Limits...
Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals.

Davies KT, Tsagkogeorga G, Rossiter SJ - BMC Evol. Biol. (2014)

Bottom Line: As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems.We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings.Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species.

View Article: PubMed Central - PubMed

Affiliation: School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK. k.t.j.davies@qmul.ac.uk.

ABSTRACT

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 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 sensory system development - suggests crucial roles in regulating gene expression and 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 auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems.

Results: Phylogenetic reconstructions of concatenated CNEs broadly recovered 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 CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing 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 inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that 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 is 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.

Show MeSH

Related in: MedlinePlus

RADAR plots of the estimated relative rates of CNEs located in the same genomic regions as putative ‘hearing/deafness’ genes for (A) bats and (B) cetaceans. Numbers refer to each of the putatively associated genes (see Additional file 1: Table S5). Colours correspond to the following groups and species: Old world fruit bats (dark grey); echolocating Yinpterchiroptera (green); Yangochiroptera (brown); Common minke whale (blue) and Bottlenose dolphin (light grey).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4302572&req=5

Fig5: RADAR plots of the estimated relative rates of CNEs located in the same genomic regions as putative ‘hearing/deafness’ genes for (A) bats and (B) cetaceans. Numbers refer to each of the putatively associated genes (see Additional file 1: Table S5). Colours correspond to the following groups and species: Old world fruit bats (dark grey); echolocating Yinpterchiroptera (green); Yangochiroptera (brown); Common minke whale (blue) and Bottlenose dolphin (light grey).

Mentions: In total CNE alignments from 113 and 118 genomic regions located proximally to putative hearing/deafness and auditory system development genes were compared across bats and cetaceans respectively (see Figures 4 and 5). The distribution of relative rates for this subset of CNEs broadly matched that of the whole sample (Additional file 6: Figure S5). Within bats, several CNEs from Yangochiroptera appeared to have a faster relative rate of evolution compared to Old World fruit bats and echolocating Yinpterochiroptera (see Figure 5). However, the median rate and standard deviation across this sample of CNEs from Old World fruit bats, echolocating Yinpterochiroptera and Yangochiroptera are 0.950 ± 0.26 SD; 1.008 ± 0.26 SD; 1.120 ± 0.36 SD respectively, and thus are similar. For cetaceans, the median rate and standard deviation were 0.775 ± 0.23 SD for the non-echolocating minke whale, and 0.846 ± 0.28 SD for the echolocating dolphin.Figure 4


Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals.

Davies KT, Tsagkogeorga G, Rossiter SJ - BMC Evol. Biol. (2014)

RADAR plots of the estimated relative rates of CNEs located in the same genomic regions as putative ‘hearing/deafness’ genes for (A) bats and (B) cetaceans. Numbers refer to each of the putatively associated genes (see Additional file 1: Table S5). Colours correspond to the following groups and species: Old world fruit bats (dark grey); echolocating Yinpterchiroptera (green); Yangochiroptera (brown); Common minke whale (blue) and Bottlenose dolphin (light grey).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4302572&req=5

Fig5: RADAR plots of the estimated relative rates of CNEs located in the same genomic regions as putative ‘hearing/deafness’ genes for (A) bats and (B) cetaceans. Numbers refer to each of the putatively associated genes (see Additional file 1: Table S5). Colours correspond to the following groups and species: Old world fruit bats (dark grey); echolocating Yinpterchiroptera (green); Yangochiroptera (brown); Common minke whale (blue) and Bottlenose dolphin (light grey).
Mentions: In total CNE alignments from 113 and 118 genomic regions located proximally to putative hearing/deafness and auditory system development genes were compared across bats and cetaceans respectively (see Figures 4 and 5). The distribution of relative rates for this subset of CNEs broadly matched that of the whole sample (Additional file 6: Figure S5). Within bats, several CNEs from Yangochiroptera appeared to have a faster relative rate of evolution compared to Old World fruit bats and echolocating Yinpterochiroptera (see Figure 5). However, the median rate and standard deviation across this sample of CNEs from Old World fruit bats, echolocating Yinpterochiroptera and Yangochiroptera are 0.950 ± 0.26 SD; 1.008 ± 0.26 SD; 1.120 ± 0.36 SD respectively, and thus are similar. For cetaceans, the median rate and standard deviation were 0.775 ± 0.23 SD for the non-echolocating minke whale, and 0.846 ± 0.28 SD for the echolocating dolphin.Figure 4

Bottom Line: As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems.We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings.Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species.

View Article: PubMed Central - PubMed

Affiliation: School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK. k.t.j.davies@qmul.ac.uk.

ABSTRACT

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 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 sensory system development - suggests crucial roles in regulating gene expression and 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 auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems.

Results: Phylogenetic reconstructions of concatenated CNEs broadly recovered 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 CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing 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 inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that 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 is 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.

Show MeSH
Related in: MedlinePlus