Abstract
Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5ʹ (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.
Highlights
Thrips (Thysanoptera) are serious pests and disease vectors on many economically important crops throughout the world [1,2]
Intraspecific distances could not be determined for the 16 species with a single representative, but Nearest-Neighbor (NN) distances for all morphological species were more than 5%
This pattern supported the presence of a barcode gap
Summary
Thrips (Thysanoptera) are serious pests and disease vectors on many economically important crops throughout the world [1,2]. Identification of most thrips to a species level is difficult because of their small size, subtle morphological differentiation [3], intraspecific polymorphisms [4], and sexual dimorphisms [5]. Molecular identification of thrips has major advantages to morphology-based analysis because it overcomes the complexities introduced by morphological variation among life stages and the inconspicuous morphological differences among species [3,6]. Several gene regions have been employed for species discrimination [7, 8] and phylogenetic analysis [9]. Crespi et al [10] employed the nuclear 18S and mitochondrial gene cytochrome c oxidase I (COI) genes to examine phylogenetic relationships between two PLOS ONE | DOI:10.1371/journal.pone.0146014. Crespi et al [10] employed the nuclear 18S and mitochondrial gene cytochrome c oxidase I (COI) genes to examine phylogenetic relationships between two PLOS ONE | DOI:10.1371/journal.pone.0146014 January 7, 2016
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