ML tree from PhyML analysis of data set 2 (1,553 sequences).

<p>Some clusters collapsed. Numbers in parentheses following names are number of sequences within that group. Numbers on branches are RAxML bootstrap values followed by SH-like support values from PhyML expressed as a percentage, both shown only if ≥ 50. Asterisk indicates species not recovered as monophyletic.</p

Subtree for <i>Australothis</i> and <i>Helicoverpa</i> clade, from PhyML analysis of data set 2 (1,553 sequences).

<p>Species clusters collapsed. Numbers in parentheses following names are number of sequences within that group. Numbers on branches are RAxML bootstrap values followed by SH-like support values from PhyML expressed as a percentage, both shown only if ≥ 50. Asterisk indicates species incongruence due to misidentifications (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160895#sec008" target="_blank">discussion</a>).</p

ML tree for data set 1 (132 taxa).

<p>Well-supported terminal clusters (species or species groups) collapsed. Numbers in parentheses following names are number of sequences within that group. Asterisk indicates species not recovered as monophyletic. Numbers on branches are RAxML bootstrap values followed by SH-like support values from PhyML expressed as a percentage, both shown only if ≥ 50.</p

DNA Barcoding the Heliothinae (Lepidoptera: Noctuidae) of Australia and Utility of DNA Barcodes for Pest Identification in Helicoverpa and Relatives

<div><p><i>Helicoverpa</i> and <i>Heliothis</i> species include some of the world’s most significant crop pests, causing billions of dollars of losses globally. As such, a number are regulated quarantine species. For quarantine agencies, the most crucial issue is distinguishing native species from exotics, yet even this task is often not feasible because of poorly known local faunas and the difficulties of identifying closely related species, especially the immature stages. DNA barcoding is a scalable molecular diagnostic method that could provide the solution to this problem, however there has been no large-scale test of the efficacy of DNA barcodes for identifying the Heliothinae of any region of the world to date. This study fills that gap by DNA barcoding the entire heliothine moth fauna of Australia, bar one rare species, and comparing results with existing public domain resources. We find that DNA barcodes provide robust discrimination of all of the major pest species sampled, but poor discrimination of Australian <i>Heliocheilus</i> species, and we discuss ways to improve the use of DNA barcodes for identification of pests.</p></div

Evaluation of six candidate DNA barcode loci for identification of five important invasive grasses in eastern Australia

<div><p>Invasive grass weeds reduce farm productivity, threaten biodiversity, and increase weed control costs. Identification of invasive grasses from native grasses has generally relied on the morphological examination of grass floral material. DNA barcoding may provide an alternative means to identify co-occurring native and invasive grasses, particularly during early growth stages when floral characters are unavailable for analysis. However, there are no universal loci available for grass barcoding. We herein evaluated the utility of six candidate loci (<i>atpF</i> intron, <i>matK</i>, <i>ndhK-ndhC</i>, <i>psbE—petL</i>, ETS and ITS) for barcode identification of several economically important invasive grass species frequently found among native grasses in eastern Australia. We evaluated these loci in 66 specimens representing five invasive grass species (<i>Chloris gayana</i>, <i>Eragrostis curvula</i>, <i>Hyparrhenia hirta</i>, <i>Nassella neesiana</i>, <i>Nassella trichotoma</i>) and seven native grass species. Our results indicated that, while no single locus can be universally used as a DNA barcode for distinguishing the grass species examined in this study, two plastid loci (<i>atpF</i> and <i>matK</i>) showed good distinguishing power to separate most of the taxa examined, and could be used as a dual locus to distinguish several of the invasive from the native species. Low PCR success rates were evidenced among two nuclear loci (ETS and ITS), and few species were amplified at these loci, however ETS was able to genetically distinguish the two important invasive <i>Nassella</i> species. Multiple loci analyses also suggested that ETS played a crucial role in allowing identification of the two <i>Nassella</i> species in the multiple loci combinations.</p></div