Revealing cryptic diversity and population divergence in subtropical aphids through DNA barcoding

Abstract

Aphids are worldwide distributed pests, which feed on plant sap and cause serious losses to agricultural and forestry industries. Relatively few comprehensive studies have been conducted on aphid diversity in subtropics, although these regions may harbour hidden aphid diversity due to high plant diversity. In this study, we conducted DNA barcoding analysis for aphids in subtropical regions based on a comprehensive DNA barcode reference library including 5821 sequences and related ecological information (e.g. geography, host plant) of 379 morphospecies. In the reference library, 2140 sequences and related data of 151 morphospecies belonging to 77 genera and 11 subfamilies were newly produced by the current study. The average Kimura 2‐parameter distances within species, genera and subfamilies were 0.92%, 3.55% and 8.3%, respectively. The minimum interspecific distances were greater than the maximum intraspecific distances in 79.8% species, suggesting that barcode gaps existed in most aphid species. Automatic barcode gap discovery, Barcode Index Number, Bayesian Poisson tree processes and generalized mixed Yule‐coalescent revealed 419, 401, 462 and 455 single species‐representing clusters, respectively. A total of 32 morphospecies were assigned to more than one subclade respectively, suggesting geography or host plant‐mediated divergences and the existence of cryptic diversity. This study demonstrates that subtropical regions should have a higher species diversity of aphids, and cryptic species in certain morphospecies indicated in this study need to be investigated based on integrative taxonomic practices in the future. The DNA barcode reference library constructed herein provides a robust baseline data set to support future research in taxonomy, phylogenetics, ecology and evolution of aphids.

Delimiting species, revealing cryptic diversity, and population divergence in Qinghai‐Tibet Plateau weevils through DNA barcoding

“…Whereas ABGD and ASAP effectively identified barcode gaps based on inter‐ and intra‐GD values to segment the data (Puillandre et al., 2012 , 2021). In line with prior research, these two approaches produced relatively conservative outcomes (Hsiao & Oberprieler, 2024 ; Li et al., 2023 ; Song et al., 2018 ). Higher intra‐GD such as L. siahus (6.08%) and lower inter‐GD such as L .…”

“…In our study, accurate delimitation was achieved for 79.25% of morphospecies when the threshold of genetic distance was set at 2%. However, further scientific algorithms are required for species delimitation to avoid relying solely on empirical genetic distance thresholds (Li et al., 2023 ).…”

“…There is no standardized algorithm or input parameter that can optimally restore the true species boundary for all organisms (Ratnasingham & Hebert, 2013 ). Especially when dealing with large‐scale datasets, it becomes imperative to adopt an integrated approach to effectively classify species (Li et al., 2023 ; Song et al., 2018 ).…”

“…We utilized Origin 2018 to visualize and represent the distribution of genetic distances through histograms and scatter plots (Moberly et al., 2018 ). Identical sequences were condensed into unique haplotypes using DNAsp, which were subsequently employed for phylogenetic analyses (Li et al., 2023 ; Librado & Rozas, 2009 ). Phylogenetic inference analyses were conducted using maximum likelihood (ML).…”

“…When four or more species delimitation methods grouped sequences of morphospecies into a single MOTU, we considered the results of both morphological identification and molecular species delimitation to be consistent. Conversely, if sequences of the same morphospecies were grouped into more than one MOTUs by four or more species delimitation methods, or if sequences of different morphospecies were grouped into the same MOTU, we classified these cases as “taxonomic warnings” (Li et al., 2023 ).…”