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Adaptive radiations are characterized by an increase in species and/or phenotypic diversity as organisms fill open ecological niches. Often, the putative adaptive radiation has been studied without explicit comparison to the patterns and rates of evolution of closely related clades, leaving open the question whether notable changes in evolutionary process indeed occurred at the origin of the group. Anolis lizards are an oft-used model for investigating the tempo and mode of adaptive radiations. Most of the prior research on the diversification of Anolis morphology has focused on the post-cranium because of its significance towards subdivision of the arboreal habitat. But the remarkable diversity in head shape in anoles has not been as thoroughly investigated. It remains unknown whether the tempo or mode of head shape diversification changed as anoles diversified. We performed geometric morphometric analysis of skull shape across a sample of 12 Iguanian families (110 species), including anoles. Anolis lizards occupy a unique area and a wider region of morphological space compared to the 11 other families examined. We did not find a difference in the evolutionary rate of head shape diversification between anoles and their relatives. Rather, the extraordinary amount of skull diversity arose through a distinct mode of evolution; anoles moved into novel regions by relatively large morphological transitions across morphological space compared to their relatives. Our results demonstrate that traits not directly tied to the adaptive shift of a lineage into unique ecological spaces may undergo exceptional patterns of change as the clade diversifies. 

Amniote skulls are diverse in shape and skeletal composition, which is the basis of much adaptive diversification within this clade. Major differences in skull shape are established early in development, at a critical developmental interval spanning the initial outgrowth and fusion of the facial processes. In birds, this is orchestrated by domains of Shh and Fgf8 expression, known as the frontonasal ectodermal zone (FEZ). It is unclear whether this model of facial development applies to species with diverse facial skeletons, especially species possessing a skull morphology representative of early amniotes. By investigating facial morphogenesis in the lizard, Anolis sagrei, we show that reptilian skull development is driven by the same genes as mammals and birds, but the manner in which those genes regulate facial development is clade-specific. These genes are not expressed in the frontal-nasal prominence, the region of the avian FEZ. Downregulating Shh and Fgf8 signaling disrupts normal facial development, but in pathway-specific ways. Our results demonstrate that early facial morphogenesis in lizards does not conform to the FEZ model. Lizard skull development may be more representative of the ancestral amniote than other model species with highly derived facial skeletons suggesting that the FEZ may be an avian-specific novelty. 

Abstract Library preparation protocols for most sequencing technologies involve PCR amplification of the template DNA, which open the possibility that a given template DNA molecule is sequenced multiple times. Reads arising from this phenomenon, known as PCR duplicates, inflate the cost of sequencing and can jeopardize the reliability of affected experiments. Despite the pervasiveness of this artefact, our understanding of its causes and of its impact on downstream statistical analyses remains essentially empirical. Here, we develop a general quantitative model of amplification distortions in sequencing data sets, which we leverage to investigate the factors controlling the occurrence of PCR duplicates. We show that the PCR duplicate rate is determined primarily by the ratio between library complexity and sequencing depth, and that amplification noise (including in its dependence on the number of PCR cycles) only plays a secondary role for this artefact. We confirm our predictions using new and published RAD‐seq libraries and provide a method to estimate library complexity and amplification noise in any data set containing PCR duplicates. We discuss how amplification‐related artefacts impact downstream analyses, and in particular genotyping accuracy. The proposed framework unites the numerous observations made on PCR duplicates and will be useful to experimenters of all sequencing technologies where DNA availability is a concern. 

Adaptive thermal tolerance plasticity can dampen the negative effects of warming. However, our knowledge of tolerance plasticity is lacking for embryonic stages that are relatively immobile and may benefit the most from an adaptive plastic response. We tested for heat hardening capacity (a rapid increase in thermal tolerance that manifests in minutes to hours) in embryos of the lizard Anolis sagrei. We compared the survival of a lethal temperature exposure between embryos that either did (hardened) or did not (not hardened) receive a high but non-lethal temperature pre-treatment. We also measured heart rates (HRs) at common garden temperatures before and after heat exposures to assess metabolic consequences. 'Hardened' embryos had significantly greater survival after lethal heat exposure relative to 'not hardened' embryos. That said, heat pre-treatment led to a subsequent increase in embryo HR that did not occur in embryos that did not receive pre-treatment, indicative of an energetic cost of mounting the heat hardening response. Our results are not only consistent with adaptive thermal tolerance plasticity in these embryos (greater heat survival after heat exposure), but also highlight associated costs. Thermal tolerance plasticity may be an important mechanism by which embryos respond to warming that warrants greater consideration. 

Abstract Phenotypic variation among species is a product of evolutionary changes to developmental programs^1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium—an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that theEmx2locus experienced lineage-specific patterns of acceleratedcis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show thatEmx2is a critical upstream regulator of patagium development. Moreover, we identify differentcis-regulatory elements that may be responsible for driving increasedEmx2expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence thatEmx2expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation ofEmx2was altered by distinctcis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty. 

Abstract How developmental modifications produce key innovations, which subsequently allow for rapid diversification of a clade into new adaptive zones, has received much attention. However, few studies have used a robust comparative framework to investigate the influence of evolutionary and developmental constraints on the origin of key innovations, such as the adhesive toe pad of lizards. Adhesive toe pads evolved independently at least 16 times in lizards, allowing us to examine whether the patterns observed are general evolutionary phenomena or unique, lineage-specific events. We performed a high-resolution comparison of plantar scale development in 14 lizard species in Anolis and geckos, encompassing five independent origins of toe pads (one in Anolis, four in geckos). Despite substantial evolutionary divergence between Anolis and geckos, we find that these clades have undergone similar developmental modifications to generate their adhesive toe pads. Relative to the ancestral plantar scale development, in which scale ridges form synchronously along the digit, both padded geckos and Anolis exhibit scansor formation in a distal-to-proximal direction. Both clades have undergone developmental repatterning and, following their origin, modifications in toe pad morphology occurred through relatively minor developmental modifications, suggesting that developmental constraints governed the diversification of the adhesive toe pad in lizards. 

Among the most specialized integumentary outgrowths in amniotes are the adhesive, scale-like scansors and lamellae on the digits of anoles and geckos. Less well-known are adhesive tail pads exhibited by 21 gecko genera. While described over 120 years ago, no studies have quantified their possible adhesive function or described their embryonic development. Here, we characterize adult and embryonic morphology and adhesive performance of crested gecko ( Correlophus ciliatus ) tail pads. Additionally, we use embryonic data to test whether tail pads are serial homologues to toe pads. External morphology and histology of C . ciliatus tail pads are largely similar to tail pads of closely related geckos. Functionally, C . ciliatus tail pads exhibit impressive adhesive ability, hypothetically capable of holding up to five times their own mass. Tail pads develop at approximately the same time during embryogenesis as toe pads. Further, tail pads exhibit similar developmental patterns to toe pads, which are markedly different from non-adhesive gecko toes and tails. Our data provide support for the serial homology of adhesive tail pads with toe pads.