Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families

Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex.

Geometric design of antireflective leafhopper brochosomes

In nature, leafhoppers cover their body surfaces with brochosomes as a protective coating. These leafhopper-produced brochosomes are hollow, buckyball-shaped, nanoscopic spheroids with through-holes distributed across their surfaces, representing a class of deployable optical materials that are rare in nature. Despite their discovery in the 1950s, it remains unknown why the sizes of brochosomes and their through-holes consistently fall within the range of hundreds of nanometers across different leafhopper species. Here, we demonstrate that the hierarchical geometries of brochosomes are engineered within a narrow size range with through-hole architecture to significantly reduce light reflection. By utilizing two-photon polymerization three-dimensional printing to fabricate high-fidelity synthetic brochosomes, we investigated the optical form-to-function relationship of brochosomes. Our results show that the diameters of brochosomes are engineered within a specific size range to maximize broadband light scattering, while the secondary through-holes are designed to function as short-wavelength, low-pass filters, further reducing light reflection. These synergistic effects enable brochosomes to achieve a substantial reduction in specular reflection, by up to approximately 80 to 94%, across a broadband wavelength range. Importantly, brochosomes represent a biological example demonstrating short-wavelength, low-pass filter functionality. Furthermore, our results indicate that the geometries of natural brochosomes may have evolved to effectively reduce reflection from ultraviolet to visible light, thereby enabling leafhoppers to evade predators whose vision spectrum encompasses both ultraviolet and visible light. Our findings offer key design insights into a class of deployable bioinspired optical materials with potential applications in omnidirectional antireflection coatings, optical encryption, and multispectral camouflage.

The genomic basis of temporal niche evolution in a diurnal rodent

Patterns of diel activity-how animals allocate their activity throughout the 24-h daily cycle-play key roles in shaping the internal physiology of an animal and its relationship with the external environment.1,2,3,4,5 Although shifts in diel activity patterns have occurred numerous times over the course of vertebrate evolution,6 the genomic correlates of such transitions remain unknown. Here, we use the African striped mouse (Rhabdomys pumilio), a species that transitioned from the ancestrally nocturnal diel niche of its close relatives to a diurnal one,7,8,9,10,11 to define patterns of naturally occurring molecular variation in diel niche traits. First, to facilitate genomic analyses, we generate a chromosome-level genome assembly of the striped mouse. Next, using transcriptomics, we show that the switch to daytime activity in this species is associated with a realignment of daily rhythms in peripheral tissues with respect to the light:dark cycle and the central circadian clock. To uncover selection pressures associated with this temporal niche shift, we perform comparative genomic analyses with closely related rodent species and find evidence of relaxation of purifying selection on striped mouse genes in the rod phototransduction pathway. In agreement with this, electroretinogram measurements demonstrate that striped mice have functional differences in dim-light visual responses compared with nocturnal rodents. Taken together, our results show that striped mice have undergone a drastic change in circadian organization and provide evidence that the visual system has been a major target of selection as this species transitioned to a novel temporal niche.

Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review

Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.

Enhanced short-wavelength sensitivity in the blue-tongued skink, Tiliqua rugosa

Despite lizards using a wide range of color signals, the limited variation in photoreceptor spectral sensitivities across lizards suggests only weak selection for species-specific, spectral tuning of photoreceptors. Some species, however, have enhanced short wavelength sensitivity, which likely helps with the detection of signals rich in ultraviolet and short wavelengths. In this study, we examined the visual system of Tiliqua rugosa, which has a UV/blue tongue, to gain insight into this species' visual ecology. We used electroretinograms, opsin sequencing and immunohistochemical labelling to characterize whole eye spectral sensitivity and the elements that shape it. Our findings reveal that T. rugosa expresses all five opsins typically found in lizards (SWS1, SWS2, RH1, RH2 and LWS) but possesses greatly enhanced short wavelength sensitivity compared to other diurnal lizards. This enhanced short wavelength sensitivity is characterized by a broadening of the spectral sensitivity curve of the eye towards shorter wavelengths while the peak sensitivity of the eye at longer wavelengths (560 nm) remains similar to other diurnal lizards. While an increased abundance of SWS1 photoreceptors is thought to mediate elevated ultraviolet sensitivity in a couple of other lizard species, SWS1 photoreceptor abundance remains low in our species. Instead, our findings suggest that short-wavelength sensitivity is driven by multiple factors which include a potentially red-shifted SWS1 photoreceptor and the absence of short-wavelength absorbing oil droplets. Examining the coincidence of enhanced short-wavelength sensitivity with blue tongues among lizards of this genus will provide further insight into the co-evolution of conspecific signals and whole-eye spectral sensitivity.

Using Classical and Operant Conditioning to Train a Shifting Behavior in Juvenile False Water Cobras (Hydrodynastes gigas)

Simple Summary

Positive reinforcement training, a form of operant conditioning that rewards learners for specific behaviors to increase the frequency of that behavior, is widely used as a management tool in modern zoological facilities. This type of training offers several benefits, including improved safety, reduction in animal stress, increased choice and control, and many others. Snakes have been shown to learn using operant conditioning, yet the use of positive reinforcement training is not a widespread practice for these animals. A shaping plan, which describes the steps necessary to achieve the ultimate behavioral goal of following a target into a secondary container from their primary enclosure, was developed for false water cobras (Hydrodynastes gigas). Snakes were given food rewards for performing behaviors related to each goal detailed in the plan. Completion of this shaping plan resulted in a reduction of stress behaviors as the training progressed, as well as a decrease in time between the presentation and snakes interacting with the target.

Abstract

All animals have the capacity to learn through operant conditioning and other types of learning, and as a result, zoos and other animal care facilities have shifted towards the use of positive reinforcement training to shape the behavior of animals under their care. Training offers animals the choice to participate in their own husbandry routines and veterinary procedures, while also providing mental stimulation. By adopting these practices, the welfare of animals in human care has improved, but it has not been applied equally across taxa. Snakes are frequently overlooked in the discussion of choice and control in a captive setting, likely due to the historical misinterpretation of their intelligence and behavioral needs. In this study, a shaping plan was developed for 28 juvenile false water cobras (Hydrodynastes gigas), a rear-fanged venomous species, from four clutches. Snakes were rewarded with food when completing behaviors related to the ultimate goal of following a target into a shift container. The purpose of this study is to incorporate the trained behaviors in routine husbandry practices, while preventing unnecessary stress in the snakes and risk to the keeper.

Size of Snake Eyes Correlates With Habitat Types and Diel Activity Patterns

Eye size influences visual acuity, sensitivity, and temporal resolution and is a result of vertebrate adaptation to the environment. The habitats of snake species are diverse, ranging from fossorial, terrestrial, arboreal, to aquatic. They also demonstrate a variety of behavioral and physiological characteristics, such as activity time, feeding patterns, and prey detection. In this study, we comparatively investigated how the relative eye size (i.e., eye diameter vs. head width) associated with the ecological (i.e., habitat), behavioral (i.e., diel activity pattern, foraging strategy), and physiological traits (i.e., the presence of pits), respectively, across six snake families from Taiwan. Among the traits we examined, we found that terrestrial and/or diurnal snakes tended to exhibit the larger relative eye size, indicating the evolutionary responses of eye size to changes in habitat types and activity patterns, respectively, while no evidence of how foraging strategies and the presence of pits affected snake eye size was found. Our findings not only shed light on the adaptive significance of the visual system in diversifying the behaviors and the environments exploited in snakes, but also underline the interactive effects of multidimensional evolutionary attributes (e.g., behavior, ecology, physiology and phylogeny) on the evolution of optimal visual performance.

Not just shades of grey: life is full of colour for the ocellate river stingray (Potamotrygon motoro)

Previous studies have shown that marine stingrays have the anatomical and physiological basis for colour vision, with cone spectral sensitivity in the blue to green range of the visible spectrum. Behavioural studies on Glaucostegus typus also showed that blue and grey can be perceived and discriminated. The present study is the first to assess visual opsin genetics in the ocellate river stingray (Potamotrygon motoro) and test whether individuals perceive colour in two alternative forced choice experiments. Retinal transcriptome profiling using RNA-Seq and quantification demonstrated the presence of lws and rh2 cone opsin genes and a highly expressed single rod (rh1) opsin gene. Spectral tuning analysis predicted these vitamin A1-based visual photopigments to exhibit spectral absorbance maxima at 461 nm (rh2), 496 nm (rh1) and 555 nm (lws); suggesting the presence of dichromacy in this species. Indeed, P. motoro demonstrates the potential to be equally sensitive to wavelengths from 380 to 600 nm of the visible spectrum. Behavioural results showed that red and green plates, as well as blue and yellow plates, were readily discriminated based on colour; however, brightness differences also played a part in the discrimination of blue and yellow. Red hues of different brightness were distinguished significantly above chance level from one another. In conclusion, the genetic and behavioural results support prior data on marine stingrays. However, this study suggests that freshwater stingrays of the family Potamotrygonidae may have a visual colour system that has ecologically adapted to a riverine habitat.

Exploiting common senses: sensory ecology meets wildlife conservation and management

Multidisciplinary approaches to conservation and wildlife management are often effective in addressing complex, multi-factor problems. Emerging fields such as conservation physiology and conservation behaviour can provide innovative solutions and management strategies for target species and systems. Sensory ecology combines the study of 'how animals acquire' and process sensory stimuli from their environments, and the ecological and evolutionary significance of 'how animals respond' to this information. We review the benefits that sensory ecology can bring to wildlife conservation and management by discussing case studies across major taxa and sensory modalities. Conservation practices informed by a sensory ecology approach include the amelioration of sensory traps, control of invasive species, reduction of human-wildlife conflicts and relocation and establishment of new populations of endangered species. We illustrate that sensory ecology can facilitate the understanding of mechanistic ecological and physiological explanations underlying particular conservation issues and also can help develop innovative solutions to ameliorate conservation problems.

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence. Minor differences in the amino acid sequences of the opsins are known to lead to large differences in the spectral peak of absorbance (i.e. the λmax value). In our prior studies, we developed a new approach that combined homology modeling and molecular dynamics simulations to gather structural information associated with chromophore conformation, then used it to generate statistical models for the accurate prediction of λmax values for photopigments derived from Rh1 and Rh2 amino acid sequences. In the present study, we test our novel approach to predict the λmax of phylogenetically distant Sws2 cone opsins. To build a model that can predict the λmax using our approach presented in our prior studies, we selected a spectrally-diverse set of 11 teleost Sws2 photopigments for which both amino acid sequence information and experimentally measured λmax values are known. The final first-order regression model, consisting of three terms associated with chromophore conformation, was sufficient to predict the λmax of Sws2 photopigments with high accuracy. This study further highlights the breadth of our approach in reliably predicting λmax values of Sws2 cone photopigments, evolutionary-more distant from template bovine RH1, and provided mechanistic insights into the role of known spectral tuning sites.