Bio-Protection Research Centre, PO Box 84, Lincoln University, Lincoln 7647, New Zealand.
Evol Bioinform Online. 2012;8:1-37. doi: 10.4137/EBO.S8532. Epub 2011 Dec 8.
Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, "tip to root", for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg's reciprocal monophyly, (P(AB)),1 (2) Rodrigo's (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits might be drawn. In the species cases here, the results clearly indicate that there is a need for more gene sampling to substantiate either the new cohort of species indicated for B. tabaci or to detect the established subspecies taxonomy of L. dispar. Given the ease of use through the Geneious species delimitation plugins, similar analysis of such multi-gene datasets would be easily accommodated. Overall, the tip to root approach described here is recommended where careful consideration of species delimitation is required to support crucial biosecurity decisions based on accurate species identification.
物种划分直接影响全球生物安全。它是各国政府在贸易流动和实施生物安全措施以保护国家免受入侵物种威胁方面决策的关键因素。在这里，我们概述了一种新的物种划分方法，“从尖端到底部”，用于两种极具入侵性的昆虫害虫，烟粉虱（甘薯粉虱）和舞毒蛾（亚洲舞毒蛾）。这两个物种都对生物安全构成威胁，但它们说明了最复杂的生物安全划分问题所呈现的极端系统发育分辨率；烟粉虱具有极高的种内遗传变异性，舞毒蛾由相对不明显的亚种组成。本研究测试了一系列分析选项，以确定它们作为提供更严格的物种划分措施的工具的适用性，从而为生物安全提供更具防御性的物种分配和未知物的鉴定。这里使用的是越来越多的被认为适用于生物安全的已建立的 DNA 条码数据集（COI）的数据。所采用的分析方法包括常用的 Kimura 双参数（K2P）种间距离加上另外四种更严格的分类群独特性度量，（1）罗森伯格的互惠单系性（P(AB)），1（2）罗德里戈的（P（随机独特）），2（3）系统发生分类指数（gsi），3 和（4）广义混合 Yule 合并（GMYC）。4,5 对于这两个昆虫数据集，方法的比较分析表明，K2P 距离方法不能捕获与其他三种方法相同的物种独特性水平；在烟粉虱中，用 K2P 距离识别的独特群体比以前多，而在舞毒蛾中，在预定义的亚种内，明显的变异较少。P(AB)、P(randomly distinct) 和 gsi 的结果一致性为遗传界限可能划定的位置提供了更大的统计置信度。在这些物种的情况下，结果清楚地表明，需要更多的基因采样来证实烟粉虱新的物种群或检测舞毒蛾已建立的亚种分类。考虑到 Geneious 物种划分插件的易用性，很容易适应这种多基因数据集的类似分析。总体而言，这里描述的从尖端到底部的方法建议在需要仔细考虑物种划分以支持基于准确物种识别的关键生物安全决策时使用。
