Journal Article

Singleton molecular species delimitation based on COI-5P barcode sequences revealed high cryptic/undescribed diversity for Chinese katydids (Orthoptera: Tettigoniidae)

Guo, Huifang, Chai, Jinyan, Che, Xuting, Shi, Fuming, Zhou, Zhijun, Han, Li

2019

Overview

Background DNA barcoding has been developed as a useful tool for species discrimination. Several sequence-based species delimitation methods, such as Barcode Index Number (BIN), REfined Single Linkage (RESL), Automatic Barcode Gap Discovery (ABGD), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP), were used. Our aim was to estimate Chinese katydid biodiversity using standard DNA barcode cytochrome c oxidase subunit I (COI-5P) sequences. Results Detection of a barcoding gap by similarity-based analyses and clustering-base analyses indicated that 131 identified morphological species (morphospecies) were assigned to 196 BINs and were divided into four categories: (i) MATCH (83/131 = 64.89%), morphospecies were a perfect match between morphospecies and BINs (including 61 concordant BINs and 22 singleton BINs); (ii) MERGE (14/131 = 10.69%), morphospecies shared its unique BIN with other species; (iii) SPLIT (33/131 = 25.19%, when 22 singleton species were excluded, it rose to 33/109 = 30.28%), morphospecies were placed in more than one BIN; (iv) MIXTURE (4/131 = 5.34%), morphospecies showed a more complex partition involving both a merge and a split. Neighbor-joining (NJ) analyses showed that nearly all BINs and most morphospecies formed monophyletic cluster with little variation. The molecular operational taxonomic units (MOTUs) were defined considering only the more inclusive clades found by at least four of seven species delimitation methods. Our results robustly supported 61 of 109 (55.96%) morphospecies represented by more than one specimen, 159 of 213 (74.65%) concordant BINs, and 3 of 8 (37.5%) discordant BINs. Conclusions Molecular species delimitation analyses generated a larger number of MOTUs compared with morphospecies. If these MOTU splits are proven to be true, Chinese katydids probably contain a seemingly large proportion of cryptic/undescribed taxa. Future amplification of additional molecular markers, particularly from the nuclear DNA, may be especially useful for specimens that were identified here as problematic taxa.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Animal Systematics/Taxonomy/Biogeography / Animals / Bar codes / Base Sequence / Bayes Theorem / Bayesian analysis / Biodiversity / Biomedical and Life Sciences / Clustering / Clustering-based method, Similarity-based method / Cryptic species / Cytochrome / Cytochrome c / Cytochrome oxidase / Cytochrome-c oxidase / Cytochromes / Deoxyribonucleic acid / DNA / DNA barcoding / DNA Barcoding, Taxonomic - methods / Entomology / Evolutionary Biology / Gene sequencing / Genetic aspects / Genetic Variation / Genetics and Population Dynamics / Genomes / Hybridization / Identification / Katydids / Life Sciences / Methods / Mitochondrial DNA / Morphology / Multiculturalism & pluralism / Nucleotide sequence / Orthoptera / Orthoptera - classification / Orthoptera - genetics / Oxidases / Phylogeny / Research Article / Speciation and evolutionary genetics / Species / Species delimitation / Species Specificity / Taxa / Taxonomy