A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans

The origin, evolution, and molecular diversity of the chemokine system

Chemokine signalling performs key functions in cell migration via chemoattraction, such as attracting leukocytes to the site of infection during host defence. The system consists of a ligand, the chemokine, usually secreted outside the cell, and a chemokine receptor on the surface of a target cell that recognises the ligand. Several noncanonical components interact with the system. These include a variety of molecules that usually share some degree of sequence similarity with canonical components and, in some cases, are known to bind to canonical components and/or to modulate cell migration. Whereas canonical components have been described in vertebrate lineages, the distribution of the noncanonical components is less clear. Uncertainty over the relationships between canonical and noncanonical components hampers our understanding of the evolution of the system. We used phylogenetic methods, including gene-tree to species-tree reconciliation, to untangle the relationships between canonical and noncanonical components, identify gene duplication events, and clarify the origin of the system. We found that unrelated ligand groups independently evolved chemokine-like functions. We found noncanonical ligands outside vertebrates, such as TAFA "chemokines" found in urochordates. In contrast, all receptor groups are vertebrate-specific and all-except ACKR1-originated from a common ancestor in early vertebrates. Both ligand and receptor copy numbers expanded through gene duplication events at the base of jawed vertebrates, with subsequent waves of innovation occurring in bony fish and mammals.

The monoaminergic system is a bilaterian innovation

Monoamines like serotonin, dopamine, and adrenaline/noradrenaline (epinephrine/norepinephrine) act as neuromodulators in the nervous system. They play a role in complex behaviours, cognitive functions such as learning and memory formation, as well as fundamental homeostatic processes such as sleep and feeding. However, the evolutionary origin of the genes required for monoaminergic modulation is uncertain. Using a phylogenomic approach, in this study, we show that most of the genes involved in monoamine production, modulation, and reception originated in the bilaterian stem group. This suggests that the monoaminergic system is a bilaterian novelty and that its evolution may have contributed to the Cambrian diversification.

Identifying and addressing methodological incongruence in phylogenomics: A review

The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning-one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one-size-fits-all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.

nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets

MOTIVATION

Compositional heterogeneity-when the proportions of nucleotides and amino acids are not broadly similar across the dataset-is a cause of a great number of phylogenetic artefacts. Whilst a variety of methods can identify it post-hoc, few metrics exist to quantify compositional heterogeneity prior to the computationally intensive task of phylogenetic tree reconstruction. Here we assess the efficacy of one such existing, widely used, metric: Relative Composition Frequency Variability (RCFV), using both real and simulated data.

RESULTS

Our results show that RCFV can be biased by sequence length, the number of taxa, and the number of possible character states within the dataset. However, we also find that missing data does not appear to have an appreciable effect on RCFV. We discuss the theory behind this, the consequences of this for the future of the usage of the RCFV value and propose a new metric, nRCFV, which accounts for these biases. Alongside this, we present a new software that calculates both RCFV and nRCFV, called nRCFV_Reader.

AVAILABILITY AND IMPLEMENTATION

nRCFV has been implemented in RCFV_Reader, available at: https://github.com/JFFleming/RCFV_Reader . Both our simulation and real data are available at Datadryad: https://doi.org/10.5061/dryad.wpzgmsbpn .

Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals

Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a "deep diversity" of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

Rhodopsins at a glance

Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, bacteriorhodopsin, was reported to be present in the cell membrane of an extreme halophilic archaeon, Halobacterium salinarum, 95 years later. Although these findings were made by physiological observation of pigmented tissue and cell bodies, recent progress in genomic and metagenomic analyses has revealed that there are more than 10,000 microbial rhodopsins and 9000 animal rhodopsins with large diversity and tremendous new functionality. In this Cell Science at a Glance article and accompanying poster, we provide an overview of the diversity of functions, structures, color discrimination mechanisms and optogenetic applications of these two rhodopsin families, and will also highlight the third distinctive rhodopsin family, heliorhodopsin.

New Tardigrade Opsins and Differential Expression Analyses Show Ontogenic Variation in Light Perception

Opsins are light-sensitive proteins involved in many photoreceptive processes, including, but not limited to, vision and regulation of circadian rhythms. Arthropod (e.g., insects, spiders, centipedes, and crabs) opsins have been extensively researched, but the relationships and function of opsins found in lineages that are evolutionarily closely related to the arthropods remains unclear. Multiple, independent, opsin duplications are known in Tardigrada (the water bears), evidencing that protostome opsin duplications are not limited to the Arthropoda. However, the relationships, function, and expression of these new opsins are still unknown. Here, we use two tardigrade transcriptomes with deep coverage to greatly expand our knowledge of the diversity of tardigrade opsins. We reconstruct the phylogenetic relationships of the tardigrade opsins and investigate their ontogenetic expression. We found that while tardigrades have multiple opsins that evolved from lineage-specific duplications of well-understood arthropod opsins, their expression levels change during ontogeny such that most of these opsins are not co-temporally expressed. Co-temporal expression of multiple opsins underpins color vision in Arthropoda and Vertebrata. Our results clearly show duplications of both rhabdomeric and ciliary opsins within Tardigrada, forming clades specific to both the Heterotardigrada and Eutardigrada in addition to multiple independent duplications within genera. However, lack of co-temporal, ontogenetic, expression suggests that while tardigrades possess multiple opsins, they are unlikely to be able to distinguish color.

Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins

Animals have evolved light-sensitive G protein-coupled receptors, known as opsins, to detect coherent and ambient light for visual and nonvisual functions. These opsins have evolved to satisfy the particular lighting niches of the organisms that express them. While many unique patterns of evolution have been identified in mammals for rod and cone opsins, far less is known about the atypical mammalian opsins. Using genomic data from over 400 mammalian species from 22 orders, unique patterns of evolution for each mammalian opsins were identified, including photoisomerases, RGR-opsin (RGR) and peropsin (RRH), as well as atypical opsins, encephalopsin (OPN3), melanopsin (OPN4), and neuropsin (OPN5). The results demonstrate that OPN5 and rhodopsin show extreme conservation across all mammalian lineages. The cone opsins, SWS1 and LWS, and the nonvisual opsins, OPN3 and RRH, demonstrate a moderate degree of sequence conservation relative to other opsins, with some instances of lineage-specific gene loss. Finally, the photoisomerase, RGR, and the best-studied atypical opsin, OPN4, have high sequence diversity within mammals. These conservation patterns are maintained in human populations. Importantly, all mammalian opsins retain key amino acid residues important for conjugation to retinal-based chromophores, permitting light sensitivity. These patterns of evolution are discussed along with known functions of each atypical opsin, such as in circadian or metabolic physiology, to provide insight into the observed patterns of evolutionary constraint.