Research Article |
Corresponding author: Zhi-Jun Zhou ( zhijunzhou@163.com ) Academic editor: Fernando Montealegre-Z
© 2016 Hui-Fang Guo, Bei Guan, Fu-Ming Shi, Zhi-Jun Zhou.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Guo H-F, Guan B, Shi F-M, Zhou Z-J (2016) DNA Barcoding of genus Hexacentrus in China reveals cryptic diversity within Hexacentrus japonicus (Orthoptera, Tettigoniidae). ZooKeys 596: 53-63. https://doi.org/10.3897/zookeys.596.8669
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DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Hence, a study was undertaken to establish DNA barcodes for all morphologically determined Hexacentrus species in China collections. In total, 83 specimens of five Hexacentrus species were barcoded using standard mitochondrial cytochrome c oxidase subunit I (COI) gene. Except for H. japonicus, barcode gaps were present in the remaining Hexacentrus species. Taxon ID tree generated seven BOLD’s barcode index numbers (BINs), four of which were in agreement with the morphological species. For H. japonicus, the maximum intraspecific divergence (4.43%) produced a minimal overlap (0.64%), and 19 specimens were divided into three different BINs. There may be cryptic species within the current H. japonicus. This study adds to a growing body of DNA barcodes that have become available for katydids, and shows that a DNA barcoding approach enables the identification of known Hexacentrus species with a very high resolution.
BOLD, China, DNA Barcoding, Hexacentrus , species delineation
DNA barcoding employs short, standardized gene regions (5' segment of mitochondrial cytochrome oxidase subunit I for animals) as an internal tag to enable metazoan species identification (
In this study, our objective is to assess the utility of DNA barcoding for closely related katydid species, belonging to the genus Hexacentrus (Serville, 1831) in China. Hexacentrus is mainly distributed in Australian, Afrotropical and Oriental realms. Hexacentrus is a particularly speciose genus, containing 24 known species (
All specimens were collected by hand or sweeping method during their active season (July–November). Hexacentrus species were all gathered in China from 12 localities, with the latitude from 18.70°N to 41.80°N and the longitude from 97.83°E to 123.38°E. One or more specimens were chosen from each locality in order to include as many morphologically distinguishable individuals per site as possible. Specimens were collected and stored in 100% ethanol at -20 °C and were deposited in the Hebei University Museum. Species-level identification was based on the original morphological descriptions, locality data and additional information. Details on all specimens (sampling location, GPS coordinates, voucher number, BOLD number, etc.) are available within the “DNA Barcoding of Hexacentrus in China, BHC” project in the Barcode of Life Data Systems (BOLD. www.barcodinglife.org).
Total DNA was extracted from the muscle of one hind leg of each specimens using TIANamp Genomic DNA Kit in accordance with the manufacturer’s instructions. The standardized gene regions of animals DNA barcoding was amplified using the primers COBU (5'-TYT CAA CAA AYC AYA ARG ATA TTG G-3') and COBL (5'-TAA ACT TCW GGR TGW CCA AAR AAT CA-3') (
Consensus sequence of both directions was assembled using SeqMan in Lasergene and verification of ambiguities and unexpected stop codons were performed in EditSeq (
The analyses were restricted to the subset of sequences, which met barcode standards (sequence length > 500bp, < 1% ambiguous bases, bidirectional sequencing, country specification). Intra- and inter-specific genetic distances were based on the Kimura-2-parameter (K2P) model (Kimura 1980) using the ‘distance summary’ tool in BOLD. The barcode gap was defined by intraspecific vs. interspecific [nearest neighbor (NN)] genetic distance of species. A globally unique identifier (i.e. BIN) then was assigned to each sequence cluster, creating an interim taxonomic system because the members of a particular BIN often correspond to a biological species. Character based DNA barcoding used the nucleotide variation in each position across DNA regions as diagnostic characters.
COI sequences were recovered from 86 of the 91 specimens that were analyzed with barcode compliant records from 83 specimens representing five species. Three records have no barcode compliant records because of low quality of trace file. A number of 80 barcodes belong to four previously identified species whereas three analyzed specimens were only identified to genus level because they are female; they probably are H. yunnaneus due to collection in Yunnan and separated from other specimens. The 658bp length sequences without indel (insertion/deletion) had full-length records. COI sequences were translated to amino acid sequences to check for stop codons and shifts in reading frame that might indicate the presence of nuclear mitochondrial copies (numts), but none were detected. Diagnostic character analysis was consistent with that of traditional external appearance discrimination. H. expansus only having one specimen was not analyzed, thus lacking diagnostic character.
Mean intraspecies divergence was 1.32% (ranged between 0.57% and 2.43%), and maximum intraspecies divergence 4.43% was observed in H. japonicus (Table
Mean and maximum intraspecific and nearest neighbor (NN) distance for all specimens.
Species | Mean intraspecific distance | Max intraspecific distance | Nearest neighbor | Distance to NN |
---|---|---|---|---|
Hexacentrus expansus | N/A | N/A | Hexacentrus unicolor | 13.19 |
Hexacentrus japonicus | 2.43 | 4.43 | Hexacentrus mundus | 3.79 |
Hexacentrus mundus | 0.57 | 0.93 | Hexacentrus japonicus | 3.79 |
Hexacentrus sp. | 0.72 | 1.08 | Hexacentrus unicolor | 9.72 |
Hexacentrus unicolor | 1.19 | 3.79 | Hexacentrus sp. | 9.72 |
Singleton species (H. expansus) were excluded from barcode gap analysis. Except for H. japonicus, barcode gap was present in the remaining Hexacentrus species (Fig.
The taxon ID tree was divided into seven clades represented by different BINs (Fig.
Taxon ID tree revealed seven well-differentiated haplogroups. Process ID, location, and BINs were shown in the tree. The clusters with a blue box indicated there may be two new putative ‘cryptic species’ within H. japonicus. The clade with a black box indicated the specimen had more mutation within H. unicolor.
Forty-four diagnostic characters were found in the study (Table
Character-based DNA barcodes for four Hexacentrus species of COI gene. A_7* means A is at the 7th position.
Species | Diagnostic characters | Characters no. | Specimen no. |
---|---|---|---|
Hexacentrus sp. | A_7* G_184 C_247 A_301 A_304 T_346 G_391 C_400 G_424 C_463 C_472 C_500 T_517 G_550 G_586 C_607 A_619 C_622 C_625 G_628 | 20 | 3 |
Hexacentrus unicolor | T_25 T_136 T_223 A_227 T_322 T_379 T_424 G_487 A_502 C_517 T_529 C_530 G_532 C_550 C_586 G_619 T_631 | 17 | 54 |
Hexacentrus mundus | T_34 T_118 C_187 T_397 A_643 | 5 | 6 |
Hexacentrus japonicus | T_460 C_514 | 2 | 19 |
The present study evaluated the efficacy of using DNA barcodes for the identification of Hexacentrus in China and provided a group of sequences associated with the identified species. Using these DNA barcoding, not only can one delineate the boundaries between species, but also assign taxonomic status to unknown specimens from known species.
Hexacentrus unicolor was controversial, and H. plantaris (Burmeister, 1838) and Tedla sellata (Walker, 1869) were considered as its synonyms. H. unicolor is distributed in south of the Yangtze River. In this study, however, one specimen was collected from Henan. In fact, molecular data support H. unicolor as a single group, with all specimens sharing one BIN (BOLD: ACD 7247). The specimen with black box (Fig.
DNA barcoding, as one effective tool in insect taxonomy, had been already applied widely. It can rapidly acquire molecular data, simplifying species classification and identification. Yet, DNA barcodes has been argued to be unreliable for consistent species identification by many authors due to a number of drawbacks (
Species boundaries were hard to delimit only based on morphologyas, and analyses including additional sources of information such as molecular data, biogeography, behavior and ecology has been called integrative taxonomy which has been shown to be very useful (
The ideal situation would be that each species was represented by sequence from its type material, particularly the holotype. Type specimens were also dried specimens and DNA degraded at different level, so not only amplification was difficult, but also the damage of specimens can’t be neglected. Recently,
We are grateful to the following people for collecting specimens and providing valuable comments during the manuscript preparation: Qiong Song; Ji–Yuan Feng; Zhi–Lin Chen; Bao–Jie Du; Xun Bian. This study was supported by National Natural Science Foundation of China (No. 31471985), and Excellent Youth Scholars Program of Higher Education of Hebei Province (No. BJ2014006).