A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility – from order to species

Rodents are the largest order of mammals and contain several model organisms important to scientific research in a variety of fields, yet no large set of genomic markers have been designed for this group to date, hindering evolutionary studies into relationships of the group as a whole. Here we present a genomic probe set designed and optimized for rodents with a protocol easy to replicate with little laboratory investment. This design utilizes an anchored hybrid enrichment approach specifically targeting rodents to generate longer loci with a higher mutation rate than existing vertebrate probes to provide utility at various taxonomic levels. Using a test set of rodents from all five suborders we successfully obtained alignments for 416 of the 418 target loci with an average of 1,379 base pairs per locus and a total alignment of more than half a million base pairs. This genomic dataset performed well in all phylogenetic analyses, especially in recent phylogenetic splits, with ample parsimoniously-informative sites within genera and even within species, showing more than four times as many single nucleotide polymorphisms per locus than a recent vertebrate ultra-conserved elements study. Additional support is provided in resolving basal clades in Rodentia. By providing this probe design, we hope that more labs can easily generate data for answering questions in rodents from species delimitation to understanding relationships among families in rapid radiations.

Methods
Probes designed using MyBaits (Chafin et al. 2018) with the mouse-60-way alignment from UCSC along with a subset of probes from Lemmon et al. 2012. Each traget site ranged from 240-400bps and was split into 21 tiled probes for five species (one per suborder of rodent). For more details on the methods see linked manuscript from Molecular Ecology Resources.

啮齿目（Rodentia）是哺乳动物中物种多样性最高的类群，包含多个在多领域科学研究中具有重要价值的模式生物，但迄今为止尚未针对该类群开发大规模基因组标记（genomic markers），这极大阻碍了针对整个啮齿类类群演化关系的进化生物学研究。在此，我们报道一套专为啮齿类设计并优化的基因组探针组（genomic probe set），其实验方案操作简便，仅需极低的实验室投入即可复刻。该设计采用专门针对啮齿类优化的锚定杂交富集（anchored hybrid enrichment）策略，可获得相较于现有脊椎动物探针更长的靶位点序列，且突变率更高，因此可适用于不同分类层级的研究。我们使用涵盖啮齿目全部5个亚目的测试样本集，成功获取了418个靶位点中416个的比对序列，每个靶位点平均长度为1379个碱基对（base pair, bp），总比对序列长度超过50万个碱基对。该基因组数据集在所有系统发育分析（phylogenetic analysis）中均表现优异，尤其在新近分化的类群分支解析上效果突出；其属内甚至种内包含大量简约信息位点（parsimoniously-informative site），每个靶位点的单核苷酸多态性（single nucleotide polymorphism, SNP）数量是近期一项脊椎动物超保守元件研究的4倍以上。此外，该数据集可为啮齿目基部演化支的解析提供有力支持。本次公开该探针设计方案，旨在帮助更多实验室便捷地获取相关数据，以解答啮齿类研究中的各类问题——从物种种群界定，到理解快速辐射演化类群间的科间演化关系。

### 实验方法
本探针基于MyBaits（Chafin et al. 2018）工具设计，使用来自UCSC的小鼠60物种全基因组比对数据，并结合Lemmon等（2012）开发的部分探针序列。每个靶位点长度介于240~400 bp之间，针对5个物种（啮齿目5个亚目各1个）设计了21个重叠探针。如需了解实验方法的更多细节，请参阅《Molecular Ecology Resources》刊发的相关联机手稿。