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Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives the search for novel sources of information to solve these difficult phylogenetic problems. A recent example, the presence and absence of microRNA families, has been vigorously promoted as an ideal source of phylogenetic data and has been applied to several perennial phylogenetic problems. The utility of such data for phylogenetic inference hinges critically both on developing stochastic models that provide a reasonable description of the process that give rise to these data, and also on the careful validation of those models in real inference scenarios. Remarkably, however, the statistical behavior and phylogenetic utility of microRNA data have not yet been rigorously characterized. Here we explore the behavior and performance of microRNA presence/absence data under a variety of evolutionary models and reexamine datasets from several previous studies. We find that highly heterogeneous rates of microRNA gain and loss, pervasive secondary loss, and sampling error collectively render microRNA-based inference of phylogeny difficult. Moreover, our reanalyses fundamentally alter the conclusions for four of the five studies that we reexamined. Our results indicate that the capacity of miRNA data to resolve the tree of life has been overstated, and we urge caution in their application and interpretation.

In biology, “many-to-one mapping” occurs when multiple morphological forms can meet a particular functional demand. Knowledge of this mapping is crucial for understanding how selection on performance shapes the evolution of morphological diversity. Past research has focused primarily on the potential for geometrically alternative morphological designs to produce equivalent performance outcomes. Here, we ask whether the material properties of biological tissues hold similar potential. Through a phylogenetic comparative study of Anolis lizards, we show that the architectural design and mineral density of the femur trade off in a many-to-one functional system, yielding a morphospace featuring parallel isolines in size-relative bending strength. Anole femur evolution has largely tracked a narrow band of strength isolines over phylogenetic timescales, suggesting that geometry and mineral content shape the course of macroevolution through compensatory effects on performance. Despite this conserved evolutionary relationship, insular and continental species evolve strong bones differently, likely reflecting underlying ecological differences. Mainland anoles, which exhibit fast-paced life histories, typically have femora with lower mineralization and thinner walls than island species, which exhibit the opposite strategy. Together, our results reveal an overlooked dimension in the relationship between form and function, expanding our understanding of how many-to-one mapping can shape patterns of phenotypic diversity. [ABSTRACT FROM AUTHOR]

For centuries, biogeographers have examined the factors that produce patterns of biodiversity across regions. The study of islands has proved particularly fruitful and has led to the theory that geographic area and isolation influence species colonization, extinction and speciation such that larger islands have more species and isolated islands have fewer species (that is, positive species-area and negative species-isolation relationships) (1-4). However, experimental tests of this theory have been limited, owing to the difficulty in experimental manipulation of islands at the scales at which speciation and long-distance colonization are relevant (5). Here we have used the human-aided transport of exotic anole lizards among Caribbean islands as such a test at an appropriate scale. In accord with theory, as anole colonizations have increased, islands impoverished in native species have gained the most exotic species, the past influence of speciation on island biogeography has been obscured, and the species-area relationship has strengthened while the species-isolation relationship has weakened. Moreover, anole biogeography increasingly reflects anthropogenic rather than geographic processes. Unlike the island biogeography of the past that was determined by geographic area and isolation, in the Anthropocene--an epoch proposed for the present time interval--island biogeography is dominated by the economic isolation of human populations., The number of species (that is, richness) on islands is theorized to be a function of colonization and in situ speciation that add species, and extinction that subtracts them (1-6). [...]

Geographical variation in sexual size dimorphism (SSD) can result from the combined effects of environmental and sexual selection. To understand the determinants of SSD across geographical landscapes, we tested for relationships between SSD and climatic variables in the widespread lizard Anolis carolinensis. To distinguish alternative hypotheses for observed patterns of variation in SSD, we also examined sex-specific patterns of body size evolution and asked whether SSD was associated with certain patterns of sexual shape dimorphism. We found strong evidence for Rensch's rule (an increase in male-biased SSD with average body size) in A. carolinensis and evidence for the reversed version of Bergmann's rule (an increase in body size towards warmer environments) in males. Across populations, SSD was positively related to temperature; however, female body size was not related to any climatic variable, suggesting that the latitudinal gradient of SSD might be driven by a gradient in the intensity of sexual selection acting on males. Sexual size dimorphism was positively correlated with sexual dimorphism in head shape and negatively correlated with limb length dimorphism, suggesting that sexual selection in males might drive the evolution of SSD and that differences in size and limb shape between sexes might represent alternative strategies to avoid competition for the same resources. [ABSTRACT FROM AUTHOR]

Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes. Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats. Using generalized dissimilarity modelling and multiple matrix regression, we found that genome‐wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure. We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies. Our results suggest an environmental basis for population‐level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature. [ABSTRACT FROM AUTHOR]