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Brown AL, Hamman EA, Shima JS, Wares JP, Osenberg CW. Extended phenotypes on coral reefs: cryptic phenotypes modulate coral-vermetid interactions. Ecology 2021; 102:e03215. [PMID: 33010033 DOI: 10.1002/ecy.3215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/04/2020] [Accepted: 08/17/2020] [Indexed: 11/09/2022]
Abstract
Phenotypic variation can lead to variation in the strength and outcome of species interactions. Variation in phenotypic traits can arise due to plastic responses to environmental stimuli, underlying genetic variation, or both, and may reflect differences in the focal organism or aspects of the extended phenotype (e.g., associated microbes). We used a reciprocal transplant experiment of Porites corals to evaluate the role of plasticity vs. heritable diversity on phenotypic traits and performance of corals that varied in their prior exposure to vermetid gastropods, an organism known to reduce coral growth and survival. We measured a suite of phenotypic traits associated with coral performance, many of which showed a plastic response to vermetid exposure. Vermetids decreased calcification of corals, increased microbial diversity, and shifted microbial composition. Most traits also showed a signature of previous exposure environment that persisted even when exposure was reversed: i.e., under the same conditions, corals naïve to vermetids had slower calcification rates, thicker tissues, higher Symbiodiniaceae densities, and different microbiomes than corals previously exposed to vermetids. We suggest the phenotypic differences are heritable, as reefs with and without vermetids were comprised of two different mitotypes, that revealed high, consistent genetic variation. Vermetids were only found on the fast-growing coral mitotype that was characterized by thin tissue, and that likely had a history of disturbance. As extended phenotypes can have community impacts, we suggest vermetid, in addition to microbes, are part of the extended community phenotype of these corals. Coral genotypes can establish different reef trajectories, with thin-tissue types more prone to disturbance and subsequent colonization by other species, like vermetids, which can further facilitate the degradation of coral reefs. The effects of the extended phenotype of species likely influence heterogeneity across landscapes as well as temporal differences in community composition.
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Affiliation(s)
- A L Brown
- Odum School of Ecology, University of Georgia, Athens, Georgia, 30601, USA.,School of Natural Resources and the Environment, University of Florida, Gainesville, Florida, 32601, USA
| | - E A Hamman
- Odum School of Ecology, University of Georgia, Athens, Georgia, 30601, USA.,School of Science and Engineering, Tulane University, New Orleans, Louisiana, 70118, USA
| | - J S Shima
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - J P Wares
- Odum School of Ecology, University of Georgia, Athens, Georgia, 30601, USA.,Genetics Department, University of Georgia, Athens, Georgia, 30601, USA
| | - C W Osenberg
- Odum School of Ecology, University of Georgia, Athens, Georgia, 30601, USA
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2
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A framework for in situ molecular characterization of coral holobionts using nanopore sequencing. Sci Rep 2020; 10:15893. [PMID: 32985530 PMCID: PMC7522235 DOI: 10.1038/s41598-020-72589-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/03/2020] [Indexed: 01/21/2023] Open
Abstract
Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.
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3
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Robicheau BM, Chase EE, Hoeh WR, Harris JL, Stewart DT, Breton S. Evaluating the utility of the female-specific mitochondrial f-orf gene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida). PeerJ 2018; 6:e5007. [PMID: 29915706 PMCID: PMC6004104 DOI: 10.7717/peerj.5007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
Freshwater mussels (order: Unionida) represent one of the most critically imperilled groups of animals; consequently, there exists a need to establish a variety of molecular markers for population genetics and systematic studies in this group. Recently, two novel mitochondrial protein-coding genes were described in unionoids with doubly uniparental inheritance of mtDNA. These genes are the f-orf in female-transmitted mtDNA and the m-orf in male-transmitted mtDNA. In this study, whole F-type mitochondrial genome sequences of two morphologically similar Lampsilis spp. were compared to identify the most divergent protein-coding regions, including the f-orf gene, and evaluate its utility for population genetic and phylogeographic studies in the subfamily Ambleminae. We also tested whether the f-orf gene is phylogenetically informative at the species level. Our preliminary results indicated that the f-orf gene could represent a viable molecular marker for population- and species-level studies in freshwater mussels.
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Affiliation(s)
- Brent M Robicheau
- Department of Biology, Acadia University, Wolfville, Canada.,Current affiliation: Department of Biology, Life Science Centre, Dalhousie University, Halifax, Canada
| | - Emily E Chase
- Department of Biology, Acadia University, Wolfville, Canada
| | - Walter R Hoeh
- Department of Biological Sciences, Kent State University, Kent, United States of America
| | - John L Harris
- Department of Biological Sciences, Arkansas State University, Jonesboro, United States of America
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
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4
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Govindarajan AF, Carman MR, Khaidarov MR, Semenchenko A, Wares JP. Mitochondrial diversity in Gonionemus (Trachylina:Hydrozoa) and its implications for understanding the origins of clinging jellyfish in the Northwest Atlantic Ocean. PeerJ 2017; 5:e3205. [PMID: 28439470 PMCID: PMC5398274 DOI: 10.7717/peerj.3205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/20/2017] [Indexed: 02/04/2023] Open
Abstract
Determining whether a population is introduced or native to a region can be challenging due to inadequate taxonomy, the presence of cryptic lineages, and poor historical documentation. For taxa with resting stages that bloom episodically, determining origin can be especially challenging as an environmentally-triggered abrupt appearance of the taxa may be confused with an anthropogenic introduction. Here, we assess diversity in mitochondrial cytochrome oxidase I sequences obtained from multiple Atlantic and Pacific locations, and discuss the implications of our findings for understanding the origin of clinging jellyfish Gonionemus in the Northwest Atlantic. Clinging jellyfish are known for clinging to seagrasses and seaweeds, and have complex life cycles that include resting stages. They are especially notorious as some, although not all, populations are associated with severe sting reactions. The worldwide distribution of Gonionemus has been aptly called a “zoogeographic puzzle” and our results refine rather than resolve the puzzle. We find a relatively deep divergence that may indicate cryptic speciation between Gonionemus from the Northeast Pacific and Northwest Pacific/Northwest Atlantic. Within the Northwest Pacific/Northwest Atlantic clade, we find haplotypes unique to each region. We also find one haplotype that is shared between highly toxic Vladivostok-area populations and some Northwest Atlantic populations. Our results are consistent with multiple scenarios that involve both native and anthropogenic processes. We evaluate each scenario and discuss critical directions for future research, including improving the resolution of population genetic structure, identifying possible lineage admixture, and better characterizing and quantifying the toxicity phenotype.
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Affiliation(s)
| | - Mary R Carman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States
| | - Marat R Khaidarov
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia.,Far Eastern Federal University, Vladivostok, Russia
| | | | - John P Wares
- Department of Genetics, University of Georgia, Athens, United States.,Odum School of Ecology, University of Georgia, Athens, United States
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5
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Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P, Barbe V. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications. Mol Ecol Resour 2017; 17:1054-1071. [DOI: 10.1111/1755-0998.12640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 11/01/2016] [Accepted: 11/15/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Roberto Arrigoni
- Red Sea Research Center; Division of Biological and Environmental Science and Engineering; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milan 20126 Italy
| | | | - Francesca Benzoni
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milan 20126 Italy
- Institut de Recherche pour le Développement; UMR227 Coreus2; 101 Promenade Roger Laroque BP A5 Noumea Cedex 98848 New Caledonia
| | - Fabrizio Stefani
- Water Research Institute-National Research Council (IRSA-CNR); Via del Mulino 19 Brugherio I-20861 Italy
| | - Eric Karsenti
- Ecole Normale Supérieure; Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197; Paris F-75005 France
- Directors’ Research; European Molecular Biology Laboratory; Meyerhofstr. 1 Heidelberg 69117 Germany
| | - Olivier Jaillon
- CEA/DSV/IG/Genoscope; Evry Cedex France
- Université d'Evry; UMR 8030; Evry CP5706 France
| | - Fabrice Not
- UPMC-CNRS; UMR 7144; Station Biologique de Roscoff; Place Georges Teissier Roscoff 29680 France
| | - Flavia Nunes
- Ifremer Centre Bretagne; DYNECO; Laboratoire d’Écologie Benthique Côtière (LEBCO); 29280 Plouzané France
| | - Claude Payri
- Institut de Recherche pour le Développement; UMR227 Coreus2; 101 Promenade Roger Laroque BP A5 Noumea Cedex 98848 New Caledonia
| | - Patrick Wincker
- CEA/DSV/IG/Genoscope; Evry Cedex France
- Université d'Evry; UMR 8030; Evry CP5706 France
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Arrigoni R, Berumen ML, Huang D, Terraneo TI, Benzoni F. Cyphastrea (Cnidaria : Scleractinia : Merulinidae) in the Red Sea: phylogeny and a new reef coral species. INVERTEBR SYST 2017. [DOI: 10.1071/is16035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The scleractinian coral Cyphastrea is a common and widespread genus throughout the coral reefs of the Indo-Pacific. Little is known about the phylogenetic relationships within this taxon and species identification is based mainly on traditional skeletal characters, such as the number of septa, septa cycles, growth form and corallite dimensions. Here we present the first focussed reconstruction of phylogenetic relationships among Cyphastrea species, analysing 57 colonies from the Red Sea, where five morphospecies live in sympatry. Analyses based on three loci (nuclear histone H3, 28S rDNA and a mitochondrial intergenic region) reveal the existence of three well-supported molecular lineages. None of the five previously defined morphospecies are monophyletic and they cluster into two clades, suggesting the need of a systematic revision in Cyphastrea. The third lineage is described as C. magna Benzoni & Arrigoni, sp. nov., a new reef coral species collected from the northern and central Red Sea. Cyphastrea magna Benzoni & Arrigoni, sp. nov. is characterised by the largest corallite diameter among known Cyphastrea species, a wide trabecular columella >1/4 of calice width, and 12 equal primary septa. This study suggests that morphology-based taxonomy in Cyphastrea may not identify monophyletic units and strengthens the application of genetics in coral systematics.
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7
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Cui S, Luo X, Chen D, Sun J, Chu H, Li C, Jiang Z. The adder (Vipera berus) in Southern Altay Mountains: population characteristics, distribution, morphology and phylogenetic position. PeerJ 2016; 4:e2342. [PMID: 27602300 PMCID: PMC4991858 DOI: 10.7717/peerj.2342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/18/2016] [Indexed: 11/20/2022] Open
Abstract
As the most widely distributed snake in Eurasia, the adder (Vipera berus) has been extensively investigated in Europe but poorly understood in Asia. The Southern Altay Mountains represent the adder's southern distribution limit in Central Asia, whereas its population status has never been assessed. We conducted, for the first time, field surveys for the adder at two areas of Southern Altay Mountains using a combination of line transects and random searches. We also described the morphological characteristics of the collected specimens and conducted analyses of external morphology and molecular phylogeny. The results showed that the adder distributed in both survey sites and we recorded a total of 34 sightings. In Kanas river valley, the estimated encounter rate over a total of 137 km transects was 0.15 ± 0.05 sightings/km. The occurrence of melanism was only 17%. The small size was typical for the adders in Southern Altay Mountains in contrast to other geographic populations of the nominate subspecies. A phylogenetic tree obtained by Bayesian Inference based on DNA sequences of the mitochondrial cytochrome b (1,023 bp) grouped them within the Northern clade of the species but failed to separate them from the subspecies V. b. sachalinensis. Our discovery extends the distribution range of V. berus and provides a basis for further researches. We discuss the hypothesis that the adder expands its distribution border to the southwest along the mountains' elevation gradient, but the population abundance declines gradually due to a drying climate.
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Affiliation(s)
- Shaopeng Cui
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Luo
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Daiqiang Chen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jizhou Sun
- Kanas National Nature Reserve , Buerjin , Urumqi , China
| | - Hongjun Chu
- College of Resources and Environment Sciences, Xinjiang University, Urumqi, China; Altay Management Station, Mt. Kalamaili Ungulate Nature Reserve, Altay, China
| | - Chunwang Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhigang Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
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8
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Capel KCC, Migotto AE, Zilberberg C, Lin MF, Forsman Z, Miller DJ, Kitahara MV. Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): Implications for species identification. Gene 2016; 590:270-7. [PMID: 27234370 DOI: 10.1016/j.gene.2016.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
Members of the azooxanthellate coral genus Tubastraea are invasive species with particular concern because they have become established and are fierce competitors in the invaded areas in many parts of the world. Pacific Tubastraea species are spreading fast throughout the Atlantic Ocean, occupying over 95% of the available substrate in some areas and out-competing native endemic species. Approximately half of all known coral species are azooxanthellate but these are seriously under-represented compared to zooxanthellate corals in terms of the availability of mitochondrial (mt) genome data. In the present study, the complete mt DNA sequences of Atlantic individuals of the invasive scleractinian species Tubastraea coccinea and Tubastraea tagusensis were determined and compared to the GenBank reference sequence available for a Pacific "T. coccinea" individual. At 19,094bp (compared to 19,070bp for the GenBank specimen), the mt genomes assembled for the Atlantic T. coccinea and T. tagusensis were among the longest sequence determined to date for "Complex" scleractinians. Comparisons of genomes data showed that the "T. coccinea" sequence deposited on GenBank was more closely related to that from Dendrophyllia arbuscula than to the Atlantic Tubastraea spp., in terms of genome length and base pair similarities. This was confirmed by phylogenetic analysis, suggesting that the former was misidentified and might actually be a member from the genus Dendrophyllia. In addition, although in general the COX1 locus has a slow evolutionary rate in Scleractinia, it was the most variable region of the Tubastraea mt genome and can be used as markers for genus or species identification. Given the limited data available for azooxanthellate corals, the results presented here represent an important contribution to our understanding of phylogenetic relationships and the evolutionary history of the Scleractinia.
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Affiliation(s)
- K C C Capel
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - A E Migotto
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - C Zilberberg
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M F Lin
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Z Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, USA
| | - D J Miller
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - M V Kitahara
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil; Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
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Forsman Z, Wellington GM, Fox GE, Toonen RJ. Clues to unraveling the coral species problem: distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits. PeerJ 2015; 3:e751. [PMID: 25674364 PMCID: PMC4319317 DOI: 10.7717/peerj.751] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/15/2015] [Indexed: 02/01/2023] Open
Abstract
Morphological variation in the geographically widespread coral Porites lobata can make it difficult to distinguish from other massive congeneric species. This morphological variation could be attributed to geographic variability, phenotypic plasticity, or a combination of such factors. We examined genetic and microscopic morphological variability in P. lobata samples from the Galápagos, Easter Island, Tahiti, Fiji, Rarotonga, and Australia. Panamanian P. evermanni specimens were used as a previously established distinct outgroup against which to test genetic and morphological methods of discrimination. We employed a molecular analysis of variance (AMOVA) based on ribosomal internal transcribed spacer region (ITS) sequence, principal component analysis (PCA) of skeletal landmarks, and Mantel tests to compare genetic and morphological variation. Both genetic and morphometric methods clearly distinguished P. lobata and P. evermanni, while significant genetic and morphological variance was attributed to differences among geographic regions for P. lobata. Mantel tests indicate a correlation between genetic and morphological variation for P. lobata across the Pacific. Here we highlight landmark morphometric measures that correlate well with genetic differences, showing promise for resolving species of Porites, one of the most ubiquitous yet challenging to identify architects of coral reefs.
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Affiliation(s)
- Zac Forsman
- Hawai‘i Institute of Marine Biology, Kāne‘ohe, HI, USA
| | | | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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