DOI: 10.5061/dryad.x69p8czjx
title: A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility – from order to species

description: 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.
description: 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.
description: Dataset includes: 1) Three .tre files; Astral
 LPP, Astral polytomy test, and IQ-tree ultra-fast bootstrap.
 2) List of probes in .csv format a total of 46,893 probes
 designed for 446 loci and totally 5.6Mbps. This file can be used to
 directly order the <em>rodent418probe </em>set from Agilent of
 similar company. The first 25,116 probes are new rodent specific probes
 and are labeled as follows: species, Name of locus,
 probe number Example: mR001p1 = mouse locus 1 probe
 1   The species key is as
 follows; m = mouse, <i>Mus
 musculus</i>, genome version <i>mm10</i> 
 k = Ord's kangaroo rat, <i>Dipodomys
 ordii</i>, genome version <i>dipOrd1</i> 
 g = guinea pig, <i>Cavia porcellus</i>, genome
 version <i>cavPor3</i> s = 13-lined
 ground squirrel, <i>Ictidomys tridecemlineatus</i> , genome
 version <i>speTri2</i> c = Chinese
 hamster, <i>Crietulus griseus</i> , genome version
 <i>criGri1</i> gr = <i>Gerbilus
 robustus </i>(from the sequences you sent me)
 sm = <i>Sigmodon mascotensis <i>
 </i></i>(from the sequences you sent me)
 n = <i>Nesomys rufus</i> <i> </i>(from
 the sequences you sent me)  
 This covers 239 new rodent probes (labeled R001 - R239) as well
 as a set for RAG1 and IRBP (labeled as such). This file also includes the
 vertebrate probes (n=21,777) from the 205 loci that passed the filtering.
 These are the same probes from Lemmon <i>et al.</i> 2012 and
 are labeled the same names as in the paper had (frist and L then the locus
 number then a species abbreviation then probe number, i.e. L5D1 is locus 5
 designed from <i>Danio rerio</i> probe 1).
   3) Full sequecnes for all new rodent
 targets in .csv format.   4)
 Reference sequences pulled from the mm10 genome in .fasta format used for
 retrival of targets after sequencing.