34 phyla, while vertebrates represent one subphylum and insects a (very large) class. Thus, the clades excepting vertebrates and insects encompass almost all of animal diversity. Consequently, the barcoding challenge in invertebrates is that of barcoding animals in general. While standard extraction, cleaning, PCR methods, and universal primers work for many taxa, taxon-specific challenges arise because of the shear genetic and biochemical diversity present across the kingdom, and because problems arising as a result of this diversity, and solutions to them, are still poorly characterized for many metazoan clades. The objective of this chapter is to emphasize general approaches, and give practical advice for overcoming the diverse challenges that may be encountered across animal taxa, but we stop short of providing an exhaustive inventory. Rather, we encourage researchers, especially those working on poorly studied taxa, to carefully consider methodological issues presented below, when standard approaches perform poorly.
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Affiliation(s)
- Nathaniel Evans
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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25
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Addamo AM, Reimer JD, Taviani M, Freiwald A, Machordom A. Desmophyllum dianthus (Esper, 1794) in the scleractinian phylogeny and its intraspecific diversity. PLoS One 2012; 7:e50215. [PMID: 23209679 PMCID: PMC3509136 DOI: 10.1371/journal.pone.0050215] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 10/22/2012] [Indexed: 11/25/2022] Open
Abstract
The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the “robust” clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.
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Affiliation(s)
- Anna M Addamo
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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Aranda M, DeSalvo MK, Bayer T, Medina M, Voolstra CR. Evolutionary insights into scleractinian corals using comparative genomic hybridizations. BMC Genomics 2012; 13:501. [PMID: 22994626 PMCID: PMC3469353 DOI: 10.1186/1471-2164-13-501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/11/2012] [Indexed: 12/04/2022] Open
Abstract
Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization). Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.
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Affiliation(s)
- Manuel Aranda
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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27
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Brockman SA, McFadden CS. The mitochondrial genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports intramolecular recombination as the primary mechanism of gene rearrangement in octocoral mitochondrial genomes. Genome Biol Evol 2012; 4:994-1006. [PMID: 22975720 PMCID: PMC3468961 DOI: 10.1093/gbe/evs074] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene content and nucleotide composition are, however, identical to most other octocorals, and the additional length is due to the presence of two large, noncoding intergenic regions. Relative to the presumed ancestral octocoral gene order, in P. aldersladei a block of three protein-coding genes (nad6–nad3–nad4l) has been translocated and inverted. Mapping the distribution of mt gene arrangements onto a taxonomically comprehensive phylogeny of Octocorallia suggests that all of the known octocoral gene orders have evolved by successive inversions of one or more evolutionarily conserved blocks of protein-coding genes. This mode of genome evolution is unique among Metazoa, and contrasts strongly with that observed in Hexacorallia, in which extreme gene shuffling has occurred among taxonomic orders. Two of the four conserved gene blocks found in Octocorallia are, however, also conserved in the linear mt genomes of Medusozoa and in one group of Demospongiae. We speculate that the rate and mechanism of gene rearrangement in octocorals may be influenced by the presence in their mt genomes of mtMutS, a putatively active DNA mismatch repair protein that may also play a role in mediating intramolecular recombination.
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28
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Miyazawa H, Yoshida MA, Tsuneki K, Furuya H. Mitochondrial genome of a Japanese placozoan. Zoolog Sci 2012; 29:223-8. [PMID: 22468831 DOI: 10.2108/zsj.29.223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Placozoans are marine invertebrates found in tropical and subtropical waters. Their body plan is among the simplest of free-living animals. The present study determined the mitochondrial genome sequence of a placozoan collected on the coast of Shirahama, Wakayama, Honshu, Japan, and compared it with those of Trichoplax adhaerens from the Red Sea and of three strains from the Caribbean Sea. The sequences of mitochondrial respiratory chain of the Japanese placozoan genes are very similar to those of the BZ49 strain from the Caribbean Sea. However, there are distinct differences in gene arrangement, such as the location of two open reading frames. This Japanese placozoan is therefore distinguishable from the other strains. Based on current knowledge of placozoan 16S diversity our 'Shirahama' strain most likely represents the H15 lineage, known from the Philippines. In the mitochondrial genome of placozoans, substitution rates are slower than in bilaterians, whereas the rate of rearrangements is faster.
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Affiliation(s)
- Hideyuki Miyazawa
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
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29
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Nunes FLD, Norris RD, Knowlton N. Long distance dispersal and connectivity in amphi-Atlantic corals at regional and basin scales. PLoS One 2011; 6:e22298. [PMID: 21799816 PMCID: PMC3142122 DOI: 10.1371/journal.pone.0022298] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/23/2011] [Indexed: 11/24/2022] Open
Abstract
Among Atlantic scleractinian corals, species diversity is highest in the Caribbean, but low diversity and high endemism are observed in various peripheral populations in central and eastern Atlantic islands and along the coasts of Brazil and West Africa. The degree of connectivity between these distantly separated populations is of interest because it provides insight into processes at both evolutionary and ecological time scales, such as speciation, recruitment dynamics and the persistence of coral populations. To assess connectivity in broadly distributed coral species of the Atlantic, DNA sequence data from two nuclear markers were obtained for six coral species spanning their distributional ranges. At basin-wide scales, significant differentiation was generally observed among populations in the Caribbean, Brazil and West Africa. Concordance of patterns in connectivity among co-distributed taxa indicates that extrinsic barriers, such as the Amazon freshwater plume or long stretches of open ocean, restrict dispersal of coral larvae from region to region. Within regions, dispersal ability appears to be influenced by aspects of reproduction and life history. Two broadcasting species, Siderastrea siderea and Montastraea cavernosa, were able to maintain gene flow among populations separated by as much as 1,200 km along the coast of Brazil. In contrast, brooding species, such as Favia gravida and Siderastrea radians, had more restricted gene flow along the Brazilian coast.
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Affiliation(s)
- Flavia L D Nunes
- Laboratory of Artificial and Natural Evolution, University of Geneva, Geneva, Switzerland.
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30
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Miller KJ, Rowden AA, Williams A, Häussermann V. Out of their depth? Isolated deep populations of the cosmopolitan coral Desmophyllum dianthus may be highly vulnerable to environmental change. PLoS One 2011; 6:e19004. [PMID: 21611159 PMCID: PMC3097177 DOI: 10.1371/journal.pone.0019004] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/25/2011] [Indexed: 11/19/2022] Open
Abstract
Deep sea scleractinian corals will be particularly vulnerable to the effects of
climate change, facing loss of up to 70% of their habitat as the
Aragonite Saturation Horizon (below which corals are unable to form calcium
carbonate skeletons) rises. Persistence of deep sea scleractinian corals will
therefore rely on the ability of larvae to disperse to, and colonise, suitable
shallow-water habitat. We used DNA sequence data of the internal transcribed
spacer (ITS), the mitochondrial ribosomal subunit (16S) and mitochondrial
control region (MtC) to determine levels of gene flow both within and among
populations of the deep sea coral Desmophyllum dianthus in SE
Australia, New Zealand and Chile to assess the ability of corals to disperse
into different regions and habitats. We found significant genetic subdivision
among the three widely separated geographic regions consistent with isolation
and limited contemporary gene flow. Furthermore, corals from different depth
strata (shallow <600 m, mid 1000–1500 m, deep >1500 m) even on the
same or nearby seamounts were strongly differentiated, indicating limited
vertical larval dispersal. Genetic differentiation with depth is consistent with
the stratification of the Subantarctic Mode Water, Antarctic Intermediate Water,
the Circumpolar Deep and North Pacific Deep Waters in the Southern Ocean, and we
propose that coral larvae will be retained within, and rarely migrate among,
these water masses. The apparent absence of vertical larval dispersal suggests
deep populations of D. dianthus are unlikely to colonise
shallow water as the aragonite saturation horizon rises and deep waters become
uninhabitable. Similarly, assumptions that deep populations will act as refuges
for shallow populations that are impacted by activities such as fishing or
mining are also unlikely to hold true. Clearly future environmental management
strategies must consider both regional and depth-related isolation of deep-sea
coral populations.
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Affiliation(s)
- Karen J Miller
- Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia.
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Budd AF, Nunes FLD, Weil E, Pandolfi JM. Polymorphism in a common Atlantic reef coral (Montastraea cavernosa) and its long-term evolutionary implications. Evol Ecol 2011. [DOI: 10.1007/s10682-010-9460-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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McFADDEN CATHERINES, BENAYAHU YEHUDA, PANTE ERIC, THOMA JANAN, NEVAREZ PANDREW, FRANCE SCOTTC. Limitations of mitochondrial gene barcoding in Octocorallia. Mol Ecol Resour 2010; 11:19-31. [DOI: 10.1111/j.1755-0998.2010.02875.x] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - YEHUDA BENAYAHU
- Department of Zoology, George S. Wise Faculty of Life Sciences, University of Tel Aviv, Ramat Aviv, Tel Aviv 69978, Israel
| | - ERIC PANTE
- Department of Biology, University of Louisiana at Lafayette, PO Box 42451, Lafayette, LA 70504, USA
| | - JANA N. THOMA
- Department of Biology, University of Louisiana at Lafayette, PO Box 42451, Lafayette, LA 70504, USA
| | - P. ANDREW NEVAREZ
- Department of Biology, Harvey Mudd College, Claremont, CA 91711, USA
| | - SCOTT C. FRANCE
- Department of Biology, University of Louisiana at Lafayette, PO Box 42451, Lafayette, LA 70504, USA
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