Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics ...

• Main Authors: Edwards, Scott V., Cloutier, Alison, Baker, Allan J.
• Format: Dataset
• Language: English
• Published: Dryad 2017
• Subjects: Dromaius novaehollandiae; Struthio camelus; Gavia stellata; Tinamus guttatus; Pygoscelis adeliae; biased-gene conversion; Falco peregrinus; Picoides pubescens; intron; Alligator mississippiensis; Taeniopygia guttata; Anas platyrhynchos; Nothoprocta perdicaria; Phoenicopterus ruber; Manacus vitellinus; Podiceps cristatus; conserved element; Meleagris gallopavo; Gallus gallus; Haliaeetus leucocephalus
• Online Access: https://dx.doi.org/10.5061/dryad.25f7g; https://datadryad.org/stash/dataset/doi:10.5061/dryad.25f7g

Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600 - ∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically-derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by ... : Supplementary_Files_Edwards_CNEEs_2017Supplementary Files S1, S3, S4, S5, and S6.Supplementary File S2Alignment summary measures for all loci.Supplementary_FileS2.xlsxSupplementary File S7Summary of jModelTest output for all loci.Supplementary_FileS7.xlsxSupplementary_Figures_CNEEs_Edwards_2017Supplementary Figures S1-7.Raw_data_alignments_trees_CNEEs_Syst_Biol ...