Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin

Martínez, José Gregório; Rangel-Medrano, José David; Yepes-Acevedo, Anny Johanna; Restrepo-Escobar, Natalia; Márquez, Edna J.

doi:10.1016/j.ympev.2022.107517

Cited by 5 publications

(4 citation statements)

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“…The database analyzed in the present study included 83 COI sequences of Pimelodus specimens collected during previous studies in a number of different South American basins ( Supplementary Table S2 ). These areas include the Maroni River [ 26 ], the basin of the Magdalena–Cauca and Orinoco Rivers [ 23 ], the Amazon River [ 27 , 28 ], the São Francisco River [ 29 , 30 ], the Paraíba do Sul River [ 31 ], the Paraguay River [ 32 ], the upper and lower Paraná basins [ 33 , 34 , 35 , 36 ], and the plains of the Argentinian Pampa [ 37 ]. In all these cases, the taxonomic identification of the species followed the original denomination presented in the respective study.…”

Section: Methodsmentioning

confidence: 99%

“…A recent study of Pimelodus , based on the use of molecular markers, confirmed the existence of two independent evolutionary lineages from the trans-Andean region, which were described as new species [ 23 ]. Studies of this type are still limited in the Brazilian Northeast, however, and most of the Pimelodus taxa known to occur in the hydrographic basins of the state of Maranhão have been catalogued based solely on classical taxonomic criteria [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae)

Limeira Filho,

França,

Costa

et al. 2024

Biology

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Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae)

Limeira Filho,

França,

Costa

et al. 2024

Biology

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“…Intraspeci lineage inference for C. arabica was carried out using the Single-locus Species-Discovery (SLSD) approach (Machado et al 2018) and the modi ed methodology of Martínez et al (2022), with the ITS dataset. For this purpose, we ran a Bayesian phylogenetic analysis in BEAST v2.5.0 (Bouckaert et al 2019), the best-t evolutionary model inferred in jModelTest was HKY + G (Posada 2008), a "Strict Clock" model and a "Birth-Death Process" were determined as tree prior.…”

Section: Phylogenetic Diversity Analysismentioning

confidence: 99%

Molecular evidence about ancestral origin, colonization patterns, and phylogenetic diversity of Coffea arabica, with insights in Latin America

Chica-Acosta

Aristizábal

González-Rivera

et al. 2023

Preprint

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Coffee is one of the most widely consumed agricultural products worldwide. The most well-known coffee species in the market are Coffea arabica and Coffea canephora. Currently, 42 varieties are recognized within C. arabica, but strangely, with very low levels of intraspecific genetic diversity despite its worldwide geographical distribution. In addition, little is known about its phylogeographical history. Although there exist descriptive hypotheses of worldwide colonization patterns and origin for C. arabica (by Ferreira et al. in 2019), none of them are molecularly supported. In this study, data mining and bioinformatic approaches, allowing to collect DNA sequences of the Internal Transcribed Spacer (ITS) region available up to date. All sequences were analyzed under the Relaxed-Random-Walk (RRW) methodology, aiming to estimate ancestral areas and spatiotemporal dispersion patterns, with South American insights. ITS was also used with Single Locus Species Discovery (SLSD) methodology, which allows the delimitation of putative lineages/species (cryptic diversity). RRW supported that the origin and the genetic diversity center of C. arabica species took place between Ethiopia and South Sudan. The study also found evidence of five colonization events and the dispersion of the species within Latin America. SLSD estimated two to 12 cryptic lineages/species within C. arabica depending on the algorithm used; with Latin America being home to two to six of these lineages. The results suggest that the evolutionary history and global dispersion of C. arabica is more complex than historians have registered, showing intermediary regions and ancestors unpublished nowadays, as well as a cryptic diversity being underestimated.

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“…Among the different markers used in the cited studies, microsatellites stand out as the most used tool to solve questions at micro-evolutive scale in population genetics. In this area, the Single Nucleotide Polymorphisms have been utilized for species delimitation and for exploring genetic introgression in Pimelodus species [ 37 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic insights into Cyphocharax magdalenae (Characiformes: Curimatidae): Microsatellite loci development and population analysis in the Cauca River, Colombia

Ochoa-Aristizábal,

Márquez

2024

PLoS ONE

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Cyphocharax magdalenae, a Colombian freshwater fish species, plays a vital role in nutrients distribution and serves as a significant food source for other fish species and local fishing communities. Considered a short-distance migratory species, C. magdalenae populations face substantial extinction risk due to human activities impacting their habitats. To address the lack of knowledge on genetic diversity and population structure, this study used next-generation sequencing technology to develop species-specific microsatellite loci and conducted a population genetics analysis of C. magdalenae in the middle and lower sections of the Cauca River, Colombia. Out of 30 pairs of microsatellite primers evaluated in 324 individuals, 14 loci were found to be polymorphic, at linkage equilibrium and, in at least one population, their genotypic frequencies were in Hardy-Weinberg equilibrium. Results showed high genetic diversity levels compared to other neotropical Characiformes, with inbreeding coefficients similar to those reported for phylogenetically related species. Moreover, C. magdalenae exhibits seasonal population structure (rainy-dry) consisting of two genetic stocks showing bottleneck signals and high effective population sizes. This information is essential for understanding the current species genetics and developing future management programs for this fishery resource.

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Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin

Cited by 5 publications

References 94 publications

Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae)

Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae)

Molecular evidence about ancestral origin, colonization patterns, and phylogenetic diversity of Coffea arabica, with insights in Latin America

Genetic insights into Cyphocharax magdalenae (Characiformes: Curimatidae): Microsatellite loci development and population analysis in the Cauca River, Colombia

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