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Makombu JG, Cheruiyot EK, Stomeo F, Thuo DN, Oben PM, Oben BO, Zango P, Mialhe E, Ngueguim JR, Mujibi FDN. Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon. PLoS One 2022; 17:e0263540. [PMID: 36190939 PMCID: PMC9529149 DOI: 10.1371/journal.pone.0263540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/16/2022] [Indexed: 11/07/2022] Open
Abstract
Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: allele frequency differentials, minor allele frequency profiles, and Wright’s Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis, and discriminant analysis of principal components. The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.
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Affiliation(s)
- Judith G. Makombu
- Department of Fisheries and Aquatic Resources Management, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | | | - Francesca Stomeo
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - David N. Thuo
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australia
| | - Pius M. Oben
- Department of Fisheries and Aquatic Resources Management, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | - Benedicta O. Oben
- Department of Fisheries and Aquatic Resources Management, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | - Paul Zango
- Institute of Fisheries and Aquatic Sciences, University of Douala, Yabassi, Cameroon
| | - Eric Mialhe
- Concepto Azul, Cdlavernaza Norte, Guayaquil, Ecuador
| | - Jules R. Ngueguim
- Institute of Agriculture Research for Development (IRAD), Kribi, Cameroon
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Neves JMM, Nolen ZJ, Fabré NN, Mott T, Pereira RJ. Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species. Heredity (Edinb) 2021; 127:323-333. [PMID: 34226671 PMCID: PMC8405619 DOI: 10.1038/s41437-021-00455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 06/18/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.
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Affiliation(s)
- Jessika M M Neves
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil.
| | - Zachary J Nolen
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, Planegg-Martinsried, Germany
- Department of Biology, Lund University, Lund, Sweden
| | - Nidia N Fabré
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Tamí Mott
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, Planegg-Martinsried, Germany.
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Zhou C, Feng M, Tang Y, Yang C, Meng X, Nie G. Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene. Ecol Evol 2021; 11:10502-10514. [PMID: 34367592 PMCID: PMC8328406 DOI: 10.1002/ece3.7855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 01/02/2023] Open
Abstract
Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree-based methods (NJ, ML, and bPTP) and distance-based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p-distances had similar results. Mean K2P distances and p-distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.
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Affiliation(s)
- Chuan‐jiang Zhou
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Meng‐xia Feng
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Yong‐tao Tang
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Chang‐xing Yang
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Xiao‐lin Meng
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Guo‐xing Nie
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
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Mantelatto FL, Pileggi LG, Pantaleão JAF, Magalhães C, Villalobos JL, Álvarez F. Multigene phylogeny and taxonomic revision of American shrimps of the genus Cryphiops Dana, 1852 (Decapoda, Palaemonidae) implies a proposal for reversal of precedence with Macrobrachium Spence Bate, 1868. Zookeys 2021; 1047:155-198. [PMID: 34267596 PMCID: PMC8266795 DOI: 10.3897/zookeys.1047.66933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/15/2021] [Indexed: 11/12/2022] Open
Abstract
The freshwater shrimp genus Cryphiops Dana, 1852 has a disjunct distribution in North (Mexico) and South (Brazil, Chile) America, and is composed of only six species. The current classification of genera in the Palaemonidae is controversial, based on variable morphological characters, and still far from a clear definition. Cryphiops differs from the speciose genus Macrobrachium Spence Bate, 1868 only by the absence of the hepatic spines on the carapace. Previous studies with a limited dataset suggested the necessity to link morphology and phylogeny to create an internal rearrangement in the genus to resolve the paraphyletic status. Through a molecular phylogenetic approach, the evolutionary relationships are inferred based on four (mitochondrial and nuclear) genes, among all recognized species of Cryphiops and, in combination with a taxonomic revision, a rearrangement in the systematics of the genus is suggested. The absence of hepatic spines on the carapace, the only character used to separate the genus Cryphiops, is subjective and should be considered as a homoplasy. This implies that Cryphiops and Macrobrachium are subjective synonyms and, because the latter genus is much more diverse and widely known, with several economically important species, to avoid confusion and disturbance in nomenclatural stability and keep universality, a proposal for the priority of the older synonym (Cryphiops) to be partially suppressed in favor of maintaining the prevailing use of the younger synonym (Macrobrachium) is presented. As the species of Cryphiops should be accommodated in the genus Macrobrachium, new names to replace three preoccupied specific names that, by this action, resulted to be secondary homonyms are offered.
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Affiliation(s)
- Fernando L Mantelatto
- Laboratório de Bioecologia e Sistemática de Crustáceos (LBSC), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil Universidade de São Paulo São Paulo Brazil
| | - Leonardo G Pileggi
- Laboratório de Bioecologia e Sistemática de Crustáceos (LBSC), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil Universidade de São Paulo São Paulo Brazil
| | - João A F Pantaleão
- Laboratório de Bioecologia e Sistemática de Crustáceos (LBSC), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil Universidade de São Paulo São Paulo Brazil
| | - Célio Magalhães
- Laboratório de Bioecologia e Sistemática de Crustáceos (LBSC), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil Universidade de São Paulo São Paulo Brazil.,Instituto Nacional de Pesquisas da Amazônia (INPA) (Retired), Manaus, Amazonas, Brazil Instituto Nacional de Pesquisas da Amazônia Amazonas Brazil
| | - José Luis Villalobos
- Colección Nacional de Crustáceos, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-153, 04510 Ciudad de México, Mexico Universidad Nacional Autónoma de México Mexico Mexico
| | - Fernando Álvarez
- Colección Nacional de Crustáceos, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-153, 04510 Ciudad de México, Mexico Universidad Nacional Autónoma de México Mexico Mexico
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