Background The range of body sizes in Carnivora is unparalleled in any other mammalian order—the heaviest species is 130,000 times heavier than the lightest and the longest species is 50 times longer than the shortest. However, the molecular mechanisms underlying these huge differences in body size have not been explored. Results Herein, we performed a comparative genomics analysis of 20 carnivores to explore the evolutionary basis of the order’s great variations in body size. Phylogenetic generalized least squares (PGLS) revealed that 337 genes were significantly related to both head body length and body mass; these genes were defined as body size associated genes (BSAGs). Fourteen positively-related BSAGs were found to be associated with obesity, and three of these were under rapid evolution in the extremely large carnivores, suggesting that these obesity-related BSAGs might have driven the body size expansion in carnivores. Interestingly, 100 BSAGs were statistically significantly enriched in cancer control in carnivores, and 15 of which were found to be under rapid evolution in extremely large carnivores. These results suggested that large carnivores might have evolved an effective mechanism to resist cancer, which could be regarded as molecular evidence to support Peto’s paradox. For small carnivores, we identified 15 rapidly evolving genes and found six genes with fixed amino acid changes that were reported to reduce body size. Conclusions This study brings new insights into the molecular mechanisms that drove the diversifying evolution of body size in carnivores, and provides new target genes for exploring the mysteries of body size evolution in mammals.
The epidermis plays an indispensable barrier function in animals. Some species have evolved unique epidermal structures to adapt to different environments. Aquatic and semi‐aquatic mammals (cetaceans, manatees, and hippopotamus) are good models to study the evolution of epidermal structures because of their exceptionally thickened stratum spinosum, the lack of stratum granulosum, and the parakeratotic stratum corneum. This study aimed to analyze an upstream regulatory gene transient receptor potential cation channel, subfamily V, member 3 (TRPV3) of epidermal differentiation so as to explore the association between TRPV3 evolution and epidermal changes in mammals. Inactivating mutations were detected in almost all the aquatic cetaceans and several terrestrial mammals. Relaxed selective pressure was examined in the cetacean lineages with inactivated TRPV3, which might contribute to its exceptionally thickened stratum spinosum as the significant thickening of stratum spinosum in TRPV3 knock‐out mouse. However, functional TRPV3 may exist in several terrestrial mammals due to their strong purifying selection, although they have “inactivating mutations.” Further, for intact sequences, relaxed selective constraints on the TRPV3 gene were also detected in aquatic cetaceans, manatees, and semi‐aquatic hippopotamus. However, they had intact TRPV3, suggesting that the accumulation of inactivating mutations might have lagged behind the relaxed selective pressure. The results of this study revealed the decay of TRPV3 being the genomic trace of epidermal development in aquatic and semi‐aquatic mammals. They provided insights into convergently evolutionary changes of epidermal structures during the transition from the terrestrial to the aquatic environment.
Background Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cryptorchids. However, the evolution of testicular position and the molecular mechanisms underlying the maintenance of health, including reproductive health, in ascrotal mammals are not clear. Results In the present study, comparative genomics and evolutionary analyses revealed that genes associated with the extracellular matrix and muscle, contributing to the development of the gubernaculum, were involved in the evolution of testicular position in mammals. Moreover, genes related to testicular position were significantly associated with spermatogenesis and sperm fertility. These genes showed rapid evolution and the signature of positive selection, with specific substitutions in ascrotal mammals. Genes associated with testicular position were significantly enriched in functions and pathways related to cancer, DNA repair, DNA replication, and autophagy. Conclusions Our results revealed that alterations in gubernaculum development contributed to the evolution of testicular position in mammals and provided the first support for two hypotheses for variation in testicular position in mammals, the “cooling hypothesis”, which proposes that the scrotum provides a cool environment for acutely heat-sensitive sperm and the “training hypothesis”, which proposes that the scrotum develops the sperm by exposing them to an exterior environment. Further, we identified cancer resistance and DNA repair as potential protective mechanisms in natural cryptorchids. These findings provide general insights into cryptorchidism and have implications for health and infertility both in humans and domestic mammals.
This research estimated Chinese rural residents' willingness to pay for rural solid wastes recycling project. Dichotomous choice format contingent valuation method was employed to diverse rural residents' preference. 4795 Households had been interviewed for collecting primary data, and had been estimated respondents' will by logistic regression model. It indicated that the respondents would refuse to support solid wastes recycling project due to households' income restriction. The mean annual WTP of rural residents were 23.41 Chinese Yuan per household. In conclusion the rural solid wastes recycling project is acceptable and accessible for implementation in Chinese rural area.
DNA damage response (DDR) is a complicated network to defend against physical or chemical changes in DNA in all animals. Elevated levels of ultraviolet radiation (UVR) caused DNA damage, which was a reason for the mass extinction that occurred at the Devonian/Carboniferous (D/C) boundary approximately 359 million years ago (Ma). However, the molecular adaptation of the stony coral ancestors that strangely survived the D/C boundary mass extinction is not well understood. In the present study, the molecular clock analysis using fourfold degenerate sites of 1,463 homologous genes of different stony coral species (a representative group of marine organisms with calcareous skeletons) suggested that their common ancestors originated 384.24 Ma, i.e., slightly earlier than the D/C transition. We identified 21 rapidly evolving genes (REGs) and 49 positive selection genes (PSGs) that were significantly enriched in diverse pathways, including the mitotic cell cycle process, intracellular protein transport, and DNA synthesis involved in DNA repair. Interestingly, four REGs and 21 PSGs were significantly enriched in DDR pathways, including the mitotic cell cycle process, DNA synthesis involved in DNA repair, and cellular response to DNA damage stimulus pathways. We hypothesize that enriched DDR genes are likely involved in the enhanced ability of ancient stony corals to detect and repair DNA damage. For example, the DNA polymerase epsilon catalytic subunit (POLE) gene, which encodes the DNA polymerase epsilon catalytic subunit A, mediates interaction with the other three catalytic subunits through its nonenzymatic carboxy-terminal domain. POLE may potentially enhance the binding ability to other subunits to strengthen its function because eight positive selection sites were distributed in the C-terminal of POLE and on the surface of the simulated 3D protein model. Therefore, our results demonstrated for the first time that the precise transfer of DNA information may help stony coral ancestors survive in elevated levels of ultraviolet radiation, suggesting that DDR levels may be critical to the environmental adaptation of calcareous skeletal organisms during climate change.
Foraminifera are sensitive to climate change and their species composition, shell chemical element composition and morphological characteristics are useful paleoenvironmental proxies. Coiling direction is a distinctive and easily identifiable morphological feature in trochospiral foraminifera and has been used for paleoceanographic reconstruction. Here, we conducted a field survey in a low intertidal zone in Yellow Sea for 13 months and performed a culture experiment under three temperatures and four salinities for the benthic foraminifera to seek the relationship between coiling direction and environmental factors. Our results showed that the dominant benthic foraminifera Ammonia aomoriensis (Asano, 1951) preferred sinistral direction under high temperature and had no preference with salinity. Statistical analysis showed that the ratio of sinistral/dextral in A. aomoriensis was significantly positively correlated with temperature (r = 0.5017, p = 0.0011 for field survey and r = 0.5117, p = 0.0014 for culture experiment), but had no evident relationship with salinity (p > 0.05). The ratio of sinistral/dextral was significantly negatively related with the abundance of A. aomoriensis (p < 0.05) and the ratio of sinistral/dextral was significantly positively related with the size (p < 0.05). This was the first study on the coiling direction of benthic foraminifera combining the field survey and culture experiment. Our findings suggested that the ratio of sinistral/dextral in A. aomoriensis could be used to indicate the change of temperature. This study offered new evidence for the reliability of the coiling direction as a temperature proxy and made us rethink the significance of the morphological change in biological adaptation and evolution.
Uncoupling protein 1 (UCP1) is an essential protein in the mitochondrial inner membrane that mediates non-shivering thermogenesis (NST) and plays an important role in thermoregulation and fat deposition. However, the relationship between the evolution of the UCP1 and fat deposition in the blubber layer in cetaceans remains unclear. Here, frameshift mutations, premature termination, and relaxed selection pressure (ω = 0.9557, p < 0.05) were detected in the UCP1 in cetaceans, suggesting that UCP1 was inactivated during cetacean evolution. Time estimate found that the inactivation of the UCP1 in cetaceans occurred between 53.1 and 50.2 million years ago. However, combined with findings from immunohistochemical analysis of the blubber layer of the Yangtze finless porpoise and in vitro functional assays, premature termination of cetacean UCP1 resulted in a reduction of UCP1-mediated NST capacity (about 50%) and lipolytic capacity (about 40%), both of which was beneficial to maintain blubber layer and body temperature without excessive fat consumption. This study provides new insights into the molecular mechanisms of the blubber thickening in cetaceans and highlights the importance of UCP1 attenuation in cetaceans for secondary aquatic adaptation.
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