The Gobiidae family occupy one of the most diverse habitat ranges of all fishes. One key reason for their successful colonization of different habitats is their ability to adapt to different energy ...demands. This energy requirement is related to the ability of mitochondria in cells to generate energy via oxidative phosphorylation (OXPHOS). Here, we assembled three complete mitochondrial genomes of Rhinogobius shennongensis, Rhinogobius wuyanlingensis, and Chaenogobius annularis. These mitogenomes are circular and include 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region (CR). We used comparative mitochondrial DNA (mtDNA) genome and selection pressure analyses to explore the structure and evolutionary rates of Gobiidae mitogenomics in different environments. The CmC model showed that the ω ratios of all mtDNA PCGs were <1, and that the evolutionary rate of adenosine triphosphate 8 (atp8) was faster in Gobiidae than in other mitochondrial DNA PCGs. We also found evidence of positive selection for several sites of NADH dehydrogenase (nd) 6 and atp8 genes. Thus, divergent mechanisms appear to underlie the evolution of mtDNA PCGs, which might explain the ability of Gobiidae to adapt to diverse environments. Our study provides new insights on the adaptive evolution of Gobiidae mtDNA genome and molecular mechanisms of OXPHOS.
Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and ...fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.
The gut microbiome can help the host adapt to a variety of environments and is affected by many factors. Marine carnivores have unique habitats in extreme environments. The question of whether marine ...habitats surpass phylogeny to drive the convergent evolution of the gut microbiome in marine carnivores remains unanswered. In the present study, we compared the gut microbiomes of 16 species from different habitats. Principal component analysis (PCA) and principal coordinate analysis (PCoA) separated three groups according to their gut microbiomes: marine carnivores, terrestrial carnivores, and terrestrial herbivores. The alpha diversity and niche breadth of the gut microbiome of marine carnivores were lower than those of the gut microbiome of terrestrial carnivores and terrestrial herbivores. The gut microbiome of marine carnivores harbored many marine microbiotas, including those belonging to the phyla Planctomycetes, Cyanobacteria, and Proteobacteria, and the genus Peptoclostridium. Collectively, these results revealed that marine habitats drive the convergent evolution of the gut microbiome of marine carnivores. This study provides a new perspective on the adaptive evolution of marine carnivores.
To date, the question of whether marine habitats surpass phylogeny to drive the convergent evolution of the gut microbiome in marine carnivores has not been answered. Thus, in the present study, we investigated and compared the published gut microbiome data (16S rRNA) of four marine carnivores, five terrestrial carnivores, and seven terrestrial herbivores. Our findings proved our hypothesis that marine habitats drive the convergent evolution of the gut microbiome of marine mammals.
Toll-like receptors (TLRs) encoded by the TLR multigene family play an important role in initial pathogen recognition in vertebrates. Among the TLRs, TLR2 and TLR4 may be of particular importance to ...reptiles. In order to study the evolutionary patterns and structural characteristics of TLRs, we explored the available genomes of several representative members of reptiles. 25 TLR2 genes and 19 TLR4 genes from reptiles were obtained in this study. Phylogenetic results showed that the TLR2 gene duplication occurred in several species. Evolutionary analysis by at least two methods identified 30 and 13 common positively selected codons in TLR2 and TLR4, respectively. Most positively selected sites of TLR2 and TLR4 were located in the Leucine-rich repeat (LRRs). Branch model analysis showed that TLR2 genes were under different evolutionary forces in reptiles, while the TLR4 genes showed no significant selection pressure. The different evolutionary adaptation of TLR2 and TLR4 among the reptiles might be due to their different function in recognizing bacteria. Overall, we explored the structure and evolution of TLR2 and TLR4 genes in reptiles for the first time. Our study revealed valuable information regarding TLR2 and TLR4 in reptiles, and provided novel insights into the conservation concern of natural populations.
Detection of epistatic interactions, which are referred to as nonlinear interactive effects of single nucleotide polymorphisms (SNPs), is increasingly being recognized as an important route in ...capturing the underlying genetic causes of complex diseases. Its methodological and computational challenges have been well understood, and many methods also have been proposed from different perspectives. Among them ant colony optimization (ACO)-based methods are promising due to their controllable time complexities, heuristic positive feedback search, and high detection power. Nevertheless, there is no comprehensive overview of them so far. This paper, therefore, provides a systematic review of 25 ACO-based epistasis detection methods. First, the generic ACO algorithm, as well as how it is applied to detect epistatic interactions, is briefly described. Then, an in-depth review of ACO-based methods for detecting epistatic interactions is discussed from four aspects, including path selection strategies, pheromone updating rules, fitness functions, and two-stage designs. Finally, this paper analyzes the strengths and limitations of involved methods, provides guidelines for applying them, and gives several views on the future directions of epistasis detection methods.
P. brasiliensis and L. canadensis are two otter species, which successfully occupied semi-aquatic habitats and diverged from other Mustelidae. Herein, the full-length mitochondrial genome sequences ...were constructed for these two otter species for the first time. Comparative mitochondrial genome, selection pressure, and phylogenetic independent contrasts (PICs) analyses were conducted to determine the structure and evolutionary characteristics of their mitochondrial genomes. Phylogenetic analyses were also conducted to confirm these two otter species’ phylogenetic position. The results demonstrated that the mitochondrial genome structure of P. brasiliensis and L. canadensis were consistent across Mustelidae. However, selection pressure analyses demonstrated that the evolutionary rates of mitochondrial genome protein-coding genes (PCGs) ND1, ND4, and ND4L were higher in otters than in terrestrial Mustelidae, whereas the evolutionary rates of ND2, ND6, and COX1 were lower in otters. Additionally, PIC analysis demonstrated that the evolutionary rates of ND2, ND4, and ND4L markedly correlated with a niche type. Phylogenetic analysis showed that P. brasiliensis is situated at the base of the evolutionary tree of otters, and then L. canadensis diverged from it. This study suggests a divergent evolutionary pattern of Mustelidae mitochondrial genome PCGs, prompting the otters’ adaptation to semi-aquatic habitats.
Although lake dunes are widespread in drylands, their formation, influenced by complex aeolian-fluvial interactions, remains unclear. This study focuses on the dunes around Cuona Lake on the ...Qinghai-Tibetan Plateau. By combining wind simulation and flow calculation with physical and chemical analyses of the sediments (grain size parameter statistics, elemental composition), we infer the processes of lake dune formation in this semi-arid intramontane basin. Meteorological data were used to resolve the temporal variations in wind and precipitation, and sediment transport pathways were identified from simulations based on wind and topographic data. Grain size and elemental analyses of sediment samples were used to characterize the physical and chemical composition of the Cuona Lake Basin dunes and related sediments. Our results show that dune formation in the Cuona Lake Basin occurs under the alternating control of wind and water processes. Dunes form mainly from sediment transported from the lake beach by westerly winds in the winter and spring; rivers flowing in the opposite direction (eastward) in the summer transport dune sand back to the lake beach. This process accounts for the recycling of sand in the landscape. This spatiotemporal coupling between hydrodynamic and wind transport pathways provides a continuous sediment supply for dune formation around the lake.
Livestock husbandry is a key indicator of economic development, environmental protection, and food security in the world, which is vulnerable to environmental changes and economic shocks. In our ...study on Kyrgyzstan, we quantified the effects of socio-economic and environmental factors on the dynamics of livestock sales, self-consumption, and inventory from 2006 to 2020 using a two-period livestock production model and spatial panel model. The results showed that from 2006 to 2020, more than 50% livestock were stocked annually, which means that herders in Kyrgyzstan preferred to preserve their animals as assets to deal with unknown risks. Additionally, to gain greater profit, Kyrgyz herdsmen would expand or downsize their livestock business, tailor self-consumption, and manage inventory based on the livestock market price, loan on livestock, non-herding income, and its current stock. Our study found that the development of animal husbandry in seven oblasts of Kyrgyzstan had spatial spillover effects, which indicated that the dynamics of the animal husbandry market and environment not only affected the scale of local animal husbandry but also had an important impact on adjacent oblasts. Our research contributes to ensuring the income for herdsmen and the sustainable development of animal husbandry, thereby promoting high-quality economic development in developing countries with animal husbandry as a pillar industry.
The geological transitional period from the Marine Isotope Stage (MIS) 5 to 4 during the Quaternary period is a multidimensional change involving monsoon and precipitation variation, vegetation ...dynamics, and environmental evolution. The first loess layer (L1) and the first paleosol layer (S1) in the Chines Loess Plateau provide excellent high-resolution terrestrial sediment record for this transition. In this work, grain size (GS), CaCO3 content, magnetic susceptibility (MS), and pollen composition were measured at intervals of 2-cm in two representative L1/S1 profiles in the southern Chinese Loess Plateau to reconstruct records of climatic and vegetative changes during this transition. Our results showed that, in general, the paleo-vegetation type was forest-steppe, with Pinus being the commonest tree, and Chenopodiaceae and Artemisia being common herbs in the study area. The topography had a significant impact on the distribution of paleo-vegetation. The increase of coarse particles, the decrease of magnetic susceptibility, and the rising percentage of Gramineae, Artemisia and Chenopodiaceae pollen, all indicated that the paleoclimate became cooler and drier over the transitional period. Besides, we identified a cool event at about 76.8 ka B.P. as revealed by grain-size curves, and in response to this event, the vegetation changed significantly but lagged several hundred years behind the grain size record. This study confirmed the cooling and drying tendency during the MIS 5 to 4 transition phase in the southern margin of the Chinese Loess Plateau. These findings shed light on the climatic change on vegetation evolution during the MIS 5 to 4 transition period.
The gastrointestinal tract of animals contains microbiota, forming a complex microecosystem. Gut microbes and their metabolites can regulate the development of host innate and adaptive immune ...systems. Animal immune systems maintain intestinal symbiotic microbiota homeostasis. However, relatively few studies have been published on reptiles, particularly snakes, and even fewer studies on different parts of the digestive tracts of these animals. Herein, we used 16S rRNA gene sequencing to investigate the microbial community composition and adaptability in the stomach and small and large intestines of
Proteobacteria, Bacteroidetes, and Firmicutes were most abundant in the stomach; Fusobacteria in the small intestine; and Proteobacteria, Bacteroidetes, Fusobacteria, and Firmicutes in the large intestine. No dominant genus could be identified in the stomach; however, dominant genera were evident in the small and large intestines. The microbial diversity index was significantly higher in the stomach than in the small and large intestines. Moreover, the influence of the microbial community structure on function was clarified through function prediction. Collectively, the gut microbes in the different segments of the digestive tract revealed the unique features of the
gut microbiome. Our results provide insights into the co-evolutionary relationship between reptile gut microbiota and their hosts.
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