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Zhang X, Li YL, Kaldy JE, Suonan Z, Komatsu T, Xu S, Xu M, Wang F, Liu P, Liu X, Yue S, Zhang Y, Lee KS, Liu JX, Zhou Y. Population genetic patterns across the native and invasive range of a widely distributed seagrass: Phylogeographic structure, invasive history and conservation implications. DIVERS DISTRIB 2024; 30:1-18. [PMID: 38515563 PMCID: PMC10953713 DOI: 10.1111/ddi.13803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 03/23/2024] Open
Abstract
Aim The seagrass Zostera japonica is a dramatically declined endemic species in the Northwestern Pacific from the (sub)tropical to temperate areas, however, it is also an introduced species along the Pacific coast of North America from British Columbia to northern California. Understanding the population's genetic patterns can inform the conservation and management of this species. Location North Pacific. Methods We used sequences of the nuclear rDNA internal transcribed spacer (ITS) and chloroplast trnK intron maturase (matK), and 24 microsatellite loci to survey 34 native and nonnative populations (>1000 individuals) of Z. japonica throughout the entire biogeographic range. We analysed the phylogeographic relationship, population genetic structure and genetic diversity of all populations and inferred possible origins and invasion pathways of the nonnative ones. Results All markers revealed a surprising and significant deep divergence between northern and southern populations of Z. japonica in the native region separated by a well-established biogeographical boundary. A secondary contact zone was found along the coasts of South Korea and Japan. Nonnative populations were found to originate from the central Pacific coast of Japan with multiple introductions from at least two different source populations, and secondary spread was likely aided by waterfowl. Main Conclusions The divergence of the two distinct clades was likely due to the combined effects of historical isolation, adaptation to distinct environments and a contemporary physical barrier created by the Yangtze River, and the warm northward Kuroshio Current led to secondary contact after glacial separation. Existing exchanges among the nonnative populations indicate the potential for persistence and further expansion. This study not only helps to understand the underlying evolutionary potential of a widespread seagrass species following global climate change but also provides valuable insights for conservation and restoration.
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Affiliation(s)
- Xiaomei Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - James E. Kaldy
- US EPA, Pacific Ecological Systems Division, Newport, Oregon, USA
| | - Zhaxi Suonan
- Department of Biological Sciences, Pusan National University, Pusan, Korea
| | | | - Shaochun Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Min Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Feng Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xujia Liu
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
| | - Shidong Yue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yu Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kun-Seop Lee
- Department of Biological Sciences, Pusan National University, Pusan, Korea
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yi Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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Ruan YG, Yu S, Shun-Hua Z, Yin QJ. Chloroplast genome structure and phylogenetic position of Syringodium isoetifolium (Asch.) Dandy. Mitochondrial DNA B Resour 2022; 7:370-371. [PMID: 35187232 PMCID: PMC8856113 DOI: 10.1080/23802359.2021.2003261] [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: 12/03/2022] Open
Abstract
Syringodium isoetifolium (noodle seagrass) is a dioecious perennial seagrass. In this study, the complete chloroplast genome of S. isoetifolium was successfully characterized through next-generation sequencing technology. The cp genome was 159,333 bp in length with a GC content of 35.9%, including LSC (89,055 bp), SSC (19,160 bp), and two IRs (25,559 bp). The genome encoded 131 function genes, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis indicated that S. isoetifolium was clustered with Zostera and Ruppia.
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Affiliation(s)
- Ying-Gang Ruan
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Shuo Yu
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Zhang Shun-Hua
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Qun-Jian Yin
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
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Ackiss AS, Bird CE, Akita Y, Santos MD, Tachihara K, Carpenter KE. Genetic patterns in peripheral marine populations of the fusilier fish Caesio cuning within the Kuroshio Current. Ecol Evol 2018; 8:11875-11886. [PMID: 30598783 PMCID: PMC6303744 DOI: 10.1002/ece3.4644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/25/2018] [Accepted: 09/05/2018] [Indexed: 01/16/2023] Open
Abstract
AIM Mayr's central-peripheral population model (CCPM) describes the marked differences between central and peripheral populations in genetic diversity, gene flow, and census size. When isolation leads to genetic divergence, these peripheral populations have high evolutionary value and can influence biogeographic patterns. In tropical marine species with pelagic larvae, powerful western-boundary currents have great potential to shape the genetic characteristics of peripheral populations at latitudinal extremes. We tested for the genetic patterns expected by the CCPM in peripheral populations that are located within the Kuroshio Current for the Indo-Pacific reef fish, Caesio cuning. METHODS We used a panel of 2,677 SNPs generated from restriction site-associated DNA (RAD) sequencing to investigate genetic diversity, relatedness, effective population size, and spatial patterns of population connectivity from central to peripheral populations of C. cuning along the Kuroshio Current. RESULTS Principal component and cluster analyses indicated a genetically distinct lineage at the periphery of the C. cuning species range and examination of SNPs putatively under divergent selection suggested potential for local adaptation in this region. We found signatures of isolation-by-distance and significant genetic differences between nearly all sites. Sites closest to the periphery exhibited increased within-population relatedness and decreased effective population size. MAIN CONCLUSIONS Despite the potential for homogenizing gene flow along the Kuroshio Current, peripheral populations in C. cuning conform to the predictions of the CCPM. While oceanography, habitat availability, and dispersal ability are all likely to shape the patterns found in C. cuning across this central-peripheral junction, the impacts of genetic drift and natural selection in increasing smaller peripheral populations appear to be probable influences on the lineage divergence found in the Ryukyu Islands.
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Affiliation(s)
- Amanda S. Ackiss
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia
| | - Christopher E. Bird
- Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexas
| | - Yuichi Akita
- Okinawa Prefectural Fisheries Research and Extension CenterItomanOkinawaJapan
| | - Mudjekeewis D. Santos
- Genetic Fingerprinting LaboratoryNational Fisheries Research and Development InstituteQuezon CityPhilippines
| | - Katsunori Tachihara
- Laboratory of Fisheries Biology & Coral Reef Studies, Faculty of ScienceUniversity of the RyukyusRyukyusOkinawaJapan
| | - Kent E. Carpenter
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia
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Local-Level Genetic Diversity and Structure of Matsutake Mushroom (Tricholoma matsutake) Populations in Nagano Prefecture, Japan, Revealed by 15 Microsatellite Markers. J Fungi (Basel) 2017; 3:jof3020023. [PMID: 29371541 PMCID: PMC5715919 DOI: 10.3390/jof3020023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 04/27/2017] [Accepted: 05/08/2017] [Indexed: 11/26/2022] Open
Abstract
The annual yield of matsutake mushrooms (Tricholoma matsutake) has consistently decreased in Japan over the past few decades. We used 15 polymorphic and codominant simple sequence repeat (SSR) markers, developed using next-generation sequencing, to carry out genetic analyses of 10 populations in Nagano, Japan. Using the SSRs, we identified 223 genotypes, none of which was observed in more than one population. The mean expected heterozygosity and standardized allelic richness values were 0.67 and 4.05, respectively. Many alleles appeared in only one of the 10 populations; 34 of these private alleles were detected with a mean number per population of 3.4. The fixation index (FST) and standardized genetic differentiation (G′ST) values were 0.019 and 0.028, respectively. Analysis of molecular variance (AMOVA) showed that the contribution of among population, among genets within a population, and within genets variation to the total variation was 2.91%, 11.62%, and 85.47%, respectively, with genetic differentiation being detected for all sources. Twenty-eight of 45 pairwise FST values were significantly larger than zero, and no pattern of isolation by distance was detected among the 10 populations. Bayesian-based clustering did not show clear differences among populations. These results suggest that reestablishment of a colony would be best accomplished by transplantation within a field; if this is not possible, then transplantation from within several dozen kilometers will cause little damage to the original population genetic structure.
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Population genetic structure of eelgrass (Zostera marina) on the Korean coast: Current status and conservation implications for future management. PLoS One 2017; 12:e0174105. [PMID: 28323864 PMCID: PMC5360257 DOI: 10.1371/journal.pone.0174105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 03/03/2017] [Indexed: 11/19/2022] Open
Abstract
Seagrasses provide numerous ecosystem services for coastal and estuarine environments, such as nursery functions, erosion protection, pollution filtration, and carbon sequestration. Zostera marina (common name “eelgrass”) is one of the seagrass bed-forming species distributed widely in the northern hemisphere, including the Korean Peninsula. Recently, however, there has been a drastic decline in the population size of Z. marina worldwide, including Korea. We examined the current population genetic status of this species on the southern coast of Korea by estimating the levels of genetic diversity and genetic structure of 10 geographic populations using eight nuclear microsatellite markers. The level of genetic diversity was found to be significantly lower for populations on Jeju Island [mean allelic richness (AR) = 1.92, clonal diversity (R) = 0.51], which is located approximately 155 km off the southernmost region of the Korean Peninsula, than for those in the South Sea (mean AR = 2.69, R = 0.82), which is on the southern coast of the mainland. South Korean eelgrass populations were substantially genetically divergent from one another (FST = 0.061–0.573), suggesting that limited contemporary gene flow has been taking place among populations. We also found weak but detectable temporal variation in genetic structure within a site over 10 years. In additional depth comparisons, statistically significant genetic differentiation was observed between shallow (or middle) and deep zones in two of three sites tested. Depleted genetic diversity, small effective population sizes (Ne) and limited connectivity for populations on Jeju Island indicate that these populations may be vulnerable to local extinction under changing environmental conditions, especially given that Jeju Island is one of the fastest warming regions around the world. Overall, our work will inform conservation and restoration efforts, including transplantation for eelgrass populations at the southern tip of the Korean Peninsula, for this ecologically important species.
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