Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs

Abstract

The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers.

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura

“…Indeed, trnL2 is associated to the most numerous codon families not only in Brachyura (see Supplementary Fig. S5 ) but in animal taxa 50 , 67 , 72 . It is implausible that the true trnL2 was lost before the remoulding process occurred.…”

Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

“…The double-helix stems, which play a key role in the formation of secondary structures of tRNAs, might experience strong evolutionary constraints [40]. Different substitution patterns in the stems of tRNAs were associated with different evolutionary history, and thus could provide valuable signals in phylogeny.…”

A Miocene pygmy right whale fossil from Australia

“…The living pygmy right whale, Caperea marginata ( Gray, 1846 ), is the smallest living baleen whale, and the only living representative of its lineage (Neobalaeninae). Its ecology and behaviour remains poorly understood, but it stands apart from all other whales in its skeletal structure ( Beddard, 1901 ; Buchholtz, 2011 ), visual capabilities ( Meredith et al, 2013 ), and even the evolution of its mitochondrial tRNAs ( Montelli et al, 2016 ).…”