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80 results for “squamate reptiles”
Data for: Convergent evolution of tail spines in squamate reptiles driven by microhabitat use
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Corticosterone and immune responses to dehydration in squamate reptiles
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Determinate growth is predominant and likely ancestral in squamate reptiles
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Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective
<p>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 datasets 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 nine of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can be used to build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups.</p>
FIGURE 1 in Use of scalation landmarks in geometric morphometrics of squamate reptiles: a comment on homology
FIGURE 1. Diagrams of specimens of the Crotalus viridis complex with 14 (A) and 16 (B) supralabial scales, respectively (supralabial scale rows are shaded in grey). For (A), the red dot marks a fixed landmark at the center of the series, seven scales from the first and seven scales from the last supralabial scale. Placing a corresponding fixed landmark on specimen B requires that one choose between seven scales from the first supralabial, seven scales from the last supralabial, or the suture at the center of the series, providing three mutually exclusive options (red dots). Selecting any of these options changes the topological position of the landmark relative to the first, the last, or both of these scales in the series. Fixed landmarks applied to scale rows variable in count renders secondary homology intractable, regardless of whether scales are counted from a consistent anchor point.
Data from: Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches – anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) – and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE, and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci (SqCL) set, a single integrated probe set that can generate high-quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically-disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness, and suggest areas for future improvement.
Data from: A global test of the cold-climate hypothesis for the evolution of viviparity of squamate reptiles
Aim The evolution of viviparity in squamate reptiles has attracted considerable scientific attention since the beginning of last century. The cold climate hypothesis posits that cold regions favor viviparity (and therefore the incidence of viviparous squamates is increased in these regions) because viviparous females can use thermoregulatory behavior to shorten embryonic developmental time and to reduce exposure of embryos to stressful temperatures. However, a rigorous global-scale test of the impact of viviparity on the developmental time and viability of embryos is still absent. Recently developed biophysical models and climate databases enable us to conduct a mechanistic test of this hypothesis. Location Global Time period Summer Major taxa studied Squamata Methods We integrated global climate data, a biophysical model, and developmental functions to quantify the effects of temperature on embryo developmental time, developmental viability, and energy consumption of oviparous versus viviparous embryos. To examine the accuracy of our predictions, we calculated the percentage of squamate reptiles that were viviparous in each region and assessed developmental temperature of gravid females, latitude and elevation as predictors for the percentage of squamate reptiles. Results Compared with oviparous embryos, viviparous embryos develop faster in cold regions, and experience similar embryonic developmental viability. Across most latitudes and elevations, the total energetic cost of development is lower for viviparous embryos than for oviparous embryos. Cold regions contain a higher proportion of viviparous species than do hot regions. By comparing the distribution pattern of viviparity and temperature effects on embryonic development, we found that shortened development time provided the strongest benefit of viviparity. Main conclusions Our global and biophysical model based comparison generally supports the cold climate hypothesis. Moreover, viviparity in cold climates appears beneficial primarily by shortening developmental time.
Data from: Do macrophylogenies yield stable macroevolutionary inferences? An example from squamate reptiles
Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"—large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches—provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles—each consisting of more than 4000 species—yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field.
Data from: Correlates of extinction risk in squamate reptiles: the relative importance of biology, geography, threat and range size
Aim Evaluating the relative roles of biological traits and environmental factors that predispose species to an elevated risk of extinction is of fundamental importance to macroecology. Identifying species that possess extinction-promoting traits allows targeted conservation action before precipitous declines occur. Such analyses have been carried out for several vertebrate groups, with the notable exception of reptiles. We identify traits correlating with high extinction risk in squamate reptiles, assess whether these differ with geography, taxonomy and threats, and make recommendations for future Red List assessments. Location Global. Methods We collected data on biological traits and environmental factors for a representative sample of 1139 species of squamate reptiles. We used phylogenetically controlled regression models to identify general correlates of extinction risk, threat-specific correlates of risk and realm-specific correlates of risk. We also assessed the relative importance of range size versus other factors through multiplicative bivariate models, partial regressions and variance partitioning. Results Range size was the most important predictor of extinction risk, reflecting the high frequency of reptiles assessed under range-based IUCN criteria. Habitat specialists occupying accessible ranges were at a greater risk of extinction: although these factors never contributed more than 10% to the variance in extinction risk, they showed significant interactions with range size. The predictive power of our global models ranged from 23% to 29%. The general overall pattern remained the same among geographical, taxonomic and threat-specific data subsets. Main conclusions Proactive conservation requires shortcuts to identify species at high risk of extinction. Regardless of location, squamate reptiles that are range-restricted habitat specialists living in areas highly accessible to humans are likely to become extinct first. Prioritizing species that exhibit such traits could forestall extinction. Integration of data sources on human pressures, such as accessibility of species ranges, may aid robust and time-efficient assessments of species extinction risk.
Data from: The convergent evolution of snake-like forms by divergent evolutionary pathways in squamate reptiles
Convergent evolution of phenotypes is considered evidence that evolution is deterministic. Establishing if such convergent phenotypes arose through convergent evolutionary pathways is a stronger test of determinism. We studied the evolution of snake-like body shapes in six clades of lizards, each containing species ranging from short-bodied and pentadactyl to long-bodied and limbless. We tested whether body shapes that evolved in each clade were convergent, and whether clades evolved snake-like body shapes following convergent evolutionary pathways. Our analyses showed that indeed species with the same numbers of digits in each clade evolved convergent body shapes. We then compared evolutionary pathways among clades by considering patterns of evolutionary integration and shape of relationship among body parts, patterns of vertebral evolution, and models of digit evolution. We found that all clades elongated their bodies through the addition, not elongation, of vertebrae, and had similar patterns of integration. However, patterns of integration, the body parts that were related by a linear or a threshold model, and patterns of digit evolution differed among clades. These results showed that clades followed different evolutionary pathways. This suggests an important role of historical contingency as opposed to determinism in the convergent evolution of snake-like body shapes.
Data from: Testing the role of climate in speciation: new methods and applications to squamate reptiles (lizards and snakes)
Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large-scale phylogeny to identify 242 sister-species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n=49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61–76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms.
Data from: Stage-dependence of phenotypical and phenological maternal effects: insight into squamate reptile reproductive strategies
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Data from: Curvilinear telomere length dynamics in a squamate reptile
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Data from: Correlates of extinction risk in squamate reptiles: the relative importance of biology, geography, threat and range size
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Data from: The convergent evolution of snake-like forms by divergent evolutionary pathways in squamate reptiles
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Data from: Do macrophylogenies yield stable macroevolutionary inferences? An example from squamate reptiles
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Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective
Open the record for dataset details and reuse information.
Data from: Testing the role of climate in speciation: new methods and applications to squamate reptiles (lizards and snakes)
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Data from: Evolutionary shifts in habitat aridity predict evaporative water loss across squamate reptiles
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Data from: Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
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