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Hawkins S, Zetika GA, Kinaston R, Firmando YR, Sari DM, Suniarti Y, Lucas M, Roberts P, Reepmeyer C, Maloney T, Kealy S, Stirling C, Reid M, Barr D, Kleffmann T, Kumar A, Yuwono P, Litster M, Husni M, Ririmasse M, Mahirta, Mujabuddawat M, Harriyadi, O'Connor S. Earliest known funerary rites in Wallacea after the last glacial maximum. Sci Rep 2024; 14:282. [PMID: 38168501 PMCID: PMC10762057 DOI: 10.1038/s41598-023-50294-y] [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: 05/16/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
The insular region of Wallacea has become a focal point for studying Pleistocene human ecological and cultural adaptations in island environments, however, little is understood about early burial traditions during the Pleistocene. Here we investigate maritime interactions and burial practices at Ratu Mali 2, an elevated coastal cave site on the small island of Kisar in the Lesser Sunda Islands of eastern Indonesia dated to 15,500-3700 cal. BP. This multidisciplinary study demonstrates extreme marine dietary adaptations, engagement with an extensive exchange network across open seas, and early mortuary practices. A flexed male and a female, interred in a single grave with abundant shellfish and obsidian at Ratu Mali 2 by 14.7 ka are the oldest known human burials in Wallacea with established funerary rites. These findings highlight the impressive flexibility of our species in marginal environments and provide insight into the earliest known ritualised treatment of the dead in Wallacea.
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Affiliation(s)
- Stuart Hawkins
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia.
| | - Gabriella Ayang Zetika
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | - Rebecca Kinaston
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
- Griffith Centre for Social and Cultural Research, Griffith University, Nathan, QLD, Australia
- BioArch South, Waitati, 9085, New Zealand
| | - Yulio Ray Firmando
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | - Devi Mustika Sari
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | - Yuni Suniarti
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | - Mary Lucas
- Department of Archaeology, Max Planck Institute of Geoanthropology DE, Jena, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute of Geoanthropology DE, Jena, Germany
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Christian Reepmeyer
- Commission for Archaeology of Non-European Cultures, German Archaeological Institute Division of Germany, Berlin, Germany
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society, and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Tim Maloney
- Griffith Centre for Social and Cultural Research, Griffith University, Southport, QLD, 4222, Australia
| | - Shimona Kealy
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
| | - Claudine Stirling
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, 9054, New Zealand
| | - Malcolm Reid
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, 9054, New Zealand
| | - David Barr
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, 9054, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Abhishek Kumar
- Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Pratiwi Yuwono
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
- Geoarchaeology and Archaeometry Research Group (GARG), Southern Cross University, Lismore, NSW, Australia
| | - Mirani Litster
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society, and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Muhammad Husni
- Balai Arkeologi Maluku, JI. Namalatu-Latuhalat, Ambon, Indonesia
| | - Marlon Ririmasse
- Balai Arkeologi Maluku, JI. Namalatu-Latuhalat, Ambon, Indonesia
| | - Mahirta
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | | | - Harriyadi
- Organisasi Riset Arkeologi Bahasa dan Sastra, Badan Riset dan Inovasi Nasional, Jakarta, Indonesia
| | - Sue O'Connor
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
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2
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Ip YCA, Chang JJM, Oh RM, Quek ZBR, Chan YKS, Bauman AG, Huang D. Seq' and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs. Mol Ecol 2023; 32:6223-6242. [PMID: 35716352 DOI: 10.1111/mec.16568] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 05/06/2022] [Accepted: 06/10/2022] [Indexed: 12/01/2022]
Abstract
Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.
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Affiliation(s)
- Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ren Min Oh
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zheng Bin Randolph Quek
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Yale-NUS College, National University of Singapore, Singapore, Singapore
| | - Yong Kit Samuel Chan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Andrew G Bauman
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Marine and Environmental Sciences, Nova Southeastern University, Dania Beach, Florida, USA
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Centre for Nature-Based Climate Solutions, National University of Singapore, Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
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3
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Randolph Quek ZB, Jain SS, Richards ZT, Arrigoni R, Benzoni F, Hoeksema BW, Carvajal JI, Wilson NG, Baird AH, Kitahara MV, Seiblitz IGL, Vaga CF, Huang D. A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia). Mol Phylogenet Evol 2023:107867. [PMID: 37348770 DOI: 10.1016/j.ympev.2023.107867] [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: 02/26/2023] [Revised: 05/28/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (<38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The "Robust" and "Complex" clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the "Robust" clade, transforming our understanding of the "Basal" clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution.
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Affiliation(s)
- Z B Randolph Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Yale-NUS College, National University of Singapore, Singapore 138527, Singapore.
| | - Sudhanshi S Jain
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia; Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms, Genoa Marine Centre, Stazione Zoologica Anton Dohrn-National Institute of Marine Biology, Ecology and Biotechnology, 16126 Genoa, Italy
| | - Francesca Benzoni
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Bert W Hoeksema
- Taxonomy, Systematics and Geodiversity Group, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC Groningen, The Netherlands
| | - Jose I Carvajal
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Nerida G Wilson
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Andrew H Baird
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Marcelo V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, United States of America
| | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - Claudia F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore; Centre for Nature-based Climate Solutions, National University of Singapore, Singapore 117558, Singapore.
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4
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Tan EYW, Neo ML, Huang D. Assessing taxonomic, functional and phylogenetic diversity of giant clams across the Indo‐Pacific for conservation prioritization. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Edwin Y. W. Tan
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Mei Lin Neo
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Tropical Marine Science Institute National University of Singapore Singapore Singapore
| | - Danwei Huang
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Tropical Marine Science Institute National University of Singapore Singapore Singapore
- Centre for Nature‐based Climate Solutions National University of Singapore Singapore Singapore
- Lee Kong Chian Natural History Museum National University of Singapore Singapore Singapore
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5
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Siqueira AC, Kiessling W, Bellwood DR. Fast-growing species shape the evolution of reef corals. Nat Commun 2022; 13:2426. [PMID: 35504876 PMCID: PMC9065008 DOI: 10.1038/s41467-022-30234-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/21/2022] [Indexed: 11/21/2022] Open
Abstract
Ecological interactions are ubiquitous on tropical coral reefs, where sessile organisms coexist in limited space. Within these high-diversity systems, reef-building scleractinian corals form an intricate interaction network. The role of biotic interactions among reef corals is well established on ecological timescales. However, its potential effect on macroevolutionary patterns remains unclear. By analysing the rich fossil record of Scleractinia, we show that reef coral biodiversity experienced marked evolutionary rate shifts in the last 3 million years, possibly driven by biotic interactions. Our models suggest that there was an overwhelming effect of staghorn corals (family Acroporidae) on the fossil diversity trajectories of other coral groups. Staghorn corals showed an unparalleled spike in diversification during the Pleistocene. But surprisingly, their expansion was linked with increases in both extinction and speciation rates in other coral families, driving a nine-fold increase in lineage turnover. These results reveal a double-edged effect of diversity dependency on reef evolution. Given their fast growth, staghorn corals may have increased extinction rates via competitive interactions, while promoting speciation through their role as ecosystem engineers. This suggests that recent widespread human-mediated reductions in staghorn coral cover, may be disrupting the key macroevolutionary processes that established modern coral reef ecosystems. The effect of biotic interactions among reef corals on macroevolutionary patterns is unclear. Here, the authors study the rich coral fossil record, finding that reef coral diversity experienced potentially biotic interaction-driven evolutionary rate changes, and that Staghorn corals affected fossil diversity trajectories of other coral groups.
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Affiliation(s)
- Alexandre C Siqueira
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia. .,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia.
| | - Wolfgang Kiessling
- GeoZentrum Nordbayern, Friedrich-Alexander University Erlangen - Nürnberg (FAU), Erlangen, 91054, Germany
| | - David R Bellwood
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
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6
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McClanahan T, Munbodhe V, Naggea J, Muthiga N, Bhagooli R. Rare coral and reef fish species status, possible extinctions, and associated environmental perceptions in Mauritius. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Tim McClanahan
- Wildlife Conservation Society, Global Marine Programs Bronx New York USA
| | - Vikash Munbodhe
- Department of Biosciences and Ocean Studies, Faculty of Science, and Pole of Research Excellence in Sustainable Marine Biodiversity University of Mauritius Réduit Mauritius
| | - Josheena Naggea
- Stanford University, Emmett Interdisciplinary Program in Environment and Resources Stanford California USA
| | - Nyawira Muthiga
- Wildlife Conservation Society, Global Marine Programs Bronx New York USA
- Wildlife Conservation Society, Kenya Marine Program Mombasa Kenya
| | - Ranjeet Bhagooli
- Department of Biosciences and Ocean Studies, Faculty of Science, and Pole of Research Excellence in Sustainable Marine Biodiversity University of Mauritius Réduit Mauritius
- The Society of Biology (Mauritius) Réduit Mauritius
- The Biodiversity and Environment Institute Réduit Mauritius
- Institute of Oceanography and Environment (INOS), University Malaysia Terengganu Kuala Terengganu Terengganu Malaysia
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Ng CSL, Chan YKS, Nguyen NTH, Kikuzawa YP, Sam SQ, Toh TC, Mock AYJ, Chou LM, Huang D. Coral community composition and carbonate production in an urbanized seascape. MARINE ENVIRONMENTAL RESEARCH 2021; 168:105322. [PMID: 33857701 DOI: 10.1016/j.marenvres.2021.105322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Coastal urbanization causes environmental modifications that directly and indirectly influence the distribution and functioning of coral reefs. However, the capacity of urban infrastructure to support corals and vertically accrete is less understood. Here, we investigated if coral communities on reefs and seawalls in Singapore are distinct, and examined the environmental variables influencing coral carbonate production. Surveys at 22 sites yielded 134 coral species, with richness significantly higher on reefs. Coral cover and Shannon index did not differ between habitat types. Community composition was distinct between habitat types, with seawalls supporting a higher proportion of massive and thick-plating species. 'Distance from mainland' was the single most important variable influencing normalized carbonate production rates (a function of species-specific linear extension rate and skeletal bulk density and site coral cover), which were higher further from the mainland where human activity and development pressures were greater. Our results indicate that environmental filtering strongly shapes coral communities and may influence ecosystem functioning in Singapore's urbanized reef system. The findings will guide the management of reefs on increasingly urbanized coastlines.
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Affiliation(s)
- Chin Soon Lionel Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore; Tropical Marine Science Institute, National University of Singapore, 14 Kent Ridge Road, 119223, Singapore.
| | - Yong Kit Samuel Chan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore
| | - Nhung Thi Hong Nguyen
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore
| | - Yuichi Preslie Kikuzawa
- Tropical Marine Science Institute, National University of Singapore, 14 Kent Ridge Road, 119223, Singapore
| | - Shu Qin Sam
- Tropical Marine Science Institute, National University of Singapore, 14 Kent Ridge Road, 119223, Singapore
| | - Tai Chong Toh
- Tropical Marine Science Institute, National University of Singapore, 14 Kent Ridge Road, 119223, Singapore; College of Alice and Peter Tan, National University of Singapore, 8 College Avenue East, 138615, Singapore
| | - Aidan Yong Jie Mock
- Yale-NUS College, Environmental Studies, National University of Singapore, 16 College Avenue West, 138527, Singapore
| | - Loke Ming Chou
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore; Tropical Marine Science Institute, National University of Singapore, 14 Kent Ridge Road, 119223, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore; Tropical Marine Science Institute, National University of Singapore, 14 Kent Ridge Road, 119223, Singapore; Centre for Nature-based Climate Solutions, National University of Singapore, 16 Science Drive 4, 117558, Singapore
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8
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Abstract
Abstract
Modern-day Indo-Pacific coral reefs are characterized by rapid recovery driven by pulses of coral recruitment, but Caribbean reefs exhibit low rates of recruitment and poor recovery following a wide range of disturbance events. The contrasting evolutionary history of coral taxa offers key insight into biogeographic patterns of coral resilience. Following the closure of the Isthmus of Panama approximately 2.8 million years ago, widespread extinction of Caribbean corals led to an evolutionary bottleneck that favored large and long-lived species with a relatively high reliance on asexual versus sexual reproduction. In contrast, adaptive radiation led to the evolution of superrecruiting tabular, digitate, and corymbose corals that drive the rapid recovery of modern-day Indo-Pacific reefs following disturbance. The dominance of branching growth forms and evolutionary absence of superrecruiting growth forms throughout the entire evolutionary history of the Caribbean (approximately 38 million years ago to present) may explain the exceptionally high recruitment rates on modern-day Indo-Pacific reefs and low historical recruitment on Caribbean reefs. The evolutionary history of the Caribbean coral reef-building taxa implies that, even with a reversal of ecosystem state, widespread recovery of Caribbean reefs may be limited.
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Affiliation(s)
- George Roff
- School of Biological Sciences, University of Queensland, in St. Lucia, Australia
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9
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Yip ZT, Quek RZB, Huang D. Historical biogeography of the widespread macroalga Sargassum (Fucales, Phaeophyceae). JOURNAL OF PHYCOLOGY 2020; 56:300-309. [PMID: 31677168 PMCID: PMC7187439 DOI: 10.1111/jpy.12945] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 10/16/2019] [Indexed: 05/13/2023]
Abstract
Sargassum is a cosmopolitan brown algal genus spanning the three ocean basins of the Atlantic, Pacific and Indian Oceans, inhabiting temperate, subtropical and tropical habitats. Sargassum has been postulated to have originated in the Oligocene epoch approximately 30 mya according to a broad phylogenetic analysis of brown macroalgae, but its diversification to become one of the most widespread and speciose macroalgal genera remains unclear. Here, we present a Bayesian molecular clock study, which analyzed data from the order Fucales of the brown algal crown radiation (BACR) group to reconstruct a time-calibrated phylogeny of the Sargassum clade. Our phylogeny included a total of 120 taxa with 99 Sargassum species sampled for three molecular markers - ITS-2, cox3 and rbcLS - calibrated with an unambiguous Sargassaceae fossil from between the lower and middle Miocene. The analysis revealed a much later origin of Sargassum than expected at about 6.7 mya, with the genus diversifying since approximately 4.3 mya. Current geographic distributions of Sargassum species were then analyzed in conjunction with the time-calibrated phylogeny using the dispersal-extinction-cladogenesis (DEC) model to estimate ancestral ranges of clades in the genus. Results strongly support origination of Sargassum in the Central Indo-Pacific (CIP) region with subsequent independent dispersal events into other marine realms. The longer history of diversification in the ancestral CIP range could explain the much greater diversity there relative to other marine areas today. Analyses of these dynamic processes, when fine-tuned to a higher spatial resolution, enable the identification of evolutionary hotspots and provide insights into long-term dispersal patterns.
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Affiliation(s)
- Zhi Ting Yip
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
| | - Randolph Z. B. Quek
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
- Tropical Marine Science InstituteNational University of SingaporeSingapore City119227Singapore
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10
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Simmonds SE, Fritts‐Penniman AL, Cheng SH, Mahardika GN, Barber PH. Genomic signatures of host-associated divergence and adaptation in a coral-eating snail, Coralliophila violacea (Kiener, 1836). Ecol Evol 2020; 10:1817-1837. [PMID: 32128119 PMCID: PMC7042750 DOI: 10.1002/ece3.5977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022] Open
Abstract
The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo-Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we examined the mechanisms promoting and maintaining the snails' adaptation to their coral hosts. Genome-wide single nucleotide polymorphism (SNP) data from type II restriction site-associated DNA (2b-RAD) sequencing revealed two differentiated clusters of C. violacea that were largely concordant with coral host, consistent with previous genetic results. However, the presence of some admixed genotypes indicates gene flow from one lineage to the other. Combined, these results suggest that differentiation between host-associated lineages of C. violacea is occurring in the face of ongoing gene flow, requiring strong selection. Indeed, 2.7% of all SNP loci were outlier loci (73/2,718), indicative of divergence with gene flow, driven by adaptation of each C. violacea lineage to their specific coral hosts.
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Affiliation(s)
- Sara E. Simmonds
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | | | - Samantha H. Cheng
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
- Center for Biodiversity and ConservationAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Gusti Ngurah Mahardika
- Animal Biomedical and Molecular Biology LaboratoryFaculty of Veterinary MedicineUdayana University BaliDenpasarIndonesia
| | - Paul H. Barber
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
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11
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Ip YCA, Tay YC, Gan SX, Ang HP, Tun K, Chou LM, Huang D, Meier R. From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach. Biodivers Data J 2019; 7:e46833. [PMID: 31866739 PMCID: PMC6917626 DOI: 10.3897/bdj.7.e46833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/21/2019] [Indexed: 12/27/2022] Open
Abstract
Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes ("biocodes"), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore's first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to "Biodiversity of Singapore" (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.
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Affiliation(s)
- Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Ywee Chieh Tay
- National University of Singapore, Singapore, SingaporeNational University of SingaporeSingaporeSingapore
- Temasek Life Sciences Laboratory, Singapore, SingaporeTemasek Life Sciences LaboratorySingaporeSingapore
| | - Su Xuan Gan
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Hui Ping Ang
- National Parks Board, Singapore, SingaporeNational Parks BoardSingaporeSingapore
| | - Karenne Tun
- National Parks Board, Singapore, SingaporeNational Parks BoardSingaporeSingapore
| | - Loke Ming Chou
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
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12
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Pérez-Escobar OA, Lucas E, Jaramillo C, Monro A, Morris SK, Bogarín D, Greer D, Dodsworth S, Aguilar-Cano J, Sanchez Meseguer A, Antonelli A. The Origin and Diversification of the Hyperdiverse Flora in the Chocó Biogeographic Region. FRONTIERS IN PLANT SCIENCE 2019; 10:1328. [PMID: 31867022 PMCID: PMC6910151 DOI: 10.3389/fpls.2019.01328] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Extremely high levels of plant diversity in the American tropics are derived from multiple interactions between biotic and abiotic factors. Previous studies have focused on macro-evolutionary dynamics of the Tropical Andes, Amazonia, and Brazil's Cerrado and Atlantic forests during the last decade. Yet, other equally important Neotropical biodiversity hotspots have been severely neglected. This is particularly true for the Chocó region on the north-western coast of South and Central America. This geologically complex region is Earth's ninth most biodiverse hotspot, hosting approximately 3% of all known plant species. Here, we test Gentry's [1982a,b] hypothesis of a northern Andean-Central American Pleistocene origin of the Chocoan flora using phylogenetic reconstructions of representative plant lineages in the American tropics. We show that plant diversity in the Chocó is derived mostly from Andean immigrants. Contributions from more distant biogeographical areas also exist but are fewer. We also identify a strong floristic connection between the Chocó and Central America, revealed by multiple migrations into the Chocó during the last 5 Ma. The dated phylogenetic reconstructions suggest a Plio-Pleistocene onset of the extant Chocó flora. Taken together, these results support to a limited extend Gentry's hypothesis of a Pleistocene origin and of a compound assembly of the Chocoan biodiversity hotspot. Strong Central American-Chocoan floristic affinity may be partly explained by the accretion of a land mass derived from the Caribbean plate to north-western South America. Additional densely sampled phylogenies of Chocoan lineages also well represented across the Neotropics could enlighten the role of land mass movements through time in the assembly of floras in Neotropical biodiversity hotspots.
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Affiliation(s)
- Oscar Alejandro Pérez-Escobar
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Eve Lucas
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Panama, Panama
- ISEM, U. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Alexandre Monro
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Sarah K. Morris
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Diego Bogarín
- Universidad de Costa Rica, Jardín Botánico Lankester, Cartago, Costa Rica
| | - Deborah Greer
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Department of Environment, Food and Rural Affairs, London, United Kingdom
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
| | | | | | - Alexandre Antonelli
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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13
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Zenil-Ferguson R, Burleigh JG, Freyman WA, Igić B, Mayrose I, Goldberg EE. Interaction among ploidy, breeding system and lineage diversification. THE NEW PHYTOLOGIST 2019; 224:1252-1265. [PMID: 31617595 DOI: 10.1111/nph.16184] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/14/2019] [Indexed: 05/28/2023]
Abstract
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs polyploid states) and breeding system (self-incompatible vs self-compatible states) are both thought to be drivers of differential diversification in angiosperms. We fit 29 diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits. We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization. Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.
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Affiliation(s)
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - William A Freyman
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Boris Igić
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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14
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Camara EM, Costa de Azevedo MC, Franco TP, Araújo FG. Hierarchical partitioning of fish diversity and scale-dependent environmental effects in tropical coastal ecosystems. MARINE ENVIRONMENTAL RESEARCH 2019; 148:26-38. [PMID: 31077965 DOI: 10.1016/j.marenvres.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/23/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
The spatial structure of the fish diversity and site-scale and landscape-scale environmental effects were investigated across hierarchical levels in tropical coastal ecosystems. Total diversity (γ) was hierarchically partitioned into α and β components using both the additive and multiplicative methods. A model selection based on the AICc was applied to generalized linear mixed models relating diversity measures to environmental variables and including random effects for hierarchical levels and season. Short-term seasonal effects were negligible. Spatial effects were more relevant at the site level and negligible at the subregion level, due to the high spatial heterogeneity and the natural pooling of ecosystems, respectively. Site-scale environmental effects were more relevant at the subregion level, with eutrophic conditions (continental influence) favoring the species richness (α and γ) and higher absence of species (βA) in oligotrophic conditions (marine influence). At the system level, the positive effect of the distance from the ocean on γ and higher βA in oligotrophic conditions reinforced the positive continental influence on fish diversity. Environmental homogenization processes were most likely associated with the negative effect of the pasture cover on α at the system level, and γ and βA at the site level. The negative effect of the forest cover on the later diversity measure evidenced its relevance to maintain richer but more similar assemblages, whereas the positive continental influence was most likely due to the loss of stenohaline marine species. This study evidenced that disentangling spatial, land use, and marine vs. continental effects on diversity components is critical to understand the primary determinants of the fish diversity in tropical coastal ecosystems.
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Affiliation(s)
- Ellen Martins Camara
- Universidade Federal Rural do Rio de Janeiro, Departamento de Biologia Animal, Laboratório de Ecologia de Peixes, 23897-030, Seropédica, RJ, Brazil
| | - Márcia Cristina Costa de Azevedo
- Universidade Federal Rural do Rio de Janeiro, Departamento de Biologia Animal, Laboratório de Ecologia de Peixes, 23897-030, Seropédica, RJ, Brazil
| | - Taynara Pontes Franco
- Universidade Federal Rural do Rio de Janeiro, Departamento de Biologia Animal, Laboratório de Ecologia de Peixes, 23897-030, Seropédica, RJ, Brazil
| | - Francisco Gerson Araújo
- Universidade Federal Rural do Rio de Janeiro, Departamento de Biologia Animal, Laboratório de Ecologia de Peixes, 23897-030, Seropédica, RJ, Brazil.
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15
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Lambert JW, Reichard M, Pincheira-Donoso D. Live fast, diversify non-adaptively: evolutionary diversification of exceptionally short-lived annual killifishes. BMC Evol Biol 2019; 19:10. [PMID: 30626330 PMCID: PMC6327596 DOI: 10.1186/s12862-019-1344-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/02/2019] [Indexed: 11/17/2022] Open
Abstract
Background Adaptive radiations are triggered by ecological opportunity – the access to novel niche domains with abundant available resources that facilitate the formation of new ecologically divergent species. Therefore, as new species saturate niche space, clades experience a diversity-dependent slowdown of diversification over time. At the other extreme of the radiation continuum, non-adaptively radiating lineages undergo diversification with minimal niche differentiation when ‘spatial opportunity’ (i.e. areas with suitable ‘ancestral’ ecological conditions) is available. Traditionally, most research has focused on adaptive radiations, while empirical studies on non-adaptive radiations remain lagging behind. A prolific clade of African fish with extremely short lifespan (Nothobranchius killifish), show the key evolutionary features of a candidate non-adaptive radiation – primarily allopatric species with minimal niche and phenotypic divergence. Here, we test the hypothesis that Nothobranchius killifish have non-adaptively diversified. We employ phylogenetic modelling to investigate the tempo and mode of macroevolutionary diversification of these organisms. Results Nothobranchius diversification has proceeded with minor niche differentiation and minimal morphological disparity among allopatric species. Additionally, we failed to identify evidence for a role of body size or biogeography in influencing diversification rates. Diversification has been homogeneous within this genus, with the only hotspot of species-richness not resulting from rapid diversification. However, species in sympatry show higher disparity, which may have been caused by character displacement among coexisting species. Conclusions Nothobranchius killifish have proliferated following the tempo and mode of a non-adaptive radiation. Our study confirms that this exceptionally short-lived group have diversified with minimal divergent niche adaptation, while one group of coexisting species seems to have facilitated spatial overlap among these taxa via the evolution of ecological character displacement. Electronic supplementary material The online version of this article (10.1186/s12862-019-1344-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua W Lambert
- School of Life Sciences, Joseph Banks Laboratories, Brayford Campus, University of Lincoln, Lincoln, LN6 7DL, UK
| | - Martin Reichard
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic
| | - Daniel Pincheira-Donoso
- MacroBiodiversity Lab, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK.
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16
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Underwood JN, Travers MJ, Snow M, Puotinen M, Gouws G. Cryptic lineages in the Wolf Cardinalfish living in sympatry on remote coral atolls. Mol Phylogenet Evol 2018; 132:183-193. [PMID: 30528081 DOI: 10.1016/j.ympev.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 10/11/2018] [Accepted: 12/04/2018] [Indexed: 10/27/2022]
Abstract
Coral reef health and biodiversity is under threat worldwide due to rapid climate change. However, much of the inter- and intra-specific diversity of coral reefs are undescribed even in well studied taxa such as fish. Delimiting previously unrecognised diversity is important for understanding the processes that generate and sustain biodiversity in coral reef ecosystems and informing strategies for their conservation and management. Many taxa that inhabit geographically isolated coral reefs rely on self-recruitment for population persistence, providing the opportunity for the evolution of unique genetic lineages through divergent selection and reproductive isolation. Many such lineages in corals and fish are morphologically similar or indistinguishable. Here, we report the discovery and characterisation of cryptic lineages of the Wolf Cardinalfish, Cheilodipterus artus, from the coral atolls of northwest Australia using multiple molecular markers from mitochondrial (CO1 and D-loop) and nuclear (microsatellites) DNA. Concordant results from all markers identified two highly divergent lineages that are morphologically cryptic and reproductively isolated. These lineages co-occurred at daytime resting sites, but the relative abundance of each lineage was strongly correlated with wave exposure. It appears, therefore, that fish from each lineage are better adapted to different microhabitats. Such cryptic and ecologically based diversity appears to be common in these atolls and may well aid resilience of these systems. Our results also highlight that underwater surveys based on visual identification clearly underestimate biodiversity, and that a taxonomic revision of the Cheilodipterus genus is necessary.
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Affiliation(s)
- Jim N Underwood
- Australian Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA 6009, Australia.
| | - Michael J Travers
- Australian Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA 6009, Australia; Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, PO Box 20, North Beach, Western Australia 6920, Australia
| | - Michael Snow
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, PO Box 20, North Beach, Western Australia 6920, Australia
| | - Marji Puotinen
- Australian Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA 6009, Australia
| | - Gavin Gouws
- National Research Foundation - South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown 6140, South Africa
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17
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Miller EC, Hayashi KT, Song D, Wiens JJ. Explaining the ocean's richest biodiversity hotspot and global patterns of fish diversity. Proc Biol Sci 2018; 285:20181314. [PMID: 30305433 PMCID: PMC6191688 DOI: 10.1098/rspb.2018.1314] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/07/2018] [Indexed: 01/01/2023] Open
Abstract
For most marine organisms, species richness peaks in the Central Indo-Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17 435 species total, including approximately 72% of all marine fishes and approximately 33% of all freshwater fishes). The high diversity of the Central Indo-Pacific was explained by its colonization by many lineages 5.3-34 million years ago. These relatively old colonizations allowed more time for richness to build up through in situ diversification compared to other warm-marine regions. Surprisingly, diversification rates were decoupled from marine richness patterns, with clades in low-richness cold-marine habitats having the highest rates. Unlike marine richness, freshwater diversity was largely derived from a few ancient colonizations, coupled with high diversification rates. Our results are congruent with the geological history of the marine tropics, and thus may apply to many other organisms. Beyond marine biogeography, we add to the growing number of cases where colonization and time-for-speciation explain large-scale richness patterns instead of diversification rates.
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Affiliation(s)
| | - Kenji T Hayashi
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
- Division of Biology and Medicine, Program in Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dongyuan Song
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
- Department of Ecology and Evolutionary Biology, Fudan University, Shanghai 200438, China
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
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18
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Caetano DS, O'Meara BC, Beaulieu JM. Hidden state models improve state-dependent diversification approaches, including biogeographical models. Evolution 2018; 72:2308-2324. [DOI: 10.1111/evo.13602] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/20/2018] [Accepted: 08/27/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Daniel S. Caetano
- Department of Biological Sciences; University of Arkansas; Fayetteville Arkansas 72701
| | - Brian C. O'Meara
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville Tennessee 37996-1610
| | - Jeremy M. Beaulieu
- Department of Biological Sciences; University of Arkansas; Fayetteville Arkansas 72701
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19
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Arrigoni R, Berumen ML, Stolarski J, Terraneo TI, Benzoni F. Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean. Cladistics 2018; 35:301-328. [DOI: 10.1111/cla.12346] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2018] [Indexed: 12/24/2022] Open
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
| | - Michael L. Berumen
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Saudi Arabia
| | - Jaroslaw Stolarski
- Institute of Paleobiology Polish Academy of Sciences Twarda 51/55 Warsaw PL‐00‐818 Poland
| | - Tullia I. Terraneo
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Saudi Arabia
- College of Marine and Environmental Science James Cook University Townsville QLD 4811 Australia
| | - Francesca Benzoni
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Piazza della Scienza 2 Milano 20126 Italy
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS) Laboratoire d'excellence‐CORAIL Centre IRD de Nouméa 101 Promenade Roger Laroque, BP A5 Noumea Cedex 98848 New Caledonia
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20
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Pérez-Escobar OA, Cass S, Dodsworth S. Digest: Drivers of coral diversification in a major marine biodiversity hotspot. Evolution 2018; 72:406-408. [PMID: 29319173 DOI: 10.1111/evo.13419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 12/18/2017] [Indexed: 12/19/2022]
Affiliation(s)
| | - Susannah Cass
- Trinity Centre for Biodiversity Research, Trinity College Dublin, Dublin 2, Ireland
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, United Kingdom
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