1
|
ddRAD Sequencing-Based Scanning of Genetic Variants in Sargassum fusiforme. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10070958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Sargassum fusiforme is a commercially important brown seaweed that has experienced significant population reduction both from heavy exploitation and degradation of the environment. Cultivated breed strains are also in a state of population mixing. These population stressors make it necessary to investigate the population genetics to discover best practices to conserve and breed this seaweed. In this study, the genetic diversity and population structure of S. fusiforme were investigated by the genome-wide SNP data acquired from double digest restriction site-associated DNA sequencing (ddRAD-seq). We found a low genetic diversity and a slight population differentiation within and between wild and cultivated populations, and the effective population size of S. fusiforme had experienced a continuous decline. Tajima’s D analysis showed the population contraction in wild populations may be related to copper pollution which showed a consistent trend with the increase of the sea surface temperature. The potential selection signatures may change the timing or level of gene expression, and further experiments are needed to investigate the effect of the mutation on relevant pathways. These results suggest an urgent need to manage and conserve S. fusiforme resources and biodiversity considering the accelerating change of the environment.
Collapse
|
2
|
Kwan V, Fong J, Ng CSL, Huang D. Temporal and spatial dynamics of tropical macroalgal contributions to blue carbon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154369. [PMID: 35259389 DOI: 10.1016/j.scitotenv.2022.154369] [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: 11/12/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Blue carbon ecosystems are a vital part of nature-based climate solutions due to their capacity to store and sequester carbon, but often exclude macroalgal beds even though they can form highly productive coastal ecosystems. Recent estimates of macroalgal contributions to global carbon sequestration are derived primarily from temperate kelp forests, while tropical macroalgal carbon stock in living biomass is still unclear. Here, using Singapore as a case study, we integrate field surveys and remote sensing data to estimate living macroalgal carbon stock. Results show that macroalgae in Singapore account for up to 650 Mg C biomass stock, which is greater than the aboveground carbon found in seagrass meadows but lower than that in mangrove forests. Ulva and Sargassum dominate macroalgal assemblages and biomass along the coast, with both genera exhibiting distinct spatio-temporal variation. The annual range of macroalgal biomass carbon is estimated to be 450 Mg C yr-1, or 0.77 Mg C ha-1 yr-1. Noting the uncertainties of the fate of macroalgal biomass carbon, we estimate the potential sequestration rate and find that it is comparable to mature terrestrial ecosystems such as tropical grasslands and temperate forests. This study demonstrates that macroalgal seasonality allows for a consistent amount of biomass carbon to either be exported and eventually sequestered, or harvested for utilization on an annual basis. These findings on macroalgal growth patterns and their considerable contributions to tropical coastal carbon pool add to the growing support for macroalgae to be formally included in blue carbon assessments.
Collapse
Affiliation(s)
- Valerie Kwan
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Centre for Nature-based Climate Solutions, National University of Singapore, Singapore 117558, Singapore.
| | - Jenny Fong
- Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore
| | - Chin Soon Lionel Ng
- Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Centre for Nature-based Climate Solutions, National University of Singapore, Singapore 117558, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore.
| |
Collapse
|
3
|
Nguyen XV, Nguyen-Nhat NT, Nguyen XT, Dao VH, M. Liao L, Papenbrock J. Analysis of rDNA reveals a high genetic diversity of Halophila major in the Wallacea region. PLoS One 2021; 16:e0258956. [PMID: 34679102 PMCID: PMC8535426 DOI: 10.1371/journal.pone.0258956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/08/2021] [Indexed: 11/19/2022] Open
Abstract
The genus Halophila shows the highest species diversity within the seagrass genera. Southeast Asian countries where several boundary lines exist were considered as the origin of seagrasses. We hypothesize that the boundary lines, such as Wallace's and Lydekker's Lines, may act as marine geographic barriers to the population structure of Halophila major. Seagrass samples were collected at three islands in Vietnamese waters and analyzed by the molecular maker ITS. These sequences were compared with published ITS sequences from seagrasses collected in the whole region of interest. In this study, we reveal the haplotype and nucleotide diversity, linking population genetics, phylogeography, phylogenetics and estimation of relative divergence times of H. major and other members of the Halophila genus. The morphological characters show variation. The results of the ITS marker analysis reveal smaller groups of H. major from Myanmar, Shoalwater Bay (Australia) and Okinawa (Japan) with high supporting values. The remaining groups including Sri Lanka, Viet Nam, the Philippines, Thailand, Malaysia, Indonesia, Two Peoples Bay (Australia) and Tokushima (Japan) showed low supporting values. The Wallacea region shows the highest haplotype and also nucleotide diversity. Non-significant differences were found among regions, but significant differences were presented among populations. The relative divergence times between some members of section Halophila were estimated 2.15-6.64 Mya.
Collapse
Affiliation(s)
- Xuan-Vy Nguyen
- Department of Marine Botany, Institute of Oceanography, Vietnam Academy of Science and Technology, Nha Trang, Viet Nam
- Faculty of Marine Science and Technology, Graduate University of Science and Technology, Cau Giay, Ha Noi, Viet Nam
| | - Nhu-Thuy Nguyen-Nhat
- Department of Marine Botany, Institute of Oceanography, Vietnam Academy of Science and Technology, Nha Trang, Viet Nam
| | - Xuan-Thuy Nguyen
- Department of Marine Botany, Institute of Oceanography, Vietnam Academy of Science and Technology, Nha Trang, Viet Nam
| | - Viet-Ha Dao
- Department of Marine Botany, Institute of Oceanography, Vietnam Academy of Science and Technology, Nha Trang, Viet Nam
- Faculty of Marine Science and Technology, Graduate University of Science and Technology, Cau Giay, Ha Noi, Viet Nam
| | - Lawrence M. Liao
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Jutta Papenbrock
- Institute of Botany, Leibniz University Hannover, Hannover, Germany
| |
Collapse
|
4
|
Li JJ, Liu ZY, Zhong ZH, Zhuang LC, Bi YX, Qin S. Limited Genetic Connectivity Among Sargassum horneri (Phaeophyceae) Populations in the Chinese Marginal Seas Despite Their high Dispersal Capacity. JOURNAL OF PHYCOLOGY 2020; 56:994-1005. [PMID: 32173868 DOI: 10.1111/jpy.12990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Sargassum horneri is a habitat-forming species in the Northwest Pacific and an important contributor to seaweed rafts. In this study, 131 benthic samples and 156 floating samples were collected in the Yellow Sea and East China Sea (ECS) to test the effects of seaweed rafts on population structure and connectivity. Our results revealed high levels of genetic diversity in both benthic and floating samples based on concatenated mitochondrial markers (rpl5-rps3, rnl-atp9, and cob-cox2). Phylogenetic analyses consistently supported the existence of two lineages (lineages I and II), with divergence dating to c. 0.692 Mya (95% HPD: 0.255-1.841 Mya), indicating that long-term isolation may have occurred during the mid-Pleistocene (0.126-0.781 Mya). Extended Bayesian skyline plots demonstrated a constant population size over time in lineage I and slight demographic expansion in lineage II. Both lineages were found in each marginal sea (including both benthic and floating samples), but PCoA, FST , and AMOVA analyses consistently revealed deep genetic variation between regions. Highly structured phylogeographic pattern supports limited genetic connectivity between regions. IMA analyses demonstrated that asymmetric gene flow between benthic populations in the North Yellow Sea (NYS) and ECS was extremely low (ECS→NYS, 2Nm = 0.6), implying that high dispersal capacity cannot be assumed to lead to widespread population connectivity, even without dispersal barriers. In addition, there were only a few shared haplotypes between benthic and floating samples, suggesting the existence of hidden donors for the floating masses in the Chinese marginal seas.
Collapse
Affiliation(s)
- Jing-Jing Li
- College of Oceanography, Institute of Marine Biology, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Zheng-Yi Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China
| | - Zhi-Hai Zhong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China
| | - Long-Chuan Zhuang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China
| | - Yuan-Xin Bi
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang Province, Zhoushan, 316021, China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China
| |
Collapse
|
5
|
Ng PK, Chiou YS, Liu LC, Sun Z, Shimabukuro H, Lin SM. Phylogeography and genetic connectivity of the marine macro-alga Sargassum ilicifolium (Phaeophyceae, Ochrophyta) in the northwestern Pacific 1. JOURNAL OF PHYCOLOGY 2019; 55:7-24. [PMID: 30372533 DOI: 10.1111/jpy.12806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
The evolutionary influences of historical and contemporary factors on the population connectivity and phylogeographic structure of a brown seaweed, Sargassum ilicifolium, were elucidated using the nuclear ITS2 and mitochondrial COI markers for the collections newly sampled within its distribution range in the northwestern Pacific (NWP). Significant genetic structure at variable levels was identified between populations (pairwise FST ) and among populations grouped by geographical proximity (ΦCT among regions). The adjacent groups of populations with moderate structure revealed from AMOVA appeared to have high genetic connectivity. However, a lack of genealogical concordance with the geographic distribution was uncovered for S. ilicifolium from the NWP. Such genetic homogeneity is interpreted as a result of the interaction between postglacial recolonization and dynamic oceanic current regimes in the region. Two separated glacial refugia, the South China Sea and the Okinawa Trough, in the marginal seas of east China were recognized based on the presence of endemic haplotypes and high haplotype diversity in the populations at southern China and northeast of Taiwan. Populations persisting in these refugia may have served as the source for recolonization in the NWP with the rise of sea level during the warmer interglacial periods. The role of oceanic currents in maintaining genetic connectivity of S. ilicifolium in the region was further corroborated by the coherence between the direction of oceanic currents and that of gene flow, especially along the eastern coast of Taiwan. This study underlines the interaction between historical postglacial recolonization and contemporary coastal hydrodynamics in contributing to population connectivity and distribution for this tropical seaweed in the NWP.
Collapse
Affiliation(s)
- Poh-Kheng Ng
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan, R.O.C
| | - Yu-Shan Chiou
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan, R.O.C
| | - Li-Chia Liu
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan, R.O.C
| | - Zhongmin Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266701, China
| | - Hiromori Shimabukuro
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, Hatsukaichi, Hiroshima, 739-0452, Japan
| | - Showe-Mei Lin
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan, R.O.C
| |
Collapse
|
6
|
Genetic diversity of Philippine Gracilaria salicornia (Gracilariaceae, Rhodophyta) based on mitochondrial COI-5P sequences. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-00179-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
7
|
Hu ZM, Li JJ, Sun ZM, Gao X, Yao JT, Choi HG, Endo H, Duan DL. Hidden diversity and phylogeographic history provide conservation insights for the edible seaweed Sargassum fusiforme in the Northwest Pacific. Evol Appl 2017; 10:366-378. [PMID: 28352296 PMCID: PMC5367075 DOI: 10.1111/eva.12455] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/13/2016] [Indexed: 02/03/2023] Open
Abstract
Understanding the evolutionary processes that have created diversity and the genetic potential of species to adapt to environmental change is an important premise for biodiversity conservation. Herein, we used mitochondrial trnW‐L and cox3 and plastid rbcL‐S data sets to analyze population genetic variation and phylogeographic history of the brown alga Sargassum fusiforme, whose natural resource has been largely exterminated in the Asia–Northwest Pacific in the past decades. Phylogenetic trees and network analysis consistently revealed three major haplotype groups (A, B, and C) in S. fusiforme, with A and B distributed in the Japan‐Pacific coast. Group C consisted of three subgroups (C1, C2, and C3) which were distributed in the Sea of Japan, the Yellow–Bohai Sea, and East China Sea, respectively. Isolation‐with‐migration (IMa) analysis revealed that the three groups diverged approximately during the mid‐Pleistocene (c. 756–1,224 ka). Extended Bayesian skyline plots (EBSP) showed that groups A and B underwent relatively long‐term stable population size despite a subsequent rapid demographic expansion, while subgroups C2 and C3 underwent a sudden expansion at c. 260 ka. FST and AMOVA detected low population‐level genetic variation and high degrees of divergence between groups. The cryptic diversity and phylogeographic patterns found in S. fusiforme not only are essential to understand how environmental shifts and evolutionary processes shaped diversity and distribution of coastal seaweeds but also provide additional insights for conserving and managing seaweed resources and facilitate predictions of their responses to future climate change and habitat loss.
Collapse
Affiliation(s)
- Zi-Min Hu
- Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China; Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Jing-Jing Li
- Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China; Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China; College of Earth Science University of Chinese Academy of Sciences Beijing China; Present address: Institute of Marine Biology College of Oceanography Hohai University Nanjing 210098 China
| | - Zhong-Min Sun
- Laboratory of Marine Organism Taxonomy & Phylogeny Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Xu Gao
- Research Centre for Inland Seas Kobe University Rokkodai Kobe Japan
| | - Jian-Ting Yao
- Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China; Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Han-Gil Choi
- Faculty of Biological Science and Research Institute for Basic Science Wonkwang University Iksan Korea
| | - Hikaru Endo
- Faculty of Fisheries Kagoshima University Kagoshima Japan
| | - De-Lin Duan
- Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China; Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
| |
Collapse
|
8
|
Li J, Yang Y, Chen Q, Fang L, He Z, Guo W, Qiao S, Wang Z, Guo M, Zhong C, Zhou R, Shi S. Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses. Sci Rep 2016; 6:29486. [PMID: 27380895 PMCID: PMC4933931 DOI: 10.1038/srep29486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 06/21/2016] [Indexed: 11/09/2022] Open
Abstract
Systematically investigating the impacts of Pleistocene sea-level fluctuations on mangrove plants may provide a better understanding of their demographic history and useful information for their conservation. Therefore, we conducted population genomic analyses of 88 nuclear genes to explore the population dynamics of a mangrove tree Lumnitzera racemosa across the Indo-West Pacific region. Our results revealed pronounced genetic differentiation in this species between the populations from the Indian Ocean and the Pacific Ocean, which may be attributable to the long-term isolation between the western and eastern coasts of the Malay Peninsula during sea-level drops in the Pleistocene glacial periods. The mixing of haplotypes from the two highly divergent groups was identified in a Cambodian population at almost all 88 nuclear genes, suggesting genetic admixture of the two lineages at the boundary region. Similar genetic admixture was also found in other populations from Southeast Asia based on the Bayesian clustering analysis of six nuclear genes, which suggests extensive and recent secondary contact of the two divergent lineages in Southeast Asia. Computer simulations indicated substantial migration from the Indian Ocean towards the South China Sea, which likely results in the genetic admixture in Southeast Asia.
Collapse
Affiliation(s)
- Jianfang Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Lu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Sitan Qiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhengzhen Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Miaomiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbour National Nature Reserve, Haikou 571129, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| |
Collapse
|
9
|
Dell CLA, Longo GO, Hay ME. Positive Feedbacks Enhance Macroalgal Resilience on Degraded Coral Reefs. PLoS One 2016; 11:e0155049. [PMID: 27186979 PMCID: PMC4871466 DOI: 10.1371/journal.pone.0155049] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/22/2016] [Indexed: 11/18/2022] Open
Abstract
Many reefs have shifted from coral and fish dominated habitats to less productive macroalgal dominated habitats, and current research is investigating means of reversing this phase shift. In the tropical Pacific, overfished reefs with inadequate herbivory can become dominated by the brown alga Sargassum polycystum. This alga suppresses recruitment and survival of corals and fishes, thus limiting the potential for reef recovery. Here we investigate the mechanisms that reinforce S. polycystum dominance and show that in addition to negatively affecting other species, this species acts in a self-reinforcing manner, positively promoting survival and growth of conspecifics. We found that survival and growth of both recruit-sized and mature S. polycystum fronds were higher within Sargassum beds than outside the beds and these results were found in both protected and fished reefs. Much of this benefit resulted from reduced herbivory within the Sargassum beds, but adult fronds also grew ~50% more within the beds even when herbivory did not appear to be occurring, suggesting some physiological advantage despite the intraspecific crowding. Thus via positive feedbacks, S. polycystum enhances its own growth and resistance to herbivores, facilitating its dominance (perhaps also expansion) and thus its resilience on degraded reefs. This may be a key feedback mechanism suppressing the recovery of coral communities in reefs dominated by macroalgal beds.
Collapse
Affiliation(s)
- Claire L. A. Dell
- School of Biology and Aquatic Chemical Ecology Centre, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Guilherme O. Longo
- School of Biology and Aquatic Chemical Ecology Centre, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Mark E. Hay
- School of Biology and Aquatic Chemical Ecology Centre, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| |
Collapse
|
10
|
Hu ZM, Li JJ, Sun ZM, Oak JH, Zhang J, Fresia P, Grant WS, Duan DL. Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific. Mol Ecol 2016; 24:5020-33. [PMID: 26334439 DOI: 10.1111/mec.13367] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 02/01/2023]
Abstract
A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from one another in the early Pliocene-late Miocene (c. 4.5-7.7 Ma). The remarkably deep divergences, both within and between lineages, appear to have resulted from ancient isolations, accelerated by random drift and limited genetic exchange between regions. The disjunct distributions of lineages A and C along the coasts of Japan may reflect divergence during isolation in scattered refugia. The distribution of lineage B, from the South China Sea to the Korean Peninsula, appears to reflect postglacial recolonizations of coastal habitats. These three lineages do not coincide with the three documented morphological formae in C. ocellatus, suggesting that additional cryptic species may exist in this taxon. Our study illustrates the interaction of environmental variability and demographic processes in producing lineage diversification in an intertidal seaweed and highlights the importance of phylogeographic approaches for discovering cryptic marine biodiversity.
Collapse
Affiliation(s)
- Zi-Min Hu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jing-Jing Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Min Sun
- Laboratory of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jung-Hyun Oak
- Department of Oceanography, Pusan National University, Pusan, 609-735, Korea
| | - Jie Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pablo Fresia
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, Uruguay
| | - W Stewart Grant
- Alaska Department of Fish and Game, Anchorage, AK, 99518, USA
| | - De-Lin Duan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| |
Collapse
|
11
|
Zhang J, Yao JT, Sun ZM, Fu G, Galanin DA, Nagasato C, Motomura T, Hu ZM, Duan DL. Phylogeographic data revealed shallow genetic structure in the kelp Saccharina japonica (Laminariales, Phaeophyta). BMC Evol Biol 2015; 15:237. [PMID: 26525408 PMCID: PMC4630829 DOI: 10.1186/s12862-015-0517-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/21/2015] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Population structure and genetic diversity of marine organisms in the Northwestern Pacific Ocean exhibited complex patterns. Saccharina japonica is a commercially and ecologically important kelp species widely distributed along the coast of Japan Sea. However, it is still poorly known about population genetics and phylogeographic patterns of wild S. japonica populations on a large geographic scale, which is an important contribution to breeding and conservation of this marine crop. RESULTS We collected 612 mitochondrial COI and trnW-trnL sequences. Diversity indices suggested that S. japonica populations along the coast of Hokkaido exhibited the highest genetic diversity. Bayesian Analysis of Population Structure (BAPS) revealed four clusters in the kelp species (cluster 1: Hokkaido and South Korea; cluster 2: northwestern Hokkaido; cluster 3: Far Eastern Russia; cluster 4: China). The network inferred from concatenated data exhibited two shallow genealogies corresponding to two BAPS groups (cluster 2 and cluster 3). We did not detect gene flow between the two shallow genealogies, but populations within genealogy have asymmetric gene exchange. Bayesian skyline plots and neutrality tests suggested that S. japonica experienced postglacial expansion around 10.45 ka. CONCLUSIONS The coast of Hokkaido might be the origin and diversification center of S. japonica. Gene exchange among S. japonica populations could be caused by anthropogenic interference and oceanographic regimes. Postglacial expansions and gene exchange apparently led to more shared haplotypes and less differentiation that in turn led to the present shallow phylogeographical patterns in S. japonica.
Collapse
Affiliation(s)
- Jie Zhang
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Ting Yao
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Zhong-Min Sun
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Gang Fu
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Hokkaido, Japan.
| | - Dmitry A Galanin
- Sakhalin Scientific Research Institute of Fisheries and Oceanology, Yuzhno-Sakhalinsk, 693023, Russia.
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Hokkaido, Japan.
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Hokkaido, Japan.
| | - Zi-Min Hu
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - De-Lin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| |
Collapse
|