Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia

Abstract

In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5–99.5%) and of species was low (25.6–44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1–44.6% and 25.6–31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of “correct” (97.6%) and a low percentage of “incorrect” (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are encountered in the application of genetic and morphological data to species delimitations, with taxonomic signal limited by extensive infra-specific variation and shared polymorphisms among species in both data types.

Phylogenetic lineages and the role of hybridization as driving force of evolution in grass supertribe Poodae

“…Since then, due to the sheer size of the group, usually representative genera were selected for comparative studies to gain an overview on the whole Poodae and their major groupings using morphological data, plastid DNA restriction site analysis, traditional Sanger and, more recently, plastid genome sequencing (Soreng & Davis, ; Davis & Soreng, ; Döring & al., ; Quintanar & al., ; Soreng & al., ; Schneider & al., ; Saarela & al., , ; Pimentel & al., ; Orton & al., ). Other studies focused on special groups using an in‐depth sampling of taxa, for example, within traditional Aveneae (Grebenstein & al., ; Döring, ; Saarela & al., , ; Wölk & Röser, , ; Barberá & al., ) and Poeae (Schneider & al., ; Birch & al., , ), in which especially the subtribes Poinae (Hunter & al., ; Gillespie & Soreng, ; Gillespie & al., , , , , ; Refulio‐Rodríguez & al., ; Hoffmann & al., ; Soreng & al., , ; Nosov & al., , ), Loliinae (Torrecilla & Catalán, , Catalán & al., , ; Torrecilla & al., ; Inda & al., ; Cheng & al., ; Minaya & al., ), Sesleriinae (Kuzmanović & al., ), Brizinae and Calothecinae (Essi & al., ; Persson & Rydin, ; Silva & al., ) were studied.…”

DNA barcodes successfully delimit morphospecies in a superdiverse insect genus

“…The choice of analytical method for the analysis of DNA barcode data can be of great importance in biodiversity assessments. Among a range of methods, distance‐based and tree‐based approaches are commonly used in barcoding studies (Austerlitz et al., ; Birch, Walsh, Cantrill, Holmes, & Murphy, ; Chu, Tong, & Chan, ). The instance‐based methods usually require a threshold similarity value to distinguish intraspecific and interspecific variations (Meier, Shiyang, Vaidya, & Ng, ).…”

The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements

“…Similarity-based measures are known to fail in several common situations such as variable rates of molecular evolution [43,44], gene duplication [44,45] and changes in the gene's composition [46]. Empirically, similarity-based approaches and phylogenetic methods for barcoding analysis are rarely compared explicitly even though they can produce conflicting identifications (see [47] which shows distance-based analyses performed best on Australian grasses, yet [48] who found tree-based methods worked better in Vicia).…”