Population genomics of variegated toad-headed lizard Phrynocephalus versicolor and its adaptation to the colorful sand of the Gobi Desert
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ABSTRACT:
PROVIDER: PRJNA742052 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14932294_1.fastq.gz | Fastqsanger.gz | |||
| SRR14932294_2.fastq.gz | Fastqsanger.gz | |||
| SRR14932295_1.fastq.gz | Fastqsanger.gz | |||
| SRR14932295_2.fastq.gz | Fastqsanger.gz | |||
| SRR14932296_1.fastq.gz | Fastqsanger.gz |
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Project description:The variegated toad-headed agama, Phrynocephalus versicolor, lives in the arid landscape of the Chinese Gobi Desert. We analyzed populations from three different locations which vary in substrate color and altitude: Heishankou (HSK), Guazhou County (GZ), and Ejin Banner (EJN). The substrate color is either light-yellow (GZ-y), yellow (EJN-y), or black (HSK-b); the corresponding lizard population colors largely match their substrate in the degree of melanism. We assembled the P. versicolor genome and sequenced over 90 individuals from the three different populations. Genetic divergence between populations corresponds to their geographic distribution. We inferred the genetic relationships among these populations and used selection scans and differential expression to identify genes that show signatures of selection. Slc2a11 and akap12, among other genes, are highly differentiated and may be responsible for pigment adaptation to substrate color in P. versicolor.
| S-EPMC9260186 | biostudies-literature
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of melanic variation. The goals of this study are to evaluate population evolutionary genetics associated with dark and light color variation in a lizard.
2022-06-15 | GSE179069 | GEO
Project description:Extreme environmental conditions at high altitude, such as hypobaric hypoxia, low temperature, and strong UV radiation, pose a great challenge to the survival of animals. Although the mechanisms of adaptation to high-altitude environments have attracted much attention for native plateau species, the underlying metabolic regulation remains unclear. Here, we used a multi-platform metabolomic analysis to compare metabolic profiles of liver between high- and low-altitude populations of toad-headed lizards, Phrynocephalus vlangalii, from the Qinghai-Tibet Plateau. A total of 191 differential metabolites were identified, consisting of 108 up-regulated and 83 down-regulated metabolites in high-altitude lizards as compared with values for low-altitude lizards. Pathway analysis revealed that the significantly different metabolites were associated with carbohydrate metabolism, amino acid metabolism, purine metabolism, and glycerolipid metabolism. Most intermediary metabolites of glycolysis and the tricarboxylic acid cycle were not significantly altered between the two altitudes, but most free fatty acids as well as β-hydroxybutyric acid were significantly lower in the high-altitude population. This may suggest that high-altitude lizards rely more on carbohydrates as their main energy fuel rather than lipids. Higher levels of phospholipids occurred in the liver of high-altitude populations, suggesting that membrane lipids may undergo adaptive remodeling in response to low-temperature stress at high altitude. In summary, this study demonstrates that metabolic profiles differ substantially between high- and low-altitude lizard populations, and that these differential metabolites and metabolic pathways can provide new insights to reveal mechanisms of adaptation to extreme environments at high altitude.
2024-01-16 | MTBLS6900 | MetaboLights
Project description:Diversity in animal coloration is generally associated with adaptation to their living habitats, ranging from territorial display and sexual selection to predation or predation avoidance, and thermoregulation. However, the mechanism underlying color variation in toad-headed Phrynocephalus lizards remains poorly understood. In this study, we investigated the population color variation of Phrynocephalus versicolor. We found that lizards distributed in dark substrate have darker dorsal coloration (melanic lizards) than populations living in light substrates. This characteristic may improve their camouflage effectiveness. A reciprocal substrate translocation experiment was conducted to clarify the potential role of morphological adaptation and physiological plasticity of this variation. Spectrometry technology and digital photography were used to quantify the color variation of the above-mentioned melanic and nonmelanic P. versicolor populations and their native substrate. Additionally, substrate color preference in both populations was investigated with choice experiments. Our results indicate that the melanic and nonmelanic populations with remarkable habitat color difference were significantly different on measured reflectance, luminance, and RGB values. Twenty-four hours, 30 days, and 60 days of substrate translocation treatment had little effects on dorsal color change. We also found that melanic lizards choose to live in dark substrate, while nonmelanic lizards have no preference for substrate color. In conclusion, our results support that the dorsal coloration of P. versicolor, associated with substrate color, is likely a morphological adaptation rather than phenotypic plasticity.
| S-EPMC6787858 | biostudies-literature
Project description:Hypoxia and low temperature at high altitudes are the main environmental pressures for alpine animals, inducing phenotypic plasticity at several levels. To investigate the effect of these variables on the organ mass of Phrynocephalus vlangalii, 138 individuals belonging to four populations living along an altitudinal gradient in the Qinghai-Tibet Plateau (China) were dissected to remove heart, lungs, stomach, and intestinal tract. Organ dry mass, individuals' sex, and body mass, as well as mean annual temperature and average air pressure (calculated from a 30-year-data series obtained from the National Climatic Data Center) were subjected to two-way analyses of covariance and generalized linear mixed models (GLMMs). Except for the heart, organ mass varied significantly among populations, although only lung and stomach mass increased significantly with increasing altitude. Males' heart and lung mass was higher than that of females, which might be due to their different behavior and reproductive efforts. GLMM analyses indicated that air pressure had a positive effect on heart, lung and intestinal tract mass, whereas temperature had a negative effect on these three organs. In order to explain the effect of hypoxia and low temperature on P. vlangalii's organ mass, further rigorous study on respiration, energy budget and food intake was encouraged.
| S-EPMC5015776 | biostudies-literature
Project description:We hypothesize the phylogenetic relationships of the agamid genus Phrynocephalus to assess how past environmental changes shaped the evolutionary and biogeographic history of these lizards and especially the impact of paleogeography and climatic factors. Phrynocephalus is one of the most diverse and taxonomically confusing lizard genera. As a key element of Palearctic deserts, it serves as a promising model for studies of historical biogeography and formation of arid habitats in Eurasia. We used 51 samples representing 33 of 40 recognized species of Phrynocephalus covering all major areas of the genus. Molecular data included four mtDNA (COI, ND2, ND4, Cytb; 2,703 bp) and four nuDNA protein-coding genes (RAG1, BDNF, AKAP9, NKTR; 4,188 bp). AU-tests were implemented to test for significant differences between mtDNA- and nuDNA-based topologies. A time-calibrated phylogeny was estimated using a Bayesian relaxed molecular clock with nine fossil calibrations. We reconstructed the ancestral area of origin, biogeographic scenarios, body size, and the evolution of habitat preference. Phylogenetic analyses of nuDNA genes recovered a well-resolved and supported topology. Analyses detected significant discordance with the less-supported mtDNA genealogy. The position of Phrynocephalus mystaceus conflicted greatly between the two datasets. MtDNA introgression due to ancient hybridization best explained this result. Monophyletic Phrynocephalus contained three main clades: (I) oviparous species from south-western and Middle Asia; (II) viviparous species of Qinghai-Tibetan Plateau (QTP); and (III) oviparous species of the Caspian Basin, Middle and Central Asia. Phrynocephalus originated in late Oligocene (26.9 Ma) and modern species diversified during the middle Miocene (14.8-13.5 Ma). The reconstruction of ancestral areas indicated that Phrynocephalus originated in Middle East-southern Middle Asia. Body size miniaturization likely occurred early in the history of Phrynocephalus. The common ancestor of Phrynocephalus probably preferred sandy substrates with the inclusion of clay or gravel. The time of Agaminae radiation and origin of Phrynocephalus in the late Oligocene significantly precedes the landbridge between Afro-Arabia and Eurasia in the Early Miocene. Diversification of Phrynocephalus coincides well with the mid-Miocene climatic transition when a rapid cooling of climate drove progressing aridification and the Paratethys salinity crisis. These factors likely triggered the spreading of desert habitats in Central Eurasia, which Phrynocephalus occupied. The origin of the viviparous Tibetan clade has been associated traditionally with uplifting of the QTP; however, further studies are needed to confirm this. Progressing late Miocene aridification, the decrease of the Paratethys Basin, orogenesis, and Plio-Pleistocene climate oscillations likely promoted further diversification within Phrynocephalus. We discuss Phrynocephalus taxonomy in scope of the new analyses.
| S-EPMC5863718 | biostudies-literature
Project description:BACKGROUND:Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover a broad altitudinal gradient of over 4000 m and are useful models for studies of such adaptive responses. In one of the first studies to have considered selection on mitochondrial protein-coding regions in an ectothermic group distributed over such a wide range of environments, we analysed nineteen complete mitochondrial genomes from all Chinese Phrynocephalus (including eight genomes sequenced for the first time). Initial analyses used site and branch-site model (program: PAML) approaches to examine nonsynonymous: synonymous substitution rates across the mtDNA tree. RESULTS:Ten positively selected sites were discovered, nine of which corresponded to subunits ND2, ND3, ND4, ND5, and ND6 within the respiratory chain enzyme mitochondrial Complex I (NADH Coenzyme Q oxidoreductase). Four of these sites showed evidence of general long-term selection across the group while the remainder showed evidence of episodic selection across different branches of the tree. Some of these branches corresponded to increases in altitude and/or latitude. Analyses of physicochemical changes in protein structures revealed that residue changes at sites that were under selection corresponded to major functional differences. Analyses of coevolution point to coevolution of selected sites within the ND4 subunit, with key sites associated with proton translocation across the mitochondrial membrane. CONCLUSIONS:Our results identify mitochondrial Complex I as a target for environment-mediated selection in this group of lizards, a complex that frequently appears to be under selection in other organisms. This makes these lizards good candidates for more detailed future studies of molecular evolution.
| S-EPMC5840783 | biostudies-literature
Project description:Intraspecific rearrangements of mitochondrial genomes are rarely reported in reptiles, even in vertebrates. The sunwatcher toad-headed agama, Phryncoephalus helioscopus, can serve as an excellent model for investigating the dynamic mitogenome structure at intraspecific level. To date, seven subspecies of P. helioscopus are well recognized, but little is known about the mitogenomic evolution among different subspecies. In this study, complete mitogenomes of subspecies P. helioscopus varius II and P. helioscopus cameranoi were determined by next-generation sequencing, and another P. helioscopus varius I retrieved from GenBank was compiled for comparative analysis. The nucleotide composition and the codon usage are similar to those previously published from toad-headed agamas. P. helioscopus varius II and P. helioscopus cameranoi have 23 tRNA genes, including standard 22 tRNA genes and one extra tRNA-Phe (tRNA-Phe duplication). Gene order and phylogenetic analyses in the genus Phrynocephalus support prevalent intraspecific gene rearrangement in P. helioscopus and other congener species including P. erythrurus, P. vlangalii, and P. forsythii. Six different mitochondrial gene arrangements are observed in Phrynocephalus. Overall, the occurrence of rearrangements may result from multiple independent structural dynamic events. The split of the two subspecies in P. helioscopus was dated at approximately 2.34 million years ago (Ma). Two types of gene rearrangements are found in the three mitogenomes of P. helioscopus, and this intraspecific rearrangement phenomenon can be explained by the tandem duplication/random loss (TDRL) model. Post duplication, the alternative loss types can occur in 0.23-0.72 Ma, suggesting that the duplication and fixation of these rearrangements can occur quite quickly. These findings highlight the need for more mitogenomes at the population level in order to better understand the potentially rampant intraspecific mitogenomic reorganization in Phrynocephalus.
| S-EPMC8872181 | biostudies-literature
Project description:Phrynocephalus helioscopus overview
| PRJNA815395 | ENA