DOI: 10.5061/dryad.50kd5
title: Data from: Divergent evolutionary rates in vertebrate and mammalian specific Conserved Non-coding Elements (CNEs) in echolocating mammals

description: Background - The majority of DNA contained within vertebrate genomes is
 non-coding, with a certain proportion of this thought to play regulatory
 roles during development. Conserved Non-coding Elements (CNEs) are an
 abundant group of putative regulatory sequences that are highly conserved
 across divergent groups and are thus assumed to be under strong selective
 constraint. Many CNEs may contain regulatory factor binding sites, and
 their frequent spatial association with key developmental genes – such as
 those regulating the development of the sensory systems – suggests crucial
 roles in regulating gene expression and hence cellular patterning. Yet
 surprisingly little is known about the molecular evolution of CNEs across
 diverse mammalian taxa or their role in specific phenotypic adaptations.
 We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs
 across 19 and 9 mammalian orders respectively, and tested for changes in
 the rate of evolution of CNEs located in the proximity of genes underlying
 the development or functioning of auditory systems. As we focused on CNEs
 putatively associated with genes underlying the development/functioning of
 the auditory systems, we incorporated several echolocating taxa in our
 dataset because of their highly specialised and derived auditory systems.
 Results - Phylogenetic reconstructions of concatenated CNE sequences
 broadly recovered the accepted mammal relationships despite high levels of
 sequence conservation. We found that CNE substitution rates were highest
 in rodents and lowest in primates, consistent with previous findings.
 Comparisons of substitution rates in CNEs from several genomic regions
 containing genes linked to auditory system development and hearing genes
 revealed differences between echolocating and non-echolocating taxa. Wider
 taxonomic sampling of four CNEs associated with the homeobox genes Hmx2
 and Hmx3 ¬ – which are required for mammalian inner ear development –
 revealed family-wise variation across diverse bat species. Specifically
 within one family of echolocating bats, known to utilise
 frequency-modulated echolocation calls varying widely in frequency and
 intensity, high levels of sequence divergence were found. Conclusions -
 Levels of selective constraint acting on CNEs differed both across genomic
 locations and taxa, with observed variation in substitution rates of CNEs
 among bat species. More work in needed to determine whether this variation
 can be linked to echolocation, and wider taxonomic sampling is necessary
 to fully document levels of conservation in CNEs across diverse taxa.
description: Concatenated alignments
 of vertebrate-specific CNEs for 89 genomic regions based on data from 26
 mammalian genomesVert_specCNEs.zipAlignments of four conserved non-coding elements located in the same genomic region as HMX2/3Alignments of four conserved non-coding elements located in the same genomic region as HMX2/3 in divergent mammalian species. Sequences were either taken from online sources, such as Ensembl, or sequenced directly using PCR and Sanger sequencing.HMX2_3.zip