Changes in selection intensity on the mitogenome of subterranean and fossorial rodents respective to aboveground species

Muscle architecture and muscle fibre type composition in the forelimb of two African mole-rat species, Bathyergus suillus and Heterocephalus glaber

The scratch-digging Cape dune mole-rat (Bathyergus suillus), and the chisel-toothed digging naked mole-rat (Heterocephalus glaber) are African mole-rats that differ in their digging strategy. The aim of this study was to determine if these behavioural differences are reflected in the muscle architecture and fibre-type composition of the forelimb muscles. Muscle architecture parameters of 39 forelimb muscles in both species were compared. Furthermore, muscle fibre type composition of 21 forelimb muscles were analysed using multiple staining protocols. In B. suillus, muscles involved with the power stroke of digging (limb retractors and scapula elevators), showed higher muscle mass percentage, force output and shortening capacity compared to those in H. glaber. Additionally, significantly higher percentages of glycolytic fibres were observed in the scapular elevators and digital flexors of B. suillus compared to H. glaber, suggesting that the forelimb muscles involved in digging in B. suillus provide fast, powerful motions for effective burrowing. In contrast, the m. sternohyoideus a head and neck flexor, had significantly more oxidative fibres in H. glaber compared to B. suillus. In addition, significantly greater physiological cross-sectional area and fascicle length values were seen in the neck flexor, m. sternocleidomastoideus, in H. glaber compared to B. suillus, which indicates a possible adaptation for chisel-tooth digging. While functional demands may play a significant role in muscle morphology, the phylogenetic differences between the two species may play an additional role which needs further study.

How voles adapt to subterranean lifestyle: Insights from RNA-seq

Life under the earth surface is highly challenging and associated with a number of morphological, physiological and behavioral modifications. Subterranean niche protects animals from predators, fluctuations in environmental parameters, but is characterized by high levels of carbon dioxide and low levels of oxygen and implies high energy requirements associated with burrowing. Moreover, it lacks most of the sensory inputs available above ground. The current study describes results from RNA-seq analysis of four subterranean voles from subfamily Arvicolinae: Prometheomys schaposchnikowi, Ellobius lutescens, Terricola subterraneus, and Lasiopodomys mandarinus. Original RNA-seq data were obtained for eight species, for nine species, SRA data were downloaded from the NCBI SRA database. Additionally assembled transcriptomes of Mynomes ochrogaster and Cricetulus griseus were included in the analysis. We searched for the selection signatures and parallel amino acid substitutions in a total of 19 species. Even within this limited data set, we found significant changes of dN/dS ratio by free-ratio model analysis for subterranean Arvicolinae. Parallel substitutions were detected in genes RAD23B and PYCR2. These genes are associated with DNA repair processes and response to oxidative stress. Similar substitutions were discovered in the RAD23 genes for highly specialized subterranean Heterocephalus glaber and Fukomys damarensis. The most pronounced signatures of adaptive evolution related to subterranean niche within species of Arvicolinae subfamily were detected for Ellobius lutescens. Our results suggest that genomic adaptations can occur very quickly so far as the amount of selection signatures was found to be compliant with the degree of specialization to the subterranean niche and independent from the evolutionary age of the taxon. We found that the number of genomic signatures of selection does not depend on the age of the taxon, but is positively correlated with the degree of specialization to the subterranean niche.

Signatures of Adaptation in Mitochondrial Genomes of Palearctic Subterranean Voles (Arvicolinae, Rodentia)

This study evaluates signatures of selection in the evolution of the mitochondrial DNA of voles, subfamily Arvicolinae, during the colonization of subterranean environments. The comparative sequence analysis of mitochondrial protein-coding genes of eight subterranean vole species (Prometheomys schaposchnikowi, three species of the genus Ellobius: Ellobius talpinus, Ellobius fuscocapillus and Ellobius lutescens, two species of the genus Terricola: Terricola subterraneus and Terricola daghestanicus, Lasiopodomys mandarinus, and Hyperacrius fertilis) and their closest aboveground relatives was applied using codon-substitution models. The highest number of selection signatures was detected in genes ATP8 and CYTB. The relaxation of selection was observed in most mitochondrial DNA protein-coding genes for subterranean species. The largest amount of relaxed genes is discovered in mole voles (genus Ellobius). The number of selection signatures was found to be independent of the evolutionary age of the lineage but fits the degree of specialization to the subterranean niche. The common trends of selective pressures were observed among the evolutionary ancient and highly specialized subterranean rodent families and phylogenetically young lineages of voles. It suggests that the signatures of adaptation in individual mitochondrial protein-coding genes associated with the colonization of the subterranean niche may appear within a rather short evolutionary timespan.

EvoProDom: Evolutionary modeling of protein families by assessing translocations of protein domains

Here, we introduce a novel ‘evolution of protein domains’ (EvoProDom) model for describing the evolution of proteins based on the ‘mix and merge’ of protein domains. We assembled and integrated genomic and proteomic data comprising protein domain content and orthologous proteins from 109 organisms. In EvoProDom, we characterized evolutionary events, particularly, translocations, as reciprocal exchanges of protein domains between orthologous proteins in different organisms. We showed that protein domains that translocate with highly frequency are generated by transcripts enriched in trans‐splicing events, that is, the generation of novel transcripts from the fusion of two distinct genes. In EvoProDom, we describe a general method to collate orthologous protein annotation from KEGG, and protein domain content from protein sequences using tools such as KoFamKOAL and Pfam. To summarize, EvoProDom presents a novel model for protein evolution based on the ‘mix and merge’ of protein domains rather than DNA‐based evolution models. This confers the advantage of considering chromosomal alterations as drivers of protein evolutionary events.

A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution

Detecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in the pattern of selection at protein-coding genes have been of main interest. To this end, phylogenetic branch-site codon models are routinely applied to detect changes in selective patterns along specific branches of the phylogeny. Many of these methods rely on a prespecified partition of the phylogeny to branch categories, thus treating the course of trait evolution as fully resolved and assuming that phenotypic transitions have occurred only at speciation events. Here, we present TraitRELAX, a new phylogenetic model that alleviates these strong assumptions by explicitly accounting for the uncertainty in the evolution of both trait and coding sequences. This joint statistical framework enables the detection of changes in selection intensity upon repeated trait transitions. We evaluated the performance of TraitRELAX using simulations and then applied it to two case studies. Using TraitRELAX, we found an intensification of selection in the primate SEMG2 gene in polygynandrous species compared to species of other mating forms, as well as changes in the intensity of purifying selection operating on sixteen bacterial genes upon transitioning from a free-living to an endosymbiotic lifestyle.[Evolutionary selection; intensification; $\gamma $-proteobacteria; genotype-phenotype; relaxation; SEMG2.].

Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks

In contrast to fossorial and above-ground organisms, subterranean species have adapted to the extreme stresses of living underground. We analyzed the predicted protein–protein interactions (PPIs) of all gene products, including those of stress-response genes, among nine subterranean, ten fossorial, and 13 aboveground species. We considered 10,314 unique orthologous protein families and constructed 5,879,879 PPIs in all organisms using ChiPPI. We found strong association between PPI network modulation and adaptation to specific habitats, noting that mutations in genes and changes in protein sequences were not linked directly with niche adaptation in the organisms sampled. Thus, orthologous hypoxia, heat-shock, and circadian clock proteins were found to cluster according to habitat, based on PPIs rather than on sequence similarities. Curiously, "ordered" domains were preserved in aboveground species, while "disordered" domains were conserved in subterranean organisms, and confirmed for proteins in DistProt database. Furthermore, proteins with disordered regions were found to adopt significantly less optimal codon usage in subterranean species than in fossorial and above-ground species. These findings reveal design principles of protein networks by means of alterations in protein domains, thus providing insight into deep mechanisms of evolutionary adaptation, generally, and particularly of species to underground living and other confined habitats.

Comparative forelimb morphology of scratch-digging and chisel-tooth digging African mole-rat species

Bathyergus suillus (Cape dune mole-rat) and Heterocephalus glaber (naked mole-rat) are two species of subterranean burrowing rodents. Bathyergus suillus occurs in soft sandy soils and is regarded as a scratch-digger, while H. glaber is found in hard, compact soils and is a chisel-tooth digging species. The present study aimed to determine musculoskeletal differences in the forelimb of these two species. The muscles of the forelimb, back and neck were dissected to the points of origin and insertion in the left and right forelimbs, B. suillus (n = 7) and H. glaber (n = 5). Dissected muscles were photographed before maceration to demonstrate muscle attachments. The scapular spine, acromion process and clavicle were relatively straight in B. suillus. In comparison a curved scapular spine, acromion process and clavicle were observed in H. glaber. In both species, the clavicle rested on the greater tuberosity of the humerus. In B. suillus, the deltoid tuberosity was prominent and situated more distally on the humeral shaft compared to the indistinct, more proximally situated deltoid tuberosity in H. glaber. A prominent bony structure underlying the thenar pad as well as a cartilaginous protrusion beneath the hypothenar pad were observed on the palmar surface of the manus in B. suillus. Prominent claws were observed in B. suillus. A robust m. sternohyoideus was observed in H. glaber while mm. tensor fasciae antebrachii and coracobrachialis were absent. The flexors of the antebrachium of B. suillus had additional and enlarged attachment sites. The forelimb of B. suillus may be morphologically adapted for scratch-digging with relatively large and additional forelimb muscles and robust bones. In comparison, H. glaber had a reduction in the relative size, amount of muscles as well as number of attachment sites in the forelimb muscles, while the well-developed ventral neck muscles may facilitate neck and head stabilisation during chisel-tooth digging.