Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?
© Pereira et al.; licensee BioMed Central Ltd. 2013
Received: 20 August 2012
Accepted: 5 March 2013
Published: 9 March 2013
The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region.
Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species.
Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.
KeywordsUpper Paraná River basin COI Characiformes Siluriformes Overlooked species Biodiversity.
The megadiverse Neotropical freshwater ichthyofauna is the richest in the world, with approximately 6,000 recognized species, and contributes 20-25% of the total freshwater fish fauna on Earth . However, the true extent of this diversity is still unknown although it has been estimated that 30-40% of the species inhabiting this region have not been described [1, 2]. Despite this exceptional richness, fishes from the Neotropical region belong to only 17 orders, a small number considering that the 954 species found in North America belong to 26 orders [3, 4]. Additionally, almost 80% of this fauna belongs to only three orders: Characiformes with 1,962 species, Siluriformes with 2,214 species, and Perciformes with 572 species. Approximately half of these species belong to only three families: Characidae (tetras, piranhas, and relatives) with 1,345 species, Loricariidae (armored catfishes) with 973 species, and Cichlidae (cichlids) with 571 species . Moreover, evidence based on molecular data has determined that most of the diversification of Neotropical ichthyofauna occurred recently, between 3 and 10 MYA [4–9]. All these characteristics make the taxonomic identification of this fauna a great challenge, even when using molecular approaches.
In 2003, DNA barcoding using the standardized cytochrome c oxidase subunit I gene (COI) was proposed by Hebert et al. as a method to identify species,  and since then, over 1.9 million specimens, belonging to roughly 172,000 species, have been barcoded, including 9,502 fishes (see http://www.boldsystems.org; ). The methodology uses a short (~650 bp), standardized DNA fragment from the mitochondrial COI gene to identify species based on differences in their COI sequences . The effectiveness of the barcoding system has been repeatedly demonstrated by the identification of marine [12–22] and freshwater fish species [23–32], with a success rate of well over 90%. However, many fish barcoding surveys have been conducted in relatively species-poor areas, with species belonging to several higher taxa, or relatively rich areas where only a few species were analyzed.
The Upper Parana River basin drains an area of approximately 891,000 km2 of Atlantic Rain Forest and South America Savanna (Cerrado) in the most urbanized and exploited area of Brazil. The last inventory of freshwater fish fauna found 310 valid species and 50 other putative species yet to be described , of which 80% corresponded to Characiformes and Siluriformes. Although this basin is considered the most well-studied in the Neotropical region, the number of species in the entire region remains uncertain, and new fish species are discovered after each new inventory [33–37]. The aim of the present study was to test the hypothesis that the DNA barcoding methodology can be used effectively to identify the megadiverse freshwater fish fauna of the Upper Parana River basin, a representative area of the Neotropical region. With this purpose, we analyzed 254 species (nearly 70% of the species that occur in this basin) including many congeneric species and closely related genera.
Summary of fish taxa included in this study
Number of genera
Number of species
Summary of K2P genetic divergence within different taxonomic levels from 1,244 analyzed specimens
Species with high intra-specific K2P divergences values
Intra-specific divergences (%)
Number of subclusters
Inter-subclusters divergences (%)
Intra-subclusters divergences (%)
1.7 to 2.5
0.4 to 0.5
0.2 to 0.8
1.4 to 2.5
1.6 to 2.1
1.7 to 2.2
0 to 0.5
1.9 to 5.6
0 to 1.0
0 to 0.6
2.9 to 8.0
Summary of the DNA barcoding surveys of fishes (by December 2012) highlighting the numbers of species, higher taxa, families and genera with multiple species analyzed
Number of species analyzed
Number of high taxa (order)
Number of families and families with multiple species (>2)
Number of genera and genera with multiple species (>2)
Mean value of K2P divergence of conspecific/congeneric comparisons (%)
Upper Paraná River basin
Paraíba do Sul River basin – Brazil
São Francisco River basin – Brazil
Mexico and Guatemala
Tall Lake - Philippines
Nayband National Park – Iran
In addition, the low observed congeneric K2P divergence values reflect a possible recent radiation of Neotropical freshwater fishes, compared to other freshwater fish faunas [4–9]. For example, Montoya-Burgos et al. , studying Hypostomus, and Hubert et al. , working with Serrasalmus and Pygocentrus from South America, proposed the hypothesis of recent radiation of these species (originating between 2 and 12 million years ago) and suggested that these patterns could apply to other Neotropical fish groups. In fact, our results showed that approximately 60% of congeneric comparisons from the neotropics are less than 5% divergent, contrasting with the values found among genera (mean value = 20%) (Figure 1), reinforcing this hypothesis. In summary, the large number of species associated with the recent radiation of the Neotropical ichthyofauna, could potentially pose a barrier to the use of barcoding (due the possible shared haplotypes). However, the barcoding methodology was able to correctly discriminate species in this megadiverse fauna.
On the other end of the spectrum, the high observed global conspecific mean value can be explained by the 14 species that displayed deep intra-specific divergence, which ranged from 1.4% to 8.0% among their subclusters (Table 3). The NND analyses confirm this observation, showing that 92.5% of species analyzed display intraspecific mean values of 0.36%. In addition, we reanalyzed the species using the subclusters formed by those 14 species as an independent genetic unit. This method resulted in a global conspecific value of 0.3%, consistent with the literature cited.
Low values of interspecific genetic divergence (<2%)
Generally, barcoding researchers have used a 2% divergence threshold as a heuristic cutoff value for species delimitation [13, 23, 27, 28, 40–42]. This limit is based on the distribution of intra and inter-specific K2P genetic distance values in the approximately 172,000 species that have been barcoded (http://www.boldsystems.org). However, in a review of the available literature, almost all barcoding surveys reported cases of inter-specific comparisons with low values, even below the generally accepted limit, but were still able to correctly discriminate between most species [12, 23–25, 28]. Thus, this value must be used only as a starting point to investigate divergence among specimens, and other characteristics of the species/group studied, such as their evolutionary history, should be considered before defining a species limit . Notably, AFLP (amplified fragment length polymorphism) genome scans of several closely related pairs of taxa from North American waters showed that taxa with divergences of > 2% rarely exhibited evidence of introgressive hybridization in their contact zones .
Using 2% as cutoff for delimiting species, 84 pairs of taxa (representing 53 species) showed inter-specific values below this limit and could not be discriminated using this simple divergence threshold (Additional file 3). However, in 83 cases, each species displayed a cohesive cluster of haplotypes, allowing its discrimination (Figure 2), showing a barcode gap ranging from 1.2 to 18 times between congeneric and intra-specific comparison, and thereby reinforcing the idea that the 2% cutoff value could be considered as a reasonable starting point. Only A. schubarti and A. trierythropterus shared haplotypes and could not be discriminated, but there are morphological evidences that these two species represent only one valid species (A. schubarti) (Dr. Ricardo M. Correa e Castro, personal communication). Possible explanations for the observed low inter-specific K2P genetic divergence values include the recent radiation of some groups of species , as discussed above, and the possible evolutionary rate variation of COI among different taxa [44, 45]. The 53 species studied here represent 12 genera of freshwater fishes, including some of the most specious Neotropical groups (Astyanax, Characidium, Pimelodella, Hypostomus and Trichomycterus), and 27 of the 53 species belong to only two genera (Hypostomus and Neoplecostomus) (Additional file 3). In the case of Hypostomus, Montoya-Burgos et al.  analyzed the species of this genus and suggested that the processes of divergence and radiation date back to between 4 and 12 million years ago, corroborating the observed low inter-specific values. This result can also explain the difficulties in the identification of these species, even with morphological approaches [46–49]. However, all 18 Hypostomus species could be discriminated using both genetic distance (Figure 2) and ND (Additional file 4) approaches. The same pattern was observed in Neoplecostomus. Roxo et al.  estimated that radiation of the Neoplecostomus genus occurred between 1 and 10 million years ago and that their speciation process involved mainly recent headwater capture events. As with Hypostomus, the 16 Neoplecostomus species were correctly discriminated using both barcoding approaches (genetic distance (Figure 2) and ND (Additional file 4)).
A survey of the evolution of Astyanax in the Mesoamerica region found a recent radiation of its species, with 90% of interspecific comparisons ranging from 1% to 5% . Other surveys examining Neotropical freshwater fish fauna provide similar results [9, 52]. In addition, our results showed that approximately 60% of congeneric comparisons in Astyanax were below 5% and had a global mean value of interspecific K2P genetic distances of 6.8%, relatively smaller than the values cited in the literature. Thus, we conclude that the most likely explanation for the low interspecific values observed in this study is a possible recent radiation process in the megadiverse Neotropical ichthyofauna.
In addition, we used the ND approach as a complement to the distance approach (Additional file 4) and found NDs to all species analyzed using both kinds of characters (only exclusive NDs or combined exclusive and partial shared NDs). The use of the ND approach can be useful in cases with low divergence values to more accurately identify species. Some surveys have used the ND approach as an alternative to the distance approach with a high level of success [29, 53–56]. Some authors even advocate the use of the ND approach, as it follows the same principles used in traditional morphological approaches, that is, the use of diagnostic characters [55, 57, 58]. Based on our experience, we suggest that as a first step, researchers use the fastest genetic distance approach to assign the species to a related group and then apply the ND approach to test the identification within the context of a genus, which simplifies the ND analysis by restricting the number of taxa which must be compared.
Deep intra-specific divergence (>2%)
The applicability of DNA barcoding to reveal cryptic and potentially new species, has increased our knowledge regarding biodiversity in many taxa and the use of barcoding as a tool for these purposes is becoming a reality, [28, 29, 59–72]. In the present study, 14 species (5.5%) showed deep intra-specific genetic divergence values (≥ 2%) and were further subdivided into two or more subclusters (Figure 3). Each subcluster showed a tight cluster of haplotypes with significantly higher mean values (1.4% to 8%) among them than the mean values observed within each subcluster (0 to 1%) (Table 3). Deep intra-specific divergence has been reported in barcoding analyses of the most diverse groups, many of which were considered cryptic species [28, 29, 60–71]. Another, non-exclusive explanation for the high intra-specific genetic divergence is the possibility of these subclusters to represent species not sampled, as most cases represent species that are difficult to identify. However, six of the 14 species reported here represent unique species from the genus/group present in the Upper Parana River basin (Table 3), four other species belong to a genus representing all species that occur in this hydrographic basin, and only four species belong to a genus with multiple reported species in this basin in which one species is not sampled (Table 3). In the last case, the specimens analyzed were morphologically reviewed but could not be assigned to the other unsampled species of the genus. We conclude that all these cases represent cryptic species and are strong candidates for new species.
To reinforce our hypothesis, six of these 14 species are strongly suggested in the literature as species complexes by cytogenetic markers (Ancistrus cirrhosus; Iheringichthys labrosus; Synbranchus marmoratus; Astyanax altiparanae; Hoplias intermedius; Piabina argentea). Furthermore, the intra-specific lineages of 10 species are allopatric, reinforcing the fact that such lineages have independent evolutionary histories. The presence of different haplotype lineages may be explained by possible restricted gene flow due to the fragmented nature of freshwater ecosystems, which can include many physical and chemical barriers [29, 41, 42]. To complete this scenario, some authors suggest that the freshwater fishes have a limited dispersal capability, especially among those belonging to small-sized groups, which restricts their geographical distribution and may facilitate geographical population subdivision, thereby enabling the possible creation of new species by geographic isolation (allopatry) [29, 79, 80]. In summary, our results identified at least 23 strong candidates as potential new species including extreme cases, such as P. argentea, which subdivided into six subclusters and S. marmoratus, which showed the highest value of genetic divergence among subclusters (8%), and exhibited mean values higher than those observed among inter-specific analyses (Table 3). These results reinforce the use of DNA barcoding as a powerful tool to reveal overlooked species, especially among specious and/or problematic groups.
Intra X Inter-specific distance genetic
The success of the species identification by DNA barcoding is based on the difference between the intra- and inter-specific genetic divergences, the so-called barcoding gap [10, 81–83]. In this survey, beside the relatively low values of the inter-specific genetic divergence observed (6.8% - Table 2), the barcoding gap was clear. The overall variation was about five and 22 times greater among congeneric species than within species considering respectively, a mean value of intra-specific K2P genetic divergence of 1.3% (without correction to species with high intra-specific divergence genetic) and 0.3% (considering each subcluster of the species with high intra-specific genetic divergence as a different unit). Even for the 83 cases that displayed low inter-specific divergence genetic values (<2% - Additional file 3), the barcoding gap was clear, with values raging from 1.2 to 18 times (mean = 6 times) greater among congeneric than within species. Thus, our results demonstrate the existence of barcoding gap even in those cases where the inter-specific genetic divergence is low.
Inter- and intra- specific genetic divergence values of the genera represented by >2 species.
Inters-specific genetic divergence
Max intra-specific genetic divergence (%)
Our study is the first to examine a large number of freshwater fish species from the Neotropical area. The results confirm the efficacy of using barcoding methodology to help calibrate our traditional knowledge of species diversity and to enhance our ability to identify this megadiverse fauna. Barcoding discriminated 99.2% of the analyzed species, agreeing with morphological taxonomic analysis, and our study represents an important contribution to the global barcoding library. Our study is the first to include many genera represented by multiple species, which may be why our distribution of inter-specific genetic divergence of the megadiverse Neotropical ichthyofauna is smaller than those of other surveys. This finding most likely indicates recent radiation of this fauna and reflects a high number of closely related species. Moreover, this study also showed the power of using barcode sequences to identify species with low inter-specific divergence using only the divergence genetic approach or in conjunction with the ND approach. The results also revealed cryptic speciation in some species (23 candidates for new species), which is a relevant finding considering that the Upper Parana River basin is the most well studied basin in the Neotropical area, suggesting that the number of overlooked species in the overarching Neotropical area may be large yet manageably revealed using barcoding methodology.
Finally, our study makes an important contribution to the knowledge of the rich ichthyofauna of the Upper Parana River basin, and contributes significantly to the FISH-BOL campaign (and the international Barcoding of Life project of which it is a part) by providing barcode sequence profiles for use in the identification of these species by experts and non-experts alike, and by making them available for use in other applications.
Extraction, PCR amplification, and sequencing
DNA barcoding was carried out at the Canadian Centre for DNA Barcoding (CCDB), Canada and at the Laboratory of Biology and Genetic of Fish (LBP), UNESP, Botucatu, Brazil. Total genomic DNA was isolated from the fin or muscle tissue of each specimen using one of two different methods: with a DNeasy Tissue Kit (Qiagen), according to the manufacturer’s instructions (LBP); or with vertebrate lysis buffer containing proteinase K digested overnight at 56°C and subsequent extraction using a membrane-based approach on a Biomek NX (http://www.pall.com) liquid handling station using AcroPrep96 (http://www.beckman.com) and 1 ml filter plates with 10 mm PALL glass fiber media  according to the CCDB protocol. A segment of approximately 648 bp from the 5’ end of the mitochondrial cytochrome c oxidase subunit I (COI) gene was amplified by polymerase chain reaction (PCR) using different combinations of primers: FishF1, FishR1, FishF2, FishR2 , the M13-tailed primer cocktails C_FishF1t1 – C_FishR1t1 and C_VF1LFt1 – C_VR1LRt1 , and the pair L5698-Asn  and H7271-Coi . The 12.5 μl polymerase chain reaction (PCR) mixtures included 6.25 μl 10% trehalose, 2.0 μl ultrapure water, 1.25 μl 10X PCR buffer, 0.625 μl MgCl2 (50.0 mM), 0.125 μl of each primer (0.01 mM), 0.0625 μl of each dNTP (0.05 mM), 0.625 μl Taq polymerase and 2.0 μl of DNA template. PCR was carried out in a thermocycler (Veriti® 96-Well Thermal Cycler, Applied Biosystems). The thermocycler conditions followed the protocols of Hajibabaei et al. . Amplified products were verified on 1% agarose gels. At the LBP, the PCR products were purified with ExoSap-IT® (USB Corporation) following the manufacturer’s protocol. At the CCDB, PCR products were labeled with the BigDye Terminator v.3.1 Cycle Sequencing Ready Reaction kit (Applied Biosystems) using standard methods  and were bidirectionally sequenced using an ABI3730 capillary sequencer. At the LBP, the cycle sequencing reaction was carried out using a BigDyeTM Terminator v.3.1 Cycle Sequencing Ready Reaction kit (Applied Biosystems) in a final volume of 7.0 μl containing 1.4 μl of template, 0.35 μl of primer (10 μM), 1.05 μl of buffer 5X, 0.7 μl of BigDye mix and water. The cycle sequencing conditions included initial denaturation at 96°C for 2 min followed by 35 cycles of denaturation at 96°C for 45 s, annealing at 50°C for 60 s, and extension at 60°C for 4 min. The PCR sequencing products were purified with EDTA/sodium acetate/alcohol following the protocol suggested in the BigDye™ Terminator v.3.1 Cycle Sequencing kit’s manual (Applied Biosystems). All samples were sequenced on an ABI3130 Genetic Analyzer capillary sequencer (Applied Biosystems) following the manufacturer’s instructions. Sequence data, trace files, primer details, and collection localities for specimens are available within the project FUPR on BOLD (http://v3.boldsystems.org/). Sequences have also been deposited in GenBank (Accession numbers in Additional file 1).
All sequences were analyzed using SeqScape® software v2.6 (Applied Biosystems) to obtain consensus sequences and check the occurrence of deletions, insertions, and stop codons. The sequences were aligned using tools available on BOLD v 3.0 (http://v3.boldsystems.org/). The genetic distances among and within species were calculated using the Kimura-2-Parameter (K2P) distance model . A neighbor-joining (NJ) dendrogram of K2P distances was created using MEGA v 5.0 software to provide a graphic representation of the patterning of divergence among species .
The nucleotide diagnostic (ND) approach  was carried out using only the exclusive nucleotide diagnostics for the single pair of species or the exclusive nucleotide diagnostics associated with partial shared nucleotide diagnostics for the genus that showed more than two species with low divergence values. The second option was used to provide a great number of informative nucleotide diagnostics, as a large number of species were analyzed. The nucleotide diagnostics were obtained using the BOLD v 3.0 tool (http://v3.boldsystems.org/) and were manually checked using the BioEdit Sequence Alignment Editor v 126.96.36.199 .
The species delimitation was initially carried out using 2% divergence as a cutoff value, as employed in others barcoding surveys [13, 23, 27, 28, 40–42]. The analysis of the possible cryptic speciation was applied to all species that showed at least one individual that displayed >2% divergence to others specimens.
Amplified fragment length polymorphism
Barcode of life data systems
Canadian centre for DNA barcoding
Citocromo c oxidase subunit I
Fishes from upper parana project
Laboratory of biology and genetic of fish
Milion yaers ago
Nearest neighbor distance
The authors are grateful to Renato Devidé and Ricardo Teixeira for their help with fish collection; Paul Hebert and the Biodiversity Institute of Ontario’s laboratory and informatics staff for help in the acquisition and analysis of barcode sequence data; and Ricardo C Benine, Ricardo MC Castro and Francisco Langeani for help in identification of the fish species. Financial support for this study was provided by CNPq and FAPESP in Brazil, and by Genome Canada (through the Ontario Genomics Institute) for support to the International Barcode of Life (iBOL) project and NSERC for support to the Canadian Centre for DNA Barcoding.
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