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80 results for “squamate reptiles”
Data from: A global test of the cold-climate hypothesis for the evolution of viviparity of squamate reptiles
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Data from: Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species
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Data from: Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians)
Here, I combine previously underutilized models and priors to perform more biologically-realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backwards transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for 'asymmetric.' The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical datasets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend towards recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across datasets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological datasets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.
Data from: The evolutionary economics of embryonic-sac fluids in squamate reptiles
The parchment-shelled eggs of squamate reptiles take up substantial water from the nest environment, enabling the conversion of yolk into neonatal tissue and buffering the embryo against the possibility of subsequent dry weather. During development, increasing amounts of water are stored in the embryonic sacs (i.e., membranes around the embryo: amnion, allantois, and chorion). The evolution of viviparity (prolonged uterine retention of developing embryos) means that embryonic-sac fluid storage now imposes a cost (increased maternal burdening), confers less benefit (because the mother buffers fetal water balance), and introduces a potential conflict among uterine siblings (for access to finite water supplies). Our data on nine species of squamate reptiles and published information on three species show that the embryonic-sac fluids comprise around 33% of neonatal mass in viviparous species versus 94% in full-term eggs of oviparous squamates. Data on parturition in 149 vipers (Vipera aspis, a viviparous species) show that larger offspring store more fluids in their fetal sacs and that an increase in litter size is associated with a decrease in fluid-sac mass per offspring. Overall, the evolutionary transition from oviparity to viviparity may have substantially altered selective forces on offspring packaging and created competition among offspring for access to water reserves during embryonic development.
Data from: Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
Although the morphological and physiological changes involved in pregnancy in live-bearing reptiles are well studied, the genetic mechanisms that underlie these changes are not known. We used the viviparous African Ocellated Skink, Chalcides ocellatus, as a model to identify a near complete gene expression profile associated with pregnancy using RNA-Seq analyses of uterine transcriptomes. Pregnancy in C. ocellatus is associated with upregulation of uterine genes involved with metabolism, cell proliferation and death, and cellular transport. Moreover, there are clear parallels between the genetic processes associated with pregnancy in mammals and Chalcides in expression of genes related to tissue remodeling, angiogenesis, immune system regulation, and nutrient provisioning to the embryo. In particular, the pregnant uterine transcriptome is dominated by expression of proteolytic enzymes that we speculate are involved both with remodeling the chorioallantoic placenta and histotrophy in the omphaloplacenta. Elements of the maternal innate immune system are downregulated in the pregnant uterus, indicating a potential mechanism to avoid rejection of the embryo. We found a downregulation of major histocompatability complex loci and estrogen and progesterone receptors in the pregnant uterus. This pattern is similar to mammals but cannot be explained by the mammalian model. The latter finding provides evidence that pregnancy is controlled by different endocrinological mechanisms in mammals and reptiles. Finally, 88% of the identified genes are expressed in both the pregnant and the nonpregnant uterus, and thus, morphological and physiological changes associated with C. ocellatus pregnancy are likely a result of regulation of genes continually expressed in the uterus rather than the initiation of expression of unique genes.
Data from: Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.
Data from: Vertebral evolution and the diversification of squamate reptiles
Taxonomic, morphological and functional diversity are often discordant and independent components of diversity. A fundamental and largely unanswered question in evolutionary biology is why some clades diversify primarily in some of these components and not others. Dramatic variation in trunk vertebral numbers (14 to >300) among squamate reptiles coincides with different body shapes, and snake-like body shapes have evolved numerous times. However, whether increased evolutionary rates or numbers of vertebrae underlie body shape and taxonomic diversification is unknown. Using a supertree of squamates including 1375 species, and corresponding vertebral and body shape data, we show that increased rates of evolution in vertebral numbers have coincided with increased rates and disparity in body shape evolution, but not changes in rates of taxonomic diversification. We also show that the evolution of many vertebrae has not spurred or inhibited body shape or taxonomic diversification, suggesting that increased vertebral number is not a key innovation. Our findings demonstrate that lineage attributes such as the relaxation of constraints on vertebral number can facilitate the evolution of novel body shapes, but that different factors are responsible for body shape and taxonomic diversification.
No link between population isolation and speciation rate in squamate reptiles
<p>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 co-distributed 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.</p>
Figure 1 in Comparative morphology of the dermal palate in squamate reptiles, with comments on phylogenetic implications
Figure 1. The variation of the dermal palate in squamates as classified by Lakjer (1927) (redrawn after Guibé, 1970: fig. 80). A, the palaeochoanate condition; B, the incomplete neochoanate condition; C, the neochoanate condition.
No link between population isolation and speciation rate in squamate reptiles
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Data from: Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa
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Data from: Vertebral evolution and the diversification of squamate reptiles
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Data from: The evolutionary economics of embryonic-sac fluids in squamate reptiles
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Data from: Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
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Data from: Diversification rates are more strongly related to microhabitat than climate in squamate reptiles (lizards and snakes)
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Data from: Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians)
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Data from: The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes
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The morphological diversity of the quadrate bone in squamate reptiles as revealed by high-resolution computed tomography and geometric morphometrics
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Candidate genes underlying hypomelanistic morphs in squamate reptiles
GEO Series GSE289621. Pantherophis guttatus. 6 samples. Type: Expression profiling by high throughput sequencing.
Candidate genes underlying hypomelanistic morphs in squamate reptiles
GEO Series GSE289890. Eublepharis macularius. 23 samples. Type: Expression profiling by high throughput sequencing.
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