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Cui X, Yang M, Li C, An B, Mu S, Zhang H, Chen Y, Li X, Kang X. Assessment of genetic diversity and population structure of Neocaridina denticulata sinensis in the Baiyangdian drainage area, China, using microsatellite markers and mitochondrial cox1 gene sequences. Gene 2023:147534. [PMID: 37286018 DOI: 10.1016/j.gene.2023.147534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/27/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
Neocaridina denticulata sinensis is a crustacean of major economic significance in the Baiyangdian drainage area. In this study, the first assessment of N. denticulata sinensis genetic diversity and population structure was performed based on sequence analysis of nine polymorphic microsatellite loci and the mitochondrial cytochrome oxidase subunit I (cox1) gene. Samples (n = 192) were collected from four different regions in the Baiyangdian drainage area i.e., Baiyangdian Lake, Jumahe River, Xidayang Reservoir, and Fuhe River. Microsatellite loci analysis identified high levels of genetic diversity represented by observed heterozygosity (Ho) of 0.6865∼0.9583, expected heterozygosity (He) of 0.7151∼0.8723, and polymorphism information content (PIC) of 0.6676∼0.8585. Based on the analysis of cox1 sequences, haplotype diversity (Hd) ranged from 0.568 to 0.853 while nucleotide diversity (π) ranged from 0.0029 to 0.2236. Furthermore, there was no evidence of expansion events in the N. denticulata sinensis populations. Pairwise FST revealed pronounced genetic differentiation, and clustering analyses showed defined genetic structures within the N. denticulata sinensis population. Three groups were identified from four sampled stocks, with Xidayang reservoir, and Fuhe river populations clustered in the same group. This work identified novel molecular markers and provided an important reference to guide management strategies to assist conservation of N. denticulata sinensis resources.
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Affiliation(s)
- Xiaodong Cui
- College of Life Sciences, Hebei University, Baoding, China
| | - Mei Yang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chunyu Li
- College of Life Sciences, Hebei University, Baoding, China
| | - Bo An
- College of Life Sciences, Hebei University, Baoding, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, China
| | - Han Zhang
- College of Life Sciences, Hebei University, Baoding, China
| | - Yongxia Chen
- College of Life Sciences, Hebei University, Baoding, China
| | - Xinzheng Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China.
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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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Decru E, Vranken N, Bragança PHN, Snoeks J, Van Steenberge M. Where ichthyofaunal provinces meet: the fish fauna of the Lake Edward system, East Africa. JOURNAL OF FISH BIOLOGY 2020; 96:1186-1201. [PMID: 31038741 DOI: 10.1111/jfb.13992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
Based on literature, museum collections and three recent expeditions, an annotated species list of the Lake Edward, East Africa, drainage system is presented, excluding the endemic haplochromines. A total of 34 non-Haplochromis species belonging to 10 families and 21 genera are recorded from the system. Three of these are endemic and two others have been introduced in the region. Six species are new records for the Lake Edward system. A species accumulation curve indicates that we probably covered most of the non-Haplochromis species in the area sampled during the recent expeditions, but undetected species might still be present in the Congolese part of the system, which is poorly sampled. A comparison of the species list with those of neighbouring basins confirmed the placement of the Lake Edward system within the east-coast ichthyofaunal province.
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Affiliation(s)
- Eva Decru
- Section Vertebrates, Biology Department, Royal Museum for Central Africa, Tervuren, Belgium
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium
| | - Nathan Vranken
- Section Vertebrates, Biology Department, Royal Museum for Central Africa, Tervuren, Belgium
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium
| | - Pedro H N Bragança
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jos Snoeks
- Section Vertebrates, Biology Department, Royal Museum for Central Africa, Tervuren, Belgium
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium
| | - Maarten Van Steenberge
- Section Vertebrates, Biology Department, Royal Museum for Central Africa, Tervuren, Belgium
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium
- Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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Nneji LM, Adeola AC, Mustapha MK, Oladipo SO, Djagoun CAMS, Nneji IC, Adedeji BE, Olatunde O, Ayoola AO, Okeyoyin AO, Ikhimiukor OO, Useni GF, Iyiola OA, Faturoti EO, Matouke MM, Ndifor WK, Wang YY, Chen J, Wang WZ, Kachi JB, Ugwumba OA, Ugwumba AAA, Nwani CD. DNA Barcoding Silver Butter Catfish (Schilbe intermedius) Reveals Patterns of Mitochondrial Genetic Diversity Across African River Systems. Sci Rep 2020; 10:7097. [PMID: 32341417 PMCID: PMC7184614 DOI: 10.1038/s41598-020-63837-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 04/07/2020] [Indexed: 11/30/2022] Open
Abstract
The silver butter catfish (Schilbe intermedius) is widely distributed across African river systems. To date, information on its mitochondrial genetic diversity, population structure, and historical demography are not well-established. Herein, we combined newly generated mitochondrial cytochrome c oxidase (COI) subunit I gene sequences with previously published COI sequences in the global databases to reconstruct its phylogeography, population genetic structure, and historical demography. Results from the mtDNA phylogeography and species delimitation tests (Cluster algorithm – Species Identifier, Automatic Barcode Gap Discovery and Poison Tree Process model) revealed that S. intermedius comprises at least seven geographically defined matrilines. Although the overall haplotype diversity of S. intermedius was high (h = 0.90), results showed that East (Kenya) and West (Nigeria) African populations had low levels of haplotype diversity (h = ~0.40). In addition, population genetic polymorphism and historical demographics showed that S. intermedius populations in both East and West Africa underwent severe contractions as a result of biogeographic influences. The patterns of genetic diversity and population structure were consistent with adaptive responses to historical biogeographic factors and contemporary environmental variations across African river systems. This is suggestive of the influence of historical biogeographic factors and climatic conditions on population divergence of S. intermedius across African river systems. Given our discovery of previously underappreciated diversity within S. intermedius, we recommend that this species be considered for increased conservation and management.
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Affiliation(s)
- Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China.
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China.
| | - Moshood K Mustapha
- Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Segun O Oladipo
- Department of Biosciences and Biotechnology, College of Pure and Applied Sciences, Kwara State University, Malete, Kwara State, Nigeria
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Ifeanyi C Nneji
- Department of Biological Science, Faculty of Sciences, University of Abuja, Abuja, Nigeria
| | - Babatunde E Adedeji
- Department of Zoology, Faculty of Science, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Omotoso Olatunde
- Department of Zoology, Faculty of Science, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria
| | - Odion O Ikhimiukor
- Department of Microbiology, Faculty of Science, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Oluyinka A Iyiola
- Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Emmanuel O Faturoti
- Department of Aquaculture and Fisheries Management, Faculty of Agriculture, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Moise M Matouke
- Department of Zoology, Faculty of Science, University of Douala, Douala, Cameroon
| | - Wanze K Ndifor
- Department of Zoology, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Yun-Yu Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jing Chen
- Wild Forensic Center, Kunming, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Wild Forensic Center, Kunming, China
| | - Jolly B Kachi
- Department of Biological Science, Faculty of Sciences, Federal University Lokoja, Lokoja, Nigeria
| | - Obih A Ugwumba
- Department of Zoology, Faculty of Science, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adiaha A A Ugwumba
- Department of Zoology, Faculty of Science, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Christopher D Nwani
- Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria.
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Basiita RK, Zenger KR, Jerry DR. Populations genetically rifting within a complex geological system: The case of strong structure and low genetic diversity in the migratory freshwater catfish, Bagrus docmak, in East Africa. Ecol Evol 2017; 7:6172-6187. [PMID: 28861223 PMCID: PMC5574809 DOI: 10.1002/ece3.3153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 03/31/2017] [Accepted: 04/24/2017] [Indexed: 11/18/2022] Open
Abstract
The complex geological history of East Africa has been a driving factor in the rapid evolution of teleost biodiversity. While there is some understanding of how macroevolutionary drivers have shaped teleost speciation in East Africa, there is a paucity of research into how the same biogeographical factors have affected microevolutionary processes within lakes and rivers. To address this deficiency, population genetic diversity, demography, and structure were investigated in a widely distributed and migratory (potamodromous) African teleost species, Ssemutundu (Bagrus docmak). Samples were acquired from five geographical locations in East Africa within two major drainage basins; the Albertine Rift and Lake Victoria Basin. Individuals (N = 175) were genotyped at 12 microsatellite loci and 93 individuals sequenced at the mitochondrial DNA control region. Results suggested populations from Lakes Edward and Victoria had undergone a severe historic bottleneck resulting in very low nucleotide diversity (π = 0.004 and 0.006, respectively) and negatively significant Fu values (-3.769 and -5.049; p < .05). Heterozygosity deficiencies and restricted effective population size (NeLD) suggested contemporary exposure of these populations to stress, consistent with reports of the species decline in the East African Region. High genetic structuring between drainages was detected at both historical (ɸST = 0.62 for mtDNA; p < .001) and contemporary (microsatellite FST = 0.460; p < .001) levels. Patterns of low genetic diversity and strong population structure revealed are consistent with speciation patterns that have been linked to the complex biogeography of East Africa, suggesting that these biogeographical features have operated as both macro- and micro-evolutionary forces in the formation of the East African teleost fauna.
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Affiliation(s)
- Rose Komugisha Basiita
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Marine and Environmental SciencesJames Cook UniversityTownsvilleQldAustralia
- National Agricultural Research OrganizationNational Fisheries Resources Research InstituteAquaculture Research and Development Center KajjansiKampalaUganda
| | - Kyall Richard Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Marine and Environmental SciencesJames Cook UniversityTownsvilleQldAustralia
| | - Dean Robert Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Marine and Environmental SciencesJames Cook UniversityTownsvilleQldAustralia
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