Forgotten treasures – using historic collections to assess the diversity and systematics of wide-ranging taxa: A case study using African Hinge-back Tortoises (Kinixys spp.)

分子遗传学方法在分类学中的应用以指数级的速度加速了未被识别的类群的发现，许多假定广泛分布的物种被确定为物种复合体。这意味着假定分布广泛和常见的物种可能拥有多个狭小分布和濒危的类群。因此，假定分布广泛的类群需要相当多的关注。然而，对范围横跨几个政治边界的分类群进行范围广泛的采样是昂贵、耗时的，而且受到立法限制的阻碍。因此，从科学收集中获得的基因样本是一个吸引人的选择。不幸的是，博物馆标本的DNA经常严重降解、碎裂，并被外源DNA污染。因此，加工需要广泛的预防措施、特殊设施和方法。下一代测序(NGS)和基于杂交的靶标浓缩的出现使基因研究发生了革命性的变化，极大地提高了使用历史材料的可能性。拟议的项目将应用NGS和aDNA方法，利用历史收集材料、一套线粒体和核标记以及逐步分析方案，示范性地阐明三个广泛的乌龟物种的多样性。对于选定的物种，只有少数新鲜样本可以从有限的范围部分获得，但大量的历史标本保存在科学收藏品中。这三个物种的分布范围很广，横跨撒哈拉以南非洲的13个国家。我的初步遗传分析显示，这些在形态上具有挑战性的物种的误识率很高，因此使目前的命名模式标本的分类鉴定受到质疑。此外，遗传分析和物种分布模型表明，目前公认的分布范围显然具有很高的推测性。在这个项目的框架内，将对非洲铰背龟Kinixys belliana、Kinixys belliana、K.Spekii和K.zombensis的命名模式标本和所有各自的同义词的范围内的遗传变异和分类学同一性进行重新遗传学检查。分类法将在必要时进行修订。通过将可疑标本分配给正确的物种，分布范围将得到更正和更新。该项目旨在开发一种简单、快速和具有成本效益的工作流程，以便于使用有限数量的历史样本对范围广泛的分类群的遗传多样性进行定量评估。同种基因之间的遗传差异在分类学上的相关水平将被用来校准“多位点尺度”，以将观察到的目标群体内的差异置于有意义的背景中。这将有助于可靠地识别隐秘的或被忽视的分类群。由此产生的协议可以应用于任何范围广泛的脊椎动物分类。

The implementation of molecular genetic approaches into taxonomy accelerated exponentially the discovery of unrecognized taxa and many putatively widely distributed species were identified as species complexes. This implies that putatively widespread and common species may harbor multiple narrowly distributed and endangered taxa. Consequently, putatively widespread taxa need considerably more attention. However, obtaining range-wide sampling for taxa with ranges dissecting several political borders is expensive, time consuming, and hampered by legislative restrictions. Therefore, genetic samples obtained from scientific collections represent an appealing alternative. Unfortunately, DNA of museum specimens is often heavily degraded, fragmented, and contaminated with exogenous DNA. Thus, processing requires extensive precautions, special facilities, and approaches. The advent of Next Generation Sequencing (NGS) and hybridization-based target enrichment have revolutionized genetic research and improved the possibilities for using historic material significantly. The proposed project will apply NGS and aDNA approaches to elucidate exemplarily the diversity of three wide-ranging tortoise species using historic collection material, a set of mitochondrial and nuclear markers, and a stepwise analyses protocol. For the selected species only a few fresh samples are available from restricted range portions but large numbers of historic specimens are housed in scientific collections. All three species occupy wide distribution ranges spanning across up to 13 countries in sub-Saharan Africa. My preliminary genetic analyses revealed high misidentification rates for these morphologically challenging species and thus render the current taxonomic identification of name-bearing type specimens questionable. In addition, the currently accepted distribution ranges are evidently highly speculative as demonstrated by genetic analyses as well as species distribution models. In the frame of this project range-wide genetic variation and the taxonomic identity of the name-bearing type specimens and all respective synonyms of the African Hinge-back Tortoises Kinixys belliana, K. spekii and K. zombensis will genetically be re-examined. Taxonomy will be revised where necessary. By assigning dubious specimens to the correct species, distribution ranges will be corrected and updated. The project aims to develop a simple, fast, and cost-efficient workflow that facilitates quantitative assessments of genetic diversity for wide-ranging taxa using a limited number of historic samples. Taxonomically relevant levels of genetic divergence between congeners will be used to calibrate a ‘multi-locus yardstick’ to place observed divergences within the target group into a meaningful context. This will facilitate the reliable identification of cryptic or overlooked taxa. The resulting protocol can be applied to any wide-ranging vertebrate taxon.