DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a cytochrome oxidase I (mt-Co1) DNA barcode database for species of the genus Oligoryzomys, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of Oligoryzomys, O. stramineus. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages’ delimitation, and identified diagnostic nucleotides for each species of Oligoryzomys. Phylogenetic analyses of Oligoryzomys were performed on 2 datasets including 14 of the 23 recognized species of this genus: a mt-Co1 only matrix, and a concatenated matrix including mt-Co1, cytochrome b (mt-Cytb), and intron 7 of the nuclear fibrinogen beta chain gene (i7Fgb). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys.

DNA条形码已成为分类学上复杂的群体中进行物种鉴定的标准方法。条形码处理的重要步骤是构建基于凭证的材料库，该库可通过独立方法正确识别，没有不正确的识别和旁系同源物。在这里，我们提供了一个细胞色素氧化酶我（MT-CO1）DNA条形码数据库属种小啸鼠属，基础型材料和核型标本，并被锚定的一个物种的线粒体基因组小啸鼠属，O. stramineus。为了评估新的COI序列的分类学确定，我们评估了物种的种内/种间遗传距离（条形码间隔），执行了通用混合Yule合并方法（GMYC）来确定谱系的界限，并为每种寡聚体物种鉴定了诊断核苷酸。寡聚体的系统发生分析是在2个数据集上进行的，包括该属23种公认物种中的14种：仅mt-Co1基质和包括mt-Co1，细胞色素b（mt-Cytb）和核内含子7​​的串联基质纤维蛋白原β链基因（i7Fgb）。我们在样本中回收了核线粒体易位（Numts）假基因，并鉴定了一些已发表的序列，这些序列都是Numts的病例。我们分析了非同义和同义替换的比率，与mtDNA序列相比，在Numts中的替换率更高。GMYC定界和DNA条形码缺口结果凸显了需要开展进一步工作来整合分子，核型和形态学分析以及其他采样的方法，以解决寡聚体分类学中的持续性问题。