- Morphologically cryptic taxa have proved to be a long-standing challenge for taxonomists. Lineages that show strong genomic structuring across the landscape but are phenotypically similar pose a conundrum, with traditional morphological analyses of these cryptic lineages struggling to keep up with species delimitation advances. Micro X-ray computed tomography (CT) combined with geometric morphometric analyses provides a promising avenue for identification of morphologically cryptic taxa, given its ability to detect subtle differences in anatomical structures. This approach, however, has yet to be used in combination with genomic data in a comparative analytical framework to distinguish cryptic taxa. We present an integrative approach incorporating genomic and geometric morphometric evidence to assess the species delimitation of grassland earless dragons (Tympanocryptis spp.) in north-eastern Australia. Using mitochondrial and nuclear genes (ND2 and RAG1, respectively), along with >8500 SNPs (nuclear single nucleotide polymorphisms), we assess the evolutionary independence of target lineages and several closely related species. We then integrate phylogenomic data with osteological cranial variation between lineages using landmark-based analyses of three-dimensional CT models. High levels of genomic differentiation between the three target lineages were uncovered, also supported by significant osteological differences. By incorporating multiple lines of evidence we provide strong support that there are three undescribed cryptic lineages of Tympanocryptis in north-eastern Australia that warrant taxonomic review. Our approach demonstrates the successful application of CT with integrative taxonomic approaches for cryptic species delimitation, which is broadly applicable across vertebrates containing morphologically similar yet genetically distinct lineages. Additionally, we provide a review of recent integrative taxonomic approaches for cryptic species delimitation, and an assessment of how our approach can value-add to taxonomic research.

中文翻译：

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使用系统基因组学和高分辨率 X 射线计算机断层扫描的综合方法对隐性分类群的物种定界

- 形态学上神秘的分类群已被证明是分类学家长期面临的挑战。在整个景观中显示出强大的基因组结构但表型相似的谱系构成了一个难题，对这些神秘谱系的传统形态分析难以跟上物种划界的进展。显微 X 射线计算机断层扫描 (CT) 与几何形态测量分析相结合，为识别形态学上神秘的分类群提供了一种有希望的途径，因为它能够检测解剖结构中的细微差异。然而，这种方法尚未在比较分析框架中与基因组数据结合使用，以区分神秘的分类群。我们提出了一种综合方法，结合基因组和几何形态测量证据来评估澳大利亚东北部草原无耳龙（Tympanocryptis spp.）的物种定界。使用线粒体和核基因（分别为 ND2 和 RAG1）以及 >8500 个 SNP（核单核苷酸多态性），我们评估了目标谱系和几个密切相关物种的进化独立性。然后，我们使用基于地标的三维 CT 模型分析将系统发育数据与谱系之间的骨颅骨变异相结合。发现了三个目标谱系之间的高水平基因组分化，这也得到了显着的骨学差异的支持。通过结合多条证据，我们提供了强有力的支持，即在澳大利亚东北部存在三个未描述的鼓室隐匿谱系，值得进行分类审查。我们的方法证明了 CT 与综合分类学方法对隐性物种定界的成功应用，这广泛适用于包含形态相似但遗传不同谱系的脊椎动物。此外，我们回顾了最近用于隐性物种定界的综合分类学方法，并评估了我们的方法如何为分类学研究增值。这广泛适用于包含形态相似但基因不同的谱系的脊椎动物。此外，我们回顾了最近用于隐性物种划界的综合分类学方法，并评估了我们的方法如何为分类学研究增值。这广泛适用于包含形态相似但基因不同的谱系的脊椎动物。此外，我们回顾了最近用于隐性物种定界的综合分类学方法，并评估了我们的方法如何为分类学研究增值。