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Krueger-Hadfield SA. Let's talk about sex: Why reproductive systems matter for understanding algae. JOURNAL OF PHYCOLOGY 2024; 60:581-597. [PMID: 38743848 DOI: 10.1111/jpy.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Sex is a crucial process that has molecular, genetic, cellular, organismal, and population-level consequences for eukaryotic evolution. Eukaryotic life cycles are composed of alternating haploid and diploid phases but are constrained by the need to accommodate the phenotypes of these different phases. Critical gaps in our understanding of evolutionary drivers of the diversity in algae life cycles include how selection acts to stabilize and change features of the life cycle. Moreover, most eukaryotes are partially clonal, engaging in both sexual and asexual reproduction. Yet, our understanding of the variation in their reproductive systems is largely based on sexual reproduction in animals or angiosperms. The relative balance of sexual versus asexual reproduction not only controls but also is in turn controlled by standing genetic variability, thereby shaping evolutionary trajectories. Thus, we must quantitatively assess the consequences of the variation in life cycles on reproductive systems. Algae are a polyphyletic group spread across many of the major eukaryotic lineages, providing powerful models by which to resolve this knowledge gap. There is, however, an alarming lack of data about the population genetics of most algae and, therefore, the relative frequency of sexual versus asexual processes. For many algae, the occurrence of sexual reproduction is unknown, observations have been lost in overlooked papers, or data on population genetics do not yet exist. This greatly restricts our ability to forecast the consequences of climate change on algal populations inhabiting terrestrial, aquatic, and marine ecosystems. This perspective summarizes our extant knowledge and provides some future directions to pursue broadly across micro- and macroalgal species.
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Delord C, Petit EJ, Blanchet S, Longin G, Rinaldo R, Vigouroux R, Roussel JM, Le Bail PY, Launey S. Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value. Heredity (Edinb) 2023; 131:1-14. [PMID: 37185615 PMCID: PMC10313816 DOI: 10.1038/s41437-023-00616-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
Spatial patterns of genetic variation compared across species provide information about the predictability of genetic diversity in natural populations, and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni- a major river system from the Guiana Shield -, to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, the mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as gold mining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow, and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.
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Affiliation(s)
- Chrystelle Delord
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 35042, Rennes, France.
- HYDRECO Guyane SARL, Laboratoire-Environnement de Petit Saut, 97310, Kourou, France.
- UMR MARBEC, Univ. Montpellier, IRD, Ifremer, CNRS, Sète, France.
| | - Eric J Petit
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 35042, Rennes, France
| | - Simon Blanchet
- CNRS, Station d'Ecologie Théorique et Expérimentale, UAR, 2029, Moulis, France
| | | | | | - Régis Vigouroux
- HYDRECO Guyane SARL, Laboratoire-Environnement de Petit Saut, 97310, Kourou, France
| | - Jean-Marc Roussel
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 35042, Rennes, France
| | | | - Sophie Launey
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 35042, Rennes, France
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Sooriyabandara MGC, Jayasundara JMSM, Marasinghe MSLRP, Hathurusinghe HABM, Bandaranayake AU, Jayawardane KANC, Nilanthi RMR, Rajapakse RC, Bandaranayake PCG. Genetic features of Sri Lankan elephant, Elephas maximus maximus Linnaeus revealed by high throughput sequencing of mitogenome and ddRAD-seq. PLoS One 2023; 18:e0285572. [PMID: 37310948 DOI: 10.1371/journal.pone.0285572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/26/2023] [Indexed: 06/15/2023] Open
Abstract
Elephas maximus maximus Linnaeus, the Sri Lankan subspecies is the largest and the darkest among Asian elephants. Patches of depigmented areas with no skin color on the ears, face, trunk, and belly morphologically differentiate it from the others. The elephant population in Sri Lanka is now limited to smaller areas and protected under Sri Lankan law. Despite its ecological and evolutionary importance, the relationship between Sri Lankan elephants and their phylogenetic position among Asian elephants remains controversial. While identifying genetic diversity is the key to any conservation and management strategies, limited data is currently available. To address such issues, we analyzed 24 elephants with known parental lineages with high throughput ddRAD-seq. The mitogenome suggested the coalescence time of the Sri Lankan elephant at ~0.2 million years, and sister to Myanmar elephants supporting the hypothesis of the movement of elephants in Eurasia. The ddRAD-seq approach identified 50,490 genome-wide SNPs among Sri Lankan elephants. The genetic diversity within Sri Lankan elephants assessed with identified SNPs suggests a geographical differentiation resulting in three main clusters; north-eastern, mid-latitude, and southern regions. Interestingly, though it was believed that elephants from the Sinharaja rainforest are of an isolated population, the ddRAD-based genetic analysis clustered it with the north-eastern elephants. The effect of habitat fragmentation on genetic diversity could be further assessed with more samples with specific SNPs identified in the current study.
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Affiliation(s)
| | - J M S M Jayasundara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - H A B M Hathurusinghe
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - A U Bandaranayake
- Department of Computer Engineering, Faculty of Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - R M R Nilanthi
- Department of Wildlife Conservation, Battaramulla, Sri Lanka
| | - R C Rajapakse
- Department of National Zoological Gardens, Anagarika Dharmapala Mawatha, Dehiwala, Sri Lanka
| | - P C G Bandaranayake
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
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4
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Osmond DR, King RA, Stockley B, Launey S, Stevens JR. A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales. JOURNAL OF FISH BIOLOGY 2023; 102:258-270. [PMID: 36281821 DOI: 10.1111/jfb.15258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.
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Affiliation(s)
- Daniel R Osmond
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - R Andrew King
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - Bruce Stockley
- Westcountry Rivers Trust, Rain-Charm House, Cornwall, UK
| | - Sophie Launey
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRAe, Rennes, France
| | - Jamie R Stevens
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
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Marasinghe MSLRP, Nilanthi RMR, Hathurusinghe HABM, Sooriyabandara MGC, Chandrasekara CHWMRB, Jayawardana KANC, Kodagoda MM, Rajapakse RC, Bandaranayake PCG. Revisiting traditional SSR based methodologies available for elephant genetic studies. Sci Rep 2021; 11:8718. [PMID: 33888797 PMCID: PMC8062488 DOI: 10.1038/s41598-021-88034-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants' dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.
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Affiliation(s)
- M S L R P Marasinghe
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - R M R Nilanthi
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - H A B M Hathurusinghe
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - M G C Sooriyabandara
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - C H W M R B Chandrasekara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - K A N C Jayawardana
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - M M Kodagoda
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - R C Rajapakse
- Department of National Zoological Gardens, Anagarika Dharmapala Mawatha, Dehiwala, 10350, Sri Lanka
| | - P C G Bandaranayake
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka.
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Blanchet S, Prunier JG, Paz‐Vinas I, Saint‐Pé K, Rey O, Raffard A, Mathieu‐Bégné E, Loot G, Fourtune L, Dubut V. A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks. Evol Appl 2020; 13:1195-1213. [PMID: 32684955 PMCID: PMC7359825 DOI: 10.1111/eva.12941] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 01/01/2023] Open
Abstract
Rivers are fascinating ecosystems in which the eco-evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last 10 years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from southern France, and we broadened the scope of our findings using experiments, meta-analyses, and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that-in the studied river systems-stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity-ecosystem function relationships, and the setting of reliable conservation plans.
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Affiliation(s)
- Simon Blanchet
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Jérôme G. Prunier
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
| | - Ivan Paz‐Vinas
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- Laboratoire Ecologie Fonctionnelle et EnvironnementUniversité de ToulouseUPSCNRSINPUMR‐5245 ECOLABToulouseFrance
| | - Keoni Saint‐Pé
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Olivier Rey
- IHPEUniv. MontpellierCNRSIfremerUniv. Perpignan Via DomitiaPerpignanFrance
| | - Allan Raffard
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
| | - Eglantine Mathieu‐Bégné
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- IHPEUniv. MontpellierCNRSIfremerUniv. Perpignan Via DomitiaPerpignanFrance
| | - Géraldine Loot
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Lisa Fourtune
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- PEIRENEEA 7500Université de LimogesLimogesFrance
| | - Vincent Dubut
- Aix Marseille UniversitéCNRSIRDAvignon UniversitéIMBEMarseilleFrance
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7
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Lange A, Paris JR, Gharbi K, Cézard T, Miyagawa S, Iguchi T, Studholme DJ, Tyler CR. A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus). Mol Ecol Resour 2020; 20:1007-1022. [PMID: 32293100 DOI: 10.1111/1755-0998.13166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/19/2020] [Accepted: 04/08/2020] [Indexed: 01/14/2023]
Abstract
Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach it has not been possible to confirm whether intersex fish in the wild arise from genetic males or females, or whether sex reversal occurs in the wild, as this condition can be induced experimentally in controlled exposures to WwTW effluents and a steroidal oestrogen. Using restriction site-associated DNA sequencing (RAD-seq), we identified a candidate for a genetic sex marker and validated this marker as a sex probe through PCR analyses of samples from wild roach populations from nonpolluted rivers. We also applied the sex marker to samples from roach exposed experimentally to oestrogen and oestrogenic effluents to confirm suspected phenotypic sex reversal from males to females in some treatments, and also that sex-reversed males are able to breed as females. We then show, unequivocally, that intersex in wild roach populations results from feminisation of males, but find no strong evidence for complete sex reversal in wild roach at river sites contaminated with oestrogens. The discovered marker has utility for studies in roach on chemical effects, wild stock assessments, and reducing the number of fish used where only one sex is required for experimentation. Furthermore, we show that the marker can be applied nondestructively using a fin clip or skin swab, with animal welfare benefits.
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Affiliation(s)
- Anke Lange
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Josephine R Paris
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Karim Gharbi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Timothée Cézard
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Shinichi Miyagawa
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - David J Studholme
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
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Dang BT, Rahman MA, Tran SQ, Glenner H. Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline. PLoS One 2019; 14:e0224473. [PMID: 31689298 PMCID: PMC6830773 DOI: 10.1371/journal.pone.0224473] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 10/15/2019] [Indexed: 11/19/2022] Open
Abstract
The blue swimming crab (Portunus pelagicus Linnaeus, 1758) is one of the commercially exploited crab fishery resources in Vietnam. This is the first study to provide a broad survey of genetic diversity, population structure and migration patterns of P. pelagicus along the Vietnamese coastline. The crab samples were collected from northern, central and southern Vietnam. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 32 outlier loci, 306 putatively neutral SNPs from 96 individuals were used to assess fine-scale population structure of blue swimming crab. The mean observed heterozygosity (Ho) and expected heterozygosity (He) per locus was 0.196 and 0.223, respectively. Pairwise Fst and hierarchical AMOVA supported significant differentiation of central and northern from southern populations (P<0.01). Population structure analyses revealed that P. pelagicus in the south is a separate fisheries unit from the north and center. Contemporary migration patterns supported high migration between northern and central populations and restricted genetic exchange within the southern population. In contrast, historic gene flow provides strong evidence for single panmictic population. The results are useful for understanding current status of P. pelagicus in the wild under an environment changing due to natural and anthropogenic stresses, with implications for fisheries management.
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Affiliation(s)
- Binh Thuy Dang
- Department of Biology, Institute for Biotechnology and Environment, Nha Trang University, Nha Trang City, Vietnam
| | - Muhammad Arifur Rahman
- Department of Biology, Institute for Biotechnology and Environment, Nha Trang University, Nha Trang City, Vietnam
- Department of Graduate Studies, Nha Trang University, Nha Trang City, Vietnam
| | - Sang Quang Tran
- Department of Biology, Institute for Biotechnology and Environment, Nha Trang University, Nha Trang City, Vietnam
| | - Henrik Glenner
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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