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The genus Blepharisma (Alveolata, Ciliophora) is a unicellular organism distributed worldwide, even in extreme environments, and comprises numerous species. While usually proliferating through cell division, Blepharisma undergoes sexual reproduction (conjugation) when cells are moderately starved. Conjugation is initiated by mating pheromones (gamone 1 and gamone 2) secreted by complementary mating-type cells. Gamone 1, a glycoprotein, functions in a species-specific manner, while gamone 2, an amino acid derivative, is a common molecule across species. The specific function of gamone 1 suggests the possibility that mutations in gamone 1 might have led to reproductive isolation during the evolutionary process, triggering species diversification. In this study, by comparing the amino acid sequences of gamone 1 homologs from 15 strains (representing five species), we found that mutations resulting in distinct amino acid properties occur across species boundaries and are mainly concentrated at two specific regions within gamone 1. These mutations potentially alter the binding affinity of gamone 1 to its receptors, suggesting their effect in causing reproductive isolation. The interspecies artificial conjugation conducted previously and the molecular phylogenetic tree constructed using the gamone 1 homolog sequences in this study provide insights into the speciation process within the genus Blepharisma. [ABSTRACT FROM AUTHOR]

Simple Summary: The host plants and the symbiotic relationship between bacteria and herbivorous insects play important roles in the population differentiation of phytophagous insects. However, current studies have paid limited attention to the connection between host-related differentiation and symbiotic bacterial communities in phytophagous insects. This study constructed phylogenetic trees using 58 Aphis odinae samples collected from different host plants and analyzed the symbiotic bacterial communities of samples from five commonly occurring host plants. The results indicate a partial correlation between differentiation related to host plants and the symbiotic bacterial communities in A. odinae, providing insights into the microevolutionary process between bacterial symbionts and insects. Host plants play a vital role in insect population differentiation, while symbiotic associations between bacteria and insects are ubiquitous in nature. However, existing studies have given limited attention to the connection between host-related differentiation and symbiotic bacterial communities in phytophagous insects. In this study, we collected 58 samples of Aphis odinae from different host plants in southern China and constructed phylogenetic trees to investigate their differentiation in relation to host plants. We also selected aphid samples from the five most preferred host plants and analyzed their symbiotic bacterial composition using Illumina sequencing of the V3–V4 hypervariable region of the 16S rRNA gene. The phylogeny and symbiotic bacterial community structure of A. odinae populations on different host plants showed that samples from Triadica sebifera (Euphorbiaceae) had a consistent presence of Wolbachia as the predominant secondary symbiont and suggested the possibility of undergoing differentiation. Conversely, although differentiation was observed in samples from Rhus chinensis (Anacardiaceae), no consistent presence of predominant secondary symbionts was found. Additionally, the samples from Heptapleurum heptaphyllum (Araliaceae) consistently carried Serratia, but no host differentiation was evident. In summary, this study reveals a partial correspondence between symbiotic bacterial communities and host-related differentiation in A. odinae. The findings contribute to our understanding of the microevolutionary influencing the macroevolutionary relationships between bacterial symbionts and phytophagous insects. The identification of specific symbionts associated with host-related differentiation provides valuable insights into the intricate dynamics of insect-bacteria interactions. [ABSTRACT FROM AUTHOR]

This study aimed to characterize the intestinal microbiota of wild thick-lipped grey mullets (Chelon labrosus) and explore its potential functionality on the host. Intestinal contents of anterior and posterior sections from wild fish were collected and DNA was extracted. Subsequently, the V3–V4 regions of 16S rRNA were sequenced using the Illumina technology and results were analyzed by bioinformatics pipeline. The functional profile of the microbial community was analyzed using PICRUSt software. Shannon and Simpson diversity indices were significantly higher in the posterior section of wild specimens. The overall taxonomic composition suggests a certain homogeneity in the anterior section of the intestine and heterogeneity in the posterior section. Due to this, no statistical differences were detected at any level among both intestinal sections. Predicted functions of intestinal microbiota showed the most abundant were those related to amino acid metabolism, carbohydrate metabolism, energy metabolism, membrane transport, and cell replication and repair. Furthermore, the analysis revealed microbial functional genes related to the elimination of environmental toxins. [ABSTRACT FROM AUTHOR]

Simple Summary: The aquaculture sector must be well-founded to undergo robust growth and sustainable development in the years ahead. Species diversity must reflect species compatibility and complementarity to manage the complexity in polyculture systems. There is a need for the implementation of innovative strategies that facilitate sustainable aquaculture development, enhance profitability, improve resilience, and support conservation and environmental protection. An aquaculture development scenario must look beyond the economic profitability and strategize aquatic food production systems to attain food and nutrition security and benefits for all stakeholders. Intensified agrochemical-based monoculture systems worldwide are under adoption to meet the challenge of human population growth and the ever-growing global demand for food. However, this path has been opposed and criticized because it involves overexploitation of land, monoculture of few species, excessive input of agrochemicals, and adverse impacts on human health and the environment. The wide diversity among polyculture systems practiced across the globe has created confusion over the priority of a single strategy towards sustainable aquaculture development and safer products. Herein, we highlight the significance of polyculture and integrated aquaculture practices in conveying the successful transition of the aquaculture industry towards sustainable development. So far, the established thought is that the precise selection of aquatic species and a focus on compatible and complementary species combinations are supposed to facilitate rapid progress in food production with more profitability and sustainability. Therefore, the advantages of species diversification are discussed from an ecological perspective to enforce aquaculture expansion. This account asserts that a diverse range of aquaculture practices can promote synergies among farmed species, enhance system resilience, enable conservation, decrease ecological footprints, and provide social benefits such as diversified income and local food security. [ABSTRACT FROM AUTHOR]

Sanghuangporus is a medicinal macrofungal genus typified by S. sanghuang, the very species utilized in traditional Chinese medicines by Chinese ancient people. To facilitate the medicinal application of S. sanghuang, we, for the first time, perform its genome sequencing and analyses from a monokaryon strain. A 33.34 Mb genome sequence was assembled to 26 contigs, which lead to the prediction of 8278 protein-coding genes. From these genes, the potential biosynthesis pathway of sesquiterpenoids was, for the first time, identified from Sanghuangporus, besides that of triterpenoids. While polysaccharides are the main medicinal metabolites in S. sanghuang, flavonoids are especially abundant medicinal metabolites comparing with other medicinal macrofungal groups. From the genomic perspective, S. sanghuang has a tetrapolar heterothallic mating system, and has its special nutritional strategy and advantageous medicinal properties compared with S. baumii and S. vaninii. A phylogenomics analysis indicates that Sanghuangporus emerged 15.39 million years ago and S. sanghuang has a closer phylogenetic relationship with S. baumii than S. vaninii. However, S. sanghuang shares a higher region of synteny and more orthologous genes, including carbohydrate-active enzymes with S. vaninii than S. baumii. A comparative genomics analysis with S. baumii and S. vaninii indicates that species diversification within Sanghuangporus may be driven by the translocation and translocation plus inversion of genome sequences, while the expansion and contraction of gene families may contribute to the host specificity of Sanghuangporus species. In general, the genome sequence of S. sanghuang provides insights into its medicinal application and evolution. [ABSTRACT FROM AUTHOR]

This paper outlines a thermodynamic theory of biological evolution. Beginning with a brief summary of the parallel histories of the modern evolutionary synthesis and thermodynamics, we use four physical laws and processes (the first and second laws of thermodynamics, diffusion and the maximum entropy production principle) to frame the theory. Given that open systems such as ecosystems will move towards maximizing dispersal of energy, we expect biological diversity to increase towards a level, Dmax, representing maximum entropic production (Smax). Based on this theory, we develop a mathematical model to predict diversity over the last 500 million years. This model combines diversification, post-extinction recovery and likelihood of discovery of the fossil record. We compare the output of this model with that of the observed fossil record. The model predicts that life diffuses into available energetic space (ecospace) towards a dynamic equilibrium, driven by increasing entropy within the genetic material. This dynamic equilibrium is punctured by extinction events, which are followed by restoration of Dmax through diffusion into available ecospace. Finally we compare and contrast our thermodynamic theory with the MES in relation to a number of important characteristics of evolution (progress, evolutionary tempo, form versus function, biosphere architecture, competition and fitness). [ABSTRACT FROM AUTHOR]

Simple Summary: Aristidoideae is a subfamily of Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences and eight non-coding sequences. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of the three genera. Within Aristidoideae, Aristida is sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae. Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae. [ABSTRACT FROM AUTHOR]