Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
PLoS One. 2013 Jul 12;8(7):e68242. doi: 10.1371/journal.pone.0068242. Print 2013.
Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the species criteria applied, but methods should be chosen that minimize the inference of objectively erroneous species limits. Several protocols exploit single-gene or multi-gene coalescence statistics, assignment tests or other rationales related to nuclear DNA (nDNA) allele sharing to automatically delimit species. We apply seven different species delimitation protocols to a taxonomically confusing group of Malagasy lizards (Madascincus), and compare the resulting taxonomies with two newly developed metrics: the Taxonomic index of congruence C tax which quantifies the congruence between two taxonomies, and the Relative taxonomic resolving power index R tax which quantifies the potential of an approach to capture a high number of species boundaries. The protocols differed in the total number of species proposed, between 9 and 34, and were also highly incongruent in placing species boundaries. The Generalized Mixed Yule-Coalescent approach captured the highest number of potential species boundaries but many of these were clearly contradicted by extensive nDNA admixture between sympatric mitochondrial DNA (mtDNA) haplotype lineages. Delimiting species as phenotypically diagnosable mtDNA clades failed to detect two cryptic species that are unambiguous due to a lack of nDNA gene flow despite sympatry. We also consider the high number of species boundaries and their placement by multi-gene Bayesian species delimitation as poorly reliable whereas the Bayesian assignment test approach provided a species delimitation highly congruent with integrative taxonomic practice. The present study illustrates the trade-off in taxonomy between reliability (favored by conservative approaches) and resolving power (favored by inflationist approaches). Quantifying excessive splitting is more difficult than quantifying excessive lumping, suggesting a priority for conservative taxonomies in which errors are more liable to be detected and corrected by subsequent studies.
物种的划分和描述是进化、宏观生态学和保护等众多生物学学科的基础。根据应用的物种标准，将物种划分为独立的进化谱系可能而且通常会产生不同的结果，但应选择方法，使客观错误的物种界限的推断最小化。有几种方案利用单基因或多基因聚结统计、分配测试或与核 DNA（nDNA）等位基因共享相关的其他合理方案自动划分物种。我们将七种不同的物种划分方案应用于马达加斯加蜥蜴（Madascincus）一组分类上令人困惑的群体，并将得到的分类法与两种新开发的指标进行比较：分类一致性指数 C tax，用于量化两个分类法之间的一致性，以及相对分类解析力指数 R tax，用于量化一种方法捕捉大量物种边界的潜力。这些方案在提出的物种总数上有所不同，从 9 到 34 个，而且在放置物种边界方面也存在很大的不一致性。广义混合 Yule-Coalescent 方法捕获了最多数量的潜在物种边界，但由于在共生的线粒体 DNA（mtDNA）单倍型谱系之间存在广泛的 nDNA 混合，许多这些边界都明显与广泛的 nDNA 混合相矛盾。将物种划分为表型可诊断的 mtDNA 进化枝无法检测到两个由于缺乏 nDNA 基因流而明确的隐种，尽管有共生。我们还考虑了多基因贝叶斯物种划分方法所确定的大量物种边界及其位置的不可靠性，而贝叶斯分配测试方法提供了一种与综合分类学实践高度一致的物种划分方法。本研究说明了分类学中在可靠性（保守方法倾向）和解析力（膨胀方法倾向）之间的权衡。量化过度分裂比量化过度合并更困难，这表明优先考虑保守分类学更为重要，因为在后续研究中更容易发现和纠正错误。
