Restricted accessResearch articleFirst published online 2020-04
Better Resolution for Cytochrome b than Cytochrome c Oxidase Subunit I to Identify Schizothorax Species (Teleostei: Cyprinidae) from the Tibetan Plateau and Its Adjacent Area
The genus Schizothorax is one of the most diverse groups of schizothoracine fish. Many species within this genus possess highly similar morphological characters and are very difficult to be identified accurately only based on morphology. The present study aims to test the effectiveness of mitochondrial cytochrome c oxidase subunit I (COI) gene and cytochrome b (Cytb) gene for discriminating the Schizothorax fish. A total of 185 individuals of 11 species for COI gene and 264 individuals of 23 species for Cytb gene were used for analyzing, respectively. According to the genetic distances, only one species based on COI gene and five species based on Cytb gene had “barcoding gaps,” respectively. The tree-based analysis displayed that four species based on COI gene and six species based on Cytb gene clustered monophyletic group with strong support, respectively. The optimal threshold value of Schizothorax is 0.005 based on COI gene and 0.008 based on Cytb gene. The results of genetic similarity tests performed through online BLAST showed that 108 of 185 similarity searches succeeded in identifying conspecific sequences based on COI gene and 199 of 264 succeeded in identifying conspecific sequences based on Cytb gene. Considering greater interspecific genetic distance in Kimura 2-parameter (K2P) analysis and many clades with higher supporting values in tree-based analysis, we suggest that Cytb gene has better resolution in discrimination of Schizothorax species than COI gene. However, there are still many confused clustering relationships based on molecular data currently available. Incomplete lineage sorting, the existence of possible cryptic species and problematic morphological identification, etc. might have greatly weakened the resolution of Cytb gene in discrimination of Schizothorax species.
Get full access to this article
View all access options for this article.
References
1.
AhmadS.M., BhatF.A., BalkhiM.U.H., and BhatB.A. (2014). Mitochondrial DNA variability to explore the relationship complexity of schizothoracine (Teleostei: Cyprinidae). Genetica, 142, 507–516.
2.
AkhtarT., and AliG. (2016). DNA barcoding of Schizothorax species from the Neelum and Jhelum Rivers of Azad Jammu and Kashmir. Mitochondrial DNA Part B, 1, 934–936.
3.
AltschulS.F., MaddenT.L., SchäfferA.A., ZhangJ.H., ZhangZ., MillerW., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25, 3389–3402.
4.
AnjaliK.M., MandalA., GunalanB., RubanL., AnandajothiE., ThineshsantharD., et al. (2019). Identification of six grouper species under the genus Epinephelus (Bloch, 1793) from Indian waters using PCR-RFLP of cytochrome c oxidase I (COI) gene fragment. Food Control, 101, 39–44.
5.
ArmaniA., CastigliegoL., TinacciL., GianfaldoniD., and GuidiA. (2011). Molecular characterization of icefish, (Salangidae family), using direct sequencing of mitochondrial cytochrome b gene. Food Control, 22, 888–895.
6.
BaratA., AliS., SatiJ., and SivaramanG.K. (2012). Phylogenetic analysis of fishes of the subfamily Schizothoracinae (Teleostei: Cyprinidae) from Indian Himalayas using cytochrome b gene. Indian J Fish, 59, 43–47.
7.
CaoW.X., ChenY.Y., WuY.F., and ZhuS.Q. (1980). Origin and evolution of schizothoracine fishes in relation to the upheaval of the Xizang Plateau. In Studies on the Period, Amplitude and Type of the Uplift of the Qinghai-Xizang Plateau. Tibetan Expedition Team of the Chinese Academy of Science, ed. (Science Press, Beijing), pp. 118–130.
8.
CarreraE., GarciaT., CespedesA., GonzalezI., SanzB., HernandezP.E., et al. (1998). Identification of Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) by using polymerase chain reaction amplification and restriction analysis of the mitochondrial cytochrome b gene. J Food Protect, 61, 482–486.
9.
Carrero-SarmientoD., and Hoyos-LópezR. (2018). Molecular identification and genetic diversity of Lutzomyia gomezi (Diptera: Psychodidae) using DNA-barcodes in Cordoba, Colombia. Trop Biomed, 35, 100–110.
10.
ChandraS., BaratA., SinghM., SinghB.K., and MaturaR. (2012). DNA bar-coding of Indian coldwater fishes of genus Schizothorax (family: Cyprinidae) from Western Himalaya. World J Fish Mar Sci, 4, 430–435.
11.
ChenW.T., MaX.H., ShenY.J., MaoY.T., and HeS.P. (2015). The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding. Sci Rep, 5, 17437.
12.
ChenW.T., YueX.J., and HeS.P. (2017). Genetic differentiation of the Schizothorax species complex (Cyprinidae) in the Nujiang River (upper Salween). Sci Rep, 7, 5944.
13.
ChenY.F., and CaoW.X. (2000). Schizothoracinae. In Fauna Sinica, Osteichthyes, Cypriniformes III. P.Q. Yue, ed. (Science Press, Beijing), pp. 273–335.
14.
ChenY.Y., LiR., LiC.Q., LiW.X., YangH.F., XiaoH., et al. (2018). Testing the validity of two putative sympatric species from Sinocyclocheilus (Cypriniformes: Cyprinidae) based on mitochondrial cytochrome b sequences. Zootaxa, 4476, 130–140.
15.
ChenY.Y., ZhangW., and HuangS.Y. (1982). Speciation in schizothoracid fishes of Lake Lugu. Acta Zool Sin, 28, 217–225.
16.
CollinsR.A., and CruickshankR.H. (2013). The seven deadly sins of DNA barcoding. Mol Ecol Resour, 13, 969–975.
17.
DarribaD., TaboadaG.L., DoalloR., and PosadaD. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nat Methods, 9, 772.
18.
DimmickW.W., and EddsD.R. (2002). Evolutionary genetics of the endemic schizorathicine (Cypriniformes: Cyprinidae) fishes of Lake Rara, Nepal. Biochem Syst Ecol, 30, 919–929.
19.
DingR.H. (1994). The Fishes of Sichuan, China (Sichuan Publishing House of Science and Technology, Chengdu).
20.
FelsensteinJ. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783–791.
GoelC., SahooP.K., and BaratA. (2016). Complete mitochondrial genome organization of Schizothorax plagiostomus (Heckel, 1838). Mitochondrial DNA Part A, 27, 113–114.
23.
GuindonS., DufayardJ.F., LefortV., AnisimovaM., HordijkW., and GascuelO. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol, 59, 307–321.
24.
GuoX.Z., ZhangG.R., WeiK.J., JiW., YanR.J., WeiQ.W., et al. (2019). Phylogeography of the threatened tetraploid fish, Schizothorax waltoni, in the Yarlung Tsangpo River on the southern Qinghai-Tibet Plateau: implications for conservation. Sci Rep, 9, 2704–2718.
HeD.K., and ChenY.F. (2006). Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences. J Ecol, 33, 1448–1460.
27.
HouG., ChenW.T., LuH.S., ChengF., and XieS.G. (2018). Developing a DNA barcode library for perciform fishes in the South China Sea: species identification, accuracy and cryptic diversity. Mol Ecol Resour, 18, 137–146.
28.
HubertN., Delrieu-TrottinE., IrissonJ.O., MeyerC., and PlanesS. (2010). Identifying coral reef fish larvae through DNA barcoding: a test case with the families Acanthuridae and Holocentridae. Mol Phylogenet Evol, 55, 1195–1203.
29.
IvanovaN.V., ZemlakT.S., HannerR.H., and HebertP.D. (2007). Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes, 7, 544–548.
30.
JenningsW.B., RuschiP.A., FerraroG., QuijadaC.C., Silva-MalanskiA.C.G., ProsdocimiF., et al. (2019). Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails. Genome, 62, 77–83.
31.
JiangF., FuW., ClarkeA.R., SchutzeM.K., SusantoA., ZhuS.F., et al. (2016). A high-throughput detection method for invasive fruit fly (Diptera: Tephritidae) species based on microfluidic dynamic array. Mol Ecol Resour, 16, 1378–1388.
32.
KatsuK., SuzukiT., FujinoK., MorishitaT., and NodaT. (2019). Development of a DNA marker for variety discrimination specific to “Manten-Kirari” based on an NGS-RNA sequence in Tartary buckwheat (Fagopyrum tataricum). Food Chem 295, 51–57.
33.
KimuraM. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol, 16, 111–120.
34.
KocherT.D., and StepienC.A., eds. (1997). Molecular Systematics of Fishes. (San Diego: Academic Press).
35.
KressW.J., and EricksonD.L. (2007). A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One, 2, e508.
36.
KroschM.N., SchutzeM.K., StruttF., ClarkeA.R., and CameronS.L. (2019). A transcriptome-based analytical workflow for identifying loci for species diagnosis: a case study with Bactrocera fruit flies (Diptera: Tephritidae). Austral Entomol, 58, 395–408.
37.
LeM.H., and PhamH.Q. (2018). Seasonal changes in the milt quality of Waigieu seaperch, Psammoperca waigiensis: implications for artificial propagation. J World Aquacult Soc, 49, 857–866.
38.
LehmkuhlF., and HaseleinF. (2000). Quaternary paleoenvironmental change on the Tibetan Plateau and adjacent areas (Western China and Western Mongolia). Quatern Int, 65, 121–145.
39.
LiJ.X., LiuD.Q., MaQ.Z., ZhangX.Y., DaiW., ChenY.B., et al. (2015). Discriminating Dabry's sturgeon (Acipenser dabryanus) and Chinese sturgeon (A. sinensis) based on DNA barcode and six nuclear markers. Hydrobiologia, 757, 185–196.
40.
LiJ.X., WangY., JinH.F., LiW.J., YanC.C., YanP.F., et al. (2017). Identification of Triplophysa species from the Qinghai-Tibetan Plateau (QTP) and its adjacent regions through DNA barcodes. Gene, 605, 12–19.
41.
LiM., and YuT.F. (2010). The application of DNAStar soft in research of animal virus. J Sci Teachers College Univ, 30, 61–63.
42.
LiX.Y., DengY.P., YangK., GanW.X., ZengR.K., DengL.J., et al. (2016). Genetic diversity and structure analysis of Percocypris pingi (Cypriniformes: Cyprinidae): implications for conservation and hatchery release in the Yalong River. PLoS One, 11, e0166769.
43.
LutzL., WilliamsK.A., VilletM.H., EkanemM., and SzpilaK. (2018). Species identification of adult African blowflies (Diptera: Calliphoridae) of forensic importance. Int J Legal Med, 132, 831–842.
44.
MeierR., ShiyangK., VaidyaG., and NgP.K.L. (2006). DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol, 55, 715–728.
45.
MeyerC.P., and PaulayG. (2005). DNA barcoding: error rates based on comprehensive sampling. PLoS Biol, 3, e422.
46.
MirandeJ.M. (2019). Morphology, molecules and the phylogeny of Characidae (Teleostei, Characiformes). Cladistics, 35, 282–300.
47.
NicolasV., SchaefferB., MissoupA.D., KennisJ., ColynM., DenysC., et al. (2012). Assessment of three mitochondrial genes (16S, Cytb, COI) for identifying species in the Praomyini tribe (Rodentia: Muridae). PLoS One, 7, e36586.
48.
O'HaraT.D., StöhrS., HugallA.F., ThuyB., and MartynovA. (2018). Morphological diagnoses of higher taxa in Ophiuroidea (Echinodermata) in support of a new classification. Eur J Taxon, 416, 1–35.
49.
PosadaD., and BuckleyT.R. (2004). Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol, 53, 793–808.
50.
QiD.L., GuoS.C., TangW.J., YanJ., and ZhaoX.Q. (2006). Molecular systematics of morphologically similar fishes in the Schizothoracinae in Nanmenxia River, with implication for morphological convergent evolution. Acta Zool Sin, 52, 862–870.
51.
QiuH., and ChenY.F. (2009). Age and growth of Schizothorax waltoni in the Yarlung Tsangpo River in Tibet, China. Ichthyol Res, 56, 260–265.
52.
QuM., TangW., LiuQ.H., WangD.X., and DingS.X. (2018). Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker. Mol Phylogenet Evol, 121, 46–51.
53.
RonquistF., and HuelsenbeckJ.P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574.
54.
SaitouN., and NeiM. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 4, 406–425.
55.
SeehausenO., ButlinR.K., KellerI., WagnerC.E., BoughmanJ.W., HohenloheP.A., et al. (2014). Genomics and the origin of species. Nat Rev Genet, 15, 176–192.
56.
SeifertK.A. (2009). Progress towards DNA barcoding of fungi. Mol Ecol Resour, 9, 83–89.
57.
SilasE.G. (1960). Fishes from the Kashmir valley. J Bombay Nat Hist Soc, 57, 66–77.
58.
SinghU., NautiyalP., and DewanS. (2018). Sub-speciation tendencies, genetic diversity and divergence of the Schizothorax progastus (McClelland, 1839) in tributaries of the Ganga river in Indian Himalayas. J Coldwater Fisheries, 1, 54–59.
59.
SongJ., SongZ.B., YueB.S., and ZhengW.J. (2006). Assessing genetic diversity of wild populations of Prenant's schizothoracin, Schizothorax prenanti, using AFLP markers. Environ Biol Fishes, 77, 79–86.
60.
StamatakisA., HooverP., and RougemontJ. (2008). A rapid bootstrap algorithm for the RAxML web servers. Syst Biol, 57, 758–771.
61.
StauchG., LaiZ., LehmkuhlF., and SchulteP. (2018). Environmental changes during the late Pleistocene and the Holocene in the Gonghe Basin, north-eastern Tibetan Plateau. Palaeogeogr Palaeocl, 509, 144–155.
62.
SteinkeD., ZemlakT.S., BoutillierJ.A., and HebertP.D.N. (2009). DNA barcoding of Pacific Canada's fishes. Mar Biol, 156, 2641–2647.
63.
TamuraK., PetersonD., PetersonN., StecherG., NeiM., and KumarS. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol, 28, 2731–2739.
64.
TautzD., ArctanderP., MinelliA., ThomasR.H., and VoglerA.P. (2002). DNA points the way ahead in taxonomy. Nature, 418, 479.
65.
TizardJ., PatelS., WaughJ., TavaresE., BergmannT., GillB., et al. (2019). DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation. BMC Evol Biol, 19, 52.
66.
WangQ.L., SiF., YuS.S., YuanL.L., YuQ.H., JiangX.F., and RenY.Q. (2019). Identification and adaptability of hatchery-origin Japanese flounder released into the Bohai Sea after the summer fishing moratorium. Aquaculture, 504, 164–171.
67.
WangY.K., ZhangN., WangD., WuJ.C., and ZhangX. (2018). Investigating the impacts of cascade hydropower development on the natural flow regime in the Yangtze River, China. Sci Total Environ, 624, 1187–1194.
68.
WardR.D., ZemlakT.S., InnesB.H., LastP.R., HebertP.D.N. (2005). DNA barcoding Australia's fish species. Phil Trans R Soc B, 360, 1847–1857.
69.
WeiQ.W., ChenX.H., YangD.G., LiuJ.Y., ZhuY.J., and ZhengW. (2005). Variations in spawning stock structure of Acipenser sinensis within 24 years since damming of Gezhouba dam. J Fish Sci China, 12, 452–457.
70.
WiemersM., and FiedlerK. (2007). Does the DNA barcoding gap exist?—a case study in blue butterflies (Lepidoptera: Lycaenidae). Front Zool, 4, 1–16.
71.
WuY.F., and WuC.Z. (1992). The Fishes of the Qinghai-Xizang Plateau (Sichuan Publishing House of Science and Technology, Chengdu).
72.
WyzgaB., ZawiejskaJ., and GurnellA.M. (2018). Effects and persistence of river restoration measures: ecological, management and research implications. Sci Total Environ, 628–629, 1098–1100.
73.
XiaoW.H., ZhangY.P., and LiuH.Z. (2001). Molecular systematics of Xenocyprinae (Teleostei: Cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia. Mol Phylogenet Evol, 18, 163–173.
74.
YangJ., ChenX.Y., and YangJ.X. (2009). The identity of Schizothorax griseus Pellegrin, 1931, with descriptions of three new species of schizothoracine fishes (Teleostei: Cyprinidae) from China. Zootaxa, 2006, 23–40.
75.
YangJ., YangJ.X., and ChenX.Y. (2012). A re-examination of the molecular phylogeny and biogeography of the genus Schizothorax (Teleostei: Cyprinidae) through enhanced sampling, with emphasis on the species in the Yunnan–Guizhou Plateau, China. J Zool Syst Evol Res, 50, 184–191.
76.
YeH., XiaoS.J., WangX.Q., WangZ.Y., ZhangZ.S., ZhuC.K., et al. (2018). Characterization of spleen transcriptome of Schizothorax prenanti during Aeromonas hydrophila infection. Mar Biotechnol, 20, 246–256.
77.
YueX.J., WangD., LiuS.P., YuanX.P., DuanX.B., ChenD.Q., et al. (2010). Population genetic structure of three schizothoracins from Nujiang River in Southwestern China. Acta Zool Sin, 30, 6418–6429.
78.
ZhangC.F., TongC., LudwigA., TangY.T., LiuS.J., ZhangR.Y., et al. (2018). Adaptive evolution of the Eda gene and scales loss in schizothoracine fishes in response to uplift of the Tibetan Plateau. Int J Mol Sci, 19, 2953.
79.
ZhangJ., and HannerR. (2012). Molecular approach to the identification of fish in the South China Sea. PLoS One, 7, e30621.
80.
ZhaoC.S., YangS.T., LiuJ.G., LiuC.M., HaoF.H., WangZ.G., et al. (2018). Linking fish tolerance to water quality criteria for the assessment of environmental flows: a practical method for streamflow regulation and pollution control. Water Res, 141, 96–108.
81.
ZhuY.X., ChenY., ChengQ.Q., QiaoH.Y., and ChenW.M. (2013). The complete mitochondrial genome sequence of Schizothorax macropogon (Cypriniformes: Cyprinidae). Mitochondrial DNA, 24, 237–239.
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
