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Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

  1. Raghavendran Partha
  2. Bharesh K Chauhan
  3. Zelia Ferreira
  4. Joseph D Robinson
  5. Kira Lathrop
  6. Ken K Nischal
  7. Maria Chikina  Is a corresponding author
  8. Nathan L Clark  Is a corresponding author
  1. University of Pittsburgh, United States
  2. Children’s Hospital of Pittsburgh, United States
  3. University of Pittsburgh School of Medicine, United States
  4. University of California, United States
Research Article
Cite this article as: eLife 2017;6:e25884 doi: 10.7554/eLife.25884
10 figures, 2 tables, 3 data sets and 12 additional files

Figures

Lens intrinsic membrane protein 2 (LIM2) evolutionary rates across species.

(A) Mammalian transitions to a subterranean environment occurred in four lineages shown in red. The branch lengths on the mammalian tree reflect the average evolutionary rate across 18,980 protein-coding genes. (B) LIM2 protein-coding sequence shows accelerated rates of evolution on subterranean branches compared to those on the proteome-wide average tree. (C) Relative evolutionary rates of LIM2 showed the strongest acceleration on the subterranean branches amongst all of the genes studied. Illustrations by Michelle Leveille (Artifact Graphics).

https://doi.org/10.7554/eLife.25884.003
Relative evolutionary rates of two retinal proteins across species.

Relative evolutionary rates of two retinal proteins, (A) Retinal outer segment membrane protein 1 (ROM1) and (B) Rod cell-specific G protein, subunit alpha (GNAT1), show strong acceleration in the subterranean mammals (marked in red).

https://doi.org/10.7554/eLife.25884.004
Enrichment of visual perception genes.

(A) Histogram of the rankings of 189 visual perception genes based on their mole-acceleration. We see a clear enrichment of the genes with low rank numbers, reflecting the strong signal of mole-acceleration in visual perception genes. As a control, we use four non-subterranean species, and as expected, genes involved in vision do not show convergent rate acceleration. (B) Mole-acceleration can equivalently serve as a predictor for function in visual perception. The plot shows the Precision-Recall values at varying p-value thresholds reflecting the fraction of visual perception genes significant at a particular threshold (Precision) and the fraction of visual perception genes retrieved at the same threshold (Recall). We see that mole-acceleration specifically identifies visual perception genes with high precision when compared to acceleration in two sets of four non-subterranean control species.

https://doi.org/10.7554/eLife.25884.005
Relative rates of footpad-specific keratin 9 (KRT9).

KRT9 shows strong acceleration on the subterranean branches. The image shown is the footpad of the star-nosed mole, showing characteristic hyperkeratosis. Keratin 9 mutations also lead to hyperkeratosis in mouse models and humans. Illustrations by Michelle Leveille (Artifact Graphics).

https://doi.org/10.7554/eLife.25884.008
Tissue-specific retinal and lens genes are highly accelerated in subterranean species.

(A) Ocular genes that are more tissue-specific exhibit stronger acceleration in subterranean ‘mole’ species. The y-axis represents the change in the rate of evolution on branches shifting to a subterranean environment. (B) Panels of tissue-specific genes were tested for their relative accelerations in the subterranean mammals. One hundred randomly chosen ‘background’ genes were not faster or slower on average, and provide an estimate of the variance expected for random genes. Retina- and lens-specific genes show many cases of acceleration in the subterranean environment, and their distributions are significantly elevated when compared to background (p=1.4×10−5 and 3.2 × 10−4, respectively). (C) Representation of average mole-acceleration for genes specifically expressed in four different tissues of the eye.

https://doi.org/10.7554/eLife.25884.009
Mole-acceleration of eye-specific enhancers in the Pax6 gene region.

(A) Genomic region spanning Pax6 and its neighbor Elp4. The exons and introns of the two genes are represented by black blocks and lines respectively, whereas the conserved non-coding regions analyzed are represented in light blue. The conservation signal as given by the 100 vertebrates Basewise Conservation is shown in dark blue. The mole-acceleration scores for these regions are represented in red. The three most accelerated non-coding regions identified in this analysis are consistent with the eye-specific enhancers regulating Pax6 expression in the eye. (B) The mole-acceleration scores for the three eye-specific enhancers of Pax6 are the highest among 150 regions analyzed, including enhancers of other tissues and uncharacterized non-coding regions. (C) The relative rates in each species for the most accelerated region ‘cre149’.

https://doi.org/10.7554/eLife.25884.010
Evidence of mole-acceleration in candidate eye-specific enhancers.

(A) Enrichment of mole-accelerated elements near eye developmental transcription factor genes. The bar plot shows the 17 mole-accelerated conserved non-coding elements identified. Fourteen of the 17 elements are present near transcription factor genes in the Eye set, denoted in red. (B) FANTOM5 Eye enhancers show strong mole-acceleration. The plot shows the relative proportion of FANTOM5 eye enhancers identified among all enhancers significant at the corresponding p-value threshold. We see a strong enrichment of eye enhancers identified at low mole-acceleration p-values (red points) whereas no such enrichment is observed using control-species-acceleration p-values (blue points).

https://doi.org/10.7554/eLife.25884.011
Some aboveground species show accelerated rates of evolutionary change in visual perception genes.

On the basis of the relative evolutionary rates across all species for 189 genes with the GO term annotation ‘visual perception’, we calculated the species-wise mean relative rate across of the genes. Our previous observations of mole-acceleration in visual perception genes are recapitulated here – the four subterranean mammals are among the species that show an accelerated rate across these genes. Interestingly, we find other non-subterranean species showing acceleration comparable to the subterranean mammals, indicating adaptations in visual systems.

https://doi.org/10.7554/eLife.25884.012
Author response image 1
Author response image 2

Tables

Table 1
Top 30 of 55 subterranean-accelerated genes.
https://doi.org/10.7554/eLife.25884.006
GeneP-valueTissuesDescription
LIM2*0.00084LensLens intrinsic membrane protein 2
CRYBB3*0.00087LensLens-specific crystallin, beta B3
R0M1*0.00096RetinaRetinal outer segment membrane protein 1
CRYBA1*0.00098LensLens-specific crystallin, beta Al
CRYGC*0.00119LensLens-specific crystallin, gamma C
CRYBB2*0.00128LensLens-specific crystallin, beta B2
GPR89B0.00130UbiquitousG-protein-coupled receptor 89B, pH mediator in Golgi
GNAT1*0.00133RetinaRod cell-specific G-protein, subunit alpha
GPRS9A0.00134UbiquitousG-protein-coupled receptor 89A, pH mediator in Golgi
NRL*0.00138RetinaNeural retina leucine zipper responsible for expression of rhodopsin
CRYGS*0.00146LensLens-specific crystallin, gamma S
GRM6*0.00150RetinaMetabotropic glutamate receptor 6, required for normal vision
GBX20.00165EmbryoGastrulation brain homeobox 2, developmental transcription factor
LGSN*0.00171LensLengsin, lens protein with glutamine synthetase domain
CRYBB1*0.00183LensLens-specific crystallin, beta Bl
KLHDC30.00186UbiquitousKelch-domain-containing 3, high expression in brain
KRT81#0.00186Hair and nailsKeratin 81, primarily in hair cortex
WDFY10.00192UbiquitousWD repeat and FYVE-domain-containing 1, endosomal protein
KRT9#0.00195SkinKeratin 9, specific to palms of hands and soles of feet
POMP#0.00199UbiquitousProteasome maturation protein, associated with rare skin disorder
RRH*0.00201RetinaRetinal pigment epithelium-derived rhodopsin homolog
DPCD*0.00201Ciliated cellsDeleted in primary ciliary dyskinesia; maintenance of ciliated cells
RAD54L0.00217UbiquitousRAD54-like: DNA double-strand break repair
TATDN10.00235UbiquitousTatD DNase-domain-containing 1
ITLN20.00244Small intestineIntelectin 2, may play a role in defense against pathogens
STX3*0.00245UbiquitousSyntaxin 3, associated with congenital cataracts and intellectual disability
SKJV2L*0.00254UbiquitousDEAD box protein, yeast SKI2 homolog, implicated in macular degeneration
DPY19L10.00254Ubiquitousdpy-19-like 1 (Caenorhabditis elegans), probable C-mannosyltransferase
TFPT0.00266UbiquitousTCF3 (E2A) fusion partner (in childhood leukemia)
RSI*0.00275RetinaRetinoschisin 1, extracellular protein involved in organization of retina
  1. *related to vision.

    #related to skin and hair.

  2. Refer to Supplementary file 1 for a full list of the subterranean-accelerated genes.

Table 2
Representative enriched functions in mole-accelerated genes.
https://doi.org/10.7554/eLife.25884.007
Functional annotationFold enrichmentp-valueFDR q-value
Visual perception23.166.84E-161.02E-11
Sensory perception of light stimulus22.699.12E-L66.82E-12
Sensory perception8.475.83E-102.91E-06
Neurological system process5.391.75E-076.53E-O4
Detection of light stimulus29.577.04E-072.10E-03
Detection of light stimulus involved in sensory perception56.351.92E-054.77E 02
Detection of light stimulus involved in visual perception56.351.92E-054.09E-02
Detection of external stimulus14.382 49E-054.66E-02

Data availability

The following previously published data sets were used
  1. 1
  2. 2
  3. 3

Additional files

Supplementary file 1

Subterranean-accelerated genes

The genome-wide ranking of genes whose rates are positively associated with the subterranean branches was identified on the basis of the Mann-Whitney U test p-values (column 2) that were significant at a FDR of 15% under a permutation-based FDR correction procedure (column 3). Other columns list brief gene descriptions (4), known biological function (5), tissue specificity if any (6), known disease links (7), the predominant evolutionary mode on subterranean branches as decided with codon models (8, see Materials and methods), and the subterranean species containing genetic lesions in the corresponding protein-coding sequences (9).

https://doi.org/10.7554/eLife.25884.013
Supplementary file 2

Functional enrichment in subterranean-accelerated genes

The subterranean-accelerated genes were strongly associated with specific Gene Ontology terms representing functional categories. This table presents the GO term identifier (column 1), description (column 2), the p-value representing the significance of the degree of enrichment of genes in that category among mole-accelerated genes relative to the entire set (3), the multiple test-corrected p-value (4), the degree of enrichment in the accelerated set relative to the entire set (5), the number of genes in that category in the entire analyzed gene set (6), the number of genes in the accelerated set (7), the number of genes in that category in the accelerated gene set (8), and the corresponding gene names (9).

https://doi.org/10.7554/eLife.25884.014
Supplementary file 3

Subterranean-decelerated genes

The genome-wide ranking of genes whose rates are negatively associated with the subterranean branches was identified based on the Mann-Whitney U test p-values (column 2) that are significant at a FDR of 15% under a permutation-based FDR correction procedure (column 3). Column 4 lists brief gene descriptions.

https://doi.org/10.7554/eLife.25884.015
Supplementary file 4

Functional enrichment in subterranean-decelerated genes

The specific Gene Ontology terms representing functional categories with which subterranean-decelerated genes were strongly associated. This table presents the GO term identifier (column 1), description (column 2), the p-value representing the significance of the degree of enrichment of genes in that category among mole-accelerated genes relative to the entire set (3), the multiple test-corrected p-value (4), the degree of enrichment in the accelerated set relative to the entire set (5), the number of genes in that category in the entire analyzed gene set (6), the number of genes in the accelerated set (7), the number of genes in that category in the accelerated gene set (8), and the corresponding gene names (9).

https://doi.org/10.7554/eLife.25884.016
Supplementary file 5

Results of codeml tests for positive selection in subterranean-accelerated genes

This table presents the results for the mole-accelerated genes from five codon models and the likelihood ratio tests between them. Columns B – T present the branch-site models and tests with their log likelihood values, the likelihood ratio tests between them (see Materials and methods), and some of the estimated parameters for background (conserved) and foreground (subterranean) branches (Zhang et al., 2005). Columns V – AC present the results of the pan-mammalian tests for positive selection using the sites models (M8A and M8) (Swanson et al., 2003; Yang, 2007).

https://doi.org/10.7554/eLife.25884.017
Supplementary file 6

Pseudogene study

This table lists the pseudogene status of mole-accelerated genes' orthologs in the set of species utilized for the study.

https://doi.org/10.7554/eLife.25884.018
Supplementary file 7

Eye developmental gene evolutionary rates.

This table presents the evolutionary rates of the 71 eye developmental genes. For each gene (column 1), we performed a branch-site selection model analysis to estimate two different values of dN/dS – one for the four subterranean branches on the tree (3), and one for the rest of the branches (2, see Materials and methods). The mole-acceleration is calculated as the difference between these two values (4). Column 5 indicates whether the gene was identified as a subterranean-accelerated gene using the RER methods, and column 6 lists the refSeq summary.

https://doi.org/10.7554/eLife.25884.019
Supplementary file 8

Relative rate acceleration in subterranean mammals for 150 conserved non-genic regions near Pax6

This table presents the 150 non-coding regions scanned near Pax6 and their relative rate acceleration in subterranean mammals. The first three columns represent the hg19 coordinates of the region. Column 4 represents the mole-acceleration calculated as the negative logarithm to the base 10 of the Mann-Whitney U test p-value. Column 5 provides additional information about the overlap of the region with known tissue-specific enhancers of Pax6.

https://doi.org/10.7554/eLife.25884.020
Supplementary file 9

Transcription factor genes utilized for genome-wide scan for convergently accelerated non-coding elements

This table presents the two sets of transcription factor genes used to scan for convergently accelerated non-coding elements. TF genes in the Eye set, were compiled based on a literature survey of their eye developmental role (column 2). Column 3 lists the refSeq summary. Similarly, the tissue-specificity of TF genes belonging to the ‘Other’ set is provided in column 2 of the second table.

https://doi.org/10.7554/eLife.25884.021
Supplementary file 10

Relative rate acceleration in subterranean mammals for conserved non-coding regions near developmental transcription factor genes

This table presents the 17 subterranean-accelerated non-coding regions scanned near the 40 TF genes listed in Supplementary file 9, significant at a FDR of 10%. Columns 1–3 list their hg19 coordinates. Column 4 presents the mole-acceleration calculated as the Mann-Whitney U test p-value. Column 5 lists the permutation-based FDR q-value.

https://doi.org/10.7554/eLife.25884.022
Supplementary file 11

Relative rate acceleration in subterranean mammals for putative FANTOM5 enhancer regions

This table presents the 62 subterranean-accelerated putative FANTOM5 enhancers significant at a FDR of 15%. Fantom5 element names containing the word 'eye' correspond to FANTOM5 enhancers identified as eye enhancers in this analysis. Columns 2 and 3 list each region's mm9 and hg19 coordinates respectively. Column 4 represents the mole-acceleration calculated as the Mann-Whitney U test p-value. Column 4 lists the permutation-based FDR q-value.

https://doi.org/10.7554/eLife.25884.023
Transparent reporting form
https://doi.org/10.7554/eLife.25884.024

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