Adaptive evolution of tight junction protein claudin-14 in echolocating whales

Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways

Repeated phenotypes, often referred to as 'homoplasies' in cladistic analyses, may evolve through changes in developmental processes. Genetic bases of recurrent evolution gained attention and have been studied in the past years using approaches that combine modern analytical phylogenetic tools with the stunning assemblage of new information on developmental mechanisms. In this review, we evaluated the topic under an integrated perspective, revisiting the classical definitions of convergence and parallelism and detailing comparative methods used to evaluate evolution of repeated phenotypes, which include phylogenetic inference, estimates of evolutionary rates and reconstruction of ancestral states. We provide examples to illustrate how a given methodological approach can be used to identify evolutionary patterns and evaluate developmental mechanisms associated with the intermittent expression of a given trait along the phylogeny. Finally, we address why repeated trait loss challenges strict definitions of convergence and parallelism, discussing how changes in developmental pathways might explain the high frequency of repeated trait loss in specific lineages.

The evolutionary tuning of hearing

After the transition to life on land, tympanic middle ears emerged separately in different groups of tetrapods, facilitating the efficient detection of airborne sounds and paving the way for high frequency sensitivity. The processes that brought about high-frequency hearing in mammals are tightly linked to the accumulation of coding sequence changes in inner ear genes; many of which were selected during evolution. These include proteins involved in hair bundle morphology, mechanotransduction and high endolymphatic potential, somatic electromotility for sound amplification, ribbon synapses for high-fidelity transmission of sound stimuli, and efferent synapses for the modulation of sound amplification. Here, we review the molecular evolutionary processes behind auditory functional innovation. Overall, the evidence to date supports the hypothesis that changes in inner ear proteins were central to the fine tuning of mammalian hearing.

Assessing evidence for adaptive evolution in two hearing-related genes important for high-frequency hearing in echolocating mammals

High-frequency hearing is particularly important for echolocating bats and toothed whales. Previously, studies of the hearing-related genes Prestin, KCNQ4, and TMC1 documented that adaptive evolution of high-frequency hearing has taken place in echolocating bats and toothed whales. In this study, we present two additional candidate hearing-related genes, Shh and SK2, that may also have contributed to the evolution of echolocation in mammals. Shh is a member of the vertebrate Hedgehog gene family and is required in the specification of the mammalian cochlea. SK2 is expressed in both inner and outer hair cells, and it plays an important role in the auditory system. The coding region sequences of Shh and SK2 were obtained from a wide range of mammals with and without echolocating ability. The topologies of phylogenetic trees constructed using Shh and SK2 were different; however, multiple molecular evolutionary analyses showed that those two genes experienced different selective pressures in echolocating bats and toothed whales compared to nonecholocating mammals. In addition, several nominally significant positively selected sites were detected in the nonfunctional domain of the SK2 gene, indicating that different selective pressures were acting on different parts of the SK2 gene. This study has expanded our knowledge of the adaptive evolution of high-frequency hearing in echolocating mammals.

Claudins of sea lamprey (Petromyzon marinus) - organ-specific expression and transcriptional responses to water of varying ion content

The role of lamprey epithelium tight junctions (TJs) in the regulation of salt and water balance is poorly understood. This study reported on claudin (Cldn) TJ protein transcripts of pre-metamorphic larval and post-metamorphic juvenile sea lamprey (Petromyzon marinus) and the transcriptional response of genes encoding Cldns to changed environmental ion levels. Transcripts encoding Cldn-3b, -4, -5, -10, -14, -18 and -19 were identified, and mRNA expression profiles revealed the organ-specific presence of cldn-5 and -14, broad expression of cldn-3b, -4, -10, -18 and -19 and spatial differences in the mRNA abundance of cldn-4, -3b and -14 along the ammocoete intestine. Expression profiles were qualitatively similar in ammocoetes and juvenile fishes. Transcript abundance of genes encoding Cldns in osmoregulatory organs (gill, kidney, intestine and skin) was subsequently investigated after exposure of ammocoetes to ion-poor water (IPW) and juveniles to hyperosmotic conditions [60% sea water (SW)]. IPW-acclimated ammocoetes increased mRNA abundance of nearly all cldns in the gill. Simultaneously, cldn-10 abundance increased in the skin, whereas cldn-4, -14 and -18 decreased in the kidney. Ammocoete cldn mRNA abundance in the intestine was altered in a region-specific manner. In contrast, cldn transcript abundance was mostly downregulated in osmoregulatory organs of juvenile fish acclimated to SW - cldn-3b, -10 and -19 in the gill; cldn-3b, -4, -10 and -19 in the skin; cldn-3b in the kidney; and cldn-3b and -14 in the intestine. Data support the idea that Cldn TJ proteins play an important role in the osmoregulatory physiology of pre- and post-metamorphic sea lamprey and that Cldn participation can occur across organs, in an organ-specific manner, as well as differ spatially within organs, which contributes to the regulation of salt and water balance in these fishes.

Cochlear Proteins Associated with Noise-induced Hearing Loss: An Update

Noise-induced hearing loss (NIHL) is one of the major occupational disease that has influence on the quality of life of mining workers. Several reports suggest NIHL is attributed to noise exposure at workplace and approximately 16% of hearing loss is due to it. NIHL occurs as a result of exposure to high-level noise (>85 dB) in the workplace. Noise disrupts proteins present in the micromachinery of the ear that is required for mechano-electric transduction of sound waves. High-level noise exposure can lead to hearing impairment owing to mechanical and metabolic exhaustion in cochlea, the major organ responsible for resilience of sound. Several key proteins of cochlea include tectorial membrane, inner hair cells, outer hair cells, and stereocilia are damaged due to high-level noise exposure. Numerous studies conducted in animals have shown cochlear proteins involvement in NIHL, but the pertinent literature remains limited in humans. Detection of proteins and pathways perturbed within the micromachinery of the ear after excessive sound induction leads toward the early identification of hearing loss. The situation insisted to present this review as an update on cochlear proteins associated with NIHL after an extensive literature search using several electronic databases which help to understand the pathophysiology of NIHL.

Adaptive evolution of the STRA6 genes in mammalian

Stimulated by retinoic acid 6 (STRA6) is the receptor for retinol binding protein and is relevant for the transport of retinol to specific sites such as the eye. The adaptive evolution mechanism that vertebrates have occupied nearly every habitat available on earth and adopted various lifestyles associated with different light conditions and visual challenges, as well as their role in development and adaptation is thus far unknown. In this work, we have investigated different aspects of vertebrate STRA6 evolution and used molecular evolutionary analyses to detect evidence of vertebrate adaptation to the lightless habitat. Free-ratio model revealed significant rate shifts immediately after the species divergence. The amino acid sites detected to be under positive selection are within the extracellular loops of STRA6 protein. Branch-site model A test revealed that STRA6 has undergone positive selection in the different phyla of mammalian except for the branch of rodent. The results suggest that interactions between different light environments and host may be driving adaptive change in STRA6 by competition between species. In support of this, we found that altered functional constraints may take place at some amino acid residues after speciation. We suggest that STRA6 has undergone adaptive evolution in different branch of vertebrate relation to habitat environment.