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Tian SY, Yasuhara M, Condamine FL, Huang HHM, Fernando AGS, Aguilar YM, Pandita H, Irizuki T, Iwatani H, Shin CP, Renema W, Kase T. Cenozoic history of the tropical marine biodiversity hotspot. Nature 2024; 632:343-349. [PMID: 38926582 PMCID: PMC11306107 DOI: 10.1038/s41586-024-07617-4] [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] [Received: 08/28/2023] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)1,2. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood3. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.
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Affiliation(s)
- Skye Yunshu Tian
- School of Biological Sciences, Area of Ecology and Biodiversity, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Musketeers Foundation Institute of Data Science, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Bonner Institut für Organismische Biologie, Paläontologie, Universität Bonn, Bonn, Germany.
| | - Moriaki Yasuhara
- School of Biological Sciences, Area of Ecology and Biodiversity, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Musketeers Foundation Institute of Data Science, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, Hong Kong SAR.
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Montpellier, France
| | | | - Allan Gil S Fernando
- National Institute of Geological Sciences, University of the Philippines, Diliman, Quezon City, The Philippines
| | - Yolanda M Aguilar
- Marine Geological Survey, Mines and Geosciences Bureau, Quezon City, The Philippines
| | - Hita Pandita
- Department of Geological Engineering, Faculty of Mineral Technology, Institute Teknologi Nasional Yogyakarta, Yogyakarta, Indonesia
| | - Toshiaki Irizuki
- Department of Geoscience, Interdisciplinary Graduate School of Science and Engineering, Shimane University, Matsue, Japan
| | - Hokuto Iwatani
- Division of Earth Science, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Caren P Shin
- Paleontological Research Institution, Ithaca, NY, USA
- Department of Earth and Atmospheric Sciences, Cornell University, New York, NY, USA
| | - Willem Renema
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
| | - Tomoki Kase
- National Museum of Nature and Science, Department of Geology and Paleontology, Tsukuba, Japan
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2
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Rades M, Poschet G, Gegner H, Wilke T, Reichert J. Chronic effects of exposure to polyethylene microplastics may be mitigated at the expense of growth and photosynthesis in reef-building corals. MARINE POLLUTION BULLETIN 2024; 205:116631. [PMID: 38917503 DOI: 10.1016/j.marpolbul.2024.116631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
The causes of the physiological effects of microplastic pollution, potentially harming reef-building corals, are unclear. Reasons might include increased energy demands for handling particles and immune reactions. This study is among the first assessing the effects of long-term microplastic exposure on coral physiology at realistic concentrations (200 polyethylene particles L-1). The coral species Acropora muricata, Pocillopora verrucosa, Porites lutea, and Heliopora coerulea were exposed to microplastics for 11 months, and energy reserves, metabolites, growth, and photosymbiont state were analyzed. Results showed an overall low impact on coral physiology, yet species-specific effects occurred. Specifically, H. coerulea exhibited reduced growth, P. lutea and A. muricata showed changes in photosynthetic efficiency, and A. muricata variations in taurine levels. These findings suggest that corals may possess compensatory mechanisms mitigating the effects of microplastics. However, realistic microplastic concentrations only occasionally affected corals. Yet, corals exposed to increasing pollution scenarios will likely experience more negative impacts.
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Affiliation(s)
- Marvin Rades
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany.
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hagen Gegner
- Metabolomics Core Technology Platform, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Thomas Wilke
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany
| | - Jessica Reichert
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany; Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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3
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Repetto MF, Torchin ME, Ruiz GM, Schlöder C, Freestone AL. Biogeographic and seasonal differences in consumer pressure underlie strong predation in the tropics. Proc Biol Sci 2024; 291:20240868. [PMID: 38955327 PMCID: PMC11334995 DOI: 10.1098/rspb.2024.0868] [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: 09/11/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Biotic interactions play a critical role in shaping patterns of global biodiversity. While several macroecological studies provide evidence for stronger predation in tropical regions compared with higher latitudes, results are variable even within the tropics, and the drivers of this variability are not well understood. We conducted two complementary standardized experiments on communities of sessile marine invertebrate prey and their associated predators to test for spatial and seasonal differences in predation across the tropical Atlantic and Pacific coastlines of Panama. We further tested the prediction that higher predator diversity contributes to stronger impacts of predation, using both direct observations of predators and data from extensive reef surveys. Our results revealed substantially higher predation rates and stronger effects of predators on prey in the Pacific than in the Atlantic, demonstrating striking variation within tropical regions. While regional predator diversity was high in the Atlantic, functional diversity at local scales was markedly low. Peak predation strength in the Pacific occurred during the wet, non-upwelling season when ocean temperatures were warmer and predator communities were more functionally diverse. Our results highlight the importance of regional biotic and abiotic drivers that shape interaction strength and the maintenance of tropical communities, which are experiencing rapid environmental change.
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Affiliation(s)
- Michele F. Repetto
- Department of Biology, Temple University, Philadelphia, PA19122, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
- Smithsonian Environmental Research Center, Edgewater, MD21037-0028, USA
| | - Mark E. Torchin
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Gregory M. Ruiz
- Smithsonian Environmental Research Center, Edgewater, MD21037-0028, USA
| | - Carmen Schlöder
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Amy L. Freestone
- Department of Biology, Temple University, Philadelphia, PA19122, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
- Smithsonian Environmental Research Center, Edgewater, MD21037-0028, USA
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4
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Haderlé R, Bouveret L, Chazal J, Girardet J, Iglésias S, Lopez PJ, Millon C, Valentini A, Ung V, Jung JL. eDNA-based survey of the marine vertebrate biodiversity off the west coast of Guadeloupe (French West Indies). Biodivers Data J 2024; 12:e125348. [PMID: 38948133 PMCID: PMC11214010 DOI: 10.3897/bdj.12.e125348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/19/2024] [Indexed: 07/02/2024] Open
Abstract
Background In the marine environment, knowledge of biodiversity remains incomplete for many taxa, requiring assessments to understand and monitor biodiversity loss. Environmental DNA (eDNA) metabarcoding is a powerful tool for monitoring marine biodiversity, as it enables several taxa to be characterised simultaneously in a single sample. However, the data generated by environmental DNA metabarcoding are often not easily reusable. Implementing FAIR principles and standards for eDNA-derived data can facilitate data-sharing within the scientific community. New information This study focuses on the detection of marine vertebrate biodiversity using eDNA metabarcoding on the leeward coast of Guadeloupe, a known hotspot for marine biodiversity in the French West Indies. Occurrences and DNA-derived data are shared here using DarwinCore standards combined with MIMARKS standards.
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Affiliation(s)
- Rachel Haderlé
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des Antilles, Paris, FranceInstitut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des AntillesParisFrance
- Station Marine de Dinard du Muséum National d’Histoire Naturelle, Dinard, FranceStation Marine de Dinard du Muséum National d’Histoire NaturelleDinardFrance
| | - Laurent Bouveret
- Observatoire des Mammifères Marins de l'Archipel Guadeloupéen (OMMAG), Port-Louis, Guadelupe (Fr)Observatoire des Mammifères Marins de l'Archipel Guadeloupéen (OMMAG)Port-LouisGuadelupe (Fr)
| | - Jordane Chazal
- Observatoire des Mammifères Marins de l'Archipel Guadeloupéen (OMMAG), Port-Louis, Guadelupe (Fr)Observatoire des Mammifères Marins de l'Archipel Guadeloupéen (OMMAG)Port-LouisGuadelupe (Fr)
| | - Justine Girardet
- Centre international d’intelligence artificielle en acoustique naturelle, LIS, CNRS, Université de Toulon, Toulon, FranceCentre international d’intelligence artificielle en acoustique naturelle, LIS, CNRS, Université de ToulonToulonFrance
| | - Samuel Iglésias
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des Antilles, Paris, FranceInstitut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des AntillesParisFrance
- Station Marine de Concarneau du Muséum national d’Histoire naturelle, Concarneau, FranceStation Marine de Concarneau du Muséum national d’Histoire naturelleConcarneauFrance
| | - Pascal-Jean Lopez
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques, MNHN, CNRS 8067, Sorbonne Université, IRD 207, UCN, Université des Antilles, Paris, FranceLaboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques, MNHN, CNRS 8067, Sorbonne Université, IRD 207, UCN, Université des AntillesParisFrance
| | - Cédric Millon
- Observatoire des Mammifères Marins de l'Archipel Guadeloupéen (OMMAG), Port-Louis, Guadelupe (Fr)Observatoire des Mammifères Marins de l'Archipel Guadeloupéen (OMMAG)Port-LouisGuadelupe (Fr)
| | - Alice Valentini
- Spygen, Le Bourget du Lac, FranceSpygenLe Bourget du LacFrance
| | - Visotheary Ung
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des Antilles, Paris, FranceInstitut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des AntillesParisFrance
| | - Jean-Luc Jung
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des Antilles, Paris, FranceInstitut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des AntillesParisFrance
- Station Marine de Dinard du Muséum National d’Histoire Naturelle, Dinard, FranceStation Marine de Dinard du Muséum National d’Histoire NaturelleDinardFrance
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5
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Alam L, Zolkaply SZ, Sumaila UR, Rusydy I, Kutty AA, Bari MA, Mokhtar M, Pradhoshini KP, Krishnakumar S, Musthafa MS. Risk of extinction, variability in fish species composition, and factors influencing fish biodiversity in the Malacca Strait. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:41355-41369. [PMID: 37103711 DOI: 10.1007/s11356-023-27101-2] [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: 10/31/2022] [Accepted: 04/14/2023] [Indexed: 06/19/2023]
Abstract
Fish biodiversity in Malaysia is under pressure due to overexploitation, pollution, and climatic stressors. Nevertheless, the information on fish biodiversity and species vulnerability status is not well documented in the region. Therefore, a study on fish species composition and abundance in the Malacca Strait of Malaysia has been conducted for the purpose of monitoring biodiversity, determining the risk of species extinction, and identifying factors influencing biodiversity distribution. The sampling was conducted based on a random stratified sampling method from the three zones of sampling locations, i.e., estuary, mangrove, and open sea area of Tanjung Karang and Port Klang of Malacca Strait. Higher species diversity was recorded at Tanjung Karang coastal and mangrove areas (H' = 2.71; H' = 1.64) than Port Klang coastal and mangrove areas (H' = 1.50, H' = 0.29), an indication that the Port Klang area is comparatively more vulnerable. The study also explored sampling location, habitat, and IUCN red list as the influencing factors for fish biodiversity. Applying IUCN red list, this study identified one Endangered and one Vulnerable species with the forecasted increasing landing for both species. Our findings suggest the urgent need for the implementation of conservation measures as well as the continuous monitoring of fish biodiversity in the area.
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Affiliation(s)
- Lubna Alam
- Institute for Environment and Development (LESTARI), Research Centre for Sustainability Science and Governance (SGK), Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
- Department of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Mulyorejo Street, Surabaya, 60115, Indonesia
| | - Siti Zulaiha Zolkaply
- Institute for Environment and Development (LESTARI), Research Centre for Sustainability Science and Governance (SGK), Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
- Department of Agrotechnology and Bio-Industry, Jalan Raya, Lebuhraya Timur-Barat, Bandar Jeli, 17600, Jeli, Kelantan, Malaysia
| | - Ussif Rashid Sumaila
- Institute for Environment and Development (LESTARI), Research Centre for Sustainability Science and Governance (SGK), Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
- Institute for the Oceans and Fisheries, Faculty of Science, The University of British Columbia, Vancouver, Canada
| | - Ibnu Rusydy
- Department of Geological Engineering, Faculty of Engineering, Syiah Kuala University, Banda Aceh, Indonesia
| | - Ahmad Abas Kutty
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Md Azizul Bari
- Institute for Environment and Development (LESTARI), Research Centre for Sustainability Science and Governance (SGK), Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Mazlin Mokhtar
- Institute for Environment and Development (LESTARI), Research Centre for Sustainability Science and Governance (SGK), Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
- United Nations Sustainable Development Solutions Network Asia Headquarters (UN SDSN ASIA), Sunway University, Kuala Lumpur, Malaysia
| | - Kumara Perumal Pradhoshini
- Unit of Research in Radiation Biology & Environmental Radioactivity (URRBER), P.G. & Research Department of Zoology, The New College (Autonomous), Affiliated to University of Madras, Chennai, 600 014, Tamilnadu, India
| | - Subbiah Krishnakumar
- Department of Geology, Malankara Catholic College, Mariyagiri, Kaliyakkavilai, Kaniyakumari District, 629 153, India
| | - Mohamed Saiyad Musthafa
- Institute for Environment and Development (LESTARI), Research Centre for Sustainability Science and Governance (SGK), Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia.
- Unit of Research in Radiation Biology & Environmental Radioactivity (URRBER), P.G. & Research Department of Zoology, The New College (Autonomous), Affiliated to University of Madras, Chennai, 600 014, Tamilnadu, India.
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6
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Villalobos R, Aylagas E, Pearman JK, Curdia J, Coker D, Bell AC, Brown SD, Rowe K, Lozano-Cortés D, Rabaoui LJ, Marshell A, Qurban M, Jones B, Berumen ML, Carvalho S. Biodiversity patterns of the coral reef cryptobiota around the Arabian Peninsula. Sci Rep 2024; 14:9532. [PMID: 38664507 PMCID: PMC11045746 DOI: 10.1038/s41598-024-60336-8] [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: 01/09/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
The Arabian Peninsula accounts for approximately 6% of the world's coral reefs. Some thrive in extreme environments of temperature and salinity. Using 51 Autonomous Reef Monitoring Structure (ARMS), a standardized non-destructive monitoring device, we investigated the spatial patterns of coral reef cryptobenthic diversity in four ecoregions around the Arabian Peninsula and analyzed how geographical and/or environmental drivers shape those patterns. The mitochondrial cytochrome c oxidase subunit I (COI) gene was used to identify Amplicon Sequence Variants and assign taxonomy of the cryptobenthic organisms collected from the sessile and mobile fractions of each ARMS. Cryptobenthic communities sampled from the two ecoregions in the Red Sea showed to be more diverse than those inhabiting the Arabian (Persian) Gulf and the Gulf of Oman. Geographic distance revealed a stronger relationship with beta diversity in the Mantel partial correlation than environmental distance. However, the two mobile fractions (106-500 µm and 500-2000 µm) also had a significant correlation between environmental distance and beta diversity. In our study, dispersal limitations explained the beta diversity patterns in the selected reefs, supporting the neutral theory of ecology. Still, increasing differences in environmental variables (environmental filtering) also had an effect on the distribution patterns of assemblages inhabiting reefs within short geographic distances. The influence of geographical distance in the cryptofauna assemblages makes these relevant, yet usually ignored, communities in reef functioning vulnerable to large scale coastal development and should be considered in ecosystem management of such projects.
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Affiliation(s)
- Rodrigo Villalobos
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Eva Aylagas
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - John K Pearman
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Joao Curdia
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Darren Coker
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Alyssa Clothilde Bell
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Shannon D Brown
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington, Seattle, WA, USA
| | - Katherine Rowe
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- School of Science, The University of Waikato, Hamilton, New Zealand
| | | | - Lotfi J Rabaoui
- Center for Environment & Marine Studies, Research Institute, King Fahd University of Petroleum and Minerals, 31261, Dhahran, Eastern Province, Kingdom of Saudi Arabia
- National Center for Wildlife, Riyadh, Saudi Arabia
| | - Alyssa Marshell
- Sultan Qaboos University, Al Seeb Al Khoudh SQU SEPS, 123, Muscat, Oman
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7053, Australia
| | - Mohammad Qurban
- Center for Environment & Marine Studies, Research Institute, King Fahd University of Petroleum and Minerals, 31261, Dhahran, Eastern Province, Kingdom of Saudi Arabia
- Ministry of Environment, Water and Agriculture, Riyadh, Saudi Arabia
| | - Burton Jones
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Michael Lee Berumen
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Susana Carvalho
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia.
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7
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Vicario S, Terraneo TI, Chimienti G, Maggioni D, Marchese F, Purkis SJ, Eweida AA, Rodrigue M, Benzoni F. Molecular diversity of black corals from the Saudi Arabian Red Sea: a first assessment. INVERTEBR SYST 2024; 38:IS23041. [PMID: 38744524 DOI: 10.1071/is23041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/12/2024] [Indexed: 05/16/2024]
Abstract
Black corals occur as part of benthic assemblages from shallow to deep waters in all oceans. Despite the importance in many benthic ecosystems, where these act as biodiversity aggregators, antipatharians remain poorly studied, with 75% of the known species occurring below recreational SCUBA diving depth limits. Currently, information regarding the diversity and evolutionary history is limited, with most studies focusing on Hawaii and the South Pacific Ocean. Other regions of the world have received less attention, such as the Red Sea, where only two black coral families and four genera have been recorded. We provide the first analysis of the molecular diversity of black corals in the eastern Gulf of Aqaba and the northern and central Saudi Arabian Red Sea, based on a dataset of 161 antipatharian colonies collected down to 627 m deep. Based on specimen morphology, we ascribed our material to 11 genera belonging to 4 of the 7 known Antipatharia families, i.e. Antipathidae, Aphanipathidae, Myriopathidae and Schizopathidae. The genus level phylogeny of three intergenic mitochondrial regions, the trnW-IGR-nad2 (IgrW ), nad5-IGR-nad1 (IgrN ) and cox3-IGR-cox1 was reconstructed including previously published material. Overall, we recovered six molecular clades that included exclusively Red Sea sequences, with the highest diversity occurring at mesophotic depths. This study highlights that diversity of black corals in the Red Sea is much higher than previously known, with seven new generic records, suggesting that this basin may be a hotspot for antipatharian diversity as is known for other taxa. Our results recovered unresolved relationships within the order at the familial and generic levels. This emphasises the urgent need for an integration of genomic-wide data with a re-examination of informative morphological features necessary to revise the systematics of the order at all taxonomic levels.
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Affiliation(s)
- Silvia Vicario
- Marine Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; and Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Tullia Isotta Terraneo
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Giovanni Chimienti
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia; and Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Davide Maggioni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; and Marine Research and Higher Education (MaRHE) Center, University of Milano-Bicocca, Faafu Magoodhoo, Maldives
| | - Fabio Marchese
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Sam J Purkis
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, USA; and Khaled bin Sultan Living Oceans Foundation, Annapolis, USA
| | | | | | - Francesca Benzoni
- Marine Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; and Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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8
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Kundu S, Kang HE, Kim AR, Lee SR, Kim EB, Amin MHF, Andriyono S, Kim HW, Kang K. Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae). Int J Mol Sci 2024; 25:1822. [PMID: 38339100 PMCID: PMC10855530 DOI: 10.3390/ijms25031822] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.
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Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Eun-Bi Kim
- Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea;
| | - Muhammad Hilman Fu’adil Amin
- Advance Tropical Biodiversity, Genomics, and Conservation Research Group, Department of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia;
| | - Sapto Andriyono
- Department of Marine, Faculty of Fisheries and Marine, Airlangga University, Surabaya 60115, Indonesia
| | - Hyun-Woo Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Kyoungmi Kang
- International Graduate Program of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
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9
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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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10
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Glass JR, Harrington RC, Cowman PF, Faircloth BC, Near TJ. Widespread sympatry in a species-rich clade of marine fishes (Carangoidei). Proc Biol Sci 2023; 290:20230657. [PMID: 37909084 PMCID: PMC10618865 DOI: 10.1098/rspb.2023.0657] [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: 07/18/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023] Open
Abstract
A universal paradigm describing patterns of speciation across the tree of life has been debated for decades. In marine organisms, inferring patterns of speciation using contemporary and historical patterns of biogeography is challenging due to the deficiency of species-level phylogenies and information on species' distributions, as well as conflicting relationships between species' dispersal, range size and co-occurrence. Most research on global patterns of marine fish speciation and biogeography has focused on coral reef or pelagic species. Carangoidei is an ecologically important clade of marine fishes that use coral reef and pelagic environments. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a time-calibrated phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographical distributions and divergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting sympatric geographical distributions, regardless of node age. Most species pairs coexist across large portions of their ranges. We also observe greater disparity in body length and maximum depth between sympatric relative to allopatric sister species. These and other ecological or behavioural attributes probably facilitate sympatry among the most closely related carangoids.
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Affiliation(s)
- Jessica R. Glass
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- South African Institute for Aquatic Biodiversity, Makhanda 6140, South Africa
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Richard C. Harrington
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Peter F. Cowman
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland 4810, Australia
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Yale Peabody Museum of Natural History, Division of Vertebrate Zoology. New Haven, CT 06520, USA
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11
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Fang X, Dong D, Yang M, Li X. Phylogenetics and Population Genetics of the Petrolisthes lamarckii-P. haswelli Complex in China: Old Lineage and New Species. Int J Mol Sci 2023; 24:15843. [PMID: 37958829 PMCID: PMC10648172 DOI: 10.3390/ijms242115843] [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: 10/01/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Petrolisthes lamarckii (Leach, 1821) and P. haswelli Miers, 1884 are a pair of sister species of porcelain crabs, both of which are common in the intertidal zone of southern China, typically found under rocks and in the crevices of coral reefs. However, the distribution, genetic relationship and diversity of the two species in China have not been rigorously studied. Meanwhile, P. lamarckii is considered as a complex of cryptic species due to their diverse morphological features. In this study, we identified 127 specimens of the P. lamarckii-P. haswelli complex (LH complex) and recognised a new species through morphological and molecular analysis. Furthermore, we constructed a time-calibrated phylogeny of the LH complex using three mitochondrial and two nuclear genes from all three species, finding that the divergence of the LH complex can be traced back to the Miocene epoch, and that the genetic diversity increased during the Mid-Pleistocene transition period. Glacial refugia formed during the Pleistocene climatic oscillations has been regarded as one of the contributing factors to the diversification of marine organisms in the north-western Pacific. Petrolisthes haswelli demonstrates a wide distribution along the southern coast of China, while other lineages display more restricted distributions. The research on the demographic history and gene flow of P. haswelli revealed that the Chinese coastal populations experienced an expansion event approximately 12.5 thousand years ago (Kya) and the asymmetrical gene flows were observed between the two sides of the Taiwan Strait and Qiongzhou Strait, respectively, which is likely influenced by the restriction of ocean currents.
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Affiliation(s)
- Xuefeng Fang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.F.); (M.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Dong
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.F.); (M.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Yang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.F.); (M.Y.)
| | - Xinzheng Li
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.F.); (M.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Laoshan Laboratory, Qingdao 266237, China
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12
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Zhong J, Li M, Zhang H, Qin J. Fine-Grained 3D Modeling and Semantic Mapping of Coral Reefs Using Photogrammetric Computer Vision and Machine Learning. SENSORS (BASEL, SWITZERLAND) 2023; 23:6753. [PMID: 37571537 PMCID: PMC10422330 DOI: 10.3390/s23156753] [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: 06/27/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023]
Abstract
Corals play a crucial role as the primary habitat-building organisms within reef ecosystems, forming expansive structures that extend over vast distances, akin to the way tall buildings define a city's skyline. However, coral reefs are vulnerable to damage and destruction due to their inherent fragility and exposure to various threats, including the impacts of climate change. Similar to successful city management, the utilization of advanced underwater videography, photogrammetric computer vision, and machine learning can facilitate precise 3D modeling and the semantic mapping of coral reefs, aiding in their careful management and conservation to ensure their survival. This study focuses on generating detailed 3D mesh models, digital surface models, and orthomosaics of coral habitats by utilizing underwater coral images and control points. Furthermore, an innovative multi-modal deep neural network is designed to perform the pixel-wise semantic segmentation of orthomosaics, enabling the projection of resulting semantic maps onto a 3D space. Notably, this study achieves a significant milestone by accomplishing semantic fine-grained 3D modeling and rugosity evaluation of coral reefs with millimeter-level accuracy, providing a potent means to understand coral reef variations under climate change with high spatial and temporal resolution.
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Affiliation(s)
- Jiageng Zhong
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Luoyu Road No. 129, Wuhan 430079, China; (J.Z.); (H.Z.); (J.Q.)
| | - Ming Li
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Luoyu Road No. 129, Wuhan 430079, China; (J.Z.); (H.Z.); (J.Q.)
- Institute of Geodesy and Photogrammetry, ETH Zurich, 8093 Zurich, Switzerland
| | - Hanqi Zhang
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Luoyu Road No. 129, Wuhan 430079, China; (J.Z.); (H.Z.); (J.Q.)
| | - Jiangying Qin
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Luoyu Road No. 129, Wuhan 430079, China; (J.Z.); (H.Z.); (J.Q.)
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13
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Pinheiro HT, MacDonald C, Quimbayo JP, Shepherd B, Phelps TA, Loss AC, Teixeira JB, Rocha LA. Assembly rules of coral reef fish communities along the depth gradient. Curr Biol 2023; 33:1421-1430.e4. [PMID: 36917975 DOI: 10.1016/j.cub.2023.02.040] [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: 09/28/2022] [Revised: 12/08/2022] [Accepted: 02/13/2023] [Indexed: 03/14/2023]
Abstract
Coral reefs are home to some of the most studied ecological assemblages on the planet. However, differences in large-scale assembly rules have never been studied using empirical quantitative data stratified along the depth gradient of reefs. Consequently, little is known about the small- and regional-scale effects of depth on coral reef assemblages. Using a large dataset of underwater surveys, we observed that the influence of classic biogeographic drivers on the species richness of coral reef fishes changes significantly with depth, shaping distinct assemblages governed by different rules in mesophotic coral ecosystems. We show that a general pattern of decreased taxonomic and functional richness of reef fish assemblages with depth results from convergent filtering of species composition and trophic strategies on deeper reefs across ocean basins and that at smaller scales deep-reef communities are less influenced by regional factors than shallower reefs.
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Affiliation(s)
- Hudson T Pinheiro
- Department of Ichthyology, California Academy of Sciences, San Francisco, CA 94118, USA; Center for Marine Biology, University of São Paulo, São Sebastião, SP 11612-109, Brazil.
| | - Chancey MacDonald
- Department of Ichthyology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Juan Pablo Quimbayo
- Center for Marine Biology, University of São Paulo, São Sebastião, SP 11612-109, Brazil
| | - Bart Shepherd
- Steinhart Aquarium, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Tyler A Phelps
- Department of Ichthyology, California Academy of Sciences, San Francisco, CA 94118, USA; Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Ana Carolina Loss
- Instituto Nacional da Mata Atlântica, Santa Teresa, ES 29650-000, Brazil
| | - João Batista Teixeira
- Departamento de Oceanografia, Universidade Federal do Espírito Santo, Vitória, ES 29075-910, Brazil
| | - Luiz A Rocha
- Department of Ichthyology, California Academy of Sciences, San Francisco, CA 94118, USA
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14
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Borbee EM, Ayu IP, Carvalho P, Restiana E, Setiawan F, Subhan B, Humphries AT, Madduppa H, Lane CE. Rubble fields shape planktonic protist communities in Indonesia at a local scale. J Eukaryot Microbiol 2023; 70:e12954. [PMID: 36401815 DOI: 10.1111/jeu.12954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022]
Abstract
The Coral Triangle encompasses nearly 30% of the world's coral reefs and is widely considered the epicenter of marine biodiversity. Destructive fishing practices and natural disturbances common to this region damage reefs leaving behind fields of coral rubble. While the impacts of disturbances in these ecosystems are well documented on metazoans, we have a poor understanding of their impact on microbial communities at the base of the food web. We use metabarcoding to characterize protist community composition in sites of varying fisheries management schemes and benthic profiles across the island of Lombok, Indonesia. Our study shows that rubble coverage and net primary productivity are the strongest explainers of variation in protist communities across Lombok. More specifically, rubble fields are characterized by increases in small heterotrophic protists, including ciliates and cercozoans. In addition to shifts in heterotrophic protist communities, we also observed increases in diatom relative abundance in rubble fields, which corresponded to sites with higher net primary productivity. These results are the first to characterize protist communities in tropical marine rubble fields and provide insight on environmental factors potentially driving these shifts on a local scale.
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Affiliation(s)
- Erin M Borbee
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Inna Puspa Ayu
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Paul Carvalho
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Ester Restiana
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia.,Department of Fisheries, University of Jambi, Jambi, Indonesia
| | - Fahkrizal Setiawan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Beginer Subhan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Austin T Humphries
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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15
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Sobczyk R, Serigstad B, Pabis K. High polychaete diversity in the Gulf of Guinea (West African continental margin): The influence of local and intermediate scale ecological factors on a background of regional patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160046. [PMID: 36356769 DOI: 10.1016/j.scitotenv.2022.160046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
The Tropical East Atlantic is one of the least studied areas in the world's oceans, and thus a blank spot on the map of marine studies. Shaped by dynamic currents and shifting water masses, it is a key region in discussions about marine ecology, biodiversity, and zoogeography, while facing numerous, poorly understood, and unmonitored threats associated with climate change, acidification, and pollution. Polychaete diversity was assessed along four transects along the Ghana coast, from shallow to deep bottoms and distributed along the whole upwelling marine ecoregion. Despite high sampling effort, steep species accumulation curves demonstrated the necessity of further sampling in the region. We observed zonation of fauna by depth, and a decrease in species richness from 25 m to 1000 m depth. Polychaete communities were influenced by sediment type, presence of oxygen minimum zones, and local disturbances caused by elevated barium concentrations. Similar evenness along the depth gradient reflected the importance of rare species in the community structure. Differences in phylogenetic diversity, as reflected by taxonomic distinctness, were small, which suggested high ecosystem stability. The highly variable species richness at small scale (meters) showed the importance of ecological factors giving rise to microhabitat diversity, although we also noticed intermediate scale (50-300 km) differences affecting community structure. About 44 % of the species were rare (i.e. recorded only in three or fewer samples), highlighting the level of patchiness, while one fifth was distributed on all transects, therefore along the whole upwelling ecoregion, demonstrating the influence of the regional species pool on local communities at particular stations. Our study yielded 253 species, increasing the number of polychaetes known from this region by at least 50 %. This casts doubt on previous findings regarding Atlantic bioregionalization, biodiversity estimates and endemism, which appear to have been more pronouncedly affected by sampling bias than previously thought.
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Affiliation(s)
- Robert Sobczyk
- Department of Invertebrates Zoology and Hydrobiology, University of Lodz, Lodz, Poland.
| | - Bjorn Serigstad
- Center for Development Cooperation in Fisheries, Institute of Marine Research, Bergen, Norway
| | - Krzysztof Pabis
- Department of Invertebrates Zoology and Hydrobiology, University of Lodz, Lodz, Poland
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16
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Martins NT, Macagnan LB, Cassano V, Gurgel CFD. Brazilian marine phylogeography: A literature synthesis and analysis of barriers. Mol Ecol 2022; 31:5423-5439. [PMID: 36073087 DOI: 10.1111/mec.16684] [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: 02/10/2021] [Revised: 08/15/2022] [Accepted: 08/30/2022] [Indexed: 12/24/2022]
Abstract
In the last 30 years a plethora of phylogeography studies have been published targeting Brazilian marine species. To date, several historical and extant physical and ecological processes have been identified as drivers of allopatric, sympatric and parapatric population genetic differentiation detected along the Brazilian coast. Examples of extant physical barriers include the split of the South Equatorial Current into the Brazil and North Brazil boundary currents, the mouth of major rivers (e.g., Amazon, São Francisco and Doce rivers) and coastal upwellings. Examples of historical barriers include the Vitória-Trindade seamount chain promoting genetic differentiation during periods of glacial maxima and lower sea levels. Examples of ecological speciation include adaptations to different substrata, resource use and reproductive biology. We used published data to build data sets and generalized additive models to identify patterns of spatial phylogeographical concordance across multiple taxa and markers. Our results identify Cape São Roque as the most dominant extant barrier to gene flow along the Brazilian coast, followed by the Vitória-Trindade seamount chain and Cape Santa Marta. Cape Santa Marta is the northern winter limit of the Rio da Plata plume and is intermittently influenced by the Malvinas Current. This study provides a novel explicit quantitative approach to comparative phylogeography that recognizes four Brazilian phylogeographical regions delimited by processes associated with barriers to gene flow.
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Affiliation(s)
- Nuno T Martins
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, Brazil
| | - Leonardo B Macagnan
- NUPEM - Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Valéria Cassano
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, Brazil
| | - Carlos Frederico D Gurgel
- NUPEM - Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
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17
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Hoban ML, Whitney J, Collins AG, Meyer C, Murphy KR, Reft AJ, Bemis KE. Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 2022; 10:e13790. [PMID: 35959477 PMCID: PMC9359134 DOI: 10.7717/peerj.13790] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.
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Affiliation(s)
- Mykle L. Hoban
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, Hawai‘i, United States of America
| | - Jonathan Whitney
- Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, Hawai‘i, United States of America
| | - Allen G. Collins
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine R. Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Abigail J. Reft
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine E. Bemis
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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18
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Payet SD, Pratchett MS, Saenz‐Agudelo P, Berumen ML, DiBattista JD, Harrison HB. Demographic histories shape population genomics of the common coral grouper ( Plectropomus leopardus). Evol Appl 2022; 15:1221-1235. [PMID: 36051464 PMCID: PMC9423088 DOI: 10.1111/eva.13450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/02/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here, we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50% smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~10-120 kya) and may be vulnerable to localized disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of the Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.
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Affiliation(s)
- Samuel D. Payet
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Morgan S. Pratchett
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Michael L. Berumen
- Division of Biological and Environmental Science and Engineering, Red Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Joseph D. DiBattista
- Australian Museum Research Institute, Australian MuseumSydneyNew South WalesAustralia
| | - Hugo B. Harrison
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
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19
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Cantalice KM, Alvarado-Ortega J, Bellwood DR, Siqueira AC. Rising from the Ashes: The Biogeographic Origins of Modern Coral Reef Fishes. Bioscience 2022; 72:769-777. [PMID: 35923187 PMCID: PMC9343231 DOI: 10.1093/biosci/biac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
During the excavation of Mayan tombs, little did the archaeologists know that the fossils they discovered in the tomb stones would fundamentally alter our understanding of the earliest origins of coral reef fishes. Located just 500 kilometers from the point where an asteroid impact reconfigured the world's biological systems 66 million years ago, we find the earliest origins of three typical reef fish groups. Their presence in Mexico just 3 million years after this impact finally reconciles the conflict between the fossil and phylogenetic evidence for the earliest origins of reef fishes. The incorporation of these fossils into a global reconstruction of fish evolutionary history reveals a new picture of the early biogeography of reef fishes, with strong Atlantic links. From locations associated with biological destruction and societal collapse, we see evidence of the origins of one of the world's most diverse and spectacular marine ecosystems: coral reefs.
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Affiliation(s)
- Kleyton M Cantalice
- Departamento de Paleontología and with the Instituto de Geología, Universidad Nacional Autónoma de México , Ciudad de México, México
| | - Jesús Alvarado-Ortega
- Departamento de Paleontología and with the Instituto de Geología, Universidad Nacional Autónoma de México , Ciudad de México, México
| | - David R Bellwood
- Research Hub for Coral Reef Ecosystem Functions, ARC Centre of Excellence for Coral Reef Studies, and the College of Science and Engineering, James Cook University , Townsville, Queensland, Australia
| | - Alexandre C Siqueira
- Research Hub for Coral Reef Ecosystem Functions, ARC Centre of Excellence for Coral Reef Studies, and the College of Science and Engineering, James Cook University , Townsville, Queensland, Australia
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20
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Samayoa AP, Struthers CD, Trnski T, Roberts CD, Liggins L. Molecular phylogenetics reveals the evolutionary history of marine fishes (Actinopterygii) endemic to the subtropical islands of the Southwest Pacific. Mol Phylogenet Evol 2022; 176:107584. [PMID: 35843570 DOI: 10.1016/j.ympev.2022.107584] [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: 02/25/2022] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
Abstract
Remote oceanic islands of the Pacific host elevated levels of actinopterygian (ray-finned fishes) endemism. Characterizing the evolutionary histories of these endemics has provided insight into the generation and maintenance of marine biodiversity in many regions. The subtropical islands of Lord Howe, Norfolk, and Rangitāhua (Kermadec) in the Southwest Pacific are yet to be comprehensively studied. Here, we characterize the spatio-temporal diversification of marine fishes endemic to these Southwest Pacific islands by combining molecular phylogenies and the geographic distribution of species. We built Bayesian ultrametric trees based on open-access and newly generated sequences for five mitochondrial and ten nuclear loci, and using fossil data for time calibration. We present the most comprehensive phylogenies to date for marine ray-finned fish genera, comprising 34 species endemic to the islands, including the first phylogenetic placements for 11 endemics. Overall, our topologies confirm the species status of all endemics, including three undescribed taxa. Our phylogenies highlight the predominant affinity of these endemics with the Australian fish fauna (53%), followed by the East Pacific (15%), and individual cases where the closest sister taxon of our endemic is found in the Northwest Pacific and wider Indo-Pacific. Nonetheless, for a quarter of our focal endemics, their geographic affinity remains unresolved due to sampling gaps within their genera. Our divergence time estimates reveal that the majority of endemic lineages (67.6%) diverged after the emergence of Lord Howe (6.92 Ma), the oldest subtropical island in the Southwest Pacific, suggesting that these islands have promoted diversification. However, divergence ages of some endemics pre-date the emergence of the islands, suggesting they may have originated outside of these islands, or, in some cases, ages may be overestimated due to unsampled taxa. To fully understand the role of the Southwest Pacific subtropical islands as a 'cradle' for diversification, our study advocates for further regional surveys focused on tissue collection for DNA analysis.
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Affiliation(s)
- André P Samayoa
- School of Natural Sciences, Massey University, Auckland 0745, New Zealand.
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
| | - Thomas Trnski
- Natural Sciences, Auckland Museum Tāmaki Paenga Hira, Auckland 1010, New Zealand.
| | - Clive D Roberts
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland 0745, New Zealand; Natural Sciences, Auckland Museum Tāmaki Paenga Hira, Auckland 1010, New Zealand.
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21
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Shi M, Qi L, He LS. Comparative Analysis of the Mitochondrial Genome of Galatheanthemum sp. MT-2020 (Actiniaria Galatheanthemidae) From a Depth of 9,462 m at the Mariana Trench. Front Genet 2022; 13:854009. [PMID: 35754826 PMCID: PMC9213748 DOI: 10.3389/fgene.2022.854009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
The hadal zone, which represents the deepest marine habitat on Earth (6,000–11,000 m), is a harsh environment mainly characterized by extremely high hydrostatic pressure, and this habitat is believed to have a high degree of endemism. The deep-sea anemone family Galatheanthemidae comprises two valid species exclusively from the hadal; however, no other information about this family is currently available. In the present study, a sea anemone was collected from a depth of 9,462 m at the Mariana Trench and was defined as Galatheanthemum sp. MT-2020 (Actiniaria Galatheanthemidae). The mitochondrial genome of Galatheanthemum sp. MT-2020 was circular, was 16,633 bp in length, and contained two ribosomal RNA genes, 13 protein-coding genes and two transfer RNA genes. The order of the genes of Galatheanthemum sp. MT-2020 was identical to that of the majority of the species of the order Actiniaria. The value of the AT-skew was the lowest in the whole mitochondrial genome, with a positive GC skew value for the atp8 gene, while other species, except Antholoba achates, had the negative values of the GC skew. Galatheanthemum sp. MT-2020 was clustered with another abyssal species, Paraphelliactis xishaensis, in the phylogenetic tree, and these species diverged in the early Jurassic approximately 200 Mya from the shallow-sea species. The usage ratio of valine, which is one of the five amino acids with the strongest barophilic properties, in the mitochondrial genomes of the two abyssal species was significantly higher than that in other species with habitats above the depth of 3,000 m. The ω (dN/dS) ratio of the genomes was 2.45-fold higher than that of the shallow-sea species, indicating a slower evolutionary rate. Overall, the present study is the first to provide a complete mitogenome of sea anemones from the hadal and reveal some characteristics that may be associated with adaptation to an extreme environment.
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Affiliation(s)
- Mengke Shi
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li Qi
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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22
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Boo GH, Leliaert F, Le Gall L, Coppejans E, De Clerck O, Van Nguyen T, Payri CE, Miller KA, Yoon HS. Ancient Tethyan Vicariance and Long-Distance Dispersal Drive Global Diversification and Cryptic Speciation in the Red Seaweed Pterocladiella. FRONTIERS IN PLANT SCIENCE 2022; 13:849476. [PMID: 35720545 PMCID: PMC9201827 DOI: 10.3389/fpls.2022.849476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella, of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier-a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella. Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.
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Affiliation(s)
- Ga Hun Boo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- University Herbarium, University of California, Berkeley, CA, United States
| | - Frederik Leliaert
- Meise Botanic Garden, Meise, Belgium
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Line Le Gall
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Eric Coppejans
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Tu Van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Claude E. Payri
- UMR Entropie (IRD, Ifremer, Univ Nouvelle-Calédonie, Univ La Réunion, CNRS), Nouméa, New Caledonia
| | - Kathy Ann Miller
- University Herbarium, University of California, Berkeley, CA, United States
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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23
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Chow SW, Keshavmurthy S, Reimer JD, de Voogd N, Huang H, Wang JT, Tang SL, Schupp PJ, Tan CH, Liew HC, Soong K, Subhan B, Madduppa H, Chen CA. Population genetics and demography of the coral-killing cyanobacteriosponge, Terpios hoshinota, in the Indo-West Pacific. PeerJ 2022; 10:e13451. [PMID: 35669953 PMCID: PMC9165603 DOI: 10.7717/peerj.13451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 04/26/2022] [Indexed: 01/14/2023] Open
Abstract
The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise F ST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed among most populations in the marine ecoregions of West Pacific, Coral Triangle, and Eastern Indian Ocean, but with a restricted gene flow between these regions and Maldives in the Central Indian Ocean. Demographic analyses of most T. hoshinota populations were consistent with the mutation-drift equilibrium, except for the Sulawesi Sea and Maldives, which showed bottlenecks following recent expansion. Our results suggest that while long-range dispersal might explain the capability of T. hoshinota to spread in the IWP, stable population demography might account for the long-term persistence of T. hoshinota outbreaks on local reefs.
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Affiliation(s)
- Savanna Wenhua Chow
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | | | - James Davis Reimer
- Department of Biology, Chemistry, and Marine Science, University of Ryukyus, Naha, Okinawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Nicole de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, Netherlands
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Jih-Terng Wang
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Peter J. Schupp
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the, University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Chun Hong Tan
- School of Marine and Environmental Sceinces, University of Malaysia Terengganu, Terengganu, Malaysia
| | - Hock-Chark Liew
- Sdn Bhd. Jalan Hiliran, Kuala Terengganu, Alchemy Laboratory & Services, Terengganu, Malaysia
| | - Keryea Soong
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Beginer Subhan
- Department of Marine Science & Technology, Faculty of Fisheries & Marine Sciences, IPB University, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science & Technology, Faculty of Fisheries & Marine Sciences, IPB University, Bogor, Indonesia
| | - Chaolun Allen Chen
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Department of Life Science, Tunghai University, Taichung, Taiwan
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24
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Salvetat J, Bez N, Habasque J, Lebourges-Dhaussy A, Lopes C, Roudaut G, Simier M, Travassos P, Vargas G, Bertrand A. Comprehensive spatial distribution of tropical fish assemblages from multifrequency acoustics and video fulfils the island mass effect framework. Sci Rep 2022; 12:8787. [PMID: 35610249 PMCID: PMC9130204 DOI: 10.1038/s41598-022-12409-9] [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: 11/08/2021] [Accepted: 04/27/2022] [Indexed: 11/22/2022] Open
Abstract
Tropical marine ecosystems are highly biodiverse and provide resources for small-scale fisheries and tourism. However, precise information on fish spatial distribution is lacking, which limits our ability to reconcile exploitation and conservation. We combined acoustics to video observations to provide a comprehensive description of fish distribution in a typical tropical environment, the Fernando de Noronha Archipelago (FNA) off Northeast Brazil. We identified and classified all acoustic echoes into ten fish assemblage and two triggerfish species. This opened up the possibility to relate the different spatial patterns to a series of environmental factors and the level of protection. We provide the first biomass estimation of the black triggerfish Melichthys niger, a key tropical player. By comparing the effects of euphotic and mesophotic reefs we show that more than the depth, the most important feature is the topography with the shelf-break as the most important hotspot. We also complete the portrait of the island mass effect revealing a clear spatial dissymmetry regarding fish distribution. Indeed, while primary productivity is higher downstream, fish concentrate upstream. The comprehensive fish distribution provided by our approach is directly usable to implement scientific-grounded Marine Spatial Planning.
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Affiliation(s)
- Julie Salvetat
- Pós-Graduação em Recursos Pesqueiros e Aquicultura, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil. .,MARBEC, Univ Montpellier, CNRS, IRD, Ifremer, Sète, France. .,Institut de Recherche pour le Développement, Sète, France.
| | - Nicolas Bez
- MARBEC, Univ Montpellier, CNRS, IRD, Ifremer, Sète, France.,Institut de Recherche pour le Développement, Sète, France
| | | | | | - Cristiano Lopes
- Pós-Graduação em Recursos Pesqueiros e Aquicultura, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil
| | | | - Monique Simier
- MARBEC, Univ Montpellier, CNRS, IRD, Ifremer, Sète, France.,Institut de Recherche pour le Développement, Sète, France
| | - Paulo Travassos
- Pós-Graduação em Recursos Pesqueiros e Aquicultura, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - Gary Vargas
- Pós-Graduação em Recursos Pesqueiros e Aquicultura, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - Arnaud Bertrand
- Pós-Graduação em Recursos Pesqueiros e Aquicultura, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil.,MARBEC, Univ Montpellier, CNRS, IRD, Ifremer, Sète, France.,Institut de Recherche pour le Développement, Sète, France.,Laboratório de Oceanografia Física Estuarina e Costeira, Depto. Oceanografia, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235-Cidade Universitária, Recife, PE, 50670-901, Brazil
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25
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Kurata NP, Hickerson MJ, Hoffberg SL, Gardiner N, Stiassny MLJ, Alter SE. Riverscape genomics of cichlid fishes in the lower Congo: Uncovering mechanisms of diversification in an extreme hydrological regime. Mol Ecol 2022; 31:3516-3532. [PMID: 35532943 DOI: 10.1111/mec.16495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
Freshwater fishes are notably diverse, given that freshwater habitat represents a tiny fraction of the earth's surface, but the mechanisms generating this diversity remain poorly understood. Rivers provide excellent models to understand how freshwater diversity is generated and maintained across heterogeneous habitats. In particular, the lower Congo River (LCR) consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, morphological and ecological specialization. Previous studies have suggested that the numerous high-energy rapids throughout the LCR form physical barriers to gene flow, thus facilitating diversification and speciation, generating ichthyofaunal diversity. However, this hypothesis has not been fully explored using genome-wide SNPs for fish species distributed across the LCR. Here, we examined four lamprologine cichlids endemic to the LCR that are distributed along the river without range overlap. Using genome-wide SNP data, we tested the hypotheses that high-energy rapids serve as physical barriers to gene flow that generate genetic divergence at inter- and intraspecific levels, and that gene flow occurs primarily in a downstream direction. Our results are consistent with the prediction that powerful rapids sometimes act as a barrier to gene flow but also suggest that, at certain temporal and spatial scales, they may provide multidirectional dispersal opportunities for riverine rheophilic cichlid fishes. These results highlight the complexity of diversification processes in rivers and the importance of assessing such processes across different riverscapes.
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Affiliation(s)
- Naoko P Kurata
- The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.,Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - Michael J Hickerson
- The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.,The City College of New York, 160 Convent Ave, New York, NY, 10031, USA.,Division of Invertebrate Zoology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - Sandra L Hoffberg
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA
| | - Ned Gardiner
- Department of Geography, University of Georgia, 210 Field St #204, Athens, Georgia, GA, 30602, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.,The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - S Elizabeth Alter
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.,Department of Biology and Chemistry, California State University Monterey Bay, Seaside, California, CA, 93955, USA
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26
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Titus BM, Daly M. Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes? Heredity (Edinb) 2022; 128:338-351. [PMID: 35418670 PMCID: PMC9076904 DOI: 10.1038/s41437-022-00531-3] [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: 09/09/2020] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/08/2022] Open
Abstract
Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.
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Affiliation(s)
- Benjamin M Titus
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
- Dauphin Island Sea Lab, Dauphin Island, AL, USA.
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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27
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Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar based on genetic, morphological, bioacoustic and ecological evidence. PLoS One 2022; 17:e0263764. [PMID: 35358210 PMCID: PMC8970393 DOI: 10.1371/journal.pone.0263764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.
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Genomic insights into the historical and contemporary demographics of the grey reef shark. Heredity (Edinb) 2022; 128:225-235. [PMID: 35296830 PMCID: PMC8987070 DOI: 10.1038/s41437-022-00514-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/08/2022] Open
Abstract
Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (Ne) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in Ne were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in Ne were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient Ne observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary Ne, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.
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Shahdadi A, von Wyschetzki K, Liu HC, Chu KH, Schubart CD. Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific. PLoS One 2022; 17:e0262122. [PMID: 35025933 PMCID: PMC8757990 DOI: 10.1371/journal.pone.0262122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/18/2021] [Indexed: 11/19/2022] Open
Abstract
Due to the lack of visible barriers to gene flow, it was a long-standing assumption that marine coastal species are widely distributed, until molecular studies revealed geographically structured intraspecific genetic differentiation in many taxa. Historical events of sea level changes during glacial periods are known to have triggered sequential disjunctions and genetic divergences among populations, especially of coastal organisms. The Parasesarma bidens species complex so far includes three named plus potentially cryptic species of estuarine brachyuran crabs, distributed along East to Southeast Asia. The aim of the present study is to address phylogeography and uncover real and hidden biological diversity within this complex, by revealing the underlying genetic structure of populations and species throughout their distribution ranges from Japan to West Papua, with a comparison of mitochondrial COX1 and 16S rRNA gene sequences. Our results reveal that the P. bidens species complex consists of at least five distinct clades, resulting from four main cladogenesis events during the mid to late Pleistocene. Among those clades, P. cricotum and P. sanguimanus are recovered as monophyletic taxa. Geographically restricted endemic clades are encountered in southeastern Indonesia, Japan and China respectively, whereas the Philippines and Taiwan share two clades. As individuals of the Japanese clade can also be found in Taiwan, we provide evidence of a third lineage and the occurrence of a potential cryptic species on this island. Ocean level retreats during Pleistocene ice ages and present oceanic currents appear to be the main triggers for the divergences of the five clades that are here addressed as the P. bidens complex. Secondary range expansions converted Taiwan into the point of maximal overlap, sharing populations with Japan and the Philippines, but not with mainland China.
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Affiliation(s)
- Adnan Shahdadi
- Department of Marine Biology, Faculty of Marine Sciences and Technology, University of Hormozgan, Bandar Abbas, Iran
| | | | - Hung-Chang Liu
- Land Crab Ecology Research Laboratory, Chenggong, Jhubei City, Hsinchu County, Taiwan
| | - Ka Hou Chu
- Simon F. S. Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Hong Kong Branch of Southern Marine Science and Technology Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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Lagourgue L, Leliaert F, Payri CE. Historical biogeographical analysis of the Udoteaceae (Bryopsidales, Chlorophyta) elucidates origins of high species diversity in the Central Indo-Pacific, Western Indian Ocean and Greater Caribbean regions. Mol Phylogenet Evol 2022; 169:107412. [PMID: 35031470 DOI: 10.1016/j.ympev.2022.107412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/19/2021] [Accepted: 12/07/2021] [Indexed: 11/28/2022]
Abstract
There is a growing interest in elucidating the biogeographical processes underlying biodiversity patterns of seaweeds, with recent studies largely focusing on red and brown macroalgae. This study focuses on the siphonous green algal family Udoteaceae, which is diverse and globally distributed in tropical to warm-temperate seas, and includes species that form important components of tropical reefs. We explored the historical processes that have shaped current biodiversity patterns in the family by analyzing a comprehensive dataset of 568 specimens sampled across its geographical range, and including 45 species, corresponding to 59% of the known diversity. Historical biogeographical analysis was based on a three-locus time-calibrated phylogeny, and probabilistic modeling of geographical range evolution. Many species were found to have restricted ranges, indicative of low dispersal capacity. Our analysis points toward a Western Tethys origin and early diversification of the Udoteaceae in the Triassic period. Three centers of diversity were identified, which are, in order of highest species richness, the Central Indo-Pacific, the Western Indian Ocean, and the Greater Caribbean. Different drivers have likely played a role in shaping these diversity centres. Species richness in the Central Indo-Pacific likely resulted from speciation within the region, as well as recolonization from neighbouring regions, and overlap of some wider ranged species, corroborating the "biodiversity feedback" model. Species richness in the Western Indian Ocean can be explained by ancient and more recent diversification within the region, and dispersal from the Central Indo-Pacific. The Greater Caribbean region was colonized more recently, followed by diversification within the region.
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Affiliation(s)
- Laura Lagourgue
- Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, 75252 Paris Cedex 05, France; UMR ENTROPIE (IRD, UR, UNC, CNRS, IFREMER), Institut de Recherche pour le Développement, B.P. A5 Nouméa Cedex, Nouvelle-Calédonie, 98848, France.
| | | | - Claude E Payri
- UMR ENTROPIE (IRD, UR, UNC, CNRS, IFREMER), Institut de Recherche pour le Développement, B.P. A5 Nouméa Cedex, Nouvelle-Calédonie, 98848, France
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hayashi K, Kuwamura T, Tachihara K, Reimer JD. Large host anemones can be shelters of a diverse assemblage of fish species, not just anemonefish. JOURNAL OF FISH BIOLOGY 2022; 100:40-50. [PMID: 34590316 DOI: 10.1111/jfb.14916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/18/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The mutualistic relationships between anemonefish (Amphiprion; Pomacentridae) and host sea anemones are well known, but host anemones are also used as shelter by damselfish (Pomacentridae), wrasses (Labridae) and cardinalfish (Apogonidae). The threespot dascyllus Dascyllus trimaculatus (Pomacentridae) is known to live on or near host anemones in their immature phase. Nonetheless, detailed studies on the use of host anemones by other fish species have not yet been conducted. To understand the factors that influence the use of host anemones by other fish species, this study investigated the fish biota around host anemones in the Ryukyu Archipelago. Other than Amphiprion spp. and D. trimaculatus, 10 additional species of fish (9 species of damselfish and 1 species of cardinalfish) were confirmed to temporarily use host anemones as shelter, and five species of wrasse including Labroides dimidiatus came to clean anemonefish. Logistic regression analyses (independent variable: presence or absence of other species of fish; dependent variables: anemonefish aggressiveness, size of host anemone, number of D. trimaculatus) indicated that the size of host anemones is important for the presence of fish, both in species using the anemone as temporary shelter and in cleaner species. Large host anemones can provide shelter and food resources for other species of coral reef fish as well as for anemonefish.
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Affiliation(s)
- Kina Hayashi
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Japan
| | - Tetsuo Kuwamura
- Faculty of Liberal Arts and Sciences, Chukyo University, Nagoya, Japan
| | - Katsunori Tachihara
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Japan
| | - James Davis Reimer
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Japan
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Vilaça ST, Piccinno R, Rota‐Stabelli O, Gabrielli M, Benazzo A, Matschiner M, Soares LS, Bolten AB, Bjorndal KA, Bertorelle G. Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species. Mol Ecol 2021; 30:6178-6192. [PMID: 34390061 PMCID: PMC9292604 DOI: 10.1111/mec.16113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022]
Abstract
Reconstructing past events of hybridization and population size changes are required to understand speciation mechanisms and current patterns of genetic diversity, and ultimately contribute to species' conservation. Sea turtles are ancient species currently facing anthropogenic threats including climate change, fisheries, and illegal hunting. Five of the seven extant sea turtle species are known to currently hybridize, especially along the Brazilian coast where some populations can have ~32%-42% of hybrids. Although frequently observed today, it is not clear what role hybridization plays in the evolutionary diversification of this group of reptiles. In this study, we generated whole genome resequencing data of the five globally distributed sea turtle species to estimate a calibrated phylogeny and the population size dynamics, and to understand the role of hybridization in shaping the genomes of these ancient species. Our results reveal discordant species divergence dates between mitochondrial and nuclear genomes, with a high frequency of conflicting trees throughout the nuclear genome suggesting that some sea turtle species frequently hybridized in the past. The reconstruction of the species' demography showed a general decline in effective population sizes with no signs of recovery, except for the leatherback sea turtle. Furthermore, we discuss the influence of reference bias in our estimates. We show long-lasting ancestral gene flow events within Chelonioidea that continued for millions of years after initial divergence. Speciation with gene flow is a common pattern in marine species, and it raises questions whether current hybridization events should be considered as a part of these species' evolutionary history or a conservation issue.
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Affiliation(s)
| | - Riccardo Piccinno
- Department of Sustainable Agro‐ecosystems and BioresourcesFondazione Edmund MachTrentoItaly
| | - Omar Rota‐Stabelli
- Department of Sustainable Agro‐ecosystems and BioresourcesFondazione Edmund MachTrentoItaly
| | - Maëva Gabrielli
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
| | - Andrea Benazzo
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
| | | | - Luciano S. Soares
- Archie Carr Center for Sea Turtle Research and Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Alan B. Bolten
- Archie Carr Center for Sea Turtle Research and Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Karen A. Bjorndal
- Archie Carr Center for Sea Turtle Research and Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Giorgio Bertorelle
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
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Influence of historical changes in tropical reef habitat on the diversification of coral reef fishes. Sci Rep 2021; 11:20731. [PMID: 34671048 PMCID: PMC8528860 DOI: 10.1038/s41598-021-00049-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 09/28/2021] [Indexed: 11/11/2022] Open
Abstract
Past environmental changes are expected to have profoundly impacted diversity dynamics through time. While some previous studies showed an association between past climate changes or tectonic events and important shifts in lineage diversification, it is only recently that past environmental changes have been explicitly integrated in diversification models to test their influence on diversification rates. Here, we used a global reconstruction of tropical reef habitat dynamics during the Cenozoic and phylogenetic diversification models to test the influence of (i) major geological events, (ii) reef habitat fragmentation and (iii) reef area on the diversification of 9 major clades of tropical reef fish (Acanthuridae, Balistoidea, Carangoidea, Chaetodontidae, Haemulinae, Holocentridae, Labridae, Pomacentridae and Sparidae). The diversification models revealed a weak association between paleo-habitat changes and diversification dynamics. Specifically, the fragmentation of tropical reef habitats over the Cenozoic was found to be a driver of tropical reef fish diversification for 2 clades. However, overall, our approach did not allow the identification of striking associations between diversification dynamics and paleo-habitat fragmentation in contrast with theoretical model's predictions.
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Filatov DA, Bendif EM, Archontikis OA, Hagino K, Rickaby REM. The mode of speciation during a recent radiation in open-ocean phytoplankton. Curr Biol 2021; 31:5439-5449.e5. [PMID: 34687611 DOI: 10.1016/j.cub.2021.09.073] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022]
Abstract
Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - El Mahdi Bendif
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Odysseas A Archontikis
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Kyoko Hagino
- Centre for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
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Lotterhos KE, Láruson ÁJ, Jiang LQ. Novel and disappearing climates in the global surface ocean from 1800 to 2100. Sci Rep 2021; 11:15535. [PMID: 34446758 PMCID: PMC8390509 DOI: 10.1038/s41598-021-94872-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
Marine ecosystems are experiencing unprecedented warming and acidification caused by anthropogenic carbon dioxide. For the global sea surface, we quantified the degree that present climates are disappearing and novel climates (without recent analogs) are emerging, spanning from 1800 through different emission scenarios to 2100. We quantified the sea surface environment based on model estimates of carbonate chemistry and temperature. Between 1800 and 2000, no gridpoints on the ocean surface were estimated to have experienced an extreme degree of global disappearance or novelty. In other words, the majority of environmental shifts since 1800 were not novel, which is consistent with evidence that marine species have been able to track shifting environments via dispersal. However, between 2000 and 2100 under Representative Concentrations Pathway (RCP) 4.5 and 8.5 projections, 10-82% of the surface ocean is estimated to experience an extreme degree of global novelty. Additionally, 35-95% of the surface ocean is estimated to experience an extreme degree of global disappearance. These upward estimates of climate novelty and disappearance are larger than those predicted for terrestrial systems. Without mitigation, many species will face rapidly disappearing or novel climates that cannot be outpaced by dispersal and may require evolutionary adaptation to keep pace.
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Affiliation(s)
- Katie E. Lotterhos
- grid.261112.70000 0001 2173 3359Northeastern University Marine Science Center, 430 Nahant Rd, Nahant, MA 01908 USA
| | - Áki J. Láruson
- grid.261112.70000 0001 2173 3359Northeastern University Marine Science Center, 430 Nahant Rd, Nahant, MA 01908 USA ,grid.5386.8000000041936877XDepartment of Natural Resources, Cornell University, Ithaca, NY 14850 USA
| | - Li-Qing Jiang
- grid.164295.d0000 0001 0941 7177Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD 20740 USA ,grid.3532.70000 0001 1266 2261National Centers for Environmental Information, National Oceanic and Atmospheric Administration, Silver Spring, MD 20910 USA
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Warren DL, Eytan RI, Dornburg A, Iglesias TL, Brandley MC, Wainwright PC. Reevaluating claims of ecological speciation in Halichoeres bivittatus. Ecol Evol 2021; 11:11449-11456. [PMID: 34429932 PMCID: PMC8366890 DOI: 10.1002/ece3.7936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 07/07/2021] [Indexed: 11/11/2022] Open
Abstract
Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with gene flow is the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of a deep divergence in a single mitochondrial locus between the northern and southern Gulf of Mexico, combined with a finding that these two haplotypes were associated with different habitat types ("tropical" vs. "subtropical") in the Florida Keys and Bermuda, where they overlap. Here, we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study. We find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations in the Keys. These results undermine claims of ecological speciation with gene flow in Halichoeres bivittatus. Future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences.
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Affiliation(s)
- Dan L. Warren
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Ron I. Eytan
- Department of Marine BiologyTexas A&M University at GalvestonGalvestonTexasUSA
| | - Alex Dornburg
- Department of Bioinformatics and GenomicsUniversity of North Carolina CharlotteCharlotteNorth CarolinaUSA
| | - Teresa L. Iglesias
- Animal Resources SectionOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Matthew C. Brandley
- Section of Amphibians and ReptilesCarnegie Museum of Natural HistoryPittsburghPAUSA
- Powdermill Nature ReserveCarnegie Museum of Natural HistoryRectorPennsylvaniaUSA
| | - Peter C. Wainwright
- Department of Evolution and EcologyUniversity of CaliforniaDavisCaliforniaUSA
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Torchin ME, Freestone AL, McCann L, Larson K, SchlÖder C, Steves BP, Fofonoff P, Repetto MF, Ruiz GM. Asymmetry of marine invasions across tropical oceans. Ecology 2021; 102:e03434. [PMID: 34114663 DOI: 10.1002/ecy.3434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/01/2021] [Accepted: 03/15/2021] [Indexed: 01/20/2023]
Abstract
Understanding the mechanisms of spatial variation of biological invasions, across local-to-global scales, has been a major challenge. The importance of evolutionary history for invasion dynamics was noted by Darwin, and several studies have since considered how biodiversity of source and recipient regions can influence the probability of invasions. For over a century, the Panama Canal has connected water bodies and biotas with different evolutionary histories, and created a global shipping hot spot, providing unique opportunities to test mechanisms that affect invasion patterns. Here, we test for asymmetry in both the extent of invasions and predation effects, a possible mechanism of biotic resistance, between two tropical oceans at similar latitudes. We estimated nonnative species (NNS) richness for sessile marine invertebrates, using standardized field surveys and literature synthesis, to examine whether invasions are asymmetrical, with more NNS present in the less diverse Pacific compared to the Atlantic. We also experimentally tested whether predation differentially limits the abundance and distribution of these invertebrates between oceans. In standardized surveys, observed total NNS richness was higher in the Pacific (18 NNS, 30% of all Pacific species) than the Atlantic (11 NNS, 13% of all Atlantic species). Similarly, literature-based records also display this asymmetry between coasts. When considering only the reciprocal exchange of NNS between Atlantic and Pacific biotas, NNS exchange from Atlantic to Pacific was eightfold higher than the opposite direction, exceeding the asymmetry predicted by random exchange based simply on differences of overall diversity per region. Predation substantially reduced biomass and changed NNS composition in the Pacific, but no such effects were detected on the Atlantic coast. Specifically, some dominant NNS were particularly susceptible to predation in the Pacific, supporting the hypothesis that predation may reduce the abundance of certain NNS here. These results are consistent with predictions that high diversity in source regions, and species interactions in recipient regions, shape marine invasion patterns. Our comparisons and experiments across two tropical ocean basins, suggest that global invasion dynamics are likely driven by both ecological and evolutionary factors that shape susceptibility to and directionality of invasions across biogeographic scales.
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Affiliation(s)
- Mark E Torchin
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Amy L Freestone
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama.,Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA.,Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA
| | - Linda McCann
- Smithsonian Environmental Research Center, 3150 Paradise Drive, Tiburon, California, 94920, USA
| | - Kristen Larson
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA
| | - Carmen SchlÖder
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Brian P Steves
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA
| | - Paul Fofonoff
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA
| | - Michele F Repetto
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama.,Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA.,Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA
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Miller EC. Comparing diversification rates in lakes, rivers, and the sea. Evolution 2021; 75:2055-2073. [PMID: 34181244 DOI: 10.1111/evo.14295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 05/29/2021] [Accepted: 06/06/2021] [Indexed: 12/23/2022]
Abstract
The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth's water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Such differences between rivers and lakes may be important to consider when comparing diversification broadly among freshwater and marine groups. Here I compared diversification rates of teleost fishes in marine, riverine and lacustrine habitats. I found that lakes had faster speciation and net diversification rates than other aquatic habitats. However, most freshwater diversity arose in rivers. Surprisingly, riverine and marine habitats had similar rates of net diversification on average. Biogeographic models suggest that lacustrine habitats are evolutionarily unstable, explaining the dearth of lacustrine species in spite of their rapid diversification. Collectively, these results suggest that strong diversification rate differences are unlikely to explain the freshwater paradox. Instead, this pattern may be attributable to the comparable amount of time spent in riverine and marine habitats over the 200-million-year history of teleosts.
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Jin L, Liu JJ, Xiao TW, Li QM, Lin LX, Shao XN, Ma CX, Li BH, Mi XC, Ren HB, Qiao XJ, Lian JY, Hao G, Ge XJ. Plastome-based phylogeny improves community phylogenetics of subtropical forests in China. Mol Ecol Resour 2021; 22:319-333. [PMID: 34233085 DOI: 10.1111/1755-0998.13462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.
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Affiliation(s)
- Lu Jin
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jia-Jia Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiao-Ming Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Lu-Xiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Na Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chen-Xin Ma
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bu-Hang Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hai-Bao Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Juan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ju-Yu Lian
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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41
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Hagen O, Flück B, Fopp F, Cabral JS, Hartig F, Pontarp M, Rangel TF, Pellissier L. gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity. PLoS Biol 2021; 19:e3001340. [PMID: 34252071 PMCID: PMC8384074 DOI: 10.1371/journal.pbio.3001340] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/22/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022] Open
Abstract
Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species' abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits. Commonly observed biodiversity patterns, such as α, β, and γ diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth's Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth's biodiversity.
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Affiliation(s)
- Oskar Hagen
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of
Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest,
Snow and Landscape Research, WSL, Birmensdorf, Switzerland
| | - Benjamin Flück
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of
Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest,
Snow and Landscape Research, WSL, Birmensdorf, Switzerland
| | - Fabian Fopp
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of
Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest,
Snow and Landscape Research, WSL, Birmensdorf, Switzerland
| | - Juliano S. Cabral
- Ecosystem Modeling, Center for Computational and Theoretical Biology,
University of Würzburg, Würzburg, Germany
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg,
Germany
| | | | - Thiago F. Rangel
- Department of Ecology, Institute of Biological Sciences, Federal
University of Goiás, Goiânia, Brazil
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of
Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest,
Snow and Landscape Research, WSL, Birmensdorf, Switzerland
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42
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Sampieri BR, Vieira PE, Teixeira MAL, Seixas VC, Pagliosa PR, Amaral ACZ, Costa FO. Molecular diversity within the genus Laeonereis (Annelida, Nereididae) along the west Atlantic coast: paving the way for integrative taxonomy. PeerJ 2021; 9:e11364. [PMID: 34123584 PMCID: PMC8164838 DOI: 10.7717/peerj.11364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/07/2021] [Indexed: 11/20/2022] Open
Abstract
The polychaete genus Laeonereis (Annelida, Nereididae) occurs over a broad geographic range and extends nearly across the entire Atlantic coast of America, from the USA to Uruguay. Despite the research efforts to clarify its diversity and systematics, mostly by morphological and ecological evidence, there is still uncertainty, mainly concerning the species Laeonereis culveri, which constitutes an old and notorious case of taxonomic ambiguity. Here, we revised the molecular diversity and distribution of Laeonereis species based on a multi-locus approach, including DNA sequence analyses of partial segments of the cytochrome c oxidase subunit I (COI), 16S rRNA, and 28S rRNA genes. We examined Laeonereis specimens collected from 26 sites along the American Atlantic coast from Massachusetts (USA) to Mar del Plata (Argentina). Although no comprehensive morphological examination was performed between different populations, the COI barcodes revealed seven highly divergent MOTUs, with a mean K2P genetic distance of 16.9% (from 6.8% to 21.9%), which was confirmed through four clustering algorithms. All MOTUs were geographically segregated, except for MOTUs 6 and 7 from southeastern Brazil, which presented partially overlapping ranges between Rio de Janeiro and São Paulo coast. Sequence data obtained from 16S rRNA and 28S rRNA markers supported the same MOTU delimitation and geographic segregation as those of COI, providing further evidence for the existence of seven deeply divergent lineages within the genus. The extent of genetic divergence between MOTUs observed in our study fits comfortably within the range reported for species of polychaetes, including Nereididae, thus providing a strong indication that they might constitute separate species. These results may therefore pave the way for integrative taxonomic studies, aiming to clarify the taxonomic status of the Laeonereis MOTUs herein reported.
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Affiliation(s)
- Bruno R Sampieri
- Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal.,Museu de Zoologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,Institute of Science and Innovation for Bio-Sustainability (IB-S), Universidade do Minho, Braga, Portugal
| | - Pedro E Vieira
- Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), Universidade do Minho, Braga, Portugal
| | - Marcos A L Teixeira
- Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), Universidade do Minho, Braga, Portugal
| | - Victor C Seixas
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo R Pagliosa
- Laboratório de Biodiversidade e Conservação Marinha, Universidade Federal de Santa Catarina, Florianopólis, Santa Catarina, Brazil
| | | | - Filipe O Costa
- Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), Universidade do Minho, Braga, Portugal
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43
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Bowen BW, Forsman ZH, Whitney JL, Faucci A, Hoban M, Canfield SJ, Johnston EC, Coleman RR, Copus JM, Vicente J, Toonen RJ. Species Radiations in the Sea: What the Flock? J Hered 2021; 111:70-83. [PMID: 31943081 DOI: 10.1093/jhered/esz075] [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] [Received: 03/18/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Species flocks are proliferations of closely-related species, usually after colonization of depauperate habitat. These radiations are abundant on oceanic islands and in ancient freshwater lakes, but rare in marine habitats. This contrast is well documented in the Hawaiian Archipelago, where terrestrial examples include the speciose silverswords (sunflower family Asteraceae), Drosophila fruit flies, and honeycreepers (passerine birds), all derived from one or a few ancestral lineages. The marine fauna of Hawai'i is also the product of rare colonization events, but these colonizations usually yield only one species. Dispersal ability is key to understanding this evolutionary inequity. While terrestrial fauna rarely colonize between oceanic islands, marine fauna with pelagic larvae can make this leap in every generation. An informative exception is the marine fauna that lack a pelagic larval stage. These low-dispersal species emulate a "terrestrial" mode of reproduction (brooding, viviparity, crawl-away larvae), yielding marine species flocks in scattered locations around the world. Elsewhere, aquatic species flocks are concentrated in specific geographic settings, including the ancient lakes of Baikal (Siberia) and Tanganyika (eastern Africa), and Antarctica. These locations host multiple species flocks across a broad taxonomic spectrum, indicating a unifying evolutionary phenomenon. Hence marine species flocks can be singular cases that arise due to restricted dispersal or other intrinsic features, or they can be geographically clustered, promoted by extrinsic ecological circumstances. Here, we review and contrast intrinsic cases of species flocks in individual taxa, and extrinsic cases of geological/ecological opportunity, to elucidate the processes of species radiations.
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Affiliation(s)
- Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Jonathan L Whitney
- Joint Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI
| | - Anuschka Faucci
- Math & Sciences Division, Leeward Community College, University of Hawai'i, Pearl City, HI
| | - Mykle Hoban
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | | | - Erika C Johnston
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Richard R Coleman
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Jan Vicente
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
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44
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Raja NB, Kiessling W. Out of the extratropics: the evolution of the latitudinal diversity gradient of Cenozoic marine plankton. Proc Biol Sci 2021; 288:20210545. [PMID: 33975476 DOI: 10.1098/rspb.2021.0545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many ecological and evolutionary hypotheses have been proposed to explain the latitudinal diversity gradient, i.e. the increase in species richness from the poles to the tropics. Among the evolutionary hypotheses, the 'out of the tropics' (OTT) hypothesis has received considerable attention. The OTT posits that the tropics are both a cradle and source of biodiversity for extratropical regions. To test the generality of the OTT hypothesis, we explored the spatial biodiversity dynamics of unicellular marine plankton over the Cenozoic era (the last 66 Myr). We find large-scale climatic changes during the Cenozoic shaped the diversification and dispersal of marine plankton. Origination was generally more likely in the extratropics and net dispersal was towards the tropics rather than in the opposite direction, especially during the warmer climates of the early Cenozoic. Although migration proportions varied among major plankton groups and climate phases, we provide evidence that the extratropics were a source of tropical microplankton biodiversity over the last 66 Myr.
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Affiliation(s)
- Nussaïbah B Raja
- GeoZentrum Nordbayern, Department of Geography and Geosciences, Friedrich-Alexander University Erlangen-Nürnberg, Loewenichstr. 28, 91054 Erlangen, Germany
| | - Wolfgang Kiessling
- GeoZentrum Nordbayern, Department of Geography and Geosciences, Friedrich-Alexander University Erlangen-Nürnberg, Loewenichstr. 28, 91054 Erlangen, Germany
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45
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Terraneo TI, Benzoni F, Arrigoni R, Baird AH, Mariappan KG, Forsman ZH, Wooster MK, Bouwmeester J, Marshell A, Berumen ML. Phylogenomics of Porites from the Arabian Peninsula. Mol Phylogenet Evol 2021; 161:107173. [PMID: 33813021 DOI: 10.1016/j.ympev.2021.107173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia.
| | - Francesca Benzoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Roberto Arrigoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; European Commission, Joint Research Centre (JRC), Ispra, Italy; Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121 Napoli, Italy
| | - Andrew H Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Zac H Forsman
- Hawaii Institute of Marine Biology, Kaneohe 96744, HI, USA
| | - Michael K Wooster
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Michael L Berumen
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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46
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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47
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Purwanto, Andradi‐Brown DA, Matualage D, Rumengan I, Awaludinnoer, Pada D, Hidayat NI, Amkieltiela, Fox HE, Fox M, Mangubhai S, Hamid L, Lazuardi ME, Mambrasar R, Maulana N, Mulyadi, Tuharea S, Pakiding F, Ahmadia GN. The Bird's Head Seascape Marine Protected Area network—Preventing biodiversity and ecosystem service loss amidst rapid change in Papua, Indonesia. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Purwanto
- University of Papua Manokwari West Papua Indonesia
- Coral Triangle Center Sanur Bali Indonesia
| | | | | | | | - Awaludinnoer
- The Nature Conservancy, Indonesia Coasts and Oceans Program – Raja Ampat Sorong West Papua Indonesia
| | - Defy Pada
- Conservation International Indonesia Sorong West Papua Indonesia
| | - Nur I. Hidayat
- Conservation International Indonesia Sorong West Papua Indonesia
| | - Amkieltiela
- Conservation Science Unit, WWF Indonesia Jakarta Indonesia
| | | | - Matt Fox
- Conservation International Indonesia Sorong West Papua Indonesia
| | | | - La Hamid
- Cenderawasih Bay National Park Authority, Kementerian Lingkungan Hidup dan Kehutanan Manokwari West Papua Indonesia
| | | | - Ronald Mambrasar
- Conservation International Indonesia Sorong West Papua Indonesia
| | - Nugraha Maulana
- Conservation International Indonesia Sorong West Papua Indonesia
| | - Mulyadi
- Cenderawasih Bay National Park Authority, Kementerian Lingkungan Hidup dan Kehutanan Manokwari West Papua Indonesia
| | - Syafri Tuharea
- Unit Pelaksana Teknis Dinas, Kawasan Konservasi Perairan Daerah Raja Ampat Raja Ampat West Papua Indonesia
| | | | - Gabby N. Ahmadia
- Ocean Conservation, World Wildlife Fund Washington District of Columbia USA
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48
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Forsman ZH, Ritson-Williams R, Tisthammer KH, Knapp ISS, Toonen RJ. Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae). Sci Rep 2020; 10:16995. [PMID: 33046719 PMCID: PMC7550562 DOI: 10.1038/s41598-020-73501-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/14/2020] [Indexed: 11/09/2022] Open
Abstract
The 'species' is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The 'Porites lobata species complex' consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāne'ohe Bay Hawai'i during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.
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Affiliation(s)
- Z H Forsman
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, USA.
| | | | - K H Tisthammer
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - I S S Knapp
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, USA
| | - R J Toonen
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, USA
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49
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Swift HF, Dawson MN. Demographic, Environmental, and Phenotypic Change but Genetic Consistency in the Jellyfish Mastigias papua. THE BIOLOGICAL BULLETIN 2020; 239:80-94. [PMID: 33151754 DOI: 10.1086/710663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
AbstractSpatiotemporal environmental change can produce phenotypic differences within and between populations. For scyphozoans, the effect of environmental variation on phenotype has been unclear because of multiple challenges, including difficulties delimiting populations. Marine lakes, bodies of seawater entirely surrounded by land, provide an opportunity to study discrete populations and capture responses to perturbations. We use this opportunity to compare Mastigias papua (Lesson, 1830) medusae before and after a demographic and environmental perturbation. We reconstructed mitochondrial DNA haplotype networks, measured morphological variation, and assessed swimming behavior of pre- and post-perturbation samples to evaluate two hypotheses about the source of variation: recolonization from an alternate location or endemic phenotypic variation. We found significant differences between samples in morphology (F > 9.5, P < 0.001) and in two of three behaviors (F > 8.45, P < 0.005) but no substantial genetic differentiation (ΦST = 0.03, P = 0.09). We reject the hypothesis of recolonization because pre- and post-perturbation lake medusae were genetically similar to each other and also significantly different from any potential source locations (ΦST > 0.48, P > 0.001). We could not distinguish the source of endemic variation; this will require genomic or experimental analyses. Increasing climatic variability emphasizes the need for understanding population-level responses to environmental change and how responses may be modified by sources of intraspecific variation.
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50
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Wepfer PH, Nakajima Y, Sutthacheep M, Radice VZ, Richards Z, Ang P, Terraneo T, Sudek M, Fujimura A, Toonen RJ, Mikheyev AS, Economo EP, Mitarai S. Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean. Mol Phylogenet Evol 2020; 151:106905. [DOI: 10.1016/j.ympev.2020.106905] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 11/16/2022]
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