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Hu S, Xiao S, Yang J, Zhang Z, Zhang K, Zhu Y, Zhang Y. AUV Path Planning Considering Ocean Current Disturbance Based on Cloud Desktop Technology. Sensors (Basel) 2023; 23:7510. [PMID: 37687967 PMCID: PMC10490685 DOI: 10.3390/s23177510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/11/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
In the field of ocean energy detection, Autonomous Underwater Vehicles (AUVs) offer significant advantages in terms of manpower, resource, and energy efficiency. However, the unpredictable nature of the ocean environment, particularly the real-time changes in ocean currents, poses navigational risks for AUVs. Therefore, effective path planning in dynamic environments is crucial for AUVs to perform specific tasks. This paper addresses the static path planning problem and proposes a model called the noise net double DQN network with prioritized experience replay (N-DDQNP). The N-DDQNP model combines a noise network and a prioritized experience replay mechanism to address the limited exploration and slow convergence speed issues of the DQN algorithm, which are caused by the greedy strategy and uniform sampling mechanism. The proposed approach involves constructing a double DQN network with a priority experience replay and an exploration mechanism using the noise network. Second, a compound reward function is formulated to take into account ocean current, distance, and safety factors, ensuring prompt feedback during the training process. Regarding the ocean current, the reward function is designed based on the angle between the current direction and the AUV's heading direction, considering its impact on the AUV's speed. As for the distance factor, the reward is determined by the Euclidean distance between the current position and the target point. Furthermore, the safety factor considers whether the AUV may collide with obstacles. By incorporating these three factors, the compound reward function is established. To evaluate the performance of the N-DDQNP model, experiments were conducted using real ocean data in various complex ocean environments. The results demonstrate that the path planning time of the N-DDQNP model outperforms other algorithms in different ocean current scenarios and obstacle environments. Furthermore, a user console-AUV connection has been established using spice cloud desktop technology. The cloud desktop architecture enables intuitive observation of the AUV's navigation posture and the surrounding marine environment, facilitating safer and more efficient underwater exploration and marine resource detection tasks.
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Affiliation(s)
- Siyuan Hu
- School of Futrue Technology, Tianjin University, Tianjin 300072, China;
| | - Shuai Xiao
- School of Electrical and Information Engineering, Tianjin University, Tianjin 300072, China; (J.Y.); (Y.Z.)
| | - Jiachen Yang
- School of Electrical and Information Engineering, Tianjin University, Tianjin 300072, China; (J.Y.); (Y.Z.)
| | - Zuochen Zhang
- Tianjin Zhuo Lang Technology Development Co., Ltd., Tianjin 300131, China; (Z.Z.); (K.Z.)
| | - Kunyu Zhang
- Tianjin Zhuo Lang Technology Development Co., Ltd., Tianjin 300131, China; (Z.Z.); (K.Z.)
| | - Yong Zhu
- School of Electrical and Information Engineering, Tianjin University, Tianjin 300072, China; (J.Y.); (Y.Z.)
- Tianjin Institute of Software Engineering, Tianjin 300387, China;
| | - Yubo Zhang
- Tianjin Institute of Software Engineering, Tianjin 300387, China;
- School of Software, Tiangong University, Tianjin 300387, China
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Snead AA, Tatarenkov A, Avise JC, Taylor DS, Turner BJ, Marson K, Earley RL. Out to sea: ocean currents and patterns of asymmetric gene flow in an intertidal fish species. Front Genet 2023; 14:1206543. [PMID: 37456662 PMCID: PMC10349204 DOI: 10.3389/fgene.2023.1206543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Passive dispersal via wind or ocean currents can drive asymmetric gene flow, which influences patterns of genetic variation and the capacity of populations to evolve in response to environmental change. The mangrove rivulus fish (Kryptolebias marmoratus), hereafter "rivulus," is an intertidal fish species restricted to the highly fragmented New World mangrove forests of Central America, the Caribbean, the Bahamas, and Florida. Mangrove patches are biological islands with dramatic differences in both abiotic and biotic conditions compared to adjacent habitat. Over 1,000 individual rivulus across 17 populations throughout its range were genotyped at 32 highly polymorphic microsatellites. Range-wide population genetic structure was evaluated with five complementary approaches that found eight distinct population clusters. However, an analysis of molecular variance indicated significant population genetic structure among regions, populations within regions, sampling locations within populations, and individuals within sampling locations, indicating that rivulus has both broad- and fine-scale genetic differentiation. Integrating range-wide genetic data with biophysical modeling based on 10 years of ocean current data showed that ocean currents and the distance between populations over water drive gene flow patterns on broad scales. Directional migration estimates suggested some significant asymmetries in gene flow that also were mediated by ocean currents and distance. Specifically, populations in the center of the range (Florida Keys) were identified as sinks that received migrants (and alleles) from other populations but failed to export individuals. These populations thus harbor genetic variation, perhaps even from extirpated populations across the range, but ocean currents and complex arrangements of landmasses might prevent the distribution of that genetic variation elsewhere. Hence, the inherent asymmetry of ocean currents shown to impact both genetic differentiation and directional migration rates may be responsible for the complex distribution of genetic variation across the range and observed patterns of metapopulation structure.
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Affiliation(s)
- Anthony A. Snead
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - John C. Avise
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | | | - Bruce J. Turner
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Kristine Marson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Ryan L. Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
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Wullenweber N, Hole LR, Ghaffari P, Graves I, Tholo H, Camus L. SailBuoy Ocean Currents: Low-Cost Upper-Layer Ocean Current Measurements. Sensors (Basel) 2022; 22:5553. [PMID: 35898056 DOI: 10.3390/s22155553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 02/01/2023]
Abstract
This study introduces an alternative to the existing methods for measuring ocean currents based on a recently developed technology. The SailBuoy is an unmanned surface vehicle powered by wind and solar panels that can navigate autonomously to predefined waypoints and record velocity profiles using an integrated downward-looking acoustic Doppler current profiler (ADCP). Data collected on two validation campaigns show a satisfactory correlation between the SailBuoy current records and traditional observation techniques such as bottom-mounted and moored current profilers and moored single-point current meter. While the highest correlations were found in tidal signals, strong current, and calm weather conditions, low current speeds and varying high wave and wind conditions reduced correlation considerably. Filtering out some events with the high sea surface roughness associated with high wind and wave conditions may increase the SailBuoy ADCP listening quality and lead to better correlations. Not yet resolved is a systematic offset between the measurements obtained by the SailBuoy and the reference instruments of ±0.03 m/s. Possible reasons are discussed to be the differences between instruments (various products) as well as changes in background noise levels due to environmental conditions.
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Banerjee AK, Feng H, Guo W, Harms NE, Xie H, Liang X, Xing F, Lin Y, Shao H, Guo Z, Ng WL, Huang Y. Glacial vicariance and oceanic circulation shape population structure of the coastal legume Derris trifoliata in the Indo-West Pacific. Am J Bot 2022; 109:1016-1034. [PMID: 35419829 DOI: 10.1002/ajb2.1851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
PREMISE The phylogeography of coastal plant species is shaped by contemporary and historical biogeographic processes. In this study, we aim to decipher the phylogeography of Derris trifoliata, a woody legume of relatively recent origin and wide distribution, in coastal areas in the Indo-West Pacific (IWP) region. METHODS Genetic diversity and population structure were assessed by analyzing six nuclear and three chloroplast DNA sequences from 30 populations across the species' range. Phylogeography was inferred by estimating gene flow, divergence time, historical population size changes, and historical habitat suitability using paleoclimatic niche modeling. RESULTS High genetic diversity was observed at the species level. The populations of three oceanic regions included in this study (i.e., Indian Ocean, South China Sea, and Pacific Ocean) formed distinct clades and likely diverged during the late Pleistocene. Potential barriers to gene flow were identified, including the Sunda and Sahul shelves, geographic distance, and current patterns of oceanic circulation. Analysis of changes in population size supported the bottleneck model, which was strengthened by estimates of habitat suitability across paleoclimatic conditions. CONCLUSIONS The once widespread distribution of D. trifoliata was fragmented by changes in climatic suitability and biogeographic barriers that arose following sea-level changes during the Pleistocene. In addition, contemporary patterns of oceanic circulation and geographic distance between populations appear to maintain genetic differentiation across its distribution in the IWP.
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Affiliation(s)
- Achyut Kumar Banerjee
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Hui Feng
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Wuxia Guo
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
- Department of Bioengineering, Zunyi Medical University, Zhuhai, 519041 Guangdong, China
| | - Nathan E Harms
- US Army Engineer Research and Development Center, Lewisville, TX 75057, USA
| | - Hongxian Xie
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Xinru Liang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Fen Xing
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Yuting Lin
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Huiyu Shao
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Zixiao Guo
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University, Malaysia, 43900 Sepang, Selangor, Malaysia
| | - Yelin Huang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
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Li C, Boswell KM. Estimating Water Transport from Short-Term Vessel-Based and Long-Term Bottom-Mounted Acoustic Doppler Current Profiler Measurements in an Arctic Lagoon Connected to the Beaufort Sea. Sensors (Basel) 2021; 22:s22010068. [PMID: 35009613 PMCID: PMC8747608 DOI: 10.3390/s22010068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 05/25/2023]
Abstract
Acoustic Doppler current profilers (ADCP) are quasi-remote sensing instruments widely used in oceanography to measure velocity profiles continuously. One of the applications is the quantification of land-ocean exchange, which plays a key role in the global cycling of water, heat, and materials. This exchange mostly occurs through estuaries, lagoons, and bays. Studies on the subject thus require that observations of total volume or mass transport can be achieved. Alternatively, numerical modeling is needed for the computation of transport, which, however, also requires that the model is validated properly. Since flows across an estuary, lagoon, or bay are usually non-uniform and point measurements will not be sufficient, continuous measurements across a transect are desired but cannot be performed in the long run due to budget constraints. In this paper, we use a combination of short-term transect-based measurements from a vessel-mounted ADCP and relatively long-term point measurements from a moored ADCP at the bottom to obtain regression coefficients between the transport from the vessel-based observations and the depth-averaged velocity from the bottom-based observations. The method is applied to an Arctic lagoon by using an ADCP mounted on a buoyant platform towed by a small inflatable vessel and another ADCP mounted on a bottom deployed metal frame. The vessel-based measurements were performed continuously for nearly 5 h, which was sufficient to derive a linear regression between the datasets with an R2-value of 0.89. The regression coefficients were in turn applied to the entire time for the moored instrument measurements, which are used in the interpretation of the subtidal transport variations.
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Affiliation(s)
- Chunyan Li
- Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kevin Mershon Boswell
- Institute of Environment, Florida International University, North Miami, FL 33181, USA;
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6
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Du Y, Han K, Zeng X, Ni G. Characterization and comparison of the mitochondrial genomes of the sea star Asterias amurensis (Echinodermata: Asteroidea) in East Asia. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:212-219. [PMID: 37916612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
The starfish Asterias amurensis is a marine pest native to the northwestern Pacific and has successfully invaded southern Australia. Asterias amurensis have caused substantial environmental and economic impacts in both native and non-native regions. However, little information is available about the genetic features of its native populations, especially for those in North China. Here we sequenced the complete mitochondrial genomes of five individuals from different locations in China and compared their characteristics with three mitogenomes available from Japan. Multiple analyses and comparisons revealed little difference in the gene composition, gene order, codon usage, and nucleotide content among the eight mitogenomes. However, intraspecific phylogenetic reconstruction unveiled two divergent lineages between specimens from North China plus Ushimado (Seto Inland Sea, Japan) and northern Japan (Asamushi and Onagawa). This conclusion was backed by an analysis of pairwise genetic distances, which showed that individuals from different lineages had relatively higher values (all above 2%). Based on knowledge of paleoenvironmental and tectonic activity in the northwestern Pacific, the two lineages might have originated during the Early Pliocene due to the isolation of the East China Sea from the Japan Sea/East Sea during that time, while the present-day distribution of these lineages have likely been influenced by the ocean current system.
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Affiliation(s)
- Yanzhen Du
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, China
| | - Kangkang Han
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, China
| | - Xiaoqi Zeng
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Gang Ni
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, China
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7
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Wang M, Ma Y, Cai L, Tedersoo L, Bahram M, Burgaud G, Long X, Zhang S, Li W. Seasonal dynamics of mycoplankton in the Yellow Sea reflect the combined effect of riverine inputs and hydrographic conditions. Mol Ecol 2021; 30:3624-3637. [PMID: 34002437 DOI: 10.1111/mec.15986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022]
Abstract
Little is known about how multiple factors including land-based inputs and ocean currents affect the spatiotemporal distribution of the mycoplankton in coastal regions. To explore the seasonal changes of mycoplanktonic communities and potential environmental drivers, we collected water samples from the Yellow Sea, used here as a model for subtropical sea habitats, in different seasons over two years. Compared with winter and spring, summer exhibited higher levels of fungal richness and community heterogeneity in the water column. The seasonal shifts in mycoplankton diversity and community composition were mainly ascribed to freshwater inputs, the Cold Water Mass and invasion of the Yellow Sea Warm Current. Among the physicochemical variables tested, temperature was the primary determinant of fungal diversity and showed contrasting influences on fungal richness in the surface and bottom waters during summer. In addition, we provide evidence for the community similarity and dissolved nutrients of different water bodies to highlight the potential origin of the Cold Water Mass. Our findings bring new understanding on the factors determining the dynamics of mycoplankton communities by modelling the influence of physicochemical variables and tracking the geographical distribution of certain fungal taxa.
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Affiliation(s)
- Mengmeng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yiyuan Ma
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gaëtan Burgaud
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Université de Brest, Plouzané, France
| | - Xuedan Long
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shoumei Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Geng Q, Wang Z, Tao J, Kimura MK, Liu H, Hogetsu T, Lian C. Ocean Currents Drove Genetic Structure of Seven Dominant Mangrove Species Along the Coastlines of Southern China. Front Genet 2021; 12:615911. [PMID: 33763110 PMCID: PMC7982666 DOI: 10.3389/fgene.2021.615911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
Mangrove forest ecosystems, which provide important ecological services for marine environments and human activities, are being destroyed worldwide at an alarming rate. The objective of our study was to use molecular data and analytical techniques to separate the effects of historical and contemporary processes on the distribution of mangroves and patterns of population genetic differentiation. Seven mangrove species (Acanthus ilicifolius, Aegiceras corniculatum, Avicennia marina, Bruguiera gymnorrhiza, Kandelia obovata, Lumnitzera racemosa, and Rhizophora stylosa), which are predominant along the coastlines of South China, were genotyped at nuclear (nSSR) and chloroplast (cpSSR) microsatellite markers. We estimated historical and contemporary gene flow, the genetic diversity and population structure of seven mangrove species in China. All of these seven species exhibited few haplotypes, low levels of genetic diversity (H E = 0.160-0.361, with the exception of K. obovata) and high levels of inbreeding (F IS = 0.104-0.637), which may be due to their marginal geographical distribution, human-driven and natural stressors on habitat loss and fragmentation. The distribution patterns of haplotypes and population genetic structures of seven mangrove species in China suggest historical connectivity between populations over a large geographic area. In contrast, significant genetic differentiation [F ST = 0.165-0.629 (nSSR); G ST = 0.173-0.923 (cpSSR)] indicates that populations of mangroves are isolated from one another with low levels of contemporary gene flow among populations. Our results suggest that populations of mangroves were historically more widely inter-connected and have recently been isolated, likely through a combination of ocean currents and human activities. In addition, genetic admixture in Beibu Gulf populations and populations surrounding Hainan Island and southern mainland China were attributed to asymmetric gene flow along prevailing oceanic currents in China in historical times. Even ocean currents promote genetic exchanges among mangrove populations, which are still unable to offset the effects of natural and anthropogenic fragmentation. The recent isolation and lack of gene flow among populations of mangroves may affect their long-term survival along the coastlines of South China. Our study enhances the understanding of oceanic currents contributing to population connectivity, and the effects of anthropogenic and natural habitat fragmentation on mangroves, thereby informing future conservation efforts and seascape genetics toward mangroves.
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Affiliation(s)
- Qifang Geng
- School of Life Sciences, Nanjing University, Nanjing, China
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
| | | | - Jianmin Tao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Megumi K. Kimura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Ibaraki, Japan
| | - Hong Liu
- Department of Earth and Environment, Florida International University, Miami, FL, United States
| | - Taizo Hogetsu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Chunlan Lian
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
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Harrison CS, Luo JY, Putman NF, Li Q, Sheevam P, Krumhardt K, Stevens J, Long MC. Identifying global favourable habitat for early juvenile loggerhead sea turtles. J R Soc Interface 2021; 18:20200799. [PMID: 33622144 DOI: 10.1098/rsif.2020.0799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Loggerhead sea turtles (Caretta caretta) nest globally on sandy beaches, with hatchlings dispersing into the open ocean. Where these juveniles go and what habitat they rely on remains a critical research question for informing conservation priorities. Here a high-resolution Earth system model is used to determine the biophysical geography of favourable ocean habitat for loggerhead sea turtles globally during their first year of life on the basis of ocean current transport, thermal constraints and food availability (defined here as the summed lower trophic level carbon biomass). Dispersal is simulated from eight major nesting sites distributed across the globe in four representative years using particle tracking. Dispersal densities are identified for all turtles, and for the top 15% 'best-fed' turtles that have not encountered metabolically unfavourable temperatures. We find that, globally, rookeries are positioned to disperse to regions where the lower trophic biomass is greatest within loggerheads' thermal range. Six out of the eight nesting sites are associated with strong coastal boundary currents that rapidly transport hatchlings to subtropical-subpolar gyre boundaries; narrow spatial migratory corridors exist for 'best-fed' turtles associated with these sites. Two other rookeries are located in exceptionally high-biomass tropical regions fuelled by natural iron fertilization. 'Best-fed' turtles tend to be associated with lower temperatures, highlighting the inverse relationship between temperature and lower trophic biomass. The annual mean isotherms between 20°C and the thermal tolerance of juvenile loggerheads are a rough proxy for favourable habitat for loggerheads from rookeries associated with boundary currents. Our results can be used to constrain regions for conservation efforts for each subpopulation, and better identify foraging habitat for this critical early life stage.
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Affiliation(s)
- Cheryl S Harrison
- National Center for Atmospheric Research, Boulder, CO 80305, USA.,Institute of Alpine and Arctic Research, University of Colorado, Boulder, CO 80303, USA.,School of Earth Environmental and Marine Science, University of Texas, Rio Grande Valley, Port Isabel, TX 78578, USA
| | - Jessica Y Luo
- National Center for Atmospheric Research, Boulder, CO 80305, USA.,NOAA Geophysical Fluid Dynamics Laboratory, Princeton, NJ 08540, USA
| | | | | | - Pooja Sheevam
- Institute of Alpine and Arctic Research, University of Colorado, Boulder, CO 80303, USA.,Department of Geological Sciences and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Kristen Krumhardt
- National Center for Atmospheric Research, Boulder, CO 80305, USA.,Institute of Alpine and Arctic Research, University of Colorado, Boulder, CO 80303, USA
| | - Jessica Stevens
- School of Earth Environmental and Marine Science, University of Texas, Rio Grande Valley, Port Isabel, TX 78578, USA
| | - Matthew C Long
- National Center for Atmospheric Research, Boulder, CO 80305, USA
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10
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Jahnke M, Gullström M, Larsson J, Asplund ME, Mgeleka S, Silas MO, Hoamby A, Mahafina J, Nordlund LM. Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents. Ecol Evol 2019; 9:8953-8964. [PMID: 31462994 PMCID: PMC6706205 DOI: 10.1002/ece3.5420] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/24/2019] [Accepted: 06/08/2019] [Indexed: 01/04/2023] Open
Abstract
This study is the first large-scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4-26°S and 33-48°E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale-across national borders.
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Affiliation(s)
- Marlene Jahnke
- Department of Marine Sciences—TjärnöUniversity of GothenburgStrömstadSweden
- Groningen Institute for Evolutionary Life Sciences, Section: Ecology and Evolutionary Genomics in Nature (GREEN)University of GroningenGroningenThe Netherlands
| | - Martin Gullström
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Josefine Larsson
- School of Natural Science, Technology and Environmental StudiesSödertörn UniversityStockholmSweden
| | - Maria E. Asplund
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Lovén CentreUniversity of GothenburgGothenburgSweden
| | - Said Mgeleka
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Tanzania Fisheries Research Institute (TAFIRI)Dar es SalaamTanzania
| | - Mathew Ogalo Silas
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Tanzania Fisheries Research Institute (TAFIRI)Dar es SalaamTanzania
| | - Arielle Hoamby
- Institut Halieutique et des Science Marine Toliara (IH.SM)ToliaraMadagascar
| | - Jamal Mahafina
- Institut Halieutique et des Science Marine Toliara (IH.SM)ToliaraMadagascar
| | - Lina Mtwana Nordlund
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Department of Earth SciencesUppsala UniversityVisbySweden
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Han Z, Wang Z, Gao T, Yanagimoto T, Iida K. Assessing the Speciation of a Cold Water Species, Japanese Sand Lance Ammodytes personatus, in the Northwestern Pacific by AFLP Markers. Animals (Basel) 2018; 8:ani8120224. [PMID: 30487407 PMCID: PMC6316128 DOI: 10.3390/ani8120224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/11/2018] [Accepted: 11/23/2018] [Indexed: 11/16/2022] Open
Abstract
The use of molecular techniques in biodiversity research increasingly results in the recognition of multiple divergent mitochondrial DNA (mtDNA) lineages below the morphospecies level. However, the overlapping distribution of multiple divergent lineages raises the question of whether some of these lineages are in fact cryptic species. Assessing the status of these divergent lineages, delimiting evolutionarily significant units (ESUs), and identifying the dominant evolutionary and ecological drivers are critical components of successful wildlife conservation and management strategies. Amplified fragment length polymorphism (AFLP) markers were applied to characterize the phylogeography pattern of a cold water species, the Japanese sand lance Ammodytes personatus, in warm and cold ocean currents. A total of 211 individuals sampled from 12 populations through the species' range, including samples from Kuroshio Current, Oyashio Current, Tsushima Current, and Yellow Sea, were analyzed. The Bayesian assignment probability test and Neighbor joining (NJ) analysis divided these populations into two genetically and geographically distinct clades (northern and southern clades) characterized by different sea surface temperatures. The incongruence between nuclear clades and previous mitochondrial lineages suggested that A. personatus is indeed composed of at least two genetically divergent cryptic species. Pleistocene glaciation isolation after secondary contact, local thermal adaptation, and isolation by distance may explain the observed geographic pattern of two cryptic species and genetic structure within clades.
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Affiliation(s)
- Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Zhiyong Wang
- Fishery College, Jimei University, Xiamen 361021, China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Takashi Yanagimoto
- National Research Institute of Fisheries Science, Yokohama 236-8648, Japan.
| | - Koji Iida
- Faculty of Fisheries, Hokkaido University, Hakodate 041-8611, Japan.
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12
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Wu ZY, Liu J, Provan J, Wang H, Chen CJ, Cadotte MW, Luo YH, Amorim BS, Li DZ, Milne RI. Testing Darwin's transoceanic dispersal hypothesis for the inland nettle family (Urticaceae). Ecol Lett 2018; 21:1515-1529. [PMID: 30133154 DOI: 10.1111/ele.13132] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/11/2018] [Accepted: 07/05/2018] [Indexed: 12/17/2022]
Abstract
Dispersal is a fundamental ecological process, yet demonstrating the occurrence and importance of long-distance dispersal (LDD) remains difficult, having rarely been examined for widespread, non-coastal plants. To address this issue, we integrated phylogenetic, molecular dating, biogeographical, ecological, seed biology and oceanographic data for the inland Urticaceae. We found that Urticaceae originated in Eurasia c. 69 Ma, followed by ≥ 92 LDD events between landmasses. Under experimental conditions, seeds of many Urticaceae floated for > 220 days, and remained viable after 10 months in seawater, long enough for most detected LDD events, according to oceanographic current modelling. Ecological traits analyses indicated that preferences for disturbed habitats might facilitate LDD. Nearly half of all LDD events involved dioecious taxa, so population establishment in dioecious Urticaceae requires multiple seeds, or occasional selfing. Our work shows that seawater LDD played an important role in shaping the geographical distributions of Urticaceae, providing empirical evidence for Darwin's transoceanic dispersal hypothesis.
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Affiliation(s)
- Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jie Liu
- Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jim Provan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Hong Wang
- Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Chia-Jui Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.,Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Ya-Huang Luo
- Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Bruno S Amorim
- Graduate Program in Biotechnology and Natural Resources, School of Health Sciences, State University of Amazonas, CEP, 69065-001, Manaus-AM, Brazil
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
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Fujita J, Drumm DT, Iguchi A, Ueda Y, Yamashita Y, Ito M, Tominaga O, Kai Y, Ueno M, Yamashita Y. Deep-Sea Phylogeographic Structure Shaped by Paleoenvironmental Changes and Ongoing Ocean Currents Around the Sea of Japan in a Crangonid Shrimp, Argis lar. Zoolog Sci 2017; 34:406-413. [PMID: 28990468 DOI: 10.2108/zs170014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The deep-sea crangonid shrimp, Argis lar, is a highly abundant species from the northern Pacific Ocean. We investigated its phylogeographic and demographic structure across the species' extensive range, using mitochondrial DNA sequence variation to evaluate the impact of deep-sea paleoenvironmental dynamics in the Sea of Japan on population histories. The haplotype network detected three distinct lineages with allopatric isolation, which roughly corresponded to the Sea of Japan (Lineage A), the northwestern Pacific off the Japanese Archipelago (Lineage B), and the Bering Sea/Gulf of Alaska (Lineage C). Lineage A showed relatively low haplotype and nucleotide diversity, a significantly negative value of Tajima's D, and a star-shaped network, suggesting that anoxic bottom-water in the Sea of Japan over the last glacial period may have brought about a reduction in the Sea of Japan population. Furthermore, unexpectedly, the distributions of Lineage A and B were closely related to the pathways of the two ocean currents, especially along the Sanriku Coast. This result indicated that A. lar could disperse across shallow straits through the ocean current, despite their deep-sea adult habitat. Bayesian inference of divergence time revealed that A. lar separated into three lineages approximately 1 million years before present (BP) in the Pleistocene, and then had been influenced by deep-sea paleoenvironmental change in the Sea of Japan during the last glacial period, followed by a more recent larval dispersal with the ocean current since ca. 6 kilo years BP.
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Affiliation(s)
- Junta Fujita
- 1 Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086, Japan
| | | | - Akira Iguchi
- 3 Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago, Okinawa 905-2192, Japan
| | - Yuji Ueda
- 4 Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Niigata 951-8121, Japan
| | - Yuho Yamashita
- 5 Kushiro Station, Hokkaido National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido 085-0802, Japan
| | - Masaki Ito
- 6 Hachinohe Station, Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Hachinohe, Aomori 031-0841, Japan
| | - Osamu Tominaga
- 7 Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui 917-0003, Japan
| | - Yoshiaki Kai
- 1 Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086, Japan
| | - Masahiro Ueno
- 1 Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086, Japan
| | - Yoh Yamashita
- 1 Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086, Japan
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Han Z, Zheng W, Chen G, Shui B, Liu S, Zhuang Z. Population genetic structure and larval dispersal strategy of portunid crab Charybdis bimaculata in Yellow sea and East China sea. Mitochondrial DNA 2013; 26:402-8. [PMID: 24117187 DOI: 10.3109/19401736.2013.840592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Larval dispersal may have an important effect on genetic structure of benthic species. However, different species may choose different larval dispersal strategy. To examine the population genetic structure and larval dispersal strategy of portunid crab Charybdis bimaculata, a 658 base pair (bp) fragment of mtDNA COI gene was sequenced in this species. In total, 67 individuals were collected from 5 locations in Yellow Sea and East China, and 24 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the five populations ranged from 0.2000 ± 0.1541 (Zhoushan) to 0.8333 ± 0.1265 (Nanji island), and from 0.0003 ± 0.0005 (Zhoushan) to 0.0026 ± 0.0019 (Nanji island). Analysis of molecular variance and pairwise FST revealed no significant differentiation between the Yellow Sea and the East China Sea in C. bimaculata, supporting high larval dispersal ability in this species, rejecting larval retention. Mismatch distribution revealed that C. bimaculata had undergone population expansion. Larval drift in the ocean currents, and recent range expansion could be the reasons for little genetic structure in the studied area.
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Affiliation(s)
- Zhiqiang Han
- Fishery College, Zhejiang Ocean University , Zhoushan , China
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Ujiié Y, Asami T, de Garidel-Thoron T, Liu H, Ishitani Y, de Vargas C. Longitudinal differentiation among pelagic populations in a planktic foraminifer. Ecol Evol 2012; 2:1725-37. [PMID: 22957176 PMCID: PMC3434911 DOI: 10.1002/ece3.286] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/28/2012] [Accepted: 05/01/2012] [Indexed: 11/24/2022] Open
Abstract
Evolutionary processes in marine plankton have been assumed to be dependent on the oceanic circulation system, which transports plankton between populations in marine surface waters. Gene flow facilitated by oceanic currents along longitudinal gradients may efficiently impede genetic differentiation of pelagic populations in the absence of confounding marine environmental effects. However, how responsible oceanic currents are for the geographic distribution and dispersal of plankton is poorly understood. We examined the phylogeography of the planktic foraminifer Pulleniatina obliquiloculata in the Indo-Pacific Warm Pool (IPWP) by using partial small subunit ribosomal DNA (SSU rDNA) sequences. We found longitudinal clines in the frequencies of three distinct genetic types in the IPWP area. These frequencies were correlated with environmental factors that are characteristic of three water masses in the IPWP. Noteworthy, populations inhabiting longitudinally distant water masses at the Pacific and Indian sides of the IPWP were genetically different, despite transportation of individuals via oceanic currents. These results demonstrate that populations of pelagic plankton have diverged genetically among different water masses within a single climate zone. Changes of the oceanic circulation system could have impacted the geographic patterns of dispersal and divergence of pelagic plankton.
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Affiliation(s)
- Yurika Ujiié
- Center for Advanced Marine Core Research, Kochi UniversityKochi 783-8502, Japan
| | - Takahiro Asami
- Department of Biology, Shinshu UniversityMatsumoto 390-8621, Japan
| | - Thibault de Garidel-Thoron
- CEREGE, CNRS, Aix-Marseille Université, IRD, Technopôle de l’Arbois-MéditerannéeBP80, 13545 Aix-en-Provence Cedex, France
| | - Hui Liu
- Institute of Marine and Coastal Sciences, Rutgers UniversityNew Brunswick, New Jersey 08901
| | - Yoshiyuki Ishitani
- Japan Agency for Marine-Earth Science and TechnologyYokosuka 237-0061, Japan
| | - Colomban de Vargas
- UMR CNRS 7144 Evolution du Plancton et PaleOceansStation Biologique, BP74, 29682 Roscoff, France
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