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  1. Abstract

    Myrmecophagy is one of the most common dietary specializations among vertebrates. Ants are an important food resource for many lizard species. Here, we use a large dataset on ant consumption by lizards (345 species, 33 families) to explore evolutionary and ecological correlates of myrmecophagy across the evolutionary history of lizards. Based on literature and previous empirical work, we develop and test the following hypotheses about myrmecophagy: (i) it does not occur randomly across Squamata; it is correlated with (ii) foraging mode, (iii) habitat, (iv) body size, (v) aridity, and/or (vi) species range size. We found that ant ingestion is not distributed randomly in the phylogeny, with higher ingestion concentrated in some Iguania. Myrmecophagy also evolved in Lacertoidea and it is a derived trait with relatively recent origin. Foraging mode, habitat, body size, and aridity do not influence ant ingestion. Species with smaller range sizes show high variability in ant ingestion, whereas lizards with larger ranges tend to eat a lower proportion of ants. This result confirms the general ecological pattern that specialization is more common in narrowly distributed species. We suggest that future studies should also explore dietary specialization more broadly and provide a better taxonomic resolution of ant species in the diet of lizards.

     
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  2. Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process—the propensity for population isolation—as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation—including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist—are likely to play a larger role than population isolation in controlling speciation rate variation in squamates. 
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  3. Ruane, Sara (Ed.)
    Abstract Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).] 
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  4. Abstract Aim

    Species adapt differently to contrasting environments, such as open habitats with sparse vegetation and forested habitats with dense forest cover. We investigated colonization patterns in the open and forested environments in the diagonal of open formations and surrounding rain forests (i.e. Amazonia and Atlantic Forest) in Brazil, tested whether the diversification rates were affected by the environmental conditions and identified traits that enabled species to persist in those environments.

    Location

    South America, Brazil.

    Taxon

    Squamata, Lizards.

    Methods

    We used phylogenetic information and the current distribution of species in open and forested habitats to estimate ancestral ranges and identify range shifts relative to the current habitats. To evaluate whether these environments influenced species diversification, we tested 12 models using a Hidden Geographic State Speciation and Extinction analysis. Finally, we combined phylogenetic relatedness and species traits in a machine learning framework to identify the traits permitting adaptation in those contrasting environments.

    Results

    We identified 41 total transitions between open and forested habitats, of which 80% were from the forested habitats to the open habitats. Widely distributed species had higher speciation, turnover, extinction, and extinction fraction rates than species in forested or open habitats, but had also the lower net diversification rate. Mean body temperature, microhabitat, female snout–vent length and diet were identified as putative traits that enabled adaptation to different environments, and phylogenetic relatedness was an important predictor of species occurrence.

    Main conclusions

    Transitions from forested to open habitats are most common, highlighting the importance of habitat shift in current patterns of biodiversity. The combination of phylogenetic reconstruction of ancestral distributions and the machine learning framework enables us to integrate organismal trait data, environmental data and evolutionary history in a manner that could be applied on a global scale.

     
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  5. Abstract Aim

    We investigate the biogeographical history and diversification in a treefrog lineage distributed in contrasting (open and forested) ecoregions of South America, including three biodiversity hotspots. We evaluate the role of dispersal and whether other factors such as diversity‐dependence or paleotemperatures could explain the diversification pattern for this group. Especially focusing on the savanna endemics, we illuminate the processes governing the species assembly and evolution of the Cerrado savanna.

    Location

    South American ecoregions south of the Amazon (i.e. Atlantic Forest, Cerrado, Araucaria Forest, Pampas, Central and Southern Andes).

    Taxon

    Boana pulchellagroup.

    Methods

    We built the most complete time‐calibrated phylogeny for the group to date. We then reconstructed ancestral ranges using the dispersal‐extinction‐cladogenesis (DEC) model comparing different dispersal scenarios considering distance, adjacency and ecological similarity among regions. Centre‐of‐origin hypotheses in forest and open ecoregions were also tested. Using biogeographical stochastic mapping, we additionally estimated the contribution of range shifts across different biomes. Lastly, we evaluated several diversification models, including the effect of time, diversity‐dependence and temperature‐dependence on speciation and extinction rates.

    Results

    TheBoana pulchellagroup originated during the Early Miocene (~17.5 MYA) and underwent high speciation rates during the Middle Miocene Climatic Optimum, with a decreasing trend following the Miocene Climatic Transition. We found no support for a single ecoregion acting as a centre of origin and diversification; instead, we inferred recurrent range shifts with dispersal among dissimilar adjacent ecoregions. Speciation linearly dependent on paleotemperatures, with either no or very low constant extinction rates, best explained the slowdown diversification pattern.

    Main conclusions

    Our results support a species assembly of Cerrado savanna in South America during the Miocene with intermittent interchange with rain forest habitats. Past climate changes impacted the rate new species originated with apparently no impact on extinction. Finally, the repeated habitat shifts among open/dry and forested/humid ecoregions, rather than long‐term in‐situ diversification in single areas, highlights the very dynamic historical interchange between contrasting habitats in South America, possibly contributing to its high species diversity.

     
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  6. Abstract Comprehensive assessments of species’ extinction risks have documented the extinction crisis 1 and underpinned strategies for reducing those risks 2 . Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction 3 . Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods 4–7 . Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs 6 . Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation 8 and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles. 
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  7. Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat-rich Y/W chromosome (the “toxic Y/W effect”) could accelerate aging in the heterogametic sex in some vertebrate clades. 
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