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

Guilherme J Costa-Silva,Claudio Oliveira,Fausto Foresti,Mónica S Rodriguez,Fábio F Roxo,Wolfgang Arthofer

doi:10.1371/journal.pone.0135075

Guilherme J Costa-Silva, Claudio Oliveira + Show 4 more

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https://doi.org/10.1371/journal.pone.0135075

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Abstract

The genus Rineloricaria is a Neotropical freshwater fish group with a long and problematic taxonomic history, attributed to the large number of species and the pronounced similarity among them. In the present work, taxonomic information and different molecular approaches were used to identify species boundaries and characterize independent evolutionary units. We analyzed 228 samples assembled in 53 distinct morphospecies. A general mixed yule-coalescent (GMYC) analysis indicated the existence of 70 entities, while BOLD system analyses showed the existence of 56 distinct BINs. When we used a new proposed integrative taxonomy approach, mixing the results obtained by each analysis, we identified 73 OTUs. We suggest that Rineloricaria probably has some complexity in the known species and several species not formally described yet. Our data suggested that other hyperdiverse fish groups with wide distributions can be further split into many new evolutionary taxonomic units.

Highlights

Integrative Taxonomy of the Complex Genus Rineloricaria for species delimitation based on single-locus data is the general mixed yule-coalescent (GMYC), which is widely used in biodiversity assessments and phylogenetic community ecology [6,7,8]
The genetic distance analysis revealed that 96% of the morphospecies differed from each other by more than 2% of the Kimura 2 Parameter (K2P) distance, whereas some morphospecies had a high genetic variation, and, sometimes, the variation was larger than the species divergences
In 19 cases (Fig 1 pattern B), the morphospecies were not discriminated in barcode index number (BIN) analysis; in six of these cases, the GMYC results were in accordance with the BIN determination, demonstrating that the GMYC analysis was more efficient than the BIN analysis for discriminating species of Rineloricaria, which were different from those found in other groups of organisms [9,38]

Summary

Introduction

With the implementation of the Barcoding of Life project, the gene COI has been used for some time as a tool for identification of fish species. [1] This gene has been an efficient tool for delimiting species of particular taxonomic groups and providing evidence of independent evolutionary units or operational taxonomy units (OTUs) with the recognition of genetic patterns within groups that support the traditional taxonomic studies [2,3,4].Barraclough et al [5] suggested that many factors can affect the success rate of DNA barcoding, such as the typical levels of intraspecific and interspecific variation among clades and substitution rate variation among lineages, casting doubt on the power of this method to identify and delimit species. Improved statistical methods have been proposed to analyze barcoding data that is being used to identify the "species boundaries" and thereby show the evolutionary independent units present in complex groups. Integrative Taxonomy of the Complex Genus Rineloricaria for species delimitation based on single-locus data is the general mixed yule-coalescent (GMYC), which is widely used in biodiversity assessments and phylogenetic community ecology [6,7,8]. This method identifies boundaries as a shift in branching rates on a phylogenetic tree that contains multiple species and populations. The GMYC analysis requires much computational time to identify large numbers of OTUs [9]

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