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Burgess SC, Turner AM, Johnston EC. Niche breadth and divergence in sympatric cryptic coral species ( Pocillopora spp.) across habitats within reefs and among algal symbionts. Evol Appl 2024; 17:e13762. [PMID: 39100752 PMCID: PMC11294925 DOI: 10.1111/eva.13762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/05/2024] [Accepted: 07/10/2024] [Indexed: 08/06/2024] Open
Abstract
While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co-occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 Pocillopora corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of Pocillopora, most of which cannot be reliably identified based on morphology: P. meandrina (42.9%), P. tuahiniensis (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and P. cf. effusa (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used psbA ncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of Pocillopora species differed across habitats within the reef. Sister taxa P. verrucosa and P. tuahiniensis had similar niche breadths and hosted the same specialist symbiont species (mostly Cladocopium pacificum) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa P. meandrina and P. grandis had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly C. latusorum). Pocillopora acuta had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, Durusdinium gynnii. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth-Pocillopora species with a broader habitat niche also had a broader symbiont niche. Our results show how fine-scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated.
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Affiliation(s)
- Scott C. Burgess
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Alyssa M. Turner
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Erika C. Johnston
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
- Present address:
Hawai‘i Institute of Marine BiologyKāne‘oheHawaiiUSA
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2
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Primov KD, Burdick DR, Lemer S, Forsman ZH, Combosch DJ. Genomic data reveals habitat partitioning in massive Porites on Guam, Micronesia. Sci Rep 2024; 14:17107. [PMID: 39048606 PMCID: PMC11269739 DOI: 10.1038/s41598-024-67992-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
Corals in marginal reef habitats generally exhibit less bleaching and associated mortality compared to nearby corals in more pristine reef environments. It is unclear, however, if these differences are due to environmental differences, including turbidity, or genomic differences between the coral hosts in these different environments. One particularly interesting case is in the coral genus Porites, which contains numerous morphologically similar massive Porites species inhabiting a wide range of reef habitats, from turbid river deltas and stagnant back reefs to high-energy fore reefs. Here, we generate ddRAD data for 172 Porites corals from river delta and adjacent (<0.5 km) fore reef populations on Guam to assess the extent of genetic differentiation among massive Porites corals in these two contrasting environments and throughout the island. Phylogenetic and population genomic analyses consistently identify seven different clades of massive Porites, with the two largest clades predominantly inhabiting either river deltas or fore reefs, respectively. No population structure was detected in the two largest clades, and Cladocopium was the dominant symbiont genus in all clades and environments. The perceived bleaching resilience of corals in marginal reefs may therefore be attributed to interspecific differences between morphologically similar species, in addition to potentially mediating environmental differences. Marginal reef environments may therefore not provide a suitable refuge for many reef corals in a heating world, but instead host additional cryptic coral diversity.
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Affiliation(s)
- Karim D Primov
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - David R Burdick
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA
| | - Sarah Lemer
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA
| | - Zac H Forsman
- King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| | - David J Combosch
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA
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3
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Macko P, Derka T, Čiamporová-Zaťovičová Z, Grabowski M, Čiampor F. Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries. Mol Ecol Resour 2024; 24:e13954. [PMID: 38520175 DOI: 10.1111/1755-0998.13954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.
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Affiliation(s)
- Patrik Macko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Tomáš Derka
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Zuzana Čiamporová-Zaťovičová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Fedor Čiampor
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
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4
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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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5
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Pinsky ML, Clark RD, Bos JT. Coral Reef Population Genomics in an Age of Global Change. Annu Rev Genet 2023; 57:87-115. [PMID: 37384733 DOI: 10.1146/annurev-genet-022123-102748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.
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Affiliation(s)
- Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA;
| | - René D Clark
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| | - Jaelyn T Bos
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
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6
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Starko S, Fifer JE, Claar DC, Davies SW, Cunning R, Baker AC, Baum JK. Marine heatwaves threaten cryptic coral diversity and erode associations among coevolving partners. SCIENCE ADVANCES 2023; 9:eadf0954. [PMID: 37566650 PMCID: PMC10421036 DOI: 10.1126/sciadv.adf0954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/12/2023] [Indexed: 08/13/2023]
Abstract
Climate change-amplified marine heatwaves can drive extensive mortality in foundation species. However, a paucity of longitudinal genomic datasets has impeded understanding of how these rapid selection events alter cryptic genetic structure. Heatwave impacts may be exacerbated in species that engage in obligate symbioses, where the genetics of multiple coevolving taxa may be affected. Here, we tracked the symbiotic associations of reef-building corals for 6 years through a prolonged heatwave, including known survivorship for 79 of 315 colonies. Coral genetics strongly predicted survival of the ubiquitous coral, Porites (massive growth form), with variable survival (15 to 61%) across three morphologically indistinguishable-but genetically distinct-lineages. The heatwave also disrupted strong associations between these coral lineages and their algal symbionts (family Symbiodiniaceae), with symbiotic turnover in some colonies, resulting in reduced specificity across lineages. These results highlight how heatwaves can threaten cryptic genotypes and decouple otherwise tightly coevolved relationships between hosts and symbionts.
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Affiliation(s)
- Samuel Starko
- Department of Biology, University of Victoria, PO Box 1700 Station CSC, Victoria, British Columbia V8W 2Y2, Canada
- UWA Oceans Institute and School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - James E. Fifer
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Danielle C. Claar
- Department of Biology, University of Victoria, PO Box 1700 Station CSC, Victoria, British Columbia V8W 2Y2, Canada
- Washington Department of Natural Resources, Olympia, WA 98504, USA
| | - Sarah W. Davies
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, 1200 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Andrew C. Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Julia K. Baum
- Department of Biology, University of Victoria, PO Box 1700 Station CSC, Victoria, British Columbia V8W 2Y2, Canada
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
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7
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Chang J, Nakamura K, Chao C, Luo M, Liao P. Ghost introgression facilitates genomic divergence of a sympatric cryptic lineage in Cycas revoluta. Ecol Evol 2023; 13:e10435. [PMID: 37600490 PMCID: PMC10439367 DOI: 10.1002/ece3.10435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
A cryptic lineage is a genetically diverged but morphologically unrecognized variant of a known species. Clarifying cryptic lineage evolution is essential for quantifying species diversity. In sympatric cryptic lineage divergence compared with allopatric divergence, the forces of divergent selection and mating patterns override geographical isolation. Introgression, by supplying preadapted or neutral standing genetic variations, can promote sympatric cryptic lineage divergence via selection. However, most studies concentrated on extant species introgression, ignoring the genetic legacy of introgression from extinct or unsampled lineages ("ghost introgression"). Cycads are an ideal plant for studying the influence of ghost introgression because of their common interspecific gene flow and past high extinction rate. Here, we utilized reference-based ddRADseq to clarify the role of ghost introgression in the evolution of a previously identified sympatric cryptic lineage in Cycas revoluta. After re-evaluating the evolutionary independency of cryptic lineages, the group-wise diverged single-nucleotide polymorphisms among sympatric and allopatric lineages were compared and functionally annotated. Next, we employed an approximate Bayesian computation method for hypothesis testing to clarify the cryptic lineage evolution and ghost introgression effect. SNPs with the genomic signatures of ghost introgression were further annotated. Our results reconfirmed the evolutionary independency of cryptic lineage among C. revoluta and demonstrated that ghost introgression to the noncryptic lineage facilitated their divergence. Gene function related to heat stress and disease resistance implied ecological adaptation of the main extant populations of C. revoluta.
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Affiliation(s)
- Jui‐Tse Chang
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern BiosphereHokkaido UniversitySapporoJapan
| | - Chien‐Ti Chao
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Min‐Xin Luo
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Pei‐Chun Liao
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
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8
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Richards TJ, McGuigan K, Aguirre JD, Humanes A, Bozec YM, Mumby PJ, Riginos C. Moving beyond heritability in the search for coral adaptive potential. GLOBAL CHANGE BIOLOGY 2023; 29:3869-3882. [PMID: 37310164 DOI: 10.1111/gcb.16719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 06/14/2023]
Abstract
Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change. For wild populations to persist, they must adapt. Knowledge shortfalls about corals' complex ecological and evolutionary dynamics, however, stymie predictions about potential adaptation to future conditions. Here, we review adaptation through the lens of quantitative genetics. We argue that coral adaptation studies can benefit greatly from "wild" quantitative genetic methods, where traits are studied in wild populations undergoing natural selection, genomic relationship matrices can replace breeding experiments, and analyses can be extended to examine genetic constraints among traits. In addition, individuals with advantageous genotypes for anticipated future conditions can be identified. Finally, genomic genotyping supports simultaneous consideration of how genetic diversity is arrayed across geographic and environmental distances, providing greater context for predictions of phenotypic evolution at a metapopulation scale.
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Affiliation(s)
- Thomas J Richards
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
| | - Katrina McGuigan
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
| | - J David Aguirre
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Adriana Humanes
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Yves-Marie Bozec
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
| | - Peter J Mumby
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
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9
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Matias AMA, Popovic I, Thia JA, Cooke IR, Torda G, Lukoschek V, Bay LK, Kim SW, Riginos C. Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef. Evol Appl 2023; 16:293-310. [PMID: 36793689 PMCID: PMC9923489 DOI: 10.1111/eva.13435] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/20/2022] [Accepted: 05/29/2022] [Indexed: 11/26/2022] Open
Abstract
Genomic studies are uncovering extensive cryptic diversity within reef-building corals, suggesting that evolutionarily and ecologically relevant diversity is highly underestimated in the very organisms that structure coral reefs. Furthermore, endosymbiotic algae within coral host species can confer adaptive responses to environmental stress and may represent additional axes of coral genetic variation that are not constrained by taxonomic divergence of the cnidarian host. Here, we examine genetic variation in a common and widespread, reef-building coral, Acropora tenuis, and its associated endosymbiotic algae along the entire expanse of the Great Barrier Reef (GBR). We use SNPs derived from genome-wide sequencing to characterize the cnidarian coral host and organelles from zooxanthellate endosymbionts (genus Cladocopium). We discover three distinct and sympatric genetic clusters of coral hosts, whose distributions appear associated with latitude and inshore-offshore reef position. Demographic modelling suggests that the divergence history of the three distinct host taxa ranges from 0.5 to 1.5 million years ago, preceding the GBR's formation, and has been characterized by low-to-moderate ongoing inter-taxon gene flow, consistent with occasional hybridization and introgression typifying coral evolution. Despite this differentiation in the cnidarian host, A. tenuis taxa share a common symbiont pool, dominated by the genus Cladocopium (Clade C). Cladocopium plastid diversity is not strongly associated with host identity but varies with reef location relative to shore: inshore colonies contain lower symbiont diversity on average but have greater differences between colonies as compared with symbiont communities from offshore colonies. Spatial genetic patterns of symbiont communities could reflect local selective pressures maintaining coral holobiont differentiation across an inshore-offshore environmental gradient. The strong influence of environment (but not host identity) on symbiont community composition supports the notion that symbiont community composition responds to habitat and may assist in the adaptation of corals to future environmental change.
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Affiliation(s)
- Ambrocio Melvin A. Matias
- Institute of BiologyUniversity of the Philippines DilimanQuezon CityPhilippines
- School of Biological SciencesThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Iva Popovic
- School of Biological SciencesThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Joshua A. Thia
- Bio21 Institute, School of BioSciencesThe University of MelbourneParkevilleVictoriaAustralia
| | - Ira R. Cooke
- College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Gergely Torda
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Vimoksalehi Lukoschek
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Gold Coast University HospitalQLD HealthSouthportQueenslandAustralia
| | - Line K. Bay
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
| | - Sun W. Kim
- School of Biological SciencesThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Cynthia Riginos
- School of Biological SciencesThe University of QueenslandSt. LuciaQueenslandAustralia
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10
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Bove CB, Ingersoll MV, Davies SW. Help Me, Symbionts, You're My Only Hope: Approaches to Accelerate our Understanding of Coral Holobiont Interactions. Integr Comp Biol 2022; 62:1756-1769. [PMID: 36099871 DOI: 10.1093/icb/icac141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/24/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023] Open
Abstract
Tropical corals construct the three-dimensional framework for one of the most diverse ecosystems on the planet, providing habitat to a plethora of species across taxa. However, these ecosystem engineers are facing unprecedented challenges, such as increasing disease prevalence and marine heatwaves associated with anthropogenic global change. As a result, major declines in coral cover and health are being observed across the world's oceans, often due to the breakdown of coral-associated symbioses. Here, we review the interactions between the major symbiotic partners of the coral holobiont-the cnidarian host, algae in the family Symbiodiniaceae, and the microbiome-that influence trait variation, including the molecular mechanisms that underlie symbiosis and the resulting physiological benefits of different microbial partnerships. In doing so, we highlight the current framework for the formation and maintenance of cnidarian-Symbiodiniaceae symbiosis, and the role that immunity pathways play in this relationship. We emphasize that understanding these complex interactions is challenging when you consider the vast genetic variation of the cnidarian host and algal symbiont, as well as their highly diverse microbiome, which is also an important player in coral holobiont health. Given the complex interactions between and among symbiotic partners, we propose several research directions and approaches focused on symbiosis model systems and emerging technologies that will broaden our understanding of how these partner interactions may facilitate the prediction of coral holobiont phenotype, especially under rapid environmental change.
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Affiliation(s)
- Colleen B Bove
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA 02215, USA
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11
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Humanes A, Lachs L, Beauchamp EA, Bythell JC, Edwards AJ, Golbuu Y, Martinez HM, Palmowski P, Treumann A, van der Steeg E, van Hooidonk R, Guest JR. Within-population variability in coral heat tolerance indicates climate adaptation potential. Proc Biol Sci 2022; 289:20220872. [PMID: 36043280 PMCID: PMC9428547 DOI: 10.1098/rspb.2022.0872] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Coral reefs are facing unprecedented mass bleaching and mortality events due to marine heatwaves and climate change. To avoid extirpation, corals must adapt. Individual variation in heat tolerance and its heritability underpin the potential for coral adaptation. However, the magnitude of heat tolerance variability within coral populations is largely unresolved. We address this knowledge gap by exposing corals from a single reef to an experimental marine heatwave. We found that double the heat stress dosage was required to induce bleaching in the most-tolerant 10%, compared to the least-tolerant 10% of the population. By the end of the heat stress exposure, all of the least-tolerant corals were dead, whereas the most-tolerant remained alive. To contextualize the scale of this result over the coming century, we show that under an ambitious future emissions scenario, such differences in coral heat tolerance thresholds equate to up to 17 years delay until the onset of annual bleaching and mortality conditions. However, this delay is limited to only 10 years under a high emissions scenario. Our results show substantial variability in coral heat tolerance which suggests scope for natural or assisted evolution to limit the impacts of climate change in the short-term. For coral reefs to persist through the coming century, coral adaptation must keep pace with ocean warming, and ambitious emissions reductions must be realized.
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Affiliation(s)
- Adriana Humanes
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Liam Lachs
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Elizabeth A Beauchamp
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - John C Bythell
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Alasdair J Edwards
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Helios M Martinez
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paweł Palmowski
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Achim Treumann
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eveline van der Steeg
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ruben van Hooidonk
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA.,Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - James R Guest
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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12
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Fifer JE, Yasuda N, Yamakita T, Bove CB, Davies SW. Genetic divergence and range expansion in a western North Pacific coral. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152423. [PMID: 34942242 DOI: 10.1016/j.scitotenv.2021.152423] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Coral poleward range expansions have recently been observed in response to warming oceans. Range expansion can lead to reduced genetic diversity and increased frequency of deleterious mutations that were rare in core populations, potentially limiting the ability for adaptation and persistence in novel environments. Successful expansions that overcome these founder effects and colonize new habitat have been attributed to multiple introductions from different sources, hybridization with native populations, or rapid adaptive evolution. Here, we investigate population genomic patterns of the reef-building coral Acropora hyacinthus along a latitudinal cline that includes a well-established range expansion front in Japan using 2b-RAD sequencing. A total of 184 coral samples were collected across seven sites spanning from ~24°N to near its northern range front at ~33°N. We uncover the presence of three cryptic lineages of A. hyacinthus, which occupy discrete reefs within this region. Only one lineage is present along the expansion front and we find evidence for its historical occupation of marginal habitats. Within this lineage we also find evidence of bottleneck pressures associated with expansion events including higher clonality, increased linkage disequilibrium, and lower genetic diversity in range edge populations compared to core populations. Asymmetric migration between populations was also detected with lower migration from edge sites. Lastly, we describe genomic signatures of local adaptation potentially attributed to lower winter temperatures experienced at the more recently expanded northern populations. Together these data illuminate the genomic consequences of range expansion in a coral and highlight how adaptation to discrete environments along expansion fronts may facilitate further range expansion in this temperate coral lineage.
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Affiliation(s)
- James E Fifer
- Department of Biology, Boston University, Boston, MA 02215, USA.
| | - Nina Yasuda
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki 889-2192, Japan.
| | - Takehisa Yamakita
- Marine Biodiversity and Environmental Assessment Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushimacho, Yokosuka, Kanagawa 237-0061, Japan
| | - Colleen B Bove
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA 02215, USA
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13
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Prata KE, Riginos C, Gutenkunst RN, Latijnhouwers KRW, Sánchez JA, Englebert N, Hay KB, Bongaerts P. Deep connections: divergence histories with gene flow in mesophotic
Agaricia
corals. Mol Ecol 2022; 31:2511-2527. [PMID: 35152496 PMCID: PMC9303685 DOI: 10.1111/mec.16391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/01/2022]
Abstract
Largely understudied, mesophotic coral ecosystems lie below shallow reefs (at >30 m depth) and comprise ecologically distinct communities. Brooding reproductive modes appear to predominate among mesophotic‐specialist corals and may limit genetic connectivity among populations. Using reduced representation genomic sequencing, we assessed spatial population genetic structure at 50 m depth in an ecologically important mesophotic‐specialist species Agaricia grahamae, among locations in the Southern Caribbean. We also tested for hybridisation with the closely related (but depth‐generalist) species Agaricia lamarcki, within their sympatric depth zone (50 m). In contrast to our expectations, no spatial genetic structure was detected between the reefs of Curaçao and Bonaire (~40 km apart) within A. grahamae. However, cryptic taxa were discovered within both taxonomic species, with those in A. lamarcki (incompletely) partitioned by depth and those in A. grahamae occurring sympatrically (at the same depth). Hybrid analyses and demographic modelling identified contemporary and historical gene flow among cryptic taxa, both within and between A. grahamae and A. lamarcki. These results (1) indicate that spatial connectivity and subsequent replenishment may be possible between islands of moderate geographic distances for A. grahamae, an ecologically important mesophotic species, (2) that cryptic taxa occur in the mesophotic zone and environmental selection along shallow to mesophotic depth gradients may drive divergence in depth‐generalists such as A. lamarcki, and (3) highlight that gene flow links taxa within this relativity diverse Caribbean genus.
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Affiliation(s)
- Katharine E. Prata
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
- California Academy of Sciences San Francisco CA USA
| | - Cynthia Riginos
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology University of Arizona Tuscon AZ USA
| | | | - Juan A. Sánchez
- Laboratorio de Biología Molecular Marina (BIOMMAR) Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
| | - Norbert Englebert
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
| | - Kyra B. Hay
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
| | - Pim Bongaerts
- School of Biological Sciences The University of Queensland St Lucia QLD Australia
- California Academy of Sciences San Francisco CA USA
- Caribbean Research and Management of Biodiversity Foundation Willemstad, Curaçao
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14
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Rose NH, Bay RA, Morikawa MK, Thomas L, Sheets EA, Palumbi SR. Genomic analysis of distinct bleaching tolerances among cryptic coral species. Proc Biol Sci 2021; 288:20210678. [PMID: 34641729 DOI: 10.1098/rspb.2021.0678] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Reef-building coral species are experiencing an unprecedented decline owing to increasing frequency and intensity of marine heatwaves and associated bleaching-induced mortality. Closely related species from the Acropora hyacinthus species complex differ in heat tolerance and in their association with heat-tolerant symbionts. We used low-coverage full genome sequencing of 114 colonies monitored across the 2015 bleaching event in American Samoa to determine the genetic differences among four cryptic species (termed HA, HC, HD and HE) that have diverged in these species traits. Cryptic species differed strongly at thousands of single nucleotide polymorphisms across the genome which are enriched for amino acid changes in the bleaching-resistant species HE. In addition, HE also showed two particularly divergent regions with strong signals of differentiation. One approximately 220 kb locus, HES1, contained the majority of fixed differences in HE. A second locus, HES2, was fixed in HE but polymorphic in the other cryptic species. Surprisingly, non-HE individuals with HE-like haplotypes at HES2 were more likely to bleach. At both loci, HE showed particular sequence similarity to a congener, Acropora millepora. Overall, resilience to bleaching during the third global bleaching event was strongly structured by host cryptic species, buoyed by differences in symbiont associations between these species.
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Affiliation(s)
- Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA, USA.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Megan K Morikawa
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Luke Thomas
- The UWA Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia.,Australian Institute of Marine Science, Perth, Western Australia, Australia.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
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15
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Rippe JP, Dixon G, Fuller ZL, Liao Y, Matz M. Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract. Mol Ecol 2021; 30:3468-3484. [PMID: 33894013 DOI: 10.1111/mec.15931] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/22/2021] [Accepted: 04/14/2021] [Indexed: 01/02/2023]
Abstract
Broadcast-spawning coral species have wide geographical ranges spanning strong environmental gradients, but it is unclear how much spatially varying selection these gradients actually impose. Strong divergent selection might present a considerable barrier for demographic exchange between disparate reef habitats. We investigated whether the cross-shelf gradient is associated with spatially varying selection in two common coral species, Montastraea cavernosa and Siderastrea siderea, in the Florida Keys. To this end, we generated a de novo genome assembly for M. cavernosa and used 2bRAD to genotype 20 juveniles and 20 adults of both species from each of the three reef zones to identify signatures of selection occurring within a single generation. Unexpectedly, each species was found to be composed of four genetically distinct lineages, with gene flow between them still ongoing but highly reduced in 13.0%-54.7% of the genome. Each species includes two sympatric lineages that are only found in the deep (20 m) habitat, while the other lineages are found almost exclusively on the shallower reefs (3-10 m). The two "shallow" lineages of M. cavernosa are also specialized for either nearshore or offshore: comparison between adult and juvenile cohorts indicates that cross-shelf migrants are more than twice as likely to die before reaching adulthood than local recruits. S. siderea and M. cavernosa are among the most ecologically successful species on the Florida Keys Reef Tract, and this work offers important insight into the genomic background of divergent selection and environmental specialization that may in part explain their resilience and broad environmental range.
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Affiliation(s)
- John P Rippe
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Groves Dixon
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Zachary L Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Yi Liao
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Mikhail Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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16
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Rieseberg L, Warschefsky E, O’Boyle B, Taberlet P, Ortiz‐Barrientos D, Kane NC, Sibbett B. Editorial 2021. Mol Ecol 2020. [DOI: 10.1111/mec.15759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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