The nocturnal bottleneck and the evolution of activity patterns in mammals

Maximising survival by shifting the daily timing of activity

Maximising survival requires animals to balance the competing demands of maintaining energy balance and avoiding predation. Here, quantitative modelling shows that optimising the daily timing of activity and rest based on the encountered environmental conditions enables small mammals to maximise survival. Our model shows that nocturnality is typically beneficial when predation risk is higher during the day than during the night, but this is reversed by the energetic benefit of diurnality when food becomes scarce. Empirical testing under semi‐natural conditions revealed that the daily timing of activity and rest in mice exposed to manipulations in energy availability and perceived predation risk is in line with the model’s predictions. Low food availability and decreased perceived daytime predation risk promote diurnal activity patterns. Overall, our results identify temporal niche switching in small mammals as a strategy to maximise survival in response to environmental changes in food availability and perceived predation risk.

Diurnal motor activity and "sunbathing" behaviour in crested porcupine (Hystrix cristata L., 1758)

The crested porcupine is a mainly nocturnal mammal that shows both moonlight avoidance and some diurnal motor activity, the latter as an extension of its night-time foraging behaviour. Furthermore, a peculiar daytime behaviour, described as "sunbathing", was reported as episodic in H. africaeaustralis. Between 2016 and 2019 a camera-trapping monitoring was performed within 10 porcupine settlements in order to detect the diurnal motor activity and to verify and describe the sunbathing behaviour in crested porcupine. Out of 1,003 trap days, a total of 148 events of diurnal motor activity were recorded. The diurnal motor activity occurred throughout the year mainly between December and June from 15:00 to 16:00, with no statistical difference between cubs, youngsters and adults. The sunbathing behaviour was detected for a total of 36 episodes recorded. Sunbathing was performed mainly by cubs. The sunbathing behaviour occurred only between April and June during the hottest hours of the day (11:00 to 12:00). Diurnal motor activity and sunbathing behaviour of porcupine are discussed in relation to food availability and porcupine physiology.

Transcriptomic data support a nocturnal bottleneck in the ancestor of gecko lizards

Gecko lizards are a species-rich clade of primarily-nocturnal squamate reptiles. In geckos, adaptations to nocturnality have dramatically reshaped the eye. Perhaps the most notable change is the loss of rod cells in the retina and subsequent "transmutation" of cones into a rod-like morphology and physiology. While many studies have noted the absence of some rod-specific genes, such as the visual pigment Rhodopsin (RH1), these studies have focused on just a handful of species that are nested deep in the gecko phylogeny. Thus, it is not clear whether these changes arose through convergence, are homologous and ubiquitous across geckos, or restricted to a subset of species. Here, we used de novo eye transcriptomes from five gecko species, and genomes from two additional gecko species, representing the breadth of extant gecko diversity (i.e. 4 of the 7 gecko families, spanning the deepest divergence of crown Gekkota), to show that geckos lost expression of almost the entire suite of necessary rod-cell phototransduction genes in the eye, distinct from all other squamate reptiles. Geckos are the first vertebrate group to have lost their complete rod-cell expression pathway, not just the visual pigment. In addition, all sampled species have also lost expression of the cone-opsin SWS2 visual pigment. These results strongly suggest a single loss of rod cells and subsequent cone-to-rod transmutation that occurred prior to the diversification of extant geckos.

Day and night in the subterranean: measuring daily activity patterns of subterranean rodents (Ctenomys aff. knighti) using bio-logging

While most studies of the impacts of climate change have investigated shifts in the spatial distribution of organisms, temporal shifts in the time of activity is another important adjustment made by animals in a changing world. Due to the importance of light and temperature cycles in shaping activity patterns, studies of activity patterns of organisms that inhabit extreme environments with respect to the 24-hour cyclicity of Earth have the potential to provide important insights into the interrelationships among abiotic variables, behaviour and physiology. Our previous laboratory studies with Argentinean tuco-tucos from the Monte desert (Ctenomys aff. knighti) show that these subterranean rodents display circadian activity/rest rhythms that can be synchronized by artificial light/dark cycles. Direct observations indicate that tuco-tucos emerge mainly for foraging and for removal of soil from their burrows. Here we used bio-logging devices for individual, long-term recording of daily activity/rest (accelerometry) and time on surface (light-loggers) of six tuco-tucos maintained in outdoor semi-natural enclosures. Environmental variables were measured simultaneously. Activity bouts were detected both during day and night but 77% of the highest values happened during the daytime and 47% of them coincided with time on surface. Statistical analyses indicate time of day and temperature as the main environmental factors modulating time on surface. In this context, the total duration that these subterranean animals spent on surface was high during the winter, averaging 3 h per day and time on surface occurred when underground temperature was lowest. Finally, transport of these animals to the indoor laboratory and subsequent assessment of their activity rhythms under constant darkness revealed a switch in the timing of activity. Plasticity of activity timing is not uncommon among desert rodents and may be adaptive in changing environments, such as the desert where this species lives.

Activity patterns in mammals: Circadian dominance challenged

The evidence that diel patterns of physiology and behaviour in mammals are governed by circadian ‘clocks’ is based almost entirely on studies of nocturnal rodents. The emergent circadian paradigm, however, neglects the roles of energy metabolism and alimentary function (feeding and digestion) as determinants of activity pattern. The temporal control of activity varies widely across taxa, and ungulates, microtine rodents, and insectivores provide examples in which circadian timekeeping is vestigial. The nocturnal rodent/human paradigm of circadian organisation is unhelpful when considering the broader manifestation of activity patterns in mammals.

The evidence that daily patterns of physiology and behaviour in mammals are governed by circadian ‘clocks’ is based almost entirely on studies of nocturnal rodents. This Essay proposes that the nocturnal rodent/human paradigm of circadian rhythms is unhelpful when considering the broader manifestation of temporal organisation of activity in mammals.

Evolution Shapes the Gene Expression Response to Oxidative Stress

Reactive oxygen species (ROS) play a key role in cell physiology and function. ROS represents a potential source of damage for many macromolecules including DNA. It is thought that daily changes in oxidative stress levels were an important early factor driving evolution of the circadian clock which enables organisms to predict changes in ROS levels before they actually occur and thereby optimally coordinate survival strategies. It is clear that ROS, at relatively low levels, can serve as an important signaling molecule and also serves as a key regulator of gene expression. Therefore, the mechanisms that have evolved to survive or harness these effects of ROS are ancient evolutionary adaptations that are tightly interconnected with most aspects of cellular physiology. Our understanding of these mechanisms has been mainly based on studies using a relatively small group of genetic models. However, we know comparatively little about how these mechanisms are conserved or have adapted during evolution under different environmental conditions. In this review, we describe recent work that has revealed significant species-specific differences in the gene expression response to ROS by exploring diverse organisms. This evidence supports the notion that during evolution, rather than being highly conserved, there is inherent plasticity in the molecular mechanisms responding to oxidative stress.

The role of ecological factors in shaping bat cone opsin evolution

Bats represent one of the largest and most striking nocturnal mammalian radiations, exhibiting many visual system specializations for performance in light-limited environments. Despite representing the greatest ecological diversity and species richness in Chiroptera, Neotropical lineages have been undersampled in molecular studies, limiting the potential for identifying signatures of selection on visual genes associated with differences in bat ecology. Here, we investigated how diverse ecological pressures mediate long-term shifts in selection upon long-wavelength (Lws) and short-wavelength (Sws1) opsins, photosensitive cone pigments that form the basis of colour vision in most mammals, including bats. We used codon-based likelihood clade models to test whether ecological variables associated with reliance on visual information (e.g. echolocation ability and diet) or exposure to varying light environments (e.g. roosting behaviour and foraging habitat) mediated shifts in evolutionary rates in bat cone opsin genes. Using additional cone opsin sequences from newly sequenced eye transcriptomes of six Neotropical bat species, we found significant evidence for different ecological pressures influencing the evolution of the cone opsins. While Lws is evolving under significantly lower constraint in highly specialized high-duty cycle echolocating lineages, which have enhanced sonar ability to detect and track targets, variation in Sws1 constraint was significantly associated with foraging habitat, exhibiting elevated rates of evolution in species that forage among vegetation. This suggests that increased reliance on echolocation as well as the spectral environment experienced by foraging bats may differentially influence the evolution of different cone opsins. Our study demonstrates that different ecological variables may underlie contrasting evolutionary patterns in bat visual opsins, and highlights the suitability of clade models for testing ecological hypotheses of visual evolution.

Interference competition pressure predicts the number of avian predators that shifted their timing of activity

Being active at different times facilitates the coexistence of functionally similar species. Hence, time partitioning might be induced by competition. However, the relative importance of direct interference and indirect exploitation competition on time partitioning remains unclear. The aim of this study was to investigate the relative importance of these two forms of competition on the occurrence of time-shifting among avian predator species. As a measure of interference competition pressure, we used the species richness of day-active avian predator species or of night-active avian predator species (i.e. species of Accipitriformes, Falconiformes and Strigiformes) in a particular geographical area (assemblage). As an estimate of exploitation competition pressure, we used the total species richness of avian predators in each assemblage. Estimates of the intensity of interference competition robustly predicted the number of Accipitriformes species that became crepuscular and the number of Strigiformes species that became day-active or strictly crepuscular. Interference competition pressure may depend on body size and on the total duration of the typical active period (day or night length). Our results support-to some extent-that smaller species are more likely to become time-shifters. Day length did not have an effect on the number of time-shifter species in the Accipitriformes. Among the large Strigiformes, more time-shifter species occur in areas where nights are shorter (i.e. where less of the typical time resource is available). However, in the small Strigiformes, we found the opposite, counterintuitive effect: more time-shifters where nights are longer. Exploitation competition may have had an additional positive effect on the number of time-shifters, but only in Accipitriformes, and the effect was not as robust. Our results thus support the interference competition hypothesis, suggesting that animals may have shifted their time of activity, despite phylogenetic constraints on the ability to do so, to reduce the costs of direct interactions. Our findings also highlight the influence of body size as a surrogate of competitive ability during encounters on time partitioning, at least among avian predators.

Redox control of non-shivering thermogenesis

Background

Thermogenic adipocytes reorganize their metabolism during cold exposure. Metabolic reprogramming requires readily available bioenergetics substrates, such as glucose and fatty acids, to increase mitochondrial respiration and produce heat via the uncoupling protein 1 (UCP1). This condition generates a finely-tuned production of mitochondrial reactive oxygen species (ROS) that support non-shivering thermogenesis.

Scope of review

Herein, the findings underlining the mechanisms that regulate ROS production and control of the adaptive responses tuning thermogenesis in adipocytes are described. Furthermore, this review describes the metabolic responses to substrate availability and the consequence of mitochondrial failure to switch fuel oxidation in response to changes in nutrient availability. A framework to control mitochondrial ROS threshold to maximize non-shivering thermogenesis in adipocytes is provided.

Major conclusions

Thermogenesis synchronizes fuel oxidation with an acute and transient increase of mitochondrial ROS that promotes the activation of redox-sensitive thermogenic signaling cascade and UCP1. However, an overload of substrate flux to mitochondria causes a massive and damaging mitochondrial ROS production that affects mitochondrial flexibility. Finding novel thermogenic redox targets and manipulating ROS concentration in adipocytes appears to be a promising avenue of research for improving thermogenesis and counteracting metabolic diseases.

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Mitochondrial ROS support non-shivering thermogenesis.

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Thermogenic ROS are tightly related to mitochondrial metabolic reorganization.

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Uncontrolled mitochondrial ROS production is causative of metabolic inflexibility.

Molecular Data Support an Early Shift to an Intermediate-Light Niche in the Evolution of Mammals

The visual ability and associated photic niche of early mammals is debated. The theory that ancestral mammals were nocturnal is supported by diverse adaptations. However, others argue that photopigment repertoires of early mammals are more consistent with a crepuscular niche, and support for this also comes from inferred spectral tuning of middle/long wavelength-sensitive (M/LWS) opsin sequences. Functional studies have suggested that the M/LWS pigment in the ancestor of Mammalia was either red- or green-sensitive; however, these were based on outdated phylogenies with key lineages omitted. By performing the most detailed study to date of middle/long-wave mammalian color vision, we provide the first experimental evidence that the M/LWS pigment of amniotes underwent a 9-nm spectral shift towards shorter wavelengths in the Mammalia ancestor, exceeding predictions from known critical sites. Our results suggest early mammals were yellow-sensitive, possibly representing an adaptive trade-off for both crepuscular (twilight) and nocturnal (moonlight) niches.

Taking a look into the orbit of mammalian carnivorans

In this study, we explore the relationship between orbit anatomy and different ecological factors in carnivorous mammals from a phylogenetic perspective. We calculated the frontation (α), convergence (β), and orbitotemporal (Ω) angles of the orbit from 3D coordinates of anatomical landmarks in a wide sample of carnivores with different kinds of visual strategy (i.e. photopic, scotopic, and mesopic), habitat (i.e. open, mixed, and closed), and substrate use (i.e. arboreal, terrestrial, and aquatic). We used Bloomberg's K and Pagel's λ to assess phylogenetic signal in frontation, convergence, and orbitotemporal angles. The association of orbit orientation with skull length and ecology was explored using phylogenetic generalized least squares and phylogenetic manova, respectively. Moreover, we also computed phylomorphospaces from orbit orientation. Our results indicate that there is not a clear association between orbit orientation and the ecology of living carnivorans. We hypothesize that the evolution of the orbit in mammalian carnivores represents a new case of an ecological bottleneck specific to carnivorans. New directions for future research are discussed in light of this new evidence.

Rapid Change in Mammalian Eye Shape Is Explained by Activity Pattern

The rate of morphological evolution along the branches of a phylogeny varies widely [1-6]. Although such rate variation is often assumed to reflect the strength of historical natural selection resulting in adaptation [7-14], this lacks empirical and analytical evidence. One way to demonstrate a relationship between branchwise rates and adaptation would be to show that rapid rates of evolution are linked with ecological shifts or key innovations. Here, we test for this link by determining whether activity pattern, the time of day at which species are active, explains rapid bursts of evolutionary change in eye shape. Using modern approaches to identify shifts in the rate of morphological evolution [7, 13], we find that over 74% of rapid eye-shape change during mammalian evolutionary history is directly explained by distinct selection pressures acting on nocturnal, cathemeral, and diurnal species. Our results reveal how ecological changes occurring along the branches of a phylogeny can manifest in subsequent changes in the rate of morphological evolution. Although selective pressures exerted by different activity patterns have acted uniformly across all mammals, we find differences in the rate of eye-shape evolution among orders. The key to understanding this is in how ecology itself has evolved. We find heterogeneity in how activity pattern has evolved among mammals that ultimately led to differences in the rate of eye-shape evolution among species. Our approach represents an exciting new way to pinpoint factors driving adaptation, enabling a clearer understanding of the factors that drive the evolution of biological diversity.

Day length constrains the time budget of aphid predators

Phenology shifts and range expansions cause organisms to experience novel day length - temperature correlations. Depending on the temporal niche, organisms may benefit or suffer from changes in day length, thus potentially affecting phenological adaptation. We assessed the impact of day length changes on larvae of Chrysoperla carnea (Stephens) and Episyrphus balteatus (De Geer), both of which prey on aphids. Larvae of E. balteatus are night-active, whereas those of C. carnea appear to be crepuscular. We subjected both species in climate chambers to day lengths of 16 : 8 L : D and, to circumvent diapause responses, 20 : 4 L : D. We recorded development times and predation rates of both species. E. balteatus grew 13% faster in the 16 : 8 L : D treatment and preyed on significantly more aphids. In contrast, C. carnea grew 13% faster in the 20 : 4 L : D treatment and higher predation rates in 20 : 4 L : D were marginally significant. Our results show that day length affects development and predation, but that the direction depends on species. Such differences in the use of day length may alter the efficiency of biocontrol agents in a changing climate.

Mechanisms Underlying the Visual Benefit of Cell Transplantation for the Treatment of Retinal Degenerations

The transplantation of retinal cells has been studied in animals to establish proof of its potential benefit for the treatment of blinding diseases. Photoreceptor precursors have been grafted in animal models of Mendelian-inherited retinal degenerations, and retinal pigmented epithelial cells have been used to restore visual function in animal models of age-related macular degeneration (AMD) and recently in patients. Cell therapy over corrective gene therapy in inherited retinal degeneration can overcome the genetic heterogeneity by providing one treatment for all genetic forms of the diseases. In AMD, the existence of multiple risk alleles precludes a priori the use of corrective gene therapy. Mechanistically, the experiments of photoreceptor precursor transplantation reveal the importance of cytoplasmic material exchange between the grafted cells and the host cells for functional rescue, an unsuspected mechanism and novel concept. For transplantation of retinal pigmented epithelial cells, the mechanisms behind the therapeutic benefit are only partially understood, and clinical trials are ongoing. The fascinating studies that describe the development of methodologies to produce cells to be grafted and demonstrate the functional benefit for vision are reviewed.

Opsin-based photopigments expressed in the retina of a South American pit viper, Bothrops atrox (Viperidae)

Although much is known about the visual system of vertebrates in general, studies regarding vision in reptiles, and snakes in particular, are scarce. Reptiles display diverse ocular structures, including different types of retinae such as pure cone, mostly rod, or duplex retinas (containing both rods and cones); however, the same five opsin-based photopigments are found in many of these animals. It is thought that ancestral snakes were nocturnal and/or fossorial, and, as such, they have lost two pigments, but retained three visual opsin classes. These are the RH1 gene (rod opsin or rhodopsin-like-1) expressed in rods and two cone opsins, namely LWS (long-wavelength-sensitive) and SWS1 (short-wavelength-sensitive-1) genes. Until recently, the study of snake photopigments has been largely ignored. However, its importance has become clear within the past few years as studies reconsider Walls’ transmutation theory, which was first proposed in the 1930s. In this study, the visual pigments of Bothrops atrox (the common lancehead), a South American pit viper, were examined. Specifically, full-length RH1 and LWS opsin gene sequences were cloned, as well as most of the SWS1 opsin gene. These sequences were subsequently used for phylogenetic analysis and to predict the wavelength of maximum absorbance (λ_max) for each photopigment. This is the first report to support the potential for rudimentary color vision in a South American viper, specifically a species that is regarded as being nocturnal.

Evolution and Expression of S100A7 Gene in Vertebrates

The skin is the primary barrier between the internal organs of an organism and the environment, and it provides protection from ultraviolet (UV) radiation. According to the nocturnal bottleneck hypothesis, ungulates might have traversed to the grasslands and were exposed to UV radiation subsequent to the reduction in predation pressure. UV light exposure might have increased the S100A7 expression. In order to test whether the UV radiation is associated with the selection pressure on S100A7, we acquired the complete S100A7 DNA sequences from each of 42 vertebrate species. The results suggested that the evidence of diversifying selection in S100A7 occurred at the end of Mesozoic era, and the site of positive selection was observed in the branch of Artiodactyla (even-toed ungulates). In addition, we found that the transcription level of S100A7 in cashmere goat skin correlates with UV radiation. Our results indicated that S100A7 plays a role in the signaling between the skin genes and UV radiation during evolution.

The Calyx of Held: A Hypothesis on the Need for Reliable Timing in an Intensity-Difference Encoder

The calyx of Held is the preeminent model for the study of synaptic function in the mammalian CNS. Despite much work on the synapse and associated circuit, its role in hearing remains enigmatic. We propose that the calyx is one of the key adaptations that enables an animal to lateralize transient sounds. The calyx is part of a binaural circuit that is biased toward high sound frequencies and is sensitive to intensity differences between the ears. This circuit also shows marked sensitivity to interaural time differences, but only for brief sound transients ("clicks"). In a natural environment, such transients are rare except as adventitious sounds generated by other animals moving at close range. We argue that the calyx, and associated temporal specializations, evolved to enable spatial localization of sound transients, through a neural code congruent with the circuit's sensitivity to interaural intensity differences, thereby conferring a key benefit to survival.

Evolution: A Dark Past

The cavefish Phreatichthys andruzzii has lost the capacity to perform light-mediated DNA repair. This finding provides further support for the 'nocturnal bottleneck' hypothesis which posits that many key mammalian traits originated from adaptations linked to the nocturnal lifestyle of our early evolutionary ancestors.

Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness

How the environment shapes the function and evolution of DNA repair systems is poorly understood. In a comparative study using zebrafish and the Somalian blind cavefish, Phreatichthys andruzzii, we reveal that during evolution for millions of years in continuous darkness, photoreactivation DNA repair function has been lost in P. andruzzii. We demonstrate that this loss results in part from loss-of-function mutations in pivotal DNA-repair genes. Specifically, C-terminal truncations in P. andruzzii DASH and 6-4 photolyase render these proteins predominantly cytoplasmic, with consequent loss in their functionality. In addition, we reveal a general absence of light-, UV-, and ROS-induced expression of P. andruzzii DNA-repair genes. This results from a loss of function of the D-box enhancer element, which coordinates and enhances DNA repair in response to sunlight. Our results point to P. andruzzii being the only species described, apart from placental mammals, that lacks the highly evolutionary conserved photoreactivation function. We predict that in the DNA repair systems of P. andruzzii, we may be witnessing the first stages in a process that previously occurred in the ancestors of placental mammals during the Mesozoic era.

Evolution shapes the responsiveness of the D-box enhancer element to light and reactive oxygen species in vertebrates

The circadian clock is a highly conserved cell-autonomous mechanism that directs daily rhythms in most aspects of biology. Daily entrainment by environmental signals, notably light, is essential for its function. However, our understanding of the mechanisms and the evolution of photic entrainment remains incomplete. Fish represent attractive models for exploring how light regulates the circadian clock due to the direct light sensitivity of their peripheral clocks. Central to this property is the light induced expression of clock genes that is mediated by D-box enhancer elements. Here, using zebrafish cells, we reveal that the light responsive D-box enhancer serves as a nuclear target for reactive oxygen species (ROS). We demonstrate that exposure to short wavelengths of visible light triggers increases in ROS levels via NADPH oxidase activity. Elevated ROS activates the JNK and p38 MAP kinases and in turn, induces clock gene expression via the D-box. In blind cavefish and mammals, where peripheral clocks are no longer entrained by direct illumination, ROS levels are still increased upon light exposure. However, in these species ROS no longer induces D-box driven clock gene transcription. Thus, during evolution, alterations in ROS-responsive signal transduction pathways underlie fundamental changes in peripheral clock photoentrainment.

Coexpression of nonvisual opsin, retinal G protein-coupled receptor, and visual pigments in human and bovine cone photoreceptors

PURPOSE

Retinal G protein-coupled receptor (RGR) mRNA is transcribed in the outer nuclear layer of human retinas; however, it is not known whether the RGR gene is expressed in the rod or cone photoreceptors. In this study, we investigate broader expression of the normal RGR isoform in photoreceptors of human and bovine retinas.

METHODS

We produced and validated a rabbit polyclonal antipeptide antibody (DE15) that is directed against a peptide sequence (SSLLRRWPHGSEGC) partly conserved in RGR across several species. Bovine and human retina sections were analyzed with immunohistochemical and double-label immunofluorescent staining.

RESULTS

The DE15 antibody bound specifically to overexpressed recombinant RGR, purified RGR from bovine RPE, and RGR in crude RPE membrane extracts without cross-reaction to other proteins. Immunostaining of diurnal bovine and human retinas with DE15 showed labeling of long-wavelength-sensitive and short-wavelength-sensitive cone photoreceptors and some retinal ganglion cells in both species. Strong labeling with DE15 was detected throughout the cone photoreceptor, including the outer segment, inner segment, cell body, axon, and cone pedicle, while rod outer segments were negative. Immunostaining for human exon-6-skipping RGR (RGR-d) was found primarily at the tips of the outer segment of the cones.

CONCLUSIONS

The results indicate that the cone photoreceptors in these mammals express a nonvisual opsin of the Go/RGR or tetraopsin group. RGR and the visual pigments are predominantly colocalized in the cone outer segment, which suggests functional interaction among these opsins. Human cone photoreceptors may also contain normal RGR and the aberrant RGR-d splice isoform.

Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments

BACKGROUND

Based on evolutionary patterns of the vertebrate eye, Walls (1942) hypothesized that early placental mammals evolved primarily in nocturnal habitats. However, not only Eutheria, but all mammals show photic characteristics (i.e. dichromatic vision, rod-dominated retina) suggestive of a scotopic eye design.

RESULTS

Here, we used integrative comparative genomic and phylogenetic methodologies employing the photoreceptive opsin gene family in 154 mammals to test the likelihood of a nocturnal period in the emergence of all mammals. We showed that mammals possess genomic patterns concordant with a nocturnal ancestry. The loss of the RH2, VA, PARA, PARIE and OPN4x opsins in all mammals led us to advance a probable and most-parsimonious hypothesis of a global nocturnal bottleneck that explains the loss of these genes in the emerging lineage (> > 215.5 million years ago). In addition, ancestral character reconstruction analyses provided strong evidence that ancestral mammals possessed a nocturnal lifestyle, ultra-violet-sensitive vision, low visual acuity and low orbit convergence (i.e. panoramic vision).

CONCLUSIONS

Overall, this study provides insight into the evolutionary history of the mammalian eye while discussing important ecological aspects of the photic paleo-environments ancestral mammals have occupied.

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

Melanopsin photopigments, Opn4x and Opn4m, were evolutionary selected to "see the light" in systems that regulate skin colour change. In this review, we analyse the roles of melanopsins, and how critical evolutionary developments, including the requirement for thermoregulation and ultraviolet protection, the emergence of a background adaptation mechanism in land-dwelling amphibian ancestors and the loss of a photosensitive pineal gland in mammals, may have helped sculpt the mechanisms that regulate light-controlled skin pigmentation. These mechanisms include melanopsin in skin pigment cells directly inducing skin darkening for thermoregulation/ultraviolet protection; melanopsin-expressing eye cells controlling neuroendocrine circuits to mediate background adaptation in amphibians in response to surface-reflected light; and pineal gland secretion of melatonin phased to environmental illuminance to regulate circadian and seasonal variation in skin colour, a process initiated by melanopsin-expressing eye cells in mammals, and by as yet unknown non-visual opsins in the pineal gland of non-mammals.

Photopigments and the dimensionality of animal color vision

Early color-matching studies established that normal human color vision is trichromatic. Subsequent research revealed a causal link between trichromacy and the presence in the retina of three classes of cone photopigments. Over the years, measurements of the photopigment complements of other species have expanded greatly and these are frequently used to predict the dimensionality of an animal's color vision. This review provides an account of how the linkage between the number of active photopigments and the dimensions of human color vision developed, summarizes the various mechanisms that can impact photopigment spectra and number, and provides an across-species survey to examine cases where the photopigment link to the dimensionality of color vision has been claimed. The literature reveals numerous instances where the human model fails to account for the ways in which the visual systems of other animals exploit information obtained from the presence of multiple photopigments in support of their behavior.

The evolution of cortical development: the synapsid-diapsid divergence

The cerebral cortex covers the rostral part of the brain and, in higher mammals and particularly humans, plays a key role in cognition and consciousness. It is populated with neuronal cell bodies distributed in radially organized layers. Understanding the common and lineage-specific molecular mechanisms that orchestrate cortical development and evolution are key issues in neurobiology. During evolution, the cortex appeared in stem amniotes and evolved divergently in two main branches of the phylogenetic tree: the synapsids (which led to present day mammals) and the diapsids (reptiles and birds). Comparative studies in organisms that belong to those two branches have identified some common principles of cortical development and organization that are possibly inherited from stem amniotes and regulated by similar molecular mechanisms. These comparisons have also highlighted certain essential features of mammalian cortices that are absent or different in diapsids and that probably evolved after the synapsid-diapsid divergence. Chief among these is the size and multi-laminar organization of the mammalian cortex, and the propensity to increase its area by folding. Here, I review recent data on cortical neurogenesis, neuronal migration and cortical layer formation and folding in this evolutionary perspective, and highlight important unanswered questions for future investigation.

Two sides of a coin: ecological and chronobiological perspectives of timing in the wild

Most processes within organisms, and most interactions between organisms and their environment, have distinct time profiles. The temporal coordination of such processes is crucial across levels of biological organization, but disciplines differ widely in their approaches to study timing. Such differences are accentuated between ecologists, who are centrally concerned with a holistic view of an organism in relation to its external environment, and chronobiologists, who emphasize internal timekeeping within an organism and the mechanisms of its adjustment to the environment. We argue that ecological and chronobiological perspectives are complementary, and that studies at the intersection will enable both fields to jointly overcome obstacles that currently hinder progress. However, to achieve this integration, we first have to cross some conceptual barriers, clarifying prohibitively inaccessible terminologies. We critically assess main assumptions and concepts in either field, as well as their common interests. Both approaches intersect in their need to understand the extent and regulation of temporal plasticity, and in the concept of 'chronotype', i.e. the characteristic temporal properties of individuals which are the targets of natural and sexual selection. We then highlight promising developments, point out open questions, acknowledge difficulties and propose directions for further integration of ecological and chronobiological perspectives through Wild Clock research.This article is part of the themed issue 'Wild Clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'.

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes

We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.

Evolution of Visual Processing in the Human Retina

Motion detection in humans is based on luminance differences, now shown likely to be processed by a specialized set of cone cells, separate from the cone cells that process color. Humans appear to have evolved a mechanism analogous to that proposed for the double cones of other vertebrates, lost as vision simplified in our nocturnal ancestors.

Deep-sequencing to resolve complex diversity of apicomplexan parasites in platypuses and echidnas: Proof of principle for wildlife disease investigation

The short-beaked echidna (Tachyglossus aculeatus) and the platypus (Ornithorhynchus anatinus) are iconic egg-laying monotremes (Mammalia: Monotremata) from Australasia. The aim of this study was to demonstrate the utility of diversity profiles in disease investigations of monotremes. Using small subunit (18S) rDNA amplicon deep-sequencing we demonstrated the presence of apicomplexan parasites and confirmed by direct and cloned amplicon gene sequencing Theileria ornithorhynchi, Theileria tachyglossi, Eimeria echidnae and Cryptosporidium fayeri. Using a combination of samples from healthy and diseased animals, we show a close evolutionary relationship between species of coccidia (Eimeria) and piroplasms (Theileria) from the echidna and platypus. The presence of E. echidnae was demonstrated in faeces and tissues affected by disseminated coccidiosis. Moreover, the presence of E. echidnae DNA in the blood of echidnas was associated with atoxoplasma-like stages in white blood cells, suggesting Hepatozoon tachyglossi blood stages are disseminated E. echidnae stages. These next-generation DNA sequencing technologies are suited to material and organisms that have not been previously characterised and for which the material is scarce. The deep sequencing approach supports traditional diagnostic methods, including microscopy, clinical pathology and histopathology, to better define the status quo. This approach is particularly suitable for wildlife disease investigation.

Seasonal changes in activity patterns of Japanese flying squirrel Pteromys momonga

Seasonal changes of activity patterns are an important survival strategy for several species. Seasonal changes in the activity patterns of Japanese flying squirrels (Pteromys momonga) were studied at Daibosatsu Mountain on Honshu Island, Japan from 2 June to 20 November 2007 and 11 April to 14 November 2008, to discuss their survival strategy based on the change. Activity patterns were assessed using long-term sensor camera traps at 214 sites for 14 months of a 2-year period. The cameras were placed for a total of 7317 camera trap nights over which total of 90 photographs of this species were collected from 22 of the 214 sites. Although distinct nocturnal activity was detected throughout the study period, activity patterns differed between temperate (June-September) and cold (April, May, October, and November) seasons. So, activity peaks were found to be bimodal during the temperate seasons and trimodal during the cold seasons. It is possible that the squirrels reduce their activity times per bout during the cold seasons to reduce energy loss arising from prolonged exposure to cold temperatures, as a survival strategy.

Genomic regression of claw keratin, taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes

Regressive evolution of anatomical traits often corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The evolutionary origins of snakes involved the regression of a number of anatomical traits, including limbs, taste buds and the visual system, and by analyzing serpent genomes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins are pseudogenized/deleted in snake genomes, providing additional evidence of claw-specificity. The second hypothesis is that snakes lack taste buds, an issue complicated by conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least one gustatory channel. The final hypothesis addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light-associated functions in snakes, demonstrating a pattern of gene loss similar to other dim light-adapted clades. Molecular dating estimates suggest that dim light adaptation preceded the loss of limbs, providing some bearing on interpretations of the ecological origins of snakes.

Out of the dark: 350 million years of conservatism and evolution in diel activity patterns in vertebrates

Many animals are active only during a particular time (e.g., day vs. night), a partitioning that may have important consequences for species coexistence. An open question is the extent to which this diel activity niche is evolutionarily conserved or labile. Here, we analyze diel activity data across a phylogeny of 1914 tetrapod species. We find strong phylogenetic signal, showing that closely related species tend to share similar activity patterns. Ancestral reconstructions show that nocturnality was the most likely ancestral diel activity pattern for tetrapods and many major clades within it (e.g., amphibians, mammals). Remarkably, nocturnal activity appears to have been maintained continuously in some lineages for ∼350 million years. Thus, we show that traits involved in local-scale resource partitioning can be conserved over strikingly deep evolutionary time scales. We also demonstrate a potentially important (but often overlooked) metric of niche conservatism. Finally, we show that diurnal lineages appear to have faster speciation and diversification rates than nocturnal lineages, which may explain why there are presently more diurnal tetrapod species even though diurnality appears to have evolved more recently. Overall, our results may have implications for studies of community ecology, species richness, and the evolution of diet and communication systems.

Evidence for convergent evolution of a neocortex-like structure in a late Permian therapsid

The special sensory, motor, and cognitive capabilities of mammals mainly depend upon the neocortex, which is the six-layered cover of the mammalian forebrain. The origin of the neocortex is still controversial and the current view is that larger brains with neocortex first evolved in late Triassic Mammaliaformes. Here, we report the earliest evidence of a structure analogous to the mammalian neocortex in a forerunner of mammals, the fossorial anomodont Kawingasaurus fossilis from the late Permian of Tanzania. The endocranial cavity of Kawingasaurus is almost completely ossified, which allowed a less hypothetical virtual reconstruction of the brain endocast to be generated. A parietal foramen is absent. A small pit between the cerebral hemispheres is interpreted as a pineal body. The inflated cerebral hemispheres are demarcated from each other by a median sulcus and by a possible rhinal fissure from the rest of the endocast. The encephalization quotient estimated by using the method of Eisenberg is 0.52, which is 2-3 times larger than in other nonmammalian synapsids. Another remarkable feature are the extremely ramified infraorbital canals in the snout. The shape of the brain endocast, the extremely ramified maxillary canals as well as the small frontally placed eyes suggest that special sensory adaptations to the subterranean habitat such as a well developed sense of touch and binocular vision may have driven the parallel evolution of an equivalent of the mammalian neocortex and a mammal-like lemnothalamic visual system in Kawingasaurus. The gross anatomy of the brain endocast of Kawingasaurus supports the Outgroup Hypothesis, according to which the neocortex evolved from the dorsal pallium of an amphibian-like ancestor, which receives sensory projections from the lemnothalamic pathway. The enlarged brain as well as the absence of a parietal foramen may be an indication for a higher metabolic rate of Kawingasaurus compared to other nonmammalian synapsids.

Recruitment of Rod Photoreceptors from Short-Wavelength-Sensitive Cones during the Evolution of Nocturnal Vision in Mammals

Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinas. In mice, we discovered genetic and epigenetic vestiges of short-wavelength cones in developing rods, and cell-lineage tracing validated the genesis of rods from S cones. Curiously, rods did not derive from S cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution.

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

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.