Using Different Methods to Access the Difficult Task of Delimiting Species in a Complex Neotropical Hyperdiverse Group

Costa-Silva, Guilherme J.; Rodriguez, Mónica S.; Roxo, Fábio Fernandes; Foresti, Fausto; Oliveira, Cláudio

doi:10.1371/journal.pone.0135075

Cited by 52 publications

(64 citation statements)

References 40 publications

(61 reference statements)

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“…Similar color patterns have been found for a broad variety of loricariids from the Rios Xingu and Tapajós [27]. Low genetic distances between congeners have already been reported for other members of the subfamily Hypostominae [4,19,28,29]. This pattern can also be found in other diverse groups like piranhas ( Serrasalmus & Pygocentrus ) [30].…”

Section: Discussionsupporting

confidence: 80%

“…tankei and the putative new species. Similar results were found in the loricariid genus Rineloricaria [19]. Identification via DNA barcodes is based on the observation that intraspecific genetic divergence is usually lower than interspecific divergence, leading to the so called ‘barcoding gap’[20].…”

Section: Molecular Analysesmentioning

confidence: 59%

“…albivermis , a species with thin bands and/or dots, showing that the coloration is a strong character for differentiation in this genus. Costa-Silva et al [19] proposed that recognition as a formal new species is justified even if only morphological traits or high molecular divergence distinguish a population from others.…”

Section: Discussionmentioning

confidence: 99%

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A New Species of Tiger Pleco Panaqolus (Siluriformes: Loricariidae) from the Xingu Basin, Brazil

Cramer

Sousa

2016

PLoS ONE

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Panaqolus tankei is described from the Xingu River, Brazil. The new species is diagnosed from P. albomaculatus, P. dentex, P. nix, P. nocturnus, and P. koko by its color pattern consisting of dark and light diagonal bars on the body and bands on the fins (vs. body and fins without bars or bands); from P. albivermis, P. maccus, and P. purusiensis by the width of the dark bars being more or less the same of the light bars (vs. dark bars at least two or three times wider than light bars) and from P. changae by the absence of vermiculation on the head (vs. vermiculation present on head). The new species differs from P. gnomus by the orientation of the bars from posterodorsal to anteroventral direction (vs. anterodorsal to posteroventral direction), and from P. claustellifer by the orientation of the bands in the dorsal fin that are not parallel to the margin (vs. parallel to the margin). The barcoding region (COI) was sequenced for the new species, sequences were deposited in GenBank and were compared with congeners from other drainages. With regard to the current construction of a hydroelectric power plant (a so-called mega dam) in the Xingu River, herewith we increase knowledge of the river Xingu’s ichthyofauna and, thus improve the assessment of the impacts of that construction on the river.

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Section: Discussionsupporting

confidence: 80%

Section: Molecular Analysesmentioning

confidence: 59%

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A New Species of Tiger Pleco Panaqolus (Siluriformes: Loricariidae) from the Xingu Basin, Brazil

Cramer

Sousa

2016

PLoS ONE

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“…These results in fact exceed those obtained for Rineloricaria (Siluriformes), another hyperdiverse fish genus, using a similar clustering approach, which gave only 41% full matches [78]. …”

Section: Discussionmentioning

confidence: 64%

“…Several studies propose integrative clustering delimitation methods to check for congruence in the results of the different species clustering methods into operational taxonomic units, referring to the recognition of genetic patterns within groups that supports traditional taxonomic studies [77, 78]. We used a similar approach to Costa-Silva et al [78], where the final OTUs were classified in four categories according to the degree of correspondence with the initial NJ classification of the genetic analysis ABGD, BIN and GMYC (see Fig 1): FULL MATCH—pattern A, when all clustering methods generated the same partition (congruence between ABGD, GMYC and BIN with NJ), PARTIAL MATCH—pattern B, when two analyses generated the same cluster as NJ (GMYC and ABGD, for example), PARTIAL MATCH—pattern C, when only one method (ABGD or GMYC or BIN) generated the same cluster as NJ, or DISCORDANT—pattern D, when none of the methods are in agreement; in this case, the OTUs were delimited based on the 2% cutoff criterion of the NJ analysis as defined by the initial clustering.…”

Section: Methodsmentioning

confidence: 99%

Highlighting Astyanax Species Diversity through DNA Barcoding

et al. 2016

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DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions.

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A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding

Mendoza‐Ramírez¹,

Páiz‐Medina²,

Salvatierra‐Suárez³

et al. 2022

Ecology and Evolution

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Aquatic macroinvertebrates are widely used as indicators for water quality assessment around the world. Modern strategies for environmental assessment implement molecular analysis to delimitate species of aquatic macroinvertebrates. Delimitation methods have been established to determine boundaries between species units using sequencing data from DNA barcodes and serve as first exploratory tools for taxonomic revisions. This is useful in regions such as the neotropics where aquatic macroinvertebrate habitats are threatened by human interference and DNA databases remain understudied. We asked whether the biodiversity of aquatic macroinvertebrates in a stream in Nicaragua, within the Central American Dry Corridor, could be characterized with biological indices and DNA barcoding. In this study, we combined regional biological indices (BMWP‐CR, IBF‐SV‐2010) along with distance‐based (ASAP, BIN) and tree‐based (GMYC, bPTP) delimitation methods, as well as nucleotide BLAST in public barcode databases. We collected samples from the upper, middle, and low reaches of the Petaquilla river. The three sites presented excellent water quality with the BMWP‐CR index, but evidence of high organic pollution was found in the middle reach with the IBF‐SV‐2010 index. We report a total of 219 COI sequences successfully generated from 18 families and 8 orders. Operational taxonomic units (OTUs) designation ranged from 69 to 73 using the four methods, with a congruency of 92% for barcode assignation. Nucleotide BLAST identified 14 species (27.4% of barcodes) and 33 genera (39.3% of barcodes) from query sequences in GenBank and BOLD system databases. This small number of identified OTUs may be explained by the paucity of molecular data from the Neotropical region. Our study provides valuable information about the characterization of macroinvertebrate families that are important biological indicators for the assessment of water quality in Nicaragua. The application of molecular approaches will allow the study of local diversity and further improve the application of molecular techniques for biomonitoring.

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Using Different Methods to Access the Difficult Task of Delimiting Species in a Complex Neotropical Hyperdiverse Group

Cited by 52 publications

References 40 publications

A New Species of Tiger Pleco Panaqolus (Siluriformes: Loricariidae) from the Xingu Basin, Brazil

A New Species of Tiger Pleco Panaqolus (Siluriformes: Loricariidae) from the Xingu Basin, Brazil

Highlighting Astyanax Species Diversity through DNA Barcoding

A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding

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