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Xian R, Yang R, Zhang P, Chen W, Luo Q, Chen J, Chen H. Carotenoid Differences and Genetic Diversity in Populations of Sargassum hemiphyllum and Sargassum fusiforme. Mol Biotechnol 2023; 65:1378-1386. [PMID: 36611100 DOI: 10.1007/s12033-022-00644-4] [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: 08/23/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
Sargassum hemiphyllum and Sargassum fusiforme are important benthic seaweeds that grow along the southeastern coast of China. The content of carotenoids in each population was detected by ultra-high performance liquid chromatography (UHPLC). The research results will enrich the theoretical basis and data support concerning the influencing factors of carotenoids in Sargassum. The inter-simple sequence repeat (ISSR) technique was used to study the genetic diversity of four S. hemiphyllum and two S. fusiforme populations, and the results provide a reference for the artificial cultivation of Sargassum. The total carotenoid content of Sargassum ranged from 161.79 ± 4.22 to 269.47 ± 6.15 μg/g. Among the carotenoids, β-carotene and fucoxanthin accounted for 80%, and levels in S. hemiphyllum were generally higher than those in S. fusiforme. The carotenoid contents of S. hemiphyllum from different areas were significantly different (P < 0.05), and the total carotenoids content decreased toward the southern region. The average heterozygosity H ranged from 0.29 to 0.49, and the Shannon diversity index I ranged from 0.44 to 0.69. The polymorphic loci, genetic diversity, and other indicators of S. hemiphyllum populations were higher than those of S. fusiforme, and the diversity of cultivated populations was not significantly lower. The results showed that the genetic variation of Sargassum is limited, and thus, more sexual reproduction can be attempted in breeding. Considering morphological indicators, genetic diversity indexes, and carotenoid content, S. hemiphyllum appears to have a higher commercial development value.
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Affiliation(s)
- Rui Xian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Rui Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Peng Zhang
- Zhejiang Institute of Marine Aquaculture, Wenzhou, 325005, China
| | - Weizhou Chen
- Guangdong Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Qijun Luo
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Juanjuan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Haimin Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315211, Zhejiang, China
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Lee YJ, Kim YD, Uh YR, Kim YM, Seo TH, Choi SJ, Jang CS. Complete organellar genomes of six Sargassum species and development of species-specific markers. Sci Rep 2022; 12:20981. [PMID: 36470932 PMCID: PMC9722929 DOI: 10.1038/s41598-022-25443-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Sargassum is one of the most important brown algal genera that can be used as food and raw material for medicinal purpose, and has various beneficial effects. As the classification of Sargassum species is currently based on their morphological characteristics, organellar genome sequences of Sargassum would provide important information for accurate identification of species and developing species-specific markers. We sequenced the complete organellar genomes of six Sargassum species, including the first complete chloroplast genome sequences of S. fulvellum, S. serratifolium, S. macrocarpum, and S. siliquastrum, and the first complete mitochondrial genome sequences of S. fulvellum, S. serratifolium, and S. macrocarpum. The chloroplast genomes of the 6 Sargassum species contained 139 protein-coding genes (PCGs), and the mitochondrial genomes possessed 37 PCGs. A comparative study was performed between the newly sequenced organellar genomes and 44 other species belonging to class Phaeophyceae. Phylogenetic relationships using PCGs shared by Phaeophyceae species were constructed with IQ-TREE 2 using the maximum likelihood method. In addition, we developed real-time PCR markers based on SNPs to distinguish the 6 Sargassum species. Our results provide useful information for establishing phylogenetic relationships between brown algae.
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Affiliation(s)
- Yong Jin Lee
- Plant Genomics Laboratory, Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon, Republic of Korea
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, Republic of Korea
| | - Yea Dam Kim
- Plant Genomics Laboratory, Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon, Republic of Korea
| | - Yo Ram Uh
- Plant Genomics Laboratory, Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon, Republic of Korea
| | - Yeon Mi Kim
- Plant Genomics Laboratory, Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon, Republic of Korea
| | - Tae-Ho Seo
- Coastal Production Institute, Yeosu, Republic of Korea
| | - Sung-Je Choi
- Korea National College of Agriculture and Fisheries, Jeonju, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Laboratory, Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon, Republic of Korea.
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, Republic of Korea.
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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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Potential of biogas production from the anaerobic digestion of Sargassum fulvellum macroalgae: Influences of mechanical, chemical, and biological pretreatments. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108140] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Wu X, Zhang P, Zhang Y, Wang T. The complete chloroplast genome of Sargassum hemiphyllum var. Chinense (Sargassaceae, Phaeophyceae) and its phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:278-279. [PMID: 33553644 PMCID: PMC7850454 DOI: 10.1080/23802359.2020.1863165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Sargassum hemiphyllum (Turner) C. Agardh is an important brown macroalga. In this study, we presented the complete chloroplast genome of its variety S. hemiphyllum var. chinense using genome skimming approach. Circular mapping revealed its sequence length was 124,319 bp, with a large single-copy region (LSC, 73,505 bp) and a small single copy region (SSC, 39,922 bp) separated by a pair of inverted repeats (IRs, 5446 bp). Its chloroplast genome contained 173 genes, including 139 protein-coding, 6 rRNA, and 28 tRNA genes. The phylogenetic analysis indicated that S. hemiphyllum var. chinense was closely related with S. confusum.
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Affiliation(s)
- Xiaowen Wu
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou, China
| | - Peng Zhang
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou, China
| | - Yonghua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
| | - Tiegan Wang
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou, China
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Li R, Jia X, Zhang J, Jia S, Liu T, Qu J, Wang X. The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:747036. [PMID: 34804089 PMCID: PMC8602799 DOI: 10.3389/fpls.2021.747036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/04/2021] [Indexed: 05/03/2023]
Abstract
Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii, and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events.
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Affiliation(s)
- Ruoran Li
- College of Life Sciences, Yantai University, Yantai, China
| | - Xuli Jia
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Shangang Jia,
| | - Tao Liu
- College of Life Sciences, Yantai University, Yantai, China
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Tao Liu,
| | - Jiangyong Qu
- College of Life Sciences, Yantai University, Yantai, China
- Jiangyong Qu,
| | - Xumin Wang
- College of Life Sciences, Yantai University, Yantai, China
- Xumin Wang,
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Zhang J, Yao J, Hu Z, Jueterbock A, Yotsukura N, Krupnova TN, Nagasato C, Duan D. Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica. Evol Appl 2019; 12:791-803. [PMID: 30976310 PMCID: PMC6439492 DOI: 10.1111/eva.12756] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 11/22/2018] [Accepted: 12/09/2018] [Indexed: 01/04/2023] Open
Abstract
Studies of postglacial range shifts could enhance our understanding of seaweed species' responses to climate change and hence facilitate the conservation of natural resources. However, the distribution dynamics and phylogeographic diversification of the commercially and ecologically important kelp Saccharina japonica in the Northwest Pacific (NWP) are still poorly surveyed. In this study, we analyzed the evolutionary history of S. japonica using two mitochondrial markers and 24 nuclear microsatellites. A STRUCTURE analysis revealed two partially isolated lineages: lineage H, which is scattered along the coast of Japan; and lineage P, which occurs along the west coast of the Japan Sea. Ecological niche modeling projections to the Last Glacial Maximum (LGM) revealed that the southern coasts of the Japan Sea and the Pacific side of the Oshima and Honshu Peninsulas provided the most suitable habitats for S. japonica, implying that these regions served as ancient refugia during the LGM. Ancient isolation in different refugia may explain the observed divergence between lineages P and H. An approximate Bayesian computation analysis indicated that the two lineages experienced post-LGM range expansion and that postglacial secondary contact occurred in Sakhalin. Model projections into the year 2,100 predicted that S. japonica will shift northwards and lose its genetic diversity center on the Oshima Peninsula in Hokkaido and Shimokita Peninsula in Honshu. The range shifts and evolutionary history of S. japonica improve our understanding of how climate change impacted the distribution range and diversity of this species and provide useful information for the conservation of natural resources under ongoing environmental change in the NWP.
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Affiliation(s)
- Jie Zhang
- Key Lab of Experimental Marine Biology, Institute of OceanologyChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Jianting Yao
- Key Lab of Experimental Marine Biology, Institute of OceanologyChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Zi‐Min Hu
- Key Lab of Experimental Marine Biology, Institute of OceanologyChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | | | | | | | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern BiosphereHokkaido UniversityMuroranJapan
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of OceanologyChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
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Shi LY, Li J, Wu SQ, Han J. Historical Refugia and Isolation by Distance of the Mud Snail, Bullacta exarata (Philippi, 1849) in the Northwestern Pacific Ocean. Front Genet 2018; 9:486. [PMID: 30405694 PMCID: PMC6204408 DOI: 10.3389/fgene.2018.00486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/01/2018] [Indexed: 11/13/2022] Open
Abstract
Many phylogeographic studies on marine organisms in the Northwestern Pacific have supported for the biogeographic hypotheses that isolation in the marginal seas of this region during the Pleistocene glaciation lower sea level led to population genetic divergence, and thus population expansion was a common phenomenon when the sea level rebounded. However, most of these studies were based on maternally inherited mitochondrial DNA markers with limited sample sites and therefore, were unable to reveal detailed pictures encompassing paternal line information covering of the entire range. In this study, we used the mitochondrial cytochrome c oxidase subunit I (COI) and nine nuclear microsatellite loci to investigate the phylogeography of the mud snail, Bullacta exarata (Philippi, 1849), a species endemic to the Northwestern Pacific. We sampled 14 natural populations spanning across 3800 km of the Chinese coastline, essentially covering most of the species distribution range. COI analysis identified a total of 149 haplotypes separated into two distinct groups with nine mutation steps, revealing a prominent phylogeographic structure. Nuclear microsatellite data also demonstrated a similar but weaker genetic structure. The estimated time to the most recent common ancestor between the two COI haplogroups is at ∼0.89 Ma, indicating that B. exarata populations survived the Pleistocene glaciation in the Sea of Japan and the Okinawa Trough, two marginal seas around the species range. The consistent significant patterns of isolation by distance of both COI and microsatellites suggests that limited mobility of adults and short planktonic stage of larvae may have played an important role in promoting or maintaining the genetic differentiation of B. exarata. Results from population demographic analyses support population expansion late in the Pleistocene era.
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Affiliation(s)
- Lu-Ye Shi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jia Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Shu-Qing Wu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jie Han
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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Ni G, Li Q, Ni L, Kong L, Yu H. Population subdivision of the surf clam Mactra chinensis in the East China Sea: Changjiang River outflow is not the sole driver. PeerJ 2015; 3:e1240. [PMID: 26468432 PMCID: PMC4592156 DOI: 10.7717/peerj.1240] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 08/22/2015] [Indexed: 12/03/2022] Open
Abstract
The northwestern Pacific, characterized by unique tectonic and hydrological settings, has greatly intrigued marine phylogeographers. However, current studies mostly focus on the influence of Pleistocene isolation of sea basins in population structure of species in the region, leaving the contribution of other factors (such as freshwater outflow and environmental gradients) largely unexploited. Here we shed light on the question by investigating phylogeography of the surf clam Mactra chinensis in the East China Sea (ECS). Genetic information was acquired from 501 specimens collected from its main distribution in the region, represented by mitochondrial cytochrome oxidase I (COI) and nine polymorphic microsatellite loci. A shallow and star-like phylogeny was revealed for all COI haplotypes, indicating the origin of populations from a single refugium. Although no divergent lineages existed, population subdivision was detected in both data sets. The most striking pattern was the significant differentiation between populations north and south of a biogeographic boundary—the Changjiang Estuary, suggesting a barrier effect of the freshwater outflow to gene flow. For the northern group, substructure was revealed by COI result as one southernmost population was significant different from other ones. Clear latitude gradations in allele frequencies were revealed by microsatellite analyses, likely influenced by environmental gradient factors such as temperature. Our results demonstrate that genetic subdivision can arise for populations within the ECS despite they have a single origin, and multiple mechanisms including Changjiang River outflow, environmental gradient factors and life-history traits may act in combination in the process.
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Affiliation(s)
- Gang Ni
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
| | - Qi Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
| | - Lehai Ni
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China ; Shandong Fisheries Technical Extension Station , Jinan , China
| | - Lingfeng Kong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
| | - Hong Yu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
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Wang J, Tsang LM, Dong YW. Causations of phylogeographic barrier of some rocky shore species along the Chinese coastline. BMC Evol Biol 2015; 15:114. [PMID: 26071894 PMCID: PMC4465721 DOI: 10.1186/s12862-015-0387-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 05/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Substrate, ocean current and freshwater discharge are recognized as important factors that control the larval dispersal and recruitment of intertidal species. Life history traits of individual species will determine the differential responses to these physical factors, and hence resulting in contrasting phylogeography across the same biogeographic barrier. To determine how these factors affect genetic structure of rocky shore species along the China coast, a comparative phylogeographic study of four intertidal and subtidal species was conducted using mitochondrial and nuclear DNA by combining new sequences from Siphonaria japonica with previously published sequences from three species (Cellana toreuma, Sargassum horneri and Atrina pectinata). RESULTS Analysis of molecular variance and pairwise ΦST revealed significant genetic differences between the Yellow Sea (YS) and the other two marginal seas (East China Sea, ECS and South China Sea, SCS) for rocky-shore species (S. japonica, C. toreuma, S. horneri), but not for muddy-shore species Atrina pectinata. Demographic history analysis proved that the population size of all these four species were persistent though the Last Glacial Maximum (LGM, ~20 ka BP). Migration analysis revealed that gene flow differentiated northward and southward migration for these four species. However, the inferred direction of gene flow using alternatively mitochondrial or nuclear markers was contradictory in S. japonica. CONCLUSIONS It is concluded that there is a phylogeographical break at the Yangtze River estuary for the rocky shore species and the causation of the barrier is mainly due to the unsuitable substratum and freshwater discharge. All four intertidal and subtidal species appear to have persisted through the LGM in China, indicating the lower impact of LGM on intertidal and subtidal species than generally anticipated. The imbalanced gene flow between YS and ESCS groups for these four species could be explained by historical refugia. The discordance between mitochondrial and nuclear markers in the MIGRATE analysis of S. japonica prove the importance of employing multi-locus data in biogeographic study. Climate change, land reclamation and dam construction, which are changing substrate and hydrological conditions around Yangtze River estuary, will consequently affect the biogeographic pattern of intertidal species.
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Affiliation(s)
- Jie Wang
- State Key Laboratory of Marine Environmental Science, College of Marine and Earth Sciences, Xiamen University, Xiamen, China. .,Marine Biodiversity and Global Change Laboratory, Xiamen University, Xiamen, China.
| | - Ling Ming Tsang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan.
| | - Yun-Wei Dong
- State Key Laboratory of Marine Environmental Science, College of Marine and Earth Sciences, Xiamen University, Xiamen, China. .,Marine Biodiversity and Global Change Laboratory, Xiamen University, Xiamen, China.
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Liu F, Pang S, Chen W. Complete mitochondrial genome of the brown alga Sargassum hemiphyllum (Sargassaceae, Phaeophyceae): comparative analyses. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1468-70. [PMID: 25162799 DOI: 10.3109/19401736.2014.953096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Sargassum hemiphyllum (Turner) C. Agardh is a common low intertidal brown alga in the northwestern Pacific, and two varieties (var. chinense and var. hemiphyllum) of this alga have been determined based on morphological and molecular data. In this study, we present the complete mitochondrial genome of S. hemiphyllum var. chinense. The circular-mapping S. hemiphyllum mitogenome of 34,686 bp has an overall A+T content of 63.43%, and contains 65 densely packed genes. The total intergenic spacer regions are 1597 bp, constituting 4.60% of the mitogenome. The gene content and genome organization of S. hemiphyllum are identical to that of other reported Sargassum species. The identity comparison of overall mitogenome sequences and phylogenomic analyses indicate that S. hemiphyllum has a closer evolutionary relationship with Sargassum muticum than other Sargassum species analyzed. The present mitogenomic data provide a powerful tool for definition of varieties and studies of population structure in S. hemiphyllum.
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Affiliation(s)
- Feng Liu
- a Key Laboratory of Experimental Marine Biology , Institute of Oceanology, Chinese Academy of Sciences , Qingdao , P. R. China and
| | - Shaojun Pang
- a Key Laboratory of Experimental Marine Biology , Institute of Oceanology, Chinese Academy of Sciences , Qingdao , P. R. China and
| | - Weizhou Chen
- b Marine Biology Institute, Shantou University , Shantou , P. R. China
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Cheang CC, Chu KH, Ang PO. Phylogeography of the marine macroalga Sargassum hemiphyllum (Phaeophyceae, Heterokontophyta) in northwestern Pacific. Mol Ecol 2010; 19:2933-48. [PMID: 20584136 DOI: 10.1111/j.1365-294x.2010.04685.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Sargassum hemiphyllum is commonly found in Japan and Korea, with a variety, var. chinense, that is found distributed in the southern Chinese coast. We previously reported distinct genetic differentiation between the two taxa based on the PCR-RFLP data of plastid RubiscoL-S spacer. The present study aims at elucidating the phylogeographic pattern of S. hemiphyllum based on more markers in the nuclear and extranuclear genomes, with a view to reveal the occurrence of hybridization. The two allopatrically distributed taxa were found to be genetically distinct in nuclear ITS2, plastidial Rubisco (Rbc) and mitochondrial TrnW_I (Trn) spacers. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the late Miocene (6.58-11.25 Mya). Divergence within both S. hemiphyllum and the chinense variety was observed based on Trn spacer, while the divergence in S. hemiphyllum was further confirmed in Rbc spacer. This divergence appears to correspond to the separation of the Japanese populations between the Sea of Japan and the Pacific that occurred around 0.92-2.88 Mya (the early Pleistocene). The presence of an ITS2 clone resembling var. chinense sequences in a Japanese population of S. hemiphyllum (JpNS) raises the possibility of the introgression of var. chinense individuals into S. hemiphyllum population. Compared to that between S. hemiphyllum and the chinense variety, hybridization among the Japanese and Korean populations of S. hemiphyllum is highly probable as all these individuals share a pool of nuclear ITS2 sequences, possibly attributable to incomplete concerted evolution of ITS2.
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Affiliation(s)
- Chi Chiu Cheang
- Simon F. S. Li Marine Science Laboratory, Department of Biology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
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Mattio L, Payri CE. TAXONOMIC REVISION OF SARGASSUM SPECIES (FUCALES, PHAEOPHYCEAE) FROM NEW CALEDONIA BASED ON MORPHOLOGICAL AND MOLECULAR ANALYSES(1). JOURNAL OF PHYCOLOGY 2009; 45:1374-1388. [PMID: 27032595 DOI: 10.1111/j.1529-8817.2009.00760.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sargassum C. Agardh (1820) is a taxonomically difficult genus distributed worldwide and reported as the most species-rich genus of the Fucales. It is especially abundant in the Pacific where decreasing species richness is reported to occur from west to east. New Caledonia has been recognized as one of the hotspots of Sargassum diversity; however, species lists available for this region are old and incomplete and have not yet been updated with regard to the latest taxonomic revisions published. This study aimed at revising Sargassum diversity in New Caledonia and to assess its geographic affinities with neighboring Pacific regions. We used combined morphological and DNA analyses on new collections and examined numerous type specimens. Although 45 taxa have been listed in the literature, most of them have been either transferred to synonymy since or misidentified, and in this study, only 12 taxa were recognized as occurring in New Caledonia. They belong to the subgenus Sargassum sect. Binderianae (Grunow) Mattio et Payri (2), sect. Ilicifoliae (J. Agardh) Mattio et Payri (2), sect. Polycystae Mattio et Payri. (1), sect. Sargassum (4), sect. Zygocarpicae (J. Agardh) Setch. (2), and subgenus Phyllotrichia (Aresh.) J. Agardh (1). New Caledonian Sargassum flora appeared as the second richest in the region after the Pacific coast of Australia, with which it has shown high similarity, and shared species with all neighboring regions. One species, S. turbinarioides Grunow, is considered as endemic to New Caledonia. The low genetic diversity detected among several polymorphic species belonging to sect. Sargassum is also discussed.
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Affiliation(s)
- Lydiane Mattio
- Institut de Recherche pour le Développement, UMR7138 SAE, BPA5, 98848 Nouméa, New Caledonia and Université de la Méditerranée, UMR6540 DIMAR COM, 13288 Marseille cedex 9, FranceInstitut de Recherche pour le Développement, UMR7138 SAE, BPA5, 98848 Nouméa, New Caledonia
| | - Claude Elisabeth Payri
- Institut de Recherche pour le Développement, UMR7138 SAE, BPA5, 98848 Nouméa, New Caledonia and Université de la Méditerranée, UMR6540 DIMAR COM, 13288 Marseille cedex 9, FranceInstitut de Recherche pour le Développement, UMR7138 SAE, BPA5, 98848 Nouméa, New Caledonia
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