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Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean-based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses.

Nonnative (“invasive,” “exotic,” “naturalized”) species frequently are vilified. However, some philosophers and ecologists have questioned whether nonnative species and assemblages are objectively, ahistorically identifiable as different entities relative to native species and assemblages, once selection biases are taken into account. We used an unprecedented dataset of morphology, phylogeny and assemblage content for 336 species of Anolis lizard to compare morphological and phylogenetic characteristics of variability and central tendency between native assemblages and those that include nonnative species. Equivalence tests demonstrated significant similarity between native and nonnative assemblages in trait variability, phylogenetic dispersion and mean trait values except for body size; logistic and zero‐inflated regression failed to distinguish native and nonnative assemblages. For most traits, similarity was not due to assemblages being structured randomly but rather to both native and nonnative assemblages including similar species. Without historical information, a naïve observer would be unable to identify Anolis assemblages as native or nonnative based on morphological assemblage structure or most mean assemblage trait values, but would have some success categorizing assemblages based on average body size of species in the assemblage. Significant phylogenetic and morphological clustering in native assemblages likely reflects source pools composed of close relatives that share traits, as well as some environmental filtering effects; the slightly less phylogenetically clustered but equally morphologically clustered nonnative assemblages are less constrained to proximal source pools but still probably subject to filtering. Differences between native and nonnative assemblages in mean body size likely reflect assemblage youth. The ontological status of nonnative species is discussed in the light of these results. A plain language summary is available for this article. Plain Language Summary

Summary Ectotherms such as lizards are expected to alter their behaviour and microhabitat use and experience population declines in response to rising temperatures. But the role of changing rainfall patterns on lizard behaviour and microhabitat use is not understood. We used a 5‐year rainfall manipulation experiment in a piñon pine‐juniper woodland in central New Mexico to study how a lizard species' microhabitat use varies in four different rainfall treatments. We examined ground temperatures in the sun and shade, and daily rainfall, within each treatment, during lizard activity periods, to address how lizards used sun or shade microhabitats on a daily basis. Our small‐scale rainfall and temperature measurements indicate that rainfall, not temperatures, predict lizard microhabitat use. Lizards showed a strong preference for shaded microhabitats during dry periods and used sunny microhabitats following rainfall events, regardless of treatment type. Lizards remained active during dry periods, foraging in the shade of trees. Our study shows that rainfall can influence lizard microhabitat use more than temperature in a piñon pine‐juniper woodland and the trees provide important refugia. The loss of piñon pine and juniper trees from prolonged drought threatens to limit the amount of shade available to lizards in the future. Lay Summary

The Arizona Toad (Anaxyrus microscaphus) is restricted to riverine corridors and adjacent uplands in the arid southwestern United States. As with numerous amphibians worldwide, populations are declining and face various known or suspected threats, from disease to habitat modification resulting from climate change. The Arizona Toad has been petitioned to be listed under the U.S. Endangered Species Act and was considered “warranted but precluded” citing the need for additional information – particularly regarding natural history (e.g., connectivity and dispersal ability). The objectives of this study were to characterize population structure and genetic diversity across the species’ range. We used reduced-representation genomic sequencing to genotype 3,601 single nucleotide polymorphisms in 99 Arizona Toads from ten drainages across its range. Multiple analytical methods revealed two distinct genetic groups bisected by the Colorado River; one in the northwestern portion of the range in southwestern Utah and eastern Nevada and the other in the southeastern portion of the range in central and eastern Arizona and New Mexico. We also found subtle substructure within both groups, particularly in central Arizona where toads at lower elevations were less connected than those at higher elevations. The northern and southern parts of the Arizona Toad range are not well connected genetically and could be managed as separate units. Further, these data could be used to identify source populations for assisted migration or translocations to support small or potentially declining populations.

For species with variable phenology, it is often challenging to produce reliable estimates of population dynamics or changes in occupancy. The Arizona Toad (Anaxyrus microscaphus) is a southwestern USA endemic that has been petitioned for legal protection, but status assessments are limited by a lack of information on population trends. Also, timing and consistency of Arizona Toad breeding varies greatly, making it difficult to predict optimal survey times or effort required for detection. To help fill these information gaps, we conducted breeding season call surveys during 2013–2016 and 2019 at 86 historically occupied sites and 59 control sites across the species' range in New Mexico. We estimated variation in mean dates of arrival and departure from breeding sites, changes in occupancy, and site-level extinction since 1959 with recently developed multi-season staggered-entry models, which relax the within-season closure assumption common to most occupancy models. Optimal timing of surveys in our study areas was approximately 5–30 March. Averaged across years, estimated probability of occupancy was 0.58 (SE = 0.09) for historical sites and 0.19 (SE = 0.08) for control sites. Occupancy increased from 2013 through 2019. Notably, even though observer error was trivial, annual detection probabilities varied from 0.23 to 0.75 and declined during the study; this means naïve occupancy values would have been misleading, indicating apparent declines in toad occupancy. Occupancy was lowest during the first year of the study, possibly due to changes in stream flows and conditions in many waterbodies following extended drought and recent wildfires. Although within-season closure was violated by variable calling phenology, simple multi-season models provided nearly identical estimates as staggered-entry models. Surprisingly, extinction probability was unrelated to the number of years since the first or last record at historically occupied sites. Collectively, our results suggest a lack of large, recent declines in occupancy by Arizona Toads in New Mexico, but we still lack population information from most of the species' range.

The worldwide spread of invasive species affects native biodiversity and causes economic loss, but also allows better understanding of historical biogeographic patterns. Prediction of likely invaders facilitates economic and conservation decisions and gives insight into characteristics that have allowed natural colonization over evolutionary time. However, it is not clear what types of characters best predict naturalization or even whether naturalization is predictable at all. Squamate reptiles have been understudied subjects for invasion biology. Lizards of the genus Anolis have been highly successful colonizers both recently and over evolutionary time. Nineteen of the approximately 350 described species of Anolis have established naturalized populations. We constructed models of naturalization using morphological, distributional, anthropogenic, and phylogenetic characters and compared these single character class models to each other and to a composite model incorporating all four classes. We show that (1) each class of variables significantly predicts invasion, (2) a composite model significantly outperforms each of the submodels, and (3) the final composite model displays extraordinary ability to objectively identify naturalized species of Anolis.

Extreme climatic events such as the El Niño Southern Oscillation profoundly affect many plants and animals, including amphibians, which are strongly negatively affected by drought conditions. How amphibians respond to exceptionally high precipitation as observed in La Niña events, however, remains unclear. We document the correlation between the exceedingly wet 2010-2012 La Niña and community-level changes in a leaf litter frog assemblage in Costa Rica. Relative abundances of species shifted, diversity and plot occupancy decreased, and community composition became homogenized with the onset of La Niña. These aspects remained altered for over 20 months but rebounded to pre-La Niña levels after approximately 12 months. We hypothesize that complex ecological cascades associated with excess moisture caused short-term declines in abundances of species and associated changes in community structure. If additional stressors such as disease or habitat loss are not co-occurring, frog communities can rapidly recover to pre-disturbance levels following severe climatic events.

Adaptive radiation is a widely recognized pattern of evolution wherein substantial phenotypic change accompanies rapid speciation. Adaptive radiation may be triggered by environmental opportunities resulting from dispersal to new areas or via the evolution of traits, called key innovations, that allow for invasion of new niches. Species sampling is a known source of bias in many comparative analyses, yet classic adaptive radiations have not been studied comparatively with comprehensively sampled phylogenies. In this study, we use unprecedented comprehensive phylogenetic sampling of Anolis lizard species to examine comparative evolution in this well-studied adaptive radiation. We compare adaptive radiation models within Anolis and in the Anolis clade and a potential sister lineage, the Corytophanidae. We find evidence for island (i.e., opportunity) effects and no evidence for trait (i.e., key innovation) effects causing accelerated body size evolution within Anolis. However, island effects are scale dependent: when Anolis and Corytophanidae are analyzed together, no island effect is evident. We find no evidence for an island effect on speciation rate and tenuous evidence for greater speciation rate due to trait effects. These results suggest the need for precision in treatments of classic adaptive radiations such as Anolis and further refinement of the concept of adaptive radiation.

We describe a new species of Anolis from the Andes of northern Peru. This form is similar to species formerly assigned to the genus Phenacosaurus and to Ernest Williams’ tigrinus series. That is, the new species possesses large smooth headscales, cryptic coloration, and short limbs and tail. We present new DNA and morphological data and perform a comprehensive phylogenetic analysis of the Dactyloa clade of Anolis. The new species is estimated to be close to phenotypically similar species from Peru and Venezuela. We revise the taxonomy of Dactyloa based on our estimate. Most previously recognized phylogenetically defined groups are retained with restricted species contents. Several species currently scorable only for morphological data could not be placed in any group with confidence. The species status of the enigmatic mainland form Anolis deltae should be re-examined with reference to the roquet group of southern Lesser Antillean Anolis.