Limits...
The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding.

Chen W, Ma X, Shen Y, Mao Y, He S - Sci Rep (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Maximum intraspecific divergence compared with the nearest-neighbor distancefor fish in the Nujiang River.Only species with multiple sequences (Table S1) are presented. All of these species fall above the 1:1line, indicating the presence of a ‘barcodegap.’
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f2: Maximum intraspecific divergence compared with the nearest-neighbor distancefor fish in the Nujiang River.Only species with multiple sequences (Table S1) are presented. All of these species fall above the 1:1line, indicating the presence of a ‘barcodegap.’

Mentions: As expected, a hierarchical increase in the mean genetic variation from withinspecies (mean = 0.41%, standard error[SE] = 0.000), to within congeners(mean = 2.14%, SE = 0.002), towithin families (mean = 12.47%,SE = 0.006) was observed in the K2P model (Table 1). Overall, the genetic divergence among congeneric species wasan average of approximately 5 times greater than that among individuals of the samespecies. The intraspecific divergence exhibited considerable heterogeneity andranged from 0 to 12.80%, with a mean value of 0.41% (Table S3). Notably deep conspecific distances wereobserved for Abbottina rivularis, Paramisgurnus dabryanus, andRhodeus ocellatus. Very low interspecific distances were observed amongthe two species in Creteuchiloglanis, three species in Schizothorax,and five species in Schistura. A regression analysis revealed that theintraspecific sequence divergence is not significantly correlated with the samplesize (Spearman correlation analysis: P = 0.608). A barcodinggap analysis demonstrated that a barcode gap was present in 76.74% of all analyzedspecies (Fig. 2). For Schizothorax gongshanensis, S.lissolabiatus and S. nukiangensis; Creteuchiloglanisgongshanensis and C. macropterus; and Schistura longa, S.poculi, S. prolixifasciata, S. sp., and S.vinciguerrae, the distance to the nearest neighbor was zero.


The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding.

Chen W, Ma X, Shen Y, Mao Y, He S - Sci Rep (2015)

Maximum intraspecific divergence compared with the nearest-neighbor distancefor fish in the Nujiang River.Only species with multiple sequences (Table S1) are presented. All of these species fall above the 1:1line, indicating the presence of a ‘barcodegap.’
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663501&req=5

f2: Maximum intraspecific divergence compared with the nearest-neighbor distancefor fish in the Nujiang River.Only species with multiple sequences (Table S1) are presented. All of these species fall above the 1:1line, indicating the presence of a ‘barcodegap.’
Mentions: As expected, a hierarchical increase in the mean genetic variation from withinspecies (mean = 0.41%, standard error[SE] = 0.000), to within congeners(mean = 2.14%, SE = 0.002), towithin families (mean = 12.47%,SE = 0.006) was observed in the K2P model (Table 1). Overall, the genetic divergence among congeneric species wasan average of approximately 5 times greater than that among individuals of the samespecies. The intraspecific divergence exhibited considerable heterogeneity andranged from 0 to 12.80%, with a mean value of 0.41% (Table S3). Notably deep conspecific distances wereobserved for Abbottina rivularis, Paramisgurnus dabryanus, andRhodeus ocellatus. Very low interspecific distances were observed amongthe two species in Creteuchiloglanis, three species in Schizothorax,and five species in Schistura. A regression analysis revealed that theintraspecific sequence divergence is not significantly correlated with the samplesize (Spearman correlation analysis: P = 0.608). A barcodinggap analysis demonstrated that a barcode gap was present in 76.74% of all analyzedspecies (Fig. 2). For Schizothorax gongshanensis, S.lissolabiatus and S. nukiangensis; Creteuchiloglanisgongshanensis and C. macropterus; and Schistura longa, S.poculi, S. prolixifasciata, S. sp., and S.vinciguerrae, the distance to the nearest neighbor was zero.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus