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

Map of locations sampled in this study.The numbers of the locations refer to 1) Bingzhongluo, 2) Puladi, 3) Maji, 4)County Areas of Fugong, 5) Pihe, 6) Chenggan, 7) Liuku, 8) Hongqi Dam, 9)Mangkuan, 10) Xiaopingtian, 11) Sanjiangkou, 12) Longzhen Bridge, 13)Kongguang Village, 14) Manglong River, 15) Mangkuan River, 16) MangliuRiver, and 17) Longwang Pond. Locations 1–12 are sampling sitesin the main stem, and 13–17 are located in a tributary. Locationdetails and a list of the number of samples collected per site are providedin Supplementary Table S1. Mapwas created in the ArcGIS version 10.1 and modified in Microsoft Office.
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f1: Map of locations sampled in this study.The numbers of the locations refer to 1) Bingzhongluo, 2) Puladi, 3) Maji, 4)County Areas of Fugong, 5) Pihe, 6) Chenggan, 7) Liuku, 8) Hongqi Dam, 9)Mangkuan, 10) Xiaopingtian, 11) Sanjiangkou, 12) Longzhen Bridge, 13)Kongguang Village, 14) Manglong River, 15) Mangkuan River, 16) MangliuRiver, and 17) Longwang Pond. Locations 1–12 are sampling sitesin the main stem, and 13–17 are located in a tributary. Locationdetails and a list of the number of samples collected per site are providedin Supplementary Table S1. Mapwas created in the ArcGIS version 10.1 and modified in Microsoft Office.

Mentions: We obtained mitochondrial barcodes (648 bp) for a total of 1139 fishspecimens belonging to 5 orders, 10 families, 31 genera and 46 a priori identifiedspecies from 17 locations in the NR basin (Fig. 1). This listof 46 morphological species includes 16 endemic species, 9 exotic invasive speciesand 21 widespread species (Table S3). Nodeletions, insertions or stop codons were detected in any of the amplifiedsequences, demonstrating that all of the sequences constitute functionalmitochondrial COI sequences. For the majority of species, multiple specimens(mean = 21.3 specimens per species) from distant localitieswere analyzed to document intraspecific divergence. Only three species wererepresented by a single specimen, and two species (Schizothorax nukiangensisand Triplophysa nujiangen) were represented by 226 and 107 individuals,respectively (Table S1).


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)

Map of locations sampled in this study.The numbers of the locations refer to 1) Bingzhongluo, 2) Puladi, 3) Maji, 4)County Areas of Fugong, 5) Pihe, 6) Chenggan, 7) Liuku, 8) Hongqi Dam, 9)Mangkuan, 10) Xiaopingtian, 11) Sanjiangkou, 12) Longzhen Bridge, 13)Kongguang Village, 14) Manglong River, 15) Mangkuan River, 16) MangliuRiver, and 17) Longwang Pond. Locations 1–12 are sampling sitesin the main stem, and 13–17 are located in a tributary. Locationdetails and a list of the number of samples collected per site are providedin Supplementary Table S1. Mapwas created in the ArcGIS version 10.1 and modified in Microsoft Office.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Map of locations sampled in this study.The numbers of the locations refer to 1) Bingzhongluo, 2) Puladi, 3) Maji, 4)County Areas of Fugong, 5) Pihe, 6) Chenggan, 7) Liuku, 8) Hongqi Dam, 9)Mangkuan, 10) Xiaopingtian, 11) Sanjiangkou, 12) Longzhen Bridge, 13)Kongguang Village, 14) Manglong River, 15) Mangkuan River, 16) MangliuRiver, and 17) Longwang Pond. Locations 1–12 are sampling sitesin the main stem, and 13–17 are located in a tributary. Locationdetails and a list of the number of samples collected per site are providedin Supplementary Table S1. Mapwas created in the ArcGIS version 10.1 and modified in Microsoft Office.
Mentions: We obtained mitochondrial barcodes (648 bp) for a total of 1139 fishspecimens belonging to 5 orders, 10 families, 31 genera and 46 a priori identifiedspecies from 17 locations in the NR basin (Fig. 1). This listof 46 morphological species includes 16 endemic species, 9 exotic invasive speciesand 21 widespread species (Table S3). Nodeletions, insertions or stop codons were detected in any of the amplifiedsequences, demonstrating that all of the sequences constitute functionalmitochondrial COI sequences. For the majority of species, multiple specimens(mean = 21.3 specimens per species) from distant localitieswere analyzed to document intraspecific divergence. Only three species wererepresented by a single specimen, and two species (Schizothorax nukiangensisand Triplophysa nujiangen) were represented by 226 and 107 individuals,respectively (Table S1).

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