DNA barcoding of fish fauna from low order streams of Tapajos River basin.
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ABSTRACT:
SUBMITTER: Guimaraes KLA
PROVIDER: S-EPMC6303048 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundUrbanisation has facilitated changes in the hydrological cycle, sediment dynamics and habitat loss and it has had a tremendous impact on river ecosystems. Moreover, the invasion of non-native species reduces the number of native species with the progress of urbanisation, thereby resulting in the homogenisation of fish fauna and significant decrease in diversity. However, the effects of urbanisation on fish fauna vary depending on the region, degree of urbanisation and number of years since the construction of the city. Hence, it is necessary to collect information on how fish fauna changes due to urbanisation in different regions. The target site of the present study is the Tsurumi River, of which approximately 85% of the basin is urbanised and many of the river channels have been affected by straightening and concrete channelling. Monitoring of biota has been conducted mainly in downstream areas; however, data on fish fauna in upstream areas and tributaries of the river, which have been substantially affected by urbanisation, are lacking.New informationSurveys were conducted at 71 sites in the Tsurumi River Basin during summers and winters, focusing on river channels that have been straightened or converted to concrete channels due to urbanisation. As a result of this investigation, 10 families, 28 species and 9,335 individuals were collected. Some of the fish collected included rare species, such as Tanakialanceolata, Lefuaechigonia and Pseudobagrustokiensis, indicating that, even in rivers that have been severely impacted by human activities, there are still rare indigenous species living there, albeit in limited numbers. In addition, Misgurnus sp. (clade B2), Micropterussalmoides, Lepomismacrochirus and Poeciliareticulata were confirmed to be non-native species. Misgurnus sp. (clade B2) was widespread; however, populations of carnivorous non-native alien species were small. The data are all accessible from the document "database_fish_urban_tsurumi" (https://ipt.pensoft.net/manage/resource?r=database_fish_urban_tsurumi).
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Project description:BackgroundThe 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.ResultsOf 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.ConclusionsOur 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.
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Project description:BackgroundThe Maranhão State harbours great fish diversity, but some areas are still undersampled or little known, such as the Munim River Basin in the northeast of the State. This lack of knowledge is critical when considering anthropogenic impacts on riverine systems especially in the face of major habitat destruction. These pressing threats mean that a comprehensive understanding of diversity is critical and fish checklists extremely relevant. Therefore, the present study provides a checklist of the fish species found in the Munim River Basin, Maranhão State, north-eastern Brazil, based on collected specimens.New informationA total of 123 species were recorded for the Munim River Basin, with only two non-native species, Oreochromisniloticus and Colossomamacropomum, showing that the fish assemblage has relatively high ecological integrity. In addition, 29 species could not be identified at the species level, indicating the presence of species that are probably new to science in the Basin. A predominance of species belonging to the fish orders Characiformes and Siluriformes, with Characidae being recovered as the most species-rich family (21 species) agrees with the general pattern for river basins in the Neotropical Region. The total fish diversity was estimated by extensive fieldwork, including several sampling gears, carried out in different seasons (dry and rainy) and exploring different environments with both daily and nocturnal sampling, from the Basin's source to its mouth. A total of 84 sites were sampled between 2010 and 2022, resulting in 12 years of fieldwork. Fish assemblages were distinct in the Estuary and Upper river basin sections and more similar in the Lower and Middle sections indicating environmental filtering processes. Species were weakly nested across basin sections, but unique species were found in each section (per Simpsons Index). High variability of species richness in the Middle river basin section is likely due to microhabitat heterogeneity supporting specialist fish communities.
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Project description: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 Tapajós River basin has been raised. In this paper, we report a new molecular lineage within P. nigricans of Tapajós 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 Tapajós 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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Project description:Nujiang River (NR), an essential component of the biodiversity hotspot of the Mountains of Southwest China, possesses a characteristic fish fauna and contains endemic species. Although previous studies on fish diversity in the NR have primarily consisted of listings of the fish species observed during field collections, in our study, we DNA-barcoded 1139 specimens belonging to 46 morphologically distinct fish species distributed throughout the NR basin by employing multiple analytical approaches. According to our analyses, DNA barcoding is an efficient method for the identification of fish by the presence of barcode gaps. However, three invasive species are characterized by deep conspecific divergences, generating multiple lineages and Operational Taxonomic Units (OTUs), implying the possibility of cryptic species. At the other end of the spectrum, ten species (from three genera) that are characterized by an overlap between their intra- and interspecific genetic distances form a single genetic cluster and share haplotypes. The neighbor-joining phenogram, Barcode Index Numbers (BINs) and Automatic Barcode Gap Discovery (ABGD) identified 43 putative species, while the General Mixed Yule-coalescence (GMYC) identified five more OTUs. Thus, our study established a reliable DNA barcode reference library for the fish in the NR and sheds new light on the local fish diversity.
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