Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes

Abstract

Nocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods.

Strong evolutionary convergence of receptor-binding protein spike between COVID-19 and SARS-related coronaviruses

“…The S1 subunit contains a receptorbinding domain (RBD), which harbors a receptor-binding motif (RBM) to make complete contact with the receptor (i.e., ACE2) 12,13 .Considering that 2019-nCoV and SARS-CoV are distantly related, but show high similarity in the RBD protein structure and can use the same cell receptor, ACE2 5-11 , an evolutionary convergence may have occurred between them. In the present study, we employ a recently developed molecular phyloecological approach [14][15][16] , which uses a comparative phylogenetic analysis of functional gene sequences to determine the genetic basis of phenotypic evolution, and we examine the possible molecular basis underlying the phenotypic convergence between 2019-nCoV and SARS-CoV. Our results reveal positive selection signals and evolutionary convergent amino acid sites of the spike protein in both 2019-nCoV and SARS-CoV and their related coronaviruses, providing new insights into understanding the evolutionary origin of their phenotypic convergence.…”

Seeing the light to change colour: An evolutionary perspective on the role of melanopsin in neuroendocrine circuits regulating light‐mediated skin pigmentation

“…Finally, melanopsin, which in mammals controls melatonin secretion to regulate physiological parameters that oscillate in a circadian manner, may also control melatonin levels in LEI and LPI organisms to mediate circadian/seasonal changes in skin colour (Figure 1b). The "nocturnal bottleneck hypothesis" (Gerkema, Davies, Foster, Menaker, & Hut, 2013;Wu, Wang, & Hadly, 2017) helps to explain how in the mammalian lineage, evolution selected for both certain opsins, including melanopsin (Davies, Collin, & Hunt, 2012), and the loss of an external photosensitive pineal gland. Ancient mammals lived in dark caverns during the Mesozoic era to avoid competing with the dominant diurnal reptiles.…”

Convergent evolution of bird-mammal shared characteristics for adapting to nocturnality

“…Following the MPE approach for studying the diel activity pattern of ancestral taxa 13,20-22 , we reconstructed the diel activity patterns of our focal taxa by analyzing the adaptive evolution of 33 phototransduction genes (Supplementary Table S1) involved in the rod and cone phototransduction pathway 23,24 in the context of sauropsid phylogeny (Fig. 1).…”

“…On the other hand, the traditional view, the thermal niche expansion model, invokes nocturnality as an initial driver for the evolution of endothermy in ancestral mammals that would not necessarily featured by high resting metabolic rate typical of most living mammals 2,7 . Indeed, early mammals are widely accepted as having been nocturnal 12,13 , and it has been hypothesized that the evolution of endothermy may have allowed them to overcome ambient low temperature constraints to be active at night, while diurnal ectothermic reptiles essentially depend on sunlight to increase their body temperature to operational levels 12,14 . The nocturnality hypothesis is criticized as being suitable only to mammals 1 , partly because so far only the nocturnality of the synapsid lineages (e.g., early mammals) is well known, while the possible nocturnal activity of the diapsid lineages (e.g., birds), especially during their early evolution, is unknown.…”

“…The recent development of a molecular phyloecological (MPE) approach allows us to reconstruct the diel activity pattern of ancestral taxa using molecular data 13,20-22 . The MPE approach has been applied to analyze the diel activity patterns of birds and mammals, and the results demonstrate its sensitivity to distinct animals with different diel activity patterns, showing that nocturnality, diurnality and cathemerality are featured by enhanced positive selection of dim-light vision genes (rod-expressed genes), bright-light vision genes (cone-expressed genes) and both, respectively 13,20,22 . In this study, we employed the MPE approach to reconstruct the early evolution of the diel activity patterns in diapsid lineages.…”