Innovative integration of high-throughput DNA barcoding, transcriptome-based constrained phylogenetics, hyperspectral imaging, and morphology to assess and characterize a poorly known fauna

我们提出了一种整合形态学和分子方法的物种描述新范式。非洲是一个理想的试验场，因为在任何重要的收集中都可能有数百种未被描述的物种。我们将生成所有非洲毛翅蝇家族的转录组，然后使用高通量测序技术对非洲热带地区（埃塞俄比亚的Bale Mts，刚果民主共和国的Albertine裂谷和刚果盆地以及贝宁）以前和新收集的毛翅目群落的数百个形态种的两个基因（mtCOI, 28S rRNA）进行测序。我们将使用一种保守的DNA分类学方法，基于rRNA+mtDNA分支的单一性来划分物种，并将其与现代基于聚结的多位点物种划分进行比较，以帮助开发非洲球虱的基线分类学。我们还将使用高光谱成像作为一个额外的，独立的字符集，以帮助划定困难的物种复合体。为了将新发现和重新发现的球虱多样性放在物种水平的生命树上，我们将使用转录组序列建立一个骨干系统发育，然后我们可以从我们的两个基因中填充一个物种水平的系统发育。这种完全确定的、物种丰富的、多基因的系统发育将使我们能够快速、准确地诊断出数百种目前对科学来说是新的分类群。这些新物种将用诊断示意图加以说明，并与分类学专家网络合作进行描述。该项目将成为将DNA分类学的速度和效率与经过时间考验的物种描述形态学概念结合起来的一个例子。

We propose a new paradigm of species descriptions integrating morphological and molecular methods. Africa is an ideal testing ground, because there are likely to be hundreds of undescribed species available in any significant collection. We will generate transcriptomes for all African caddisfly families, and then sequence two genes for hundreds of morphospecies (mtCOI, 28S rRNA) from previously and newly collected Trichoptera communities of Afrotropical regions (Bale Mts in Ethiopia, Albertine Rift and Congo Basin in DR Congo, and Benin) using high-thoughput sequencing technologies. We will use a conservative DNA taxonomy approach for delimiting species based on monophyly of rRNA+mtDNA clades and compare this with modern coalescent-based multi-locus species delimitations to help develop a baseline taxonomy of caddisflies in Africa. We will also use hyperspectral imaging as an additional, independent character set to help delimit difficult species complexes. To place the newly identified and rediscovered diversity of caddisflies on a species-level tree of life, we will use transcriptome sequences to build a backbone phylogeny, upon which we can then fill out a species-level phylogeny from our two genes. This fully resolved, species rich, multi-gene phylogeny will allow us to make rapid, accurate diagnoses for hundreds of taxa currently new to science. These new species will be illustrated with diagnostic schematics and described in collaboration with a network of taxonomic experts. The project will be an example of merging the speed and efficiency of DNA taxonomy with time tested morphological concepts of species description.