Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex

Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on Omocestus antigai and O. navasi, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean-montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geomet..., SNAPP input fileInput file (NEXUS format) used for phylogenomic analyses in SNAPPSNAPP_InputFile.nexSVDQuartets input fileInput file (NEXUS format) used for phylogenomic analyses in SVDQuartetsSVDQuartets_InputFile.nexBPP input filesThis ZIP folder contains the genetic datasets used to perform BPP analysesBPP.zipiBPP input filesThis ZIP folder contains the genetic and morphological datasets (males and females) used to perform iBPP analysesiBPP.zipRaw landmark coordinates of morphological traitsThis ZIP folder contains raw coordinates of landmarks used to characterize shape variation of the different morphological traits (head, pronotum, forewing and ovopositor valve) analyzed in males and females. Landmarks are stored in TPS format.LandmarkCoordinates.zipPrincipal component scores of morphological traitsPrincipal component scores (PC1 and PC2) summarizing shape variation of the different morphological traits (head, pronotum, forewing and ovopositor valve) analyzed in males and femalesMo...,

传统分类学历来依托形态学与生态学特征，以解读和划分生物多样性。近十年来，分子生态学与系统分类学领域的技术突破与概念进展，极大降低了基因组数据的生成门槛，重塑了生物多样性分析的研究范式。本文旨在阐明：传统分类学所确立的物种界定，既无法通过高通量测序（high throughput sequencing）数据得到验证，也未能通过基因组信息与其他证据来源的定量整合来获得支撑。
具体研究对象为产自比利牛斯山区的两种山地蝗虫：*Omocestus antigai*和*O. navasi*，二者最初是基于定量表型差异以及迥异的生境偏好（高山生境与地中海山地生境）被正式描述的。
为验证当前的分类界定、检验物种边界并解析促成遗传分化的因素，本研究获取了表型数据（几何形态学相关，原文截断为geomet...），并附带如下数据集文件：
1. SNAPP输入文件：用于SNAPP系统发育组学分析的NEXUS格式输入文件SNAPP_InputFile.nex
2. SVDQuartets输入文件：用于SVDQuartets系统发育组学分析的NEXUS格式输入文件SVDQuartets_InputFile.nex
3. BPP输入文件压缩包：包含用于BPP分析的基因组数据集的压缩文件BPP.zip
4. iBPP输入文件压缩包：包含用于iBPP分析的基因组与表型数据集（含雌雄个体）的压缩文件iBPP.zip
5. 形态学特征原始地标坐标：包含用于表征雌雄个体各形态性状（头部、前胸背板、前翅及产卵瓣）形状变异的地标原始坐标的压缩文件LandmarkCoordinates.zip，地标数据以TPS格式存储。
6. 形态学特征主成分得分：包含雌雄个体各形态性状（头部、前胸背板、前翅及产卵瓣）形状变异的主成分得分（PC1与PC2）的数据集（原文此处截断为Mo...）