DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods

Abstract

Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a ‘barcode gap’ and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

“…The chloroplast ribulose‐1, 5‐bisphosphate carboxylase/oxygenase large subunit gene ( rbcL ) and maturase K gene ( matK ) are the approved barcodes for land plants (CBOL Plant Working Group 2009). However, plant‐plastid barcodes typically have lower resolving power to separate closely related plant species compared to the animal barcode, and in several cases, conspecifics or recently diverged species do not form highly supported, distinct sequence clusters that allow species discrimination (Hollingsworth et al., 2016; van Velzen, Weitschek, Felici, & Bakker, 2012; Zhang et al., 2012). In fact, a uniquely identified species in a given genus is the exception rather than the rule in most plant barcoding studies (Hollingsworth, Graham, & Little, 2011).…”

Exposing the illegal trade in cycad species (Cycadophyta:Encephalartos) at two traditional medicine markets in South Africa using DNA barcoding

“…To test the efficiency of the Encephalartos DNA barcode library, we calculated species discrimination using BRONX version 2.0 (Barcode Recognition Obtained with Nucleotide eXposé's; Little and Stevenson 2007;Little 2011), which is an alignment-free algorithm that relies on the presence/absence of particular characters in the barcode sequences for identification, instead of using them all (Van Velzen et al 2012), thereby accounting for withintaxon variation (Little 2011). For this, a unified reference database was constructed for southern African Encephalartos spp.…”

Distinction and relatedness – Taxonomic and genetic studies reveal a new species group of goatfishes (Upeneus; Mullidae)

“…This is reflected by the sharing of haplotypes, the nonmonophyly or incomplete clustering of the two taxa, the shallow divergence among them, and the lack of a clear 'barcoding gap'. This pattern is a population-genetic phenomenon, whereby, under coalescent theory, haplotypes of recently separated species (aided by potentially large population sizes) coalesce to a most recent common ancestor (the shared ancestral haplotype in this case) that pre-dates the actual speciation event, causing incomplete lineage sorting (Van Velzen et al 2012). This is then reflected in para-or polyphyly and the lack of a 'barcode gap' (Van Velzen et al 2012), with shallow divergences between taxa reflecting their recent separation and indicating insufficient time for monophyly to be established (Ward et al 2005;Hubert et al 2008).…”

“…This pattern is a population-genetic phenomenon, whereby, under coalescent theory, haplotypes of recently separated species (aided by potentially large population sizes) coalesce to a most recent common ancestor (the shared ancestral haplotype in this case) that pre-dates the actual speciation event, causing incomplete lineage sorting (Van Velzen et al 2012). This is then reflected in para-or polyphyly and the lack of a 'barcode gap' (Van Velzen et al 2012), with shallow divergences between taxa reflecting their recent separation and indicating insufficient time for monophyly to be established (Ward et al 2005;Hubert et al 2008). Such a pattern of haplotypes being shared among morphologically valid species is not uncommon (Hubert et al 2008(Hubert et al , 2012Mabragaña et al 2011;Van Velzen et al 2012) and is well documented in reef fishes (Victor 2014).…”