Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples

Although species assignment of scats is important to study carnivoran biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here we evaluate the potential of two short mtDNA fragments (ATP6 [126 bp] and COI [187 bp]) to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences, and analyzed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters, uniqueness of haplotypes, or by reducing the geographic scope of the comparison. In silico comparative analyses were also performed with a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case-studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA, and allowed an assessment of prey-DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.尽管粪样的物种鉴定对于食肉目（Carnivora）生物学研究至关重要，但目前全球尚未建立统一的食肉动物鉴定检测方法，无法实现大规模常规检测与结果的可靠跨研究比对。本研究评估了两段短线粒体DNA（mitochondrial DNA, mtDNA）片段——ATP6（126 bp）与COI（187 bp）作为食肉目标准分子标记的潜力。我们对66个物种的样本进行了这两个片段中至少一段的测序。研究通过补充存档序列完成序列比对，并采用三种分析方法（基于系统发育树、基于遗传距离、基于特征位点）进行分析。种内遗传距离普遍低于种间遗传距离，使得86%（ATP6）与85%（COI）的物种均可形成可明确区分的聚类簇。值得注意的例外是近期分化的物种，其中大部分仍可通过诊断特征、单倍型（haplotype）唯一性，或缩小比对的地理范围实现鉴定。本研究同时对一段110 bp的细胞色素b（cytochrome b, cytb）片段进行了计算机比对分析，其物种鉴定成功率仅为70%，这可能源于有效信息位点较少，以及从GenBank获取的部分序列存在鉴定错误的影响。最后，我们利用粪样开展了案例研究，结果证实了我们所选的两段标记在低质量DNA样本中的适用性，并可用于评估猎物DNA的共扩增情况。ATP6未检测到猎物DNA污染的情况，而COI则出现过此类问题，后续通过设计特异性更强的引物得以解决。综上，本研究结果表明，这两段片段具备作为食肉目物种精准鉴定标准分子标记的良好潜力。