DNA Barcoding Reveals High Levels of Divergence among Mitochondrial Lineages of Brycon (Characiformes, Bryconidae)

Arruda, Pábila S. S.; Ferreira, Daniela Cristina; Oliveira, Cláudio; Vênere, Paulo César

doi:10.3390/genes10090639

Cited by 11 publications

(10 citation statements)

References 46 publications

(59 reference statements)

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“…nigricans raises a possible and interesting model to test such ideas. Different migratory fish groups such as Brycon [ 57 ], Leporinus [ 5 ], and Zungaro [ 19 ] have been showing hidden diversity, particularly in the Tapajós River basin. Overall, these results appear indicating both the high level of endemism [ 18 ] and the putative historical hybridism [ 6 ] can be important drives of fish diversity in this peculiar system.…”

Section: Resultsmentioning

confidence: 99%

Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin

2020

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Highly spread through the Amazon River basin, Prochilodus nigricans have had its taxonomic validity recently questioned, when genetic differences between Western and Eastern Amazon populations from the Brazilian shield were detected. This area has been seeing as a region of high ichthyofaunal diversity and endemism, in which the hybrid origin of the Tapajó s River basin has been raised. In this paper, we report a new molecular lineage within P. nigricans of Tapajó s River, highlighting this region still hides taxonomically significant diversity. Haplotype networks were reconstructed using the mitochondrial COI and ATP6/8 markers, which were also used to calculate genetic distances among clusters. We additionally conducted a delimiting species approach by employing a Generalized Mixed Yule-Coalescent model (GMYC) with COI sequences produced here, and previous ones published for individuals sampled across the Amazon River basin. In addition to the genetic differentiation within P. nigricans, our findings favor the hypothesis of hybrid origin of the Tapajó s River basin and reaffirm the importance of studies aiming to investigate hidden diversity to address taxonomic and biogeographic issues, that certainly benefit better biodiversity conservation actions.

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Section: Resultsmentioning

confidence: 99%

Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin

2020

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“…To guarantee even more conclusive findings on the observed genetic distances, the ''optimal threshold'' of interspecific distance was calculated, which indicated that a distance of 3.28% would be the most appropriate threshold for the delimitation of the MOTUS identified in the present study, which is consistent with the findings of a number of previous studies of different fish groups. [64][65][66] In the specific case of G. paraguensis, which was the most common species at all the sampling points and was also the most heterogeneous, given the considerable variation in banding patterns and coloration (Fig. 5), we decided to run a more detailed genetic analysis.…”

Section: Discussionmentioning

confidence: 99%

Gymnotus paraguensis, a Good Example of Phenotypic Plasticity in the Pantanal Biome, Brazil

et al. 2021

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Gymnotus is the most studied genus of the order Gymnotiformes, but the morphological similarities of the different species make it difficult to identify taxa reliably. The present study is a continuation of the ongoing research into the taxonomic diversity of the stocks of Gymnotus sold as live bait in the Pantanal, Brazil. These studies have been based on cytogenetic analyses, DNA barcoding, and the analysis of coloration patterns. The results of the cytogenetic analysis confirmed the presence of three distinct strains, recognized as Gymnotus paraguensis, G. sylvius, and G. pantanal. However, the results revealed that the molecular operational taxonomic units identified as G. paraguensis actually include a relatively diverse set of fish, separated by considerable genetic distances. As the G. paraguensis specimens also presented considerable variation in coloration patterns, further genetic diversity analyses were conducted on these individuals, to test the hypothesis that more than one species is present in this cytotaxonomic unit. The haplotype network revealed a regional pattern in the distribution of this species. The results indicate that the observed variation in coloration patterns is associated with a high degree of phenotypic plasticity in G. paraguensis. These findings emphasize the importance of using an integrative approach for a more accurate diagnosis of Gymnotus, in particular, the species marketed as live bait for the fisheries of the upper Paraguay River basin in the Brazilian Pantanal.

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“…Sequences of the mitochondrial DNA gene cytochrome c oxidase (COI) are often used to assist taxonomy and species identification following the DNA barcoding principles ( Hebert, Ratnasingham & DeWaard, 2003 ; Hajibabaei et al, 2007 ). They can also be used for biodiversity inventories ( Monaghan et al, 2009 ; Carvalho et al, 2011 ; Pereira et al, 2013 ; Machado et al, 2018 ), allowing rapid characterization of not just a given sample but of entire communities ( Carvalho et al, 2018 ; Machado et al, 2018 ; Souza et al, 2018 ; Arruda et al, 2019 ; Santos et al, 2019 ). The simplest approach to delimit species from DNA sequence data is to use the percent cut-off rule ( Fujisawa & Barraclough, 2013 ), such as the 2% intra vs .…”

Section: Introductionmentioning

confidence: 99%

Mapping the hidden diversity of the Geophagus sensu stricto species group (Cichlidae: Geophagini) from the Amazon basin

Ximenes

Bittencourt

Machado

et al. 2021

PeerJ

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South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing 10 nominal and six morphologically distinct but undescribed species. We sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delimited lineages using four different single-locus species discovery methods (mPTP-15 lineages; LocMin-14 lineages; bGMYC-18 lineages; and GMYC-30 lineages). The six morphologically distinct but undescribed species were also delimited by the majority of the species discovery methods. Five of these lineages are restricted to a single collection site or a watershed and their habitats are threatened by human activities such as deforestation, agricultural activities and construction of hydroelectric plants. Our results also highlight the importance of combining DNA and morphological data in biodiversity assessment studies especially in taxonomically diverse tropical biotas.

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DNA Barcoding Reveals High Levels of Divergence among Mitochondrial Lineages of Brycon (Characiformes, Bryconidae)

Cited by 11 publications

References 46 publications

Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin

Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin

Gymnotus paraguensis, a Good Example of Phenotypic Plasticity in the Pantanal Biome, Brazil

Mapping the hidden diversity of the Geophagus sensu stricto species group (Cichlidae: Geophagini) from the Amazon basin

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