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Zhang Q, Hu X, Deng Z, Li Y, Dong Y, Han C, Zeng X, Xiao N, Zhang X, Xu Q. Population genetics and evolutionary history of the intertidal brittle star Ophiothrix (Ophiothrix) exigua in the northern China Sea. Ecol Evol 2024; 14:e70284. [PMID: 39290668 PMCID: PMC11405633 DOI: 10.1002/ece3.70284] [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: 05/14/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/19/2024] Open
Abstract
Ophiothrix (Ophiothrix) exigua is a common brittle star in the northwestern Pacific. As a dominant species, O. exigua inhabiting the intertidal rocky ecosystem are affected by multiple environmental stressors, but molecular insights into their genetic population structure remain poorly studied. In this study, we investigated the population genetics and evolutionary history of six O. exigua populations from the northern China Sea using mitochondrial (COI, NAD4) and nuclear (ITS2, 18S) gene markers. High haplotype diversity, low nucleotide diversity, and low rates of gene differentiation among the populations of O. exigua were detected. Pairwise genetic differentiation (ΦST) statistics between different localities were negative or low and insignificant, suggesting strong gene flow of this species over the study areas. The phylogenetic analyses showed that the populations exhibited high homogeneity between localities in our study area. Demographic analyses indicated that the populations experienced sustained expansion around 0.2 million years ago. This expansion was likely related to transgressions events in the Yellow Sea during the Pleistocene period. Additional samples of O. exigua from disparate geographical locations, especially the Japan Sea and the Korean Peninsula, will be needed to unravel the population genetic patterns and evolutionary history of this species.
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Affiliation(s)
- Qian Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography MNR Qingdao China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center Qingdao China
| | - Xuying Hu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography MNR Qingdao China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center Qingdao China
| | - Zongjing Deng
- National Museum of Nature and Science Taito-ku Japan
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Bunkyo-ku Japan
| | - Yixuan Li
- Department of Biology Hong Kong Baptist University Hong Kong China
| | - Yue Dong
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography MNR Qingdao China
- College of Environmental Science and Engineering Ocean University of China Qingdao China
| | - Chen Han
- School of Ocean Sciences, China University of Geosciences Beijing China
| | - Xiaoqi Zeng
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
| | - Ning Xiao
- Institute of Oceanology, Department of Marine Organism Taxonomy and Phylogeny Chinese Academy of Sciences Qingdao China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography MNR Qingdao China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center Qingdao China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography MNR Qingdao China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center Qingdao China
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Han C, Zhang Q, Li Y, Sun Y, Dong Y, Ge M, Li Z, Hu X, Liu B, Zhang X, Wang Z, Xu Q. Chromosome-level genome assembly and annotation of the cold-water species Ophiura sarsii. Sci Data 2024; 11:560. [PMID: 38816401 PMCID: PMC11139871 DOI: 10.1038/s41597-024-03412-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024] Open
Abstract
The cold-water species Ophiura sarsii, a brittle star, is a key echinoderm in the Arctic continental shelf region, highly sensitive to climate change. However, the absence of a high-quality genome has hindered a thorough understanding of its adaptive evolution. In this study, we reported the first chromosome-level genome assembly of O. sarsii. The genome assembly totalled 1.57 Gb, encompassing 19 chromosomes with a GC content of 37.11% and a scaffold N50 length of 78.03 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment yielded a completeness estimate of 93.5% for this assembly. We predicted a total of 27,099 protein-coding genes, with 25,079 functionally annotated. The genome was comprised of 58.09% transposable elements. This chromosome-level genome of O. sarsii contributes to our understanding of the origin and evolution of marine organisms.
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Affiliation(s)
- Chen Han
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Qian Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yixuan Li
- Faculty of Science, Hong Kong Baptist University, Hong Kong, 000000, China
| | - Yuyao Sun
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yue Dong
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Meiling Ge
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Zhong Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Xuying Hu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Bing Liu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Zongling Wang
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
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Osland MJ, Hughes AR, Armitage AR, Scyphers SB, Cebrian J, Swinea SH, Shepard CC, Allen MS, Feher LC, Nelson JA, O'Brien CL, Sanspree CR, Smee DL, Snyder CM, Stetter AP, Stevens PW, Swanson KM, Williams LH, Brush JM, Marchionno J, Bardou R. The impacts of mangrove range expansion on wetland ecosystem services in the southeastern United States: Current understanding, knowledge gaps, and emerging research needs. GLOBAL CHANGE BIOLOGY 2022; 28:3163-3187. [PMID: 35100489 DOI: 10.1111/gcb.16111] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Climate change is transforming ecosystems and affecting ecosystem goods and services. Along the Gulf of Mexico and Atlantic coasts of the southeastern United States, the frequency and intensity of extreme freeze events greatly influence whether coastal wetlands are dominated by freeze-sensitive woody plants (mangrove forests) or freeze-tolerant grass-like plants (salt marshes). In response to warming winters, mangroves have been expanding and displacing salt marshes at varying degrees of severity in parts of north Florida, Louisiana, and Texas. As winter warming accelerates, mangrove range expansion is expected to increasingly modify wetland ecosystem structure and function. Because there are differences in the ecological and societal benefits that salt marshes and mangroves provide, coastal environmental managers are challenged to anticipate the effects of mangrove expansion on critical wetland ecosystem services, including those related to carbon sequestration, wildlife habitat, storm protection, erosion reduction, water purification, fisheries support, and recreation. Mangrove range expansion may also affect wetland stability in the face of extreme climatic events and rising sea levels. Here, we review the current understanding of the effects of mangrove range expansion and displacement of salt marshes on wetland ecosystem services in the southeastern United States. We also identify critical knowledge gaps and emerging research needs regarding the ecological and societal implications of salt marsh displacement by expanding mangrove forests. One consistent theme throughout our review is that there are ecological trade-offs for consideration by coastal managers. Mangrove expansion and marsh displacement can produce beneficial changes in some ecosystem services, while simultaneously producing detrimental changes in other services. Thus, there can be local-scale differences in perceptions of the impacts of mangrove expansion into salt marshes. For very specific local reasons, some individuals may see mangrove expansion as a positive change to be embraced, while others may see mangrove expansion as a negative change to be constrained.
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Affiliation(s)
- Michael J Osland
- Wetland and Aquatic Research Center, U.S. Geological Survey, Lafayette, Louisiana, USA
| | - A Randall Hughes
- Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - Anna R Armitage
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Steven B Scyphers
- Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - Just Cebrian
- Northern Gulf Institute, Mississippi State University, Stennis Space Center, Mississippi, USA
| | - Savannah H Swinea
- Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | | | | | - Laura C Feher
- Wetland and Aquatic Research Center, U.S. Geological Survey, Lafayette, Louisiana, USA
| | - James A Nelson
- University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | | | | | | | - Caitlin M Snyder
- Apalachicola National Estuarine Research Reserve, Eastpoint, Florida, USA
| | | | - Philip W Stevens
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, Florida, USA
| | - Kathleen M Swanson
- Mission-Aransas National Estuarine Research Reserve, Port Aransas, Texas, USA
| | | | - Janell M Brush
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Gainesville, Florida, USA
| | - Joseph Marchionno
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Gainesville, Florida, USA
| | - Rémi Bardou
- Northeastern University Marine Science Center, Nahant, Massachusetts, USA
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Kennedy JP, Antwis RE, Preziosi RF, Rowntree JK. Evidence for the genetic similarity rule at an expanding mangrove range limit. AMERICAN JOURNAL OF BOTANY 2021; 108:1331-1342. [PMID: 34458987 DOI: 10.1002/ajb2.1715] [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: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Host-plant genetic variation can shape associated communities of organisms. These community-genetic effects include (1) genetically similar hosts harboring similar associated communities (i.e., the genetic similarity rule) and (2) host-plant heterozygosity increasing associated community diversity. Community-genetic effects are predicted to be less prominent in plant systems with limited genetic variation, such as those at distributional range limits. Yet, empirical evidence from such systems is limited. METHODS We sampled a natural population of a mangrove foundation species (Avicennia germinans) at an expanding range limit in Florida, USA. We measured genetic variation within and among 40 host trees with 24 nuclear microsatellite loci and characterized their foliar endophytic fungal communities with internal transcribed spacer (ITS1) gene amplicon sequencing. We evaluated relationships among host-tree genetic variation, host-tree spatial location, and the associated fungal communities. RESULTS Genetic diversity was low across all host trees (mean: 2.6 alleles per locus) and associated fungal communities were relatively homogeneous (five sequence variants represented 78% of all reads). We found (1) genetically similar host trees harbored similar fungal communities, with no detectable effect of interhost geographic distance. (2) Host-tree heterozygosity had no detectable effect, while host-tree absolute spatial location affected community alpha diversity. CONCLUSIONS This research supports the genetic similarity rule within a range limit population and helps broaden the current scope of community genetics theory by demonstrating that community-genetic effects can occur even at expanding distributional limits where host-plant genetic variation may be limited. Our findings also provide the first documentation of community-genetic effects in a natural mangrove system.
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Affiliation(s)
- John Paul Kennedy
- Ecology and Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Richard F Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Jennifer K Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
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Han C, Xu Z, Liu X. Characteristics of macrofaunal assemblages and their relationships with environmental factors in a semi-enclosed bay. MARINE POLLUTION BULLETIN 2021; 167:112348. [PMID: 33865043 DOI: 10.1016/j.marpolbul.2021.112348] [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: 01/29/2021] [Revised: 03/27/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Characteristics of macrofaunal assemblages and their relationships with environmental factors in a semi-enclosed bay were studied seasonally in China. A total of 251 species were identified, including polychaetes (104 species), crustaceans (73 species), mollusks (51 species), and other phyla (23 species). Mean values of macrofaunal abundance were 1210, 2483, 3209, 3600 ind./m2 while those of biomass were 56.88, 176.15, 136.28, 265.55 g/m2, respectively. Ranges of species richness index, evenness index, Shannon-Wiener index were 1.54-8.16, 0.17-0.90, 0.69-4.78, respectively. The diversity indices were affected by bottom water salinity and pH. BIOENV analysis showed that water depth, phaeophorbide, and silt-clay proportion had important impacts on macrofaunal assemblages while abundance and biomass were affected by bottom water temperature, salinity, and water depth. Compared with historical data, macrofaunal species number, abundance and biomass showed a slight increasing trend, which may be due to the water quality improvement of this bay.
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Affiliation(s)
- Chen Han
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Zhaodong Xu
- North China Sea Environmental Monitoring Center, State Oceanic Administration, Qingdao 266033, China
| | - Xiaoshou Liu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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