Publications by authors named "Yan-Fu Qu"

Environmental temperature affects the composition, structure, and function of the gut microbial communities in host animals. To elucidate the role of gut microbiota in thermal adaptation, we designed a 2 species × 3 temperatures experiment, whereby we acclimated adult males of two agamid lizard species (warm-climate and cold-climate ) to 20, 28, and 36°C for 2 weeks and then collected their fecal and small-intestinal samples to analyze and compare the microbiota using 16S rRNA gene amplicon sequencing technology. The fecal microbiota displayed more pronounced interspecific differences in microbial community than the small-intestinal microbiota in the two species occurring in thermally different regions.

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The transforming growth factor-β (TGF-β) gene family is unique to animals and is involved in various important processes including tissue regeneration. Here, we identified 52 TGF-β family genes based on genome sequences of the gecko (Gekko japonicus), compared TGF-β genes between G. japonicus and other four reptilian species, and evaluated the expression of 14 randomly selected genes in muscle, kidney, liver, heart, and brain during tail regeneration to investigate whether their expression was tissue-dependent.

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  • The study investigates local adaptation and genomic variation in the Asiatic toad across different populations in China, focusing on how these factors relate to climate change.
  • Researchers analyzed SNP data from 94 toads and identified three genetic clusters associated with various regions, revealing that environmental variables significantly influence genetic diversity and population structure.
  • Findings suggest that climate warming poses a greater extinction risk for the Asiatic toad due to mismatches between its current genetic makeup and future environmental conditions.
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  • Multiple factors influence the gut microbiota in hosts, and its disorder can lead to various diseases.
  • Researchers examined gut microbiota in Japanese geckos by analyzing fecal samples from wild and captive geckos fed different diets (mealworms vs. fruit flies) using 16S rRNA gene sequencing.
  • The study found that mealworm-fed geckos had richer and more diverse gut microbiota, with the overall composition being linked to diet and sexual differences, highlighting the microbial contribution to metabolic and immune functions in the species.
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Residual yolk is assumed to be an important source of energy and nutrients during early life in nonmammalian amniotes. Available data show that the mean size of residual yolk is far smaller in lizards than in turtles, snakes, crocodiles, and birds, raising a question of whether residual yolk is of functional significance in lizards. Here, we compared data from 26 lizard species with those from other nonmammalian amniotes to test the hypothesis that residual yolk is functionally less significant in species producing more fully developed offspring.

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  • The liver plays a crucial role in nutrient metabolism, detoxification, and immune functions, particularly in response to pathogens from the gut.
  • Researchers used single-cell RNA sequencing to analyze the liver of the Chinese soft-shelled turtle, identifying the cellular composition of immune cells in their liver.
  • The study revealed seven distinct liver immune cell types and showed how bacterial infection changes the number and types of these cells, providing new insights into turtle liver immunology.
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  • The study tests the metabolic cold-climate adaption hypothesis by comparing gut microbiota in two cold-climate lizard species to see if it aids in their adaptation.
  • The gut microbiota analysis revealed a different composition between the species and showed that it helps promote thermal adaptation, with varying bacterial abundance.
  • The findings support the idea that gut microbiota is crucial for cold-climate adaptation in lizards, particularly highlighting P. erythrurus's stronger metabolic response at lower temperatures.
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  • Long-term studies help researchers understand how different external and internal factors influence reproductive strategies, specifically in terms of the number and size of offspring.
  • A study of red-banded wolf snakes in Zhejiang, East China, over several years showed that egg-laying dates and reproductive traits were closely linked to the size of the female snakes.
  • The findings highlight that while larger female snakes tend to produce larger eggs, they don’t necessarily sacrifice the number of offspring for egg size, challenging previous theories on reproductive investment strategies.
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Composition and diversity in gut microbiota are impacted by a wide variety of factors. The similarity of gut microbiota in related or sympatric species has been gaining recent traction. Here, 16S rRNA gene sequencing technology was employed to study the gut microbiota of three sympatric frog species, namely , , and .

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  • The study investigates how diet affects the oral and gut microbiota in wild and captive water monitor lizards by analyzing samples collected from both groups.
  • The dominant bacterial phyla found in both the oral and gut microbiota were Proteobacteria and Bacteroidota, with diverse microbiota observed in the gut compared to the mouth.
  • Results suggest that captive lizards exhibited different microbiota profiles due to their diet and environment, indicating that maintaining a wild-like diet can help preserve their natural microbiota.
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  • The Qinghai-Tibet Plateau's diverse landscape and complex climate history have significantly influenced genetic differences among the Phrynocephalus vlangalii species complex.
  • Researchers analyzed genetic data from 532 individuals, discovering a new mitochondrial clade and evidence of DNA interchange between species, suggesting recent population expansions and diversifications.
  • Geological events, such as mountain uplift during various orogeny phases, have played a crucial role in separating populations and shaping the current genetic diversity of these reptiles in northeastern Tibet.
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Body temperature is a crucial variable in animals that affects nearly every aspect of their lives. Here we analyze for the first time largescale patterns in the evolution of body temperatures across terrestrial vertebrates (tetrapods: including amphibians, mammals, birds and other reptiles). Despite the traditional view that endotherms (birds and mammals) have higher body temperatures than ectotherms, we find they are not significantly different.

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  • The study investigates the diversity and function of venom toxins in the annulated sea snake, highlighting the significance of venom in their adaptation to marine life.
  • Researchers conducted proteomic and NGS analyses, identifying three main toxin types: three-finger toxins (3-FTxs), phospholipase A (PLA), and cysteine-rich secretory protein (CRISP), with a total of 59 toxin-coding unigenes across 24 protein families.
  • The findings reveal that 3-FTxs are the primary contributors to venom toxicity, indicating that natural selection plays a crucial role in venom evolution to help sea snakes effectively prey on and defend against fast-moving marine threats.
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Coexisting species may experience population and range changes alone or jointly in response to environmental change. Here, we used six climate variables and ten modeling algorithms to predict the distribution of two species (.  and .

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The diversity of habitats generated by the Andes uplift resulted a mosaic of heterogeneous environments in South America for species to evolve a variety of ecological and physiological specializations. Species in the lizard family Liolaemidae occupy a myriad of habitats in the Andes. Here, we analyze the tempo and mode of evolution in the thermal biology of liolaemids.

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The scavenger receptor class B type 1 (SR-B1), a high-density lipoprotein (HDL) receptor, is a membrane glycoprotein that mediates selective uptake of HDL-cholesterol and cholesterol ester (CE) into cells. SR-B1 is subject to posttranslational regulation; however, the underlying mechanisms still remain obscure. Here, we identified a novel SR-B1-interacting protein, GIPC1 (GAIP-interacting protein, C terminus 1) that interacts with SR-B1 and stabilizes SR-B1 by negative regulation of its proteasomal and lysosomal degradation pathways.

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  • The study investigates the gut microbiota of the native Chinese three-keeled pond turtle and the invasive red-eared slider turtle, both raised under the same farm conditions, to understand the microbial differences that may affect their success as species.
  • Both species predominantly host Bacteroidetes and Firmicutes, with differences in the abundance of specific microbe families; the three-keeled pond turtle has a higher presence of Bacteroidaceae and Clostridiaceae, while the red-eared slider has more Porphyromonadaceae and Fusobacteriaceae.
  • The findings indicate that the three-keeled pond turtle may have a greater potential for growth and colonization due to a lower Firmic
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Background: Identifying the factors that contribute to divergence among populations in mate preferences is important for understanding of the manner in which premating reproductive isolation might arise and how this isolation may in turn contribute to the evolutionary process of population divergence. Here, we offered female northern grass lizards () a choice of males between their own population and another four populations to test whether the preferences that females display in the mating trials correlate with phenotypic adaptation to local environments, or to the neutral genetic distance measured by divergence of mitochondrial DNA sequence loci.

Results: Females showed a strong preference for native over foreign males.

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Understanding rates and patterns of change in physiological and climatic-niche variables is of urgent importance as many species are increasingly threatened by rising global temperatures. Here, we broadly test several fundamental hypotheses about physiological and niche evolution for the first time (with appropriate phylogenetic methods), using published data from 2059 vertebrate species. Our main results show that: (i) physiological tolerances to heat evolve more slowly than those to cold, (ii) the hottest climatic-niche temperatures change more slowly than the coldest climatic-niche temperatures, and (iii) physiological tolerances to heat and cold evolve more slowly than the corresponding climatic-niche variables.

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  • Captivity significantly alters the gut microbiota of the northern grass lizard (Takydromus septentrionalis), affecting microbial community structure and diversity.
  • Both wild and captive lizards share dominant microbial phyla (Proteobacteria, Firmicutes, Tenericutes), but differ in specific genera, with Citrobacter prevalent in the wild and Morganella in captivity.
  • Gene function predictions revealed that wild lizards have a greater abundance of certain genes, suggesting that captivity impacts not only microbial diversity but potentially the lizards' nutrient and immune functions.
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Monitor lizards (Varanidae) inhabit both the mainland and islands of all geological types and have diversified into an exceptionally wide range of body sizes, thus providing an ideal model for examining the role of mainland versus island in driving species evolution. Here we use phylogenetic comparative methods to examine whether a link exists between body size-driven diversification and body size-frequency distributions in varanid lizards and to test the hypothesis that island lizards differ from mainland species in evolutionary processes, body size, and life-history traits (offspring number and size). We predict that: 1) since body size drives rapid diversification in groups, a link exists between body size-driven diversification and body size-frequency distributions; 2) because of various environments on island, island species will have higher speciation, extinction, and dispersal rates, compared with mainland species; 3) as a response to stronger intraspecific competition, island species will maximize individual ability associated with body size to outcompete closely-related species, and island species will produce smaller clutches of larger eggs to increase offspring quality.

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We experimentally miniaturized freshly laid eggs of the Chinese cobra (Elapidae) by removing ∼10% and ∼20% of original yolk. We tested if yolk-reduced eggs would produce 1) normal-sized hatchlings with invariant yolk-free body mass (and thus invariant linear size) but dramatically reduced or even completely depleted residual yolk, 2) smaller hatchlings with normal-sized residual yolk but reduced yolk-free body mass, or 3) smaller hatchlings of which both yolk-free body mass and residual yolk are proportionally reduced. Yolk quantity affected hatchling linear size (both snout-vent length and tail length) and body mass.

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Background: The oviparity-viviparity transition is a major evolutionary event, likely altering the reproductive process of the organisms involved. Residual yolk, a portion of yolk remaining unutilized at hatching or birth as parental investment in care, has been investigated in many oviparous amniotes but remained largely unknown in viviparous species. Here, we used data from 20 (12 oviparous and 8 viviparous) species of snakes to see if the oviparity-viviparity transition alters the partitioning of yolk in embryonic snakes.

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Studies examining the effects of incubation temperature fluctuation on the phenotype of hatchling reptiles have shown species variation. To examine whether incubation temperature fluctuation has a key role in influencing the phenotype of hatchling Chinese skinks (Plestiodon chinensis), we incubated eggs produced by 20 females under five thermal regimes (treatments). Eggs in three treatments were incubated in three incubators, one set constant at 27°C and two ramp-programmed at 27 ± 3°C and 27 ± 5°C on a cycle of 12h (+) and 12h (-).

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The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis.

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