Air temperature drives the evolution of mid-infrared optical properties of butterfly wings

This study uncovers a correlation between the mid-infrared emissivity of butterfly wings and the average air temperature of their habitats across the world. Butterflies from cooler climates have a lower mid-infrared emissivity, which limits heat losses to surroundings, and butterflies from warmer climates have a higher mid-infrared emissivity, which enhances radiative cooling. The mid-infrared emissivity showed no correlation with other investigated climatic factors. Phylogenetic independent contrasts analysis indicates the microstructures of butterfly wings may have evolved in part to regulate mid-infrared emissivity as an adaptation to climate, rather than as phylogenetic inertia. Our findings offer new insights into the role of microstructures in thermoregulation and suggest both evolutionary and physical constraints to butterflies’ abilities to adapt to climate change.

Indagando aspectos evolutivos con filogenias: reloj molecular y otras técnicas útiles en biología comparada

The first step for evolutionary studies is usually to establish a hypothesis of relationships between members of the study group. After this, there is a wide range of possibilities depending on the researcher's interest. This contribution presents the generalities of some of the methodologies most commonly used in macroevolutionary studies: the molecular clock and the reconstruction of ancestral characters. Information on other useful techniques for comparative studies that use a phylogenetic framework is also presented, such as phylogenetic signal estimation, independent contrasts, orthonormal decomposition, and phylogenetic principal component analysis.

Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

Despite the importance of gene function to evolutionary biology, the applicability of comparative methods to gene function is poorly known. A specific case which has crystalized methodological questions is the “ortholog conjecture”, the hypothesis that function evolves faster after duplication (i.e., in paralogs), and conversely conserved between orthologs. Since the mode of functional evolution after duplication is not well known, we investigate under what reasonable evolutionary scenarios phylogenetic independent contrasts or pairwise comparisons can recover a putative signal of different functional evolution between orthologs and paralogs.We investigate three different simulation models, which represent reasonable but simplified hypotheses about gene function (our “trait”) evolution. These are time dependent trait acceleration, correlated changes in rates of both sequence and trait evolution, and asymmetric trait jump. For each model we tested phylogenetic independent contrasts and an improved pairwise comparison method which accounts for interactions between events and node age.Both approaches loose power to detect the trend of functional evolution when the functional trait accelerates for a long time following duplication, with better power of phylogenetic contrasts under intermediate scenarios. Concomitant increase in evolutionary rates of sequence and of trait after duplication can lead to both an incorrect rejection of the null under null simulations of trait evolution, and a false rejection of the ortholog conjecture under ortholog conjecture simulations by phylogenetic independent contrasts. Improved pairwise comparisons are robust to this bias. Both approaches perform equally well to trace rapid shift in traits.Considering our ignorance of gene function evolution, and the potential for bias under simple models, we recommend methodological pluralism in studying gene family evolution. Functional phylogenomics is complex and results supported by only one method should be treated with caution.

Phylogeographic Estimation and Simulation of Global Diffusive Dispersal

The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example, for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2D plane; however, the accuracy of these methods deteriorates substantially when dispersal occurs at global scales because spherical Brownian motion (SBM) differs from planar Brownian motion. No statistical method exists for estimating SBM diffusion coefficients from a given timetree and tip coordinates, and no method exists for simulating SBM along a given timetree. Here, I present new methods for simulating SBM along a given timetree, and for estimating SBM diffusivity from a given timetree and tip coordinates using a modification of Felsenstein’s independent contrasts and maximum likelihood. My simulation and fitting methods can accommodate arbitrary time-dependent diffusivities and scale efficiently to trees with millions of tips, thus enabling new analyses even in cases where planar BM would be a sufficient approximation. I demonstrate these methods using a timetree of marine and terrestrial Cyanobacterial genomes, as well as timetrees of two globally circulating Influenza B clades. My methods are implemented in the R package “castor.” [Independent contrasts; phylogenetic; random walk; simulation; spherical Brownian motion.]

Freshwater-to-marine transitions may explain the evolution of herbivory in the subgenus Mollienesia (genus Poecilia, mollies and guppies)

The ability of organisms to cross ecosystem boundaries is an important catalyst of evolutionary diversification. The genus Poecilia (mollies and guppies) is an excellent system for studying ecosystem transitions because species display a range of salinity and dietary preferences, with herbivory concentrated in the subgenus Mollienesia. We reconstructed ancestral habitats and diets across a phylogeny of the genus Poecilia, evaluated diversification rates and used phylogenetically independent contrasts to determine whether diet evolved in response to habitat transition in this group. The results suggest that ancestors of subgenus Mollienesia were exclusively herbivorous, whereas ancestral diets of other Poecilia included animals. We found that transitions across euryhaline boundaries occurred at least once in this group, probably after the divergence of the subgenus Mollienesia. Furthermore, increased salinity affiliation explained 24% of the decrease in animals in the gut, and jaw morphology was associated with the percentage of animals in the gut, but not with the percentage of species occupying saline habitats. These findings suggest that in the genus Poecilia, herbivory evolved in association with transitions from fresh to euryhaline habitats, and jaw morphology evolved in response to the appearance of herbivory. These results provide a rare example of increased diet diversification associated with the transition from freshwater to euryhaline habitats.

Is there convergence of gut microbes in blood-feeding vertebrates?

Animal microbiomes play an important role in dietary adaptation, yet the extent to which microbiome changes exhibit parallel evolution is unclear. Of particular interest is an adaptation to extreme diets, such as blood, which poses special challenges in its content of proteins and lack of essential nutrients. In this study, we assessed taxonomic signatures (by 16S rRNA amplicon profiling) and potential functional signatures (inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)) of haematophagy in birds and bats. Our goal was to test three alternative hypotheses: no convergence of microbiomes, convergence in taxonomy and convergence in function. We find a statistically significant effect of haematophagy in terms of microbial taxonomic convergence across the blood-feeding bats and birds, although this effect is small compared to the differences found between haematophagous and non-haematophagous species within the two host clades. We also find some evidence of convergence at the predicted functional level, although it is possible that the lack of metagenomic data and the poor representation of microbial lineages adapted to haematophagy in genome databases limit the power of this approach. The results provide a paradigm for exploring convergent microbiome evolution replicated with independent contrasts in different host lineages. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

Testing for correlation between traits under directional evolution

Being confounding factors, directional trends are likely to make two quantitative traits appear as spuriously correlated. By determining the probability distributions of independent contrasts when traits evolve following Brownian motions with linear trends, we show that the standard independent contrasts can not be used to test for correlation in this situation. We propose a multiple regression approach which corrects the bias caused by directional evolution.We show that our approach is equivalent to performing a Phylogenetic Generalized Least Squares (PGLS) analysis with tip times as covariables by providing a new and more general proof of the equivalence between PGLS and independent contrasts methods.Our approach is assessed and compared with three previous correlation tests on data simulated in various situations and overall outperforms all the other methods. The approach is next illustrated on a real dataset to test for correlation between hominin cranial capacity and body mass.

Functional and Phylogenetic Aspect in Modularity of Palearctic Mustelids (Carnivora, Mustelidae) Mandible

Geometric morphometrics was used to investigate morphological integration and modularity in mustelid mandible. A set of 16 two-dimensional landmarks was digitized on the mandibles of 14 extant species of Palearctic Mustelidae (genera Enhydra, Gulo, Meles, Lutra, Martes, Mustela). The original data size-corrected data and phylogenetically independent contrasts (PICs) were analyzed. Several hypotheses were tested: two and three-modules with the masseteric fossa included in corpus or ramus of the mandible. As a result, the two-module hypothesis (subdivision into the alveolar region and the ascending ramus) with masseteric fossa included in corpus for all sets of data was supported. A clear modularity in mustelid mandible is seen at interspecific level, whereas there was large within species covariation between mandibular corpus and ramus. The allometry correction reduces estimates of covariation for the mustelid mandibles. Due to the analysis of PICs the shape changes with maximum evolutionary covariation were found: elongated, sloped backward ramus and thick corpus.