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Grupstra CGB, Gómez-Corrales M, Fifer JE, Aichelman HE, Meyer-Kaiser KS, Prada C, Davies SW. Integrating cryptic diversity into coral evolution, symbiosis and conservation. Nat Ecol Evol 2024; 8:622-636. [PMID: 38351091 DOI: 10.1038/s41559-023-02319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/12/2023] [Indexed: 04/13/2024]
Abstract
Understanding how diversity evolves and is maintained is critical to predicting the future trajectories of ecosystems under climate change; however, our understanding of these processes is limited in marine systems. Corals, which engineer reef ecosystems, are critically threatened by climate change, and global efforts are underway to conserve and restore populations as attempts to mitigate ocean warming continue. Recently, sequencing efforts have uncovered widespread undescribed coral diversity, including 'cryptic lineages'-genetically distinct but morphologically similar coral taxa. Such cryptic lineages have been identified in at least 24 coral genera spanning the anthozoan phylogeny and across ocean basins. These cryptic lineages co-occur in many reef systems, but their distributions often differ among habitats. Research suggests that cryptic lineages are ecologically specialized and several examples demonstrate differences in thermal tolerance, highlighting the critical implications of this diversity for predicting coral responses to future warming. Here, we draw attention to recent discoveries, discuss how cryptic diversity affects the study of coral adaptation and acclimation to future environments, explore how it shapes symbiotic partnerships, and highlight challenges and opportunities for conservation and restoration efforts.
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Affiliation(s)
| | | | - James E Fifer
- Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA.
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Wepfer PH, Nakajima Y, Sutthacheep M, Radice VZ, Richards Z, Ang P, Terraneo T, Sudek M, Fujimura A, Toonen RJ, Mikheyev AS, Economo EP, Mitarai S. Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean. Mol Phylogenet Evol 2020; 151:106905. [DOI: 10.1016/j.ympev.2020.106905] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 11/16/2022]
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Nakajima Y, Chuang PS, Ueda N, Mitarai S. First evidence of asexual recruitment of Pocillopora acuta in Okinawa Island using genotypic identification. PeerJ 2018; 6:e5915. [PMID: 30473933 PMCID: PMC6237110 DOI: 10.7717/peerj.5915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
Okinawa Island is located near the center of the Nansei Islands (∼24–31°N), at a relatively high latitude for coral reefs. Nevertheless, more than 80 coral genera (over 400 species) are abundant in the Nansei Islands. Since March, 2017, scleractinian corals have been held in an outdoor tank at the OIST Marine Science Station at Seragaki, Onna with natural sea water flow-through in order to be used in molecular biological and physiological studies. In January, 2018, we found small pocilloporid-like colonies suspected to have originated asexually. We collected 25 small colonies and measured their sizes and weights. Also, we validated the classification and clonality of the colonies using a mitochondrial locus and nine microsatellite loci. Almost all of the small colonies collected in the outdoor tank were ≤1 cm in both width and height. The weight of dried skeletons ranged from 0.0287 to 0.1807 g. Genetic analysis determined that they were, in fact, Pocillopora acuta. Only one mitochondrial haplotype was shared and two microsatellite multilocus genotypes were detected (20 colonies of one and four colonies of the other). The mitochondrial haplotype and one microsatellite multilocus genotype for 20 colonies corresponded to those of one P. acuta colony being kept in the tank. One small colony matched both multilocus genotypes. This may have been a chimeric colony resulting from allogenic fusion. These small colonies were not produced sexually, because the only potential parent in the tank was the aforementioned P. acuta colony. Instead, they were more likely derived from asexual planula release or polyp bail-out. Corals as Pocillopora acuta have the capacity to produce clonal offspring rapidly and to adapt readily to local environments. This is the first report of asexual reproduction by planulae or expelled polyps in P. acuta at Okinawa Island.
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Affiliation(s)
- Yuichi Nakajima
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Po-Shun Chuang
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Nobuo Ueda
- Okinawa Marine Science Support Section, OIST Marine Science Station, Onna, Okinawa, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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Yang SY, Fong WL, Chow WS, Hsu CM, Chan CLC, Keshavmurthy S, Chen CA. Development of Novel Polymorphic Microsatellite Markers in Catch Bowl Coral, Isopora palifera (Scleractinia; Acroporidae) Using Next-generation Sequencing. Zool Stud 2018; 57:e32. [PMID: 31966272 PMCID: PMC6517735 DOI: 10.6620/zs.2018.57-32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022]
Abstract
Sung-Yin Yang, Wai-Ling Fong, Wenhua Savanna Chow, Chia-Min Hsu, Chia-Ling Carynn Chan, Shashank Keshavmurthy, and Chaolun Allen Chen (2018) Catch bowl coral, Isopora palifera, is a shallow- water scleractinian species distributed in the Indo-West Pacific region, and has been studied for its reproduction, symbiont diversity, and population genetics. In order to develop microsatellite markers to reveal the genetic connectivity of I. palifera in the Kenting reefs, southern Taiwan, we applied a stepwise approach including Illumina sequencing, primer screening, and validation. DNA sequences of each 6,363,035 read pairs were assembled with high coverage and sequencing depth, and 1,173,835 potential SSRs were identified. A set of 60,986 primers were designed and tested, and six novel microsatellite markers with three type motifs, including 3 di- and 3 tetra- repeats, were successfully isolated. The ranges in number of alleles per locus and observed and expected heterozygosities were 3-5, 0.444-0.538, and 0.375-0.565, respectively. Application of these loci to the genetic diversity of an I. palifera population that experienced bleaching events in the Kenting reef between 1998 and 2015 showed a signature admixture of three clusters without temporal variation. These loci are useful for studying population genetics in the genus Isopora. Our results suggest that next-generation sequencing technology is convenient and cost-effective and can be utilized to isolate microsatellites in other reef-building corals.
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Affiliation(s)
- Sung-Yin Yang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
| | - Wai-Ling Fong
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Wenhua Savanna Chow
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
- Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Chia-Min Hsu
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Chia-Ling Carynn Chan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
| | - Shashank Keshavmurthy
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
| | - Chaolun Allen Chen
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
- Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Nankang, Taipei 115, Taiwan
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Capel KCC, Toonen RJ, Rachid CTCC, Creed JC, Kitahara MV, Forsman Z, Zilberberg C. Clone wars: asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean. PeerJ 2017; 5:e3873. [PMID: 29018611 PMCID: PMC5632532 DOI: 10.7717/peerj.3873] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/09/2017] [Indexed: 11/20/2022] Open
Abstract
Although the invasive azooxanthellate corals Tubastraea coccinea and T. tagusensis are spreading quickly and outcompeting native species in the Atlantic Ocean, there is little information regarding the genetic structure and path of introduction for these species. Here we present the first data on genetic diversity and clonal structure from these two species using a new set of microsatellite markers. High proportions of clones were observed, indicating that asexual reproduction has a major role in the local population dynamics and, therefore, represents one of the main reasons for the invasion success. Although no significant population structure was found, results suggest the occurrence of multiple invasions for T. coccinea and also that both species are being transported along the coast by vectors such as oil platforms and monobouys, spreading these invasive species. In addition to the description of novel microsatellite markers, this study sheds new light into the invasive process of Tubastraea.
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Affiliation(s)
- Katia Cristina Cruz Capel
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,School of Ocean & Earth Science & Technology, Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Kane'ohe, Hawai'i, United States of America.,Coral-Sol Research, Technological Development and Innovation Network, Brazil
| | - Robert J Toonen
- School of Ocean & Earth Science & Technology, Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Kane'ohe, Hawai'i, United States of America
| | - Caio T C C Rachid
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joel C Creed
- Coral-Sol Research, Technological Development and Innovation Network, Brazil.,Departamento de Ecologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo V Kitahara
- Coral-Sol Research, Technological Development and Innovation Network, Brazil.,Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, Brazil.,Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, Brazil
| | - Zac Forsman
- School of Ocean & Earth Science & Technology, Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Kane'ohe, Hawai'i, United States of America
| | - Carla Zilberberg
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Coral-Sol Research, Technological Development and Innovation Network, Brazil
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Microsatellite markers for multiple Pocillopora genetic lineages offer new insights about coral populations. Sci Rep 2017; 7:6729. [PMID: 28751649 PMCID: PMC5532301 DOI: 10.1038/s41598-017-06776-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/16/2017] [Indexed: 11/08/2022] Open
Abstract
Population genetics of the coral genus Pocillopora have been more intensively studied than those of any other reef-building taxon. However, recent investigations have revealed that the current morphological classification is inadequate to represent genetic lineages. In this study, we isolated and characterized novel microsatellite loci from morphological Pocillopora meandrina (Type 1) and Pocillopora acuta (Type 5). Furthermore, we characterized previously reported microsatellite loci. A total of 27 loci (13 novel loci) proved useful for population genetic analyses at two sites in the Ryukyu Archipelago, in the northwestern Pacific. Clonal diversity differed in each genetic lineage. Genetic structure suggested by microsatellites corresponded to clusters in a phylogenetic tree constructed from a mitochondrial open reading frame (mtORF). In addition, we found an unknown mitochondrial haplotype of this mtORF. These microsatellite loci will be useful for studies of connectivity and genetic diversity of Pocillopora populations, and will also support coral reef conservation.
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Transcriptome profiling of Galaxea fascicularis and its endosymbiont Symbiodinium reveals chronic eutrophication tolerance pathways and metabolic mutualism between partners. Sci Rep 2017; 7:42100. [PMID: 28181581 PMCID: PMC5299600 DOI: 10.1038/srep42100] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/06/2017] [Indexed: 01/10/2023] Open
Abstract
In the South China Sea, coastal eutrophication in the Beibu Gulf has seriously threatened reef habitats by subjecting corals to chronic physiological stress. To determine how coral holobionts may tolerate such conditions, we examined the transcriptomes of healthy colonies of the galaxy coral Galaxea fascicularis and its endosymbiont Symbiodinium from two reef sites experiencing pristine or eutrophied nutrient regimes. We identified 236 and 205 genes that were differentially expressed in eutrophied hosts and symbionts, respectively. Both gene sets included pathways related to stress responses and metabolic interactions. An analysis of genes originating from each partner revealed striking metabolic integration with respect to vitamins, cofactors, amino acids, fatty acids, and secondary metabolite biosynthesis. The expression levels of these genes supported the existence of a continuum of mutualism in this coral-algal symbiosis. Additionally, large sets of transcription factors, cell signal transduction molecules, biomineralization components, and galaxin-related proteins were expanded in G. fascicularis relative to other coral species.
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Nakajima Y, Zayasu Y, Shinzato C, Satoh N, Mitarai S. Genetic differentiation and connectivity of morphological types of the broadcast-spawning coral Galaxea fascicularis in the Nansei Islands, Japan. Ecol Evol 2016; 6:1457-69. [PMID: 27087925 PMCID: PMC4775516 DOI: 10.1002/ece3.1981] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/25/2015] [Accepted: 01/03/2016] [Indexed: 11/24/2022] Open
Abstract
Population connectivity resulting from larval dispersal is essential for the maintenance or recovery of populations in marine ecosystems, including coral reefs. Studies of species diversity and genetic connectivity within species are essential for the conservation of corals and coral reef ecosystems. We analyzed mitochondrial DNA sequence types and microsatellite genotypes of the broadcast‐spawning coral, Galaxea fascicularis, from four regions in the subtropical Nansei Islands in the northwestern Pacific Ocean. Two types (soft and hard types) of nematocyst morphology are known in G. fascicularis and are significantly correlated with the length of a mitochondrial DNA noncoding sequence (soft type: mt‐L; hard type: mt‐S type). Using microsatellites, significant genetic differentiation was detected between the mitochondrial DNA sequence types in all regions. We also found a third genetic cluster (mt‐L+), and this unexpected type may be a cryptic species of Galaxea. High clonal diversity was detected in both mt‐L and mt‐S types. Significant genetic differentiation, which was found among regions within a given type (FST = 0.009–0.024, all Ps ≤ 0.005 in mt‐L; 0.009–0.032, all Ps ≤ 0.01 in mt‐S), may result from the shorter larval development than in other broadcast‐spawning corals, such as the genus Acropora. Nevertheless, intraspecific genetic diversity and connectivity have been maintained, and with both sexual and asexual reproduction, this species appears to have a potential for the recovery of populations after disturbance.
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Affiliation(s)
- Yuichi Nakajima
- Marine Biophysics Unit Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha Onna Okinawa 904-0495 Japan
| | - Yuna Zayasu
- Marine Genomics Unit Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha Onna Okinawa 904-0495 Japan
| | - Chuya Shinzato
- Marine Genomics Unit Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha Onna Okinawa 904-0495 Japan
| | - Noriyuki Satoh
- Marine Genomics Unit Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha Onna Okinawa 904-0495 Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha Onna Okinawa 904-0495 Japan
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Cryptic genetic divergence within threatened species of Acropora coral from the Indian and Pacific Oceans. CONSERV GENET 2016. [DOI: 10.1007/s10592-015-0807-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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