Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
189
datasets available to search
ShareScore release 0.9.0
Dataset results
189 results for “squamation”
Determinate growth is predominant and likely ancestral in squamate reptiles
Open the record for dataset details and reuse information.
Squamation and scale morphology at the root of jawed vertebrates
Open the record for dataset details and reuse information.
A Triassic crown squamate
Open the record for dataset details and reuse information.
Taphonomic megabiases constrain phylogenetic information in the squamate fossil record
Open the record for dataset details and reuse information.
Data from: Are there general laws for digit evolution in squamates? The loss and re-evolution of digits in a clade of fossorial lizards (Brachymeles, Scincinae)
Open the record for dataset details and reuse information.
A global analysis of viviparity in squamates highlights its prevalence in cold climates
Open the record for dataset details and reuse information.
The Jurassic rise of squamates as supported by lepidosaur disparity and evolutionary rates
Open the record for dataset details and reuse information.
Predictors of genomic diversity within North American squamates
Open the record for dataset details and reuse information.
Squamate metabolic rates decrease in winter beyond the effect of temperature
Open the record for dataset details and reuse information.
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.
Dataset for Ecomorphological diversification of squamates in the Cretaceous
<p><span>Squamates (lizards and snakes) are highly successful modern vertebrates, with over 10,000 species. Squamates have a long history, dating back to at least 240 million years ago (Ma), and showing increasing species richness in the Late Cretaceous (84 Ma) and early Paleogene (66–55 Ma). We confirm that the major expansion of dietary functional morphology happened before these diversifications, in the mid Cretaceous, 110–90 Ma. Until that time, squamates had relatively uniform tooth types, which then diversified substantially and ecomorphospace expanded to modern levels. This coincides with the Cretaceous Terrestrial Revolution, when angiosperms began to take over terrestrial ecosystems, providing new roles for plant-eating and pollinating insects, which were in turn new sources of food for herbivorous and insectivorous squamates. There was also an early Late Cretaceous (95–90 Ma) rise in jaw size disparity, driven by the diversification of marine squamates, particularly early mosasaurs. These events established modern levels of squamate feeding ecomorphology before the major steps in species diversification, confirming decoupling of diversity and disparity. In fact, squamate feeding ecomorphospace had been partially explored in the Late Jurassic and Early Cretaceous, and jaw innovation in Late Cretaceous squamates involved expansions at the extremes of morphospace. </span></p>
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: Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status
Macroevolutionary rates of diversification and anthropogenic extinction risk differ vastly throughout the Tree of Life. This results in a highly heterogeneous distribution of Evolutionary distinctiveness (ED) and threat status among species. We examine the phylogenetic distribution of ED and threat status for squamates (amphisbaenians, lizards, and snakes) using fully-sampled phylogenies containing 9574 species and expert-based estimates of threat status for ~ 4000 species. We ask whether threatened species are more closely related than would be expected by chance and whether high-risk species represent a disproportionate amount of total evolutionary history. We found currently-assessed threat status to be phylogenetically clustered at broad level in Squamata, suggesting it is critical to assess extinction risks for close relatives of threatened lineages. Our findings show no association between threat status and ED, suggesting that future extinctions may not result in a disproportionate loss of evolutionary history. Lizards in degraded tropical regions (e.g., Madagascar, India, Australia, and the West Indies) seem to be at particular risk. A low number of threatened high-ED species in areas like the Amazon, Borneo, and Papua New Guinea may be due to a dearth of adequate risk assessments. It seems we have not yet reached a tipping point of extinction risk affecting a majority of species; 63% of the assessed species are not threatened and 56% are Least Concern. Nonetheless, our results show that immediate efforts should focus on geckos, iguanas, and chameleons, representing 67% of high-ED threatened species and 57% of Unassessed high-ED lineages.
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: Squamate hatchling size and the evolutionary causes of negative offspring size allometry
Although fecundity selection is ubiquitous, in an overwhelming majority of animal lineages, small species produce smaller number of offspring per clutch. In this context, egg, hatchling and neonate sizes are absolutely larger, but smaller relative to adult body size in larger species. The evolutionary causes of this widespread phenomenon are not fully explored. The negative offspring size allometry can result from processes limiting maximal egg/offspring size forcing larger species to produce relatively smaller offspring ('upper limit'), or from a limit on minimal egg/offspring size forcing smaller species to produce relatively larger offspring ('lower limit'). Several reptile lineages have invariant clutch sizes, where females always lay either one or two eggs per clutch. These lineages offer an interesting perspective on the general evolutionary forces driving negative offspring size allometry, because an important selective factor, fecundity selection in a single clutch, is eliminated here. Under the upper limit hypotheses, large offspring should be selected against in lineages with invariant clutch sizes as well, and these lineages should therefore exhibit the same, or shallower, offspring size allometry as lineages with variable clutch size. On the other hand, the lower limit hypotheses would allow lineages with invariant clutch sizes to have steeper offspring size allometries. Using an extensive data set on the hatchling and female sizes of > 1800 species of squamates, we document that negative offspring size allometry is widespread in lizards and snakes with variable clutch sizes and that some lineages with invariant clutch sizes have unusually steep offspring size allometries. These findings suggest that the negative offspring size allometry is driven by a constraint on minimal offspring size, which scales with a negative allometry.
A global analysis of field body temperatures of active squamates in relation to climate and behaviour
<p><strong>Aim</strong>: Squamate fitness is affected by body temperature, which in turn is influenced by environmental temperatures and, in many species, by exposure to solar radiation. The biophysical drivers of body temperature have been widely studied, but we lack an integrative synthesis of actual body temperatures experienced in the field, and their relationships to environmental temperatures, across phylogeny, behaviour, and climate.</p> <p><strong>Location</strong>: Global (25 countries on six continents)</p> <p><strong>Taxa</strong>: Squamates (210 species, representing 25 families)</p> <p><strong>Methods</strong>: We measured body temperatures during activity for 20,231 individuals, and examined how body temperatures vary with substrate and air temperatures across taxa, climates, and behaviours (basking and diel activity).</p> <p><strong>Results</strong>: Heliothermic lizards had the highest body temperatures and those most weakly correlated with substrate and air temperatures. Body temperatures of non-heliothermic diurnal lizards were similar to heliotherms in relation to air temperature but to nocturnal species in relation to substrate temperatures. Diurnal snake and non-heliothermic lizard body temperatures were more strongly correlated to air and substrate temperatures than in heliotherms. Correlation parameters of all diurnal squamates vary with mean annual temperatures, especially in heliotherms, so that the thermal relations of the various categories are disparate in cold climate but convergent in warm climate. Non-heliotherms and nocturnal body temperatures are better explained by substrate temperature than by air temperature. Body temperature distributions become left-skewed in warmer-bodied species, especially in colder climate.</p> <p><strong>Main</strong> <strong>conclusions</strong>: Differences in squamate body temperatures, their environmental relationships, and frequency distributions are globally influenced by behavioural and climatic factors. Differences between behavioural categories are smaller in warm climates where environmental temperatures are generally favourable, but heliotherm body temperature remained consistently higher than all others.</p>
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.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.