Developing, calibrating and applying a genomic toolbox for species delimitation in Palearctic and tropical amphibians

开发、校准和应用用于古北界和热带两栖动物物种界定的基因组工具箱

• 批准号: 350782366
• 负责人: Professor Dr. Michael Hofreiter
• 金额: --
• 依托单位: Institut für Biochemie und Biologie
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2017
• 资助国家: 德国
• 起止时间: 2016-12-31 至 2020-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/350782366?language=en
• 关键词: Developing; calibrating; applying; genomic; toolbox

Recent years have seen a meteoric rise of ever more powerful high-througput DNA sequencing methods. These can yield data to define evolutionary lineages of organisms at ever finer scales and thus delimite species, but empirical studies comparatively testing the performance of different kinds of markers for this purpose are scarce. In the proposed project we plan assesing the performance of genomic markers in quantitative species delimitation approaches, using amphibians as a model, and with the goal to develop an affordable and efficient genomic toolbox to delimit species in this animal group. We will first generate for a set of 17 species and species complexes of European amphibians high-throughput sequencing data with various methods, i.e., sequencing of transcribed RNA (RNAseq / transcriptomics), hybrid enrichment sequencing, restriction site associated DNA sequencing (ddRADseq), hybridization capture using RAD probes (hyRADseq), and molecular inversion probes (MIP sequencing). The European target species will represent the whole continuum from very young and barely differentiated intraspecific lineages to deeply divergent, morphologically differentiated but sometimes still hybridizing lineages. We will use the current taxonomy of these species, well established by a plethora of previous thorough integrative studies, as benchmark to compare the performance of different sets of markers in species delimitation, based on multispecies coalescent methods. We will test the performance of markers of different methological origin, length, variability, and biological function in correctly delimiting these species of European amphibians. To avoid taxonomic inflation, well-performing markers must not falsely delimit fine-scale intraspecific population clusters as species, but they also should be sensitive enough to identify closely related cryptic species. Based on the empirical data from European amphibians, we will select a set of well-performing markers and bioinformatic procedures for reliable statistical species delimitation in amphibians, aiming for simple and affordable laboratory protocols. We will then apply the selected work protocol to a taxonomically convoluted group of tropical amphibians (frogs of the subgenus Brygoomantis from Madagascar) in the context of a fast-track taxonomic revision during which we envisage describing over 20 new species.

近年来，更强大的高通量DNA测序方法迅速崛起。这些可以产生数据，以更精细的尺度定义生物体的进化谱系，从而界定物种，但比较测试不同种类的标记为此目的的性能的实证研究是稀缺的。在拟议的项目中，我们计划评估基因组标记在定量物种划界方法中的性能，以两栖动物为模型，目标是开发一个负担得起的和有效的基因组工具箱，以划定该动物组中的物种。我们将首先用各种方法生成一组欧洲两栖动物的17个物种和物种复合体的高通量测序数据，即，转录RNA测序（RNAseq / transcriptomics）、杂交富集测序、限制性位点相关DNA测序（ddRADseq）、使用RAD探针的杂交捕获（hyRADseq）和分子倒置探针（MIP测序）。欧洲的目标物种将代表整个连续体，从非常年轻和几乎没有分化的种内谱系，以深刻分歧，形态分化，但有时仍然杂交谱系。我们将使用目前的分类这些物种，以及建立了大量的以前彻底的综合研究，作为基准，比较性能的不同套标记的物种划界，基于多物种合并的方法。我们将测试不同的方法学起源，长度，变异性和生物学功能的标记在正确界定这些物种的欧洲两栖动物的性能。为了避免分类学膨胀，性能良好的标记不得错误地将细尺度种内种群集群划分为物种，但它们也应该足够敏感，以识别密切相关的神秘物种。基于欧洲两栖动物的经验数据，我们将选择一套性能良好的标记和生物信息学程序，用于两栖动物可靠的统计物种划分，旨在提供简单和负担得起的实验室协议。然后，我们将适用于选定的工作协议，一个分类学上错综复杂的组的热带两栖动物（青蛙的亚属Brygoomantis从马达加斯加）的背景下，在一个快速通道的分类修订，在此期间，我们设想描述超过20个新物种。