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Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and to test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape across adults of 1294 amphibian species, 74 families and three orders, and additionally for larval stages for all families of frogs and salamanders with a biphasic ontogeny. For amphibians with a biphasic life history, pupil shape changed in many species that occupy distinct habitats before and after metamorphosis. In addition, non-elongated (circular or diamond) constricted pupils were associated with species inhabiting aquatic or underground environments, and elongated pupils (with vertical or horizontal long axes) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical and ecological mechanisms underlying the evolution of pupil shape.

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.

Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly different spectral properties from the African rift lakes. These ecological and/or biogeographic differences may have imposed divergent selective pressures on the evolution of the cichlid visual system. To test these hypotheses, we investigated the molecular evolution of the dim-light visual pigment, rhodopsin. We sequenced rhodopsin from Neotropical and African riverine cichlids and combined these data with published sequences from African cichlids. We found significant evidence for positive selection using random sites codon models in all cichlid groups, with the highest levels in African lake cichlids. Tests using branch-site and clade models that partitioned the data along ecological (lake, river) and/or biogeographic (African, Neotropical) boundaries found significant evidence of divergent selective pressures among cichlid groups. However, statistical comparisons among these models suggest that ecological, rather than biogeographic, factors may be responsible for divergent selective pressures that have shaped the evolution of the visual system in cichlids. We found that branch-site models did not perform as well as clade models for our data set, in which there was evidence for positive selection in the background. One of our most intriguing results is that the amino acid sites found to be under positive selection in Neotropical and African lake cichlids were largely nonoverlapping, despite falling into the same three functional categories: spectral tuning, retinal uptake/release, and rhodopsin dimerization. Taken together, these results would imply divergent selection across cichlid clades, but targeting similar functions. This study highlights the importance of molecular investigations of ecologically important groups and the flexibility of clade models in explicitly testing ecological hypotheses.

Studies of large-scale diversity changes and patterns of evolution can be adversely affected by a lack of understanding of alpha-taxonomy and systematics, and pachycephalosaur dinosaurs have significantly contributed to this problem. This is primarily a result of the relatively incomplete nature of the pachycephalosaur fossil record and the lack of understanding of specific and ontogenetic variation within the group. The taxon previously known as ‘Prenocephale’ brevis has been particularly problematic and has been placed in several different genera in addition to being synonymized with the species Stegoceras validum multiple times. Here we evaluate the validity of this taxon based on old and new material and using multiple, independent lines of evidence. We identify and describe the first peripheral skull elements, as well as the first juvenile and adult specimens, assignable to this taxon. These provide information on key parts of the morphology that have previously been lacking. Comparative anatomy, bivariate and multivariate morphometrics, osteohistology, and systematic analyses were used to test the hypothesis that this material is representative of a distinct taxon and to evaluate the differences between the other pachycephalosaur species of the closely related Belly River Group assemblage. No support was found for the assignment of ‘P.’ brevis to Stegoceras or Prenocephale, and thus we have erected a new genus, Foraminacephale gen. nov., to contain this species. Our data support the conclusion that the Foraminacephale brevis material represents an ontogenetic growth series of a single species distinct from St. validum. Evaluation of the two other members of the Belly River Group assemblage (Hanssuesia sternbergi and Colepiocephale lambei) was hindered by the small number of known specimens, but our results suggest that specimens currently referred to H. sternbergi may represent at least two species. We find that both ontogeny and osteohistology can vary greatly amongst even closely related species. It is therefore critical that multiple, independent lines of evidence be used to establish the ontogenetic trajectories of species prior to delineation, and that results of these analyses are used to produce robust and phylogenetically informative characters for use in phylogenetic analyses.