DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies

Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tes...

当类群在种以上阶元的分类位置存在争议时，常被标记为分类未定（incertae sedis），例如其亚属、属或亚族级的归属问题。由于难以鉴定合适的共有衍征（synapomorphies），这一问题在系统发育关系复杂的类群中普遍存在。本研究提出将DNA条形码（DNA barcode）与多位点骨干系统发育树相结合，以实现类群的属级及更高阶元分类归属判定。该采样策略所构建的分子矩阵存在大量非随机分布的缺失数据：所有研究代表类群均会被采样条形码序列，而额外的分子标记仅在小比例类群中被获取。本研究针对含1000个分类单元的系统发育树（最多涵盖100个分子标记）开展模拟分析，并以包含大量分类学未明确物种的大类群——眼灰蝶亚族（Polyommatina，鳞翅目：灰蝶科）——为实际案例，探究了缺失数据的程度与随机性对系统发育准确性的影响。我们的模拟测试...