Measuring phylogenetic signal between categorical traits and phylogenies

Identification and Evolution of Cas9 tracrRNAs

Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas)9 transactivating CRISPR RNAs (tracrRNAs) form distinct structures essential for target recognition and cleavage and dictate exchangeability between orthologous proteins. As noncoding RNAs that are often apart from the CRISPR array, their identification can be arduous. In this article, a new bioinformatic method for the detection of Cas9 tracrRNAs is presented. The approach utilizes a covariance model based on both sequence homology and predicted secondary structure to locate tracrRNAs. This method predicts a tracrRNA for 98% of CRISPR-Cas9 systems identified by us. To ensure accuracy, we also benchmark our approach against biochemically vetted tracrRNAs finding false-positive and false-negative rates of 5.5% and 7.1%, respectively. Finally, the association between Cas9 amino acid sequence-based phylogeny and tracrRNA secondary structure is evaluated, revealing strong evidence that secondary structure is evolutionarily conserved among Cas9 lineages. Altogether, our findings provide insight into Cas9 tracrRNA evolution and efforts to characterize the tracrRNA of Cas9 systems.

Floral UV Features of Plant Species From a Neotropical Savanna

Despite the wide interest in flower colours, only after the end of the nineteenth-century studies started to comprise floral UV reflection, which is invisible to humans but visible to the major groups of pollinators. Many flowers and inflorescences display colour patterns, an important signal for pollinators, promoted by the presence of at least two different colours within flowers or inflorescences, including colours in the UV waveband. For Neotropical savanna plant species, we characterised floral UV features using UV-photography and reflectance measurements. We tested (i) whether floral UV features were constrained by their shared ancestry, (ii) whether floral UV features were associated with pollinators, and (iii) whether floral UV features were associated with floral traits mediating these interactions, including floral resource, type of attraction unit and presence/absence of non-UV colour patterns. Of 80 plant species, ca. 70% were UV-patternless, most of them UV-absorbing. Approximately 30% presented one of three types of UV-patterns: bullseye, contrasting corolla markings oriented toward floral resources or contrasting reproductive structures, which were all considered as floral guides. Floral UV features were phylogenetically constrained and were associated with pollinators, floral resources and attraction unit, but not with non-UV colour patterns. UV-patternless flowers were associated with most of the pollination systems, while UV-patterned flowers were mainly associated with bee-pollination. UV-absorbing flowers comprised the only category with hawkmoth- and butterfly-pollinated flowers, and a high percentage of hummingbird-pollinated species. Nocturnal pollinated species were also commonly UV-absorbing, except for one UV-reflecting bat-pollinated species and one beetle-pollinated species with UV-reflecting stigmas. All types of floral UV features were associated with nectar; however, flowers with contrasting reproductive structures were mainly associated with pollen. There was an association between UV-absorbing species and the presence of inflorescences and intermediate attraction units. Our results evince that phylogenetic relatedness can constraint floral UV features' diversification, but combinations of evolutionary and ecological processes may be expected in this scenario.

Rethinking the use of finite element simulations in comparative biomechanics research

In the past 15 years, the finite element (FE) method has become a ubiquitous tool in the repertoire of evolutionary biologists. The method is used to estimate and compare biomechanical performance implicated as selective factors in the evolution of morphological structures. A feature common to many comparative studies using 3D FE simulations is small taxonomic sample sizes. The time-consuming nature of FE model construction is considered a main limiting factor in taxonomic breadth of comparative FE analyses. Using a composite FE model dataset, I show that the combination of small taxonomic sample sizes and comparative FE data in analyses of evolutionary associations of biomechanical performance to feeding ecology generates artificially elevated correlations. Such biases introduce false positives into interpretations of clade-level trends. Considering this potential pitfall, recommendations are provided to consider the ways FE analyses are best used to address both taxon-specific and clade-level evolutionary questions.

Conspicuousness, phylogenetic structure, and origins of Müllerian mimicry in 4000 lycid beetles from all zoogeographic regions

Biologists have reported on the chemical defences and the phenetic similarity of net-winged beetles (Coleoptera: Lycidae) and their co-mimics. Nevertheless, our knowledge has remained fragmental, and the evolution of mimetic patterns has not been studied in the phylogenetic context. We illustrate the general appearance of ~ 600 lycid species and ~ 200 co-mimics and their distribution. Further, we assemble the phylogeny using the transcriptomic backbone and ~ 570 species. Using phylogenetic information, we closely scrutinise the relationships among aposematically coloured species, the worldwide diversity, and the distribution of aposematic patterns. The emitted visual signals differ in conspicuousness. The uniform coloured dorsum is ancestral and was followed by the evolution of bicoloured forms. The mottled patterns, i.e. fasciate, striate, punctate, and reticulate, originated later in the course of evolution. The highest number of sympatrically occurring patterns was recovered in New Guinea and the Andean mountain ecosystems (the areas of the highest abundance), and in continental South East Asia (an area of moderate abundance but high in phylogenetic diversity). Consequently, a large number of co-existing aposematic patterns in a single region and/or locality is the rule, in contrast with the theoretical prediction, and predators do not face a simple model-like choice but cope with complex mimetic communities. Lycids display an ancestral aposematic signal even though they sympatrically occur with differently coloured unprofitable relatives. We show that the highly conspicuous patterns evolve within communities predominantly formed by less conspicuous Müllerian mimics and, and often only a single species displays a novel pattern. Our work is a forerunner to the detailed research into the aposematic signalling of net-winged beetles.

Impacts of growth form and phylogenetic relatedness on seed germination: A large-scale analysis of a subtropical regional flora

Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25°C; daily alternating 25/15°C for each 12 hr). Germination was low with a skewed distribution (mean = 38.9% at 25°C, and 43.3% at 25/15°C). One fifth of the species had low (<10%) and slow (4-30 days) germination, and only a few (8%) species had a high (>80%) and rapid (1.2-6.6 days) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.

Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes

Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia-legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.

Assessing the Diversity of the Form of Age-Specific Changes in Adult Mortality from Captive Mammalian Populations

Actuarial senescence (i.e., the age-specific increase in mortality rate) is pervasive across mammalian species, but our current understanding of the diversity of forms that actuarial senescence displays across species remains limited. Although several mathematical models have been proposed to model actuarial senescence, there is still no consensus on which model to use, especially when comparing mortality patterns among species. To fill this knowledge gap, we fitted and compared different forms of increase using models commonly used in senescence studies (i.e., Gompertz, Weibull, and logistic) across 61 species of mammalian captive populations using the Bayesian Survival Trajectory Analysis (BaSTA) approach. For as much as 79% of the species, a Gompertz increase of mortality with age was the most parsimonious model that satisfactorily described the shape of age-specific mortality changes in adults. This highlights that the form of the increase in mortality is mostly consistent across mammalian species and follows the Gompertz rule with some rare exceptions. The implications of that result are twofold. First, the Gompertz rate of mortality increase should be used in cross-species comparative analyses of mammals, as already done in some studies. Second, although the Gompertz model accurately describes actuarial senescence in most mammals, there are notable exceptions, and the factors causing this deviation from an exponential mortality increase during the adult stage warrant further investigation.

Global patterns and determinants of lake macrophyte taxonomic, functional and phylogenetic beta diversity

Documenting the patterns of biological diversity on Earth has always been a central challenge in macroecology and biogeography. However, for the diverse group of freshwater plants, such research program is still in its infancy. Here, we examined global variation in taxonomic, functional and phylogenetic beta diversity patterns of lake macrophytes using regional data from six continents. A data set of ca. 480 lake macrophyte community observations, together with climatic, geographical and environmental variables, was compiled across 16 regions worldwide. We (a) built the very first phylogeny comprising most freshwater plant lineages; (b) exploited a wide array of functional traits that are important to macrophyte autoecology or that relate to lake ecosystem functioning; (c) assessed if different large-scale beta diversity patterns show a clear latitudinal gradient from the equator to the poles using null models; and (d) employed evolutionary and regression models to first identify the degree to which the studied functional traits show a phylogenetic signal, and then to estimate community-environment relationships at multiple spatial scales. Our results supported the notion that ecological niches evolved independently of phylogeny in macrophyte lineages worldwide. We also showed that taxonomic and phylogenetic beta diversity followed the typical global trend with higher diversity in the tropics. In addition, we were able to confirm that species, multi-trait and lineage compositions were first and foremost structured by climatic conditions at relatively broad spatial scales. Perhaps more importantly, we showed that large-scale processes along latitudinal and elevational gradients have left a strong footprint in the current diversity patterns and community-environment relationships in lake macrophytes. Overall, our results stress the need for an integrative approach to macroecology, biogeography and conservation biology, combining multiple diversity facets at different spatial scales.

The evolution of parental care strategies in subsocial wasps

Abstract

Insect parental care strategies are particularly diverse, and prolonged association between parents and offspring may be a key precursor to the evolution of complex social traits. Macroevolutionary patterns remain obscure, however, due to the few rigorous phylogenetic analyses. The subsocial sphecid wasps are a useful group in which to study parental care because of the diverse range of strategies they exhibit. These strategies range from placing a single prey item in a pre-existing cavity to mass provisioning a pre-built nest, through to complex progressive provisioning where a female feeds larvae in different nests simultaneously as they grow. We show that this diversity stems from multiple independent transitions between states. The strategies we focus on were previously thought of in terms of a stepping-stone model in which complexity increases during evolution, ending with progressive provisioning which is a likely precursor to eusociality. We find that evolution has not always followed this model: reverse transitions are common, and the ancestral state is the most flexible rather than the simplest strategy. Progressive provisioning has evolved several times independently, but transitions away from it appear rare. We discuss the possibility that ancestral plasticity has played a role in the evolution of extended parental care.

Significance statement

Parental care behaviour leads to prolonged associations between parents and offspring, which is thought to drive the evolution of social living. Despite the importance of insect parental care for shaping the evolution of sociality, relatively few studies have attempted to reconstruct how different strategies evolve in the insects. In this study, we use phylogenetic methods to reconstruct the evolution of the diverse parental care strategies exhibited by the subsocial digger wasps (Sphecidae). Contrary to expectations, we show that parental care in this group has not increased in complexity over evolutionary time. We find that the ancestral state is not the simplest, but may be the most flexible strategy. We suggest that this flexible ancestral strategy may have allowed rapid response to changing environmental conditions which might explain the diversity in parental care strategies that we see in the digger wasps today.

Evolution and Development at the Origin of a Phylum

Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define these body plans were not fixed at the origin of the phylum, countering hypotheses regarding developmental processes governing the early evolution of animals. Instead, these burdened characters were flexible, enabling continued evolutionary innovation throughout the clades' history.

Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype

Typical avian eyes are phenotypically engineered for photopic vision (daylight). In contrast, the highly derived eyes of the barn owl (Tyto alba) are adapted for scotopic vision (dim light). The dramatic modifications distinguishing barn owl eyes from other birds include: 1) shifts in frontal orientation to improve binocularity, 2) rod-dominated retina, and 3) enlarged corneas and lenses. Some of these features parallel mammalian eye patterns, which are hypothesized to have initially evolved in nocturnal environments. Here, we used an integrative approach combining phylogenomics and functional phenotypes of 211 eye-development genes across 48 avian genomes representing most avian orders, including the stem lineage of the scotopic-adapted barn owl. Overall, we identified 25 eye-development genes that coevolved under intensified or relaxed selection in the retina, lens, cornea, and optic nerves of the barn owl. The agtpbp1 gene, which is associated with the survival of photoreceptor populations, was pseudogenized in the barn owl genome. Our results further revealed that barn owl retinal genes responsible for the maintenance, proliferation, and differentiation of photoreceptors experienced an evolutionary relaxation. Signatures of relaxed selection were also observed in the lens and cornea morphology-associated genes, suggesting that adaptive evolution in these structures was essentially structural. Four eye-development genes (ephb1, phactr4, prph2, and rs1) evolved in positive association with the orbit convergence in birds and under relaxed selection in the barn owl lineage, likely contributing to an increased reliance on binocular vision in the barn owl. Moreover, we found evidence of coevolutionary interactions among genes that are expressed in the retina, lens, and optic nerve, suggesting synergetic adaptive events. Our study disentangles the genomic changes governing the binocularity and low-light perception adaptations of barn owls to nocturnal environments while revealing the molecular mechanisms contributing to the shift from the typical avian photopic vision to the more-novel scotopic-adapted eye.