Search Results (16)

The cause of the Cambrian explosion is one of the centuries-old puzzles. For centuries, scholars from numerous disciplines have proposed various theories based on evidence such as paleontological fossils and changes in geology and climate to try to reveal the cause of the Cambrian explosion, but no satisfactory conclusion has been reached. We explored a possible cause of the Cambrian explosion based on the evolution mechanism of genome sequences of existing species. Previous studies have found that the CG- and TA-independent selection intensities and the mutual inhibition relationship between them determine the evolution state of genome sequences. Based on the evolution mechanism of genome sequences, we analyzed the distribution of CG- and TA-independent selection intensities in animals and plants. We believed that the phase transition process from the evolution mode dominated by TA-independent selection to that dominated by CG-independent selection is an important cause of the Cambrian explosion. Consequently, we deduced the evolution time corresponding to the evolution state of genome sequences and gave the origin time of species branches. The results are largely consistent with existing paleontological evidence for animal branches and some plant branches, which verifies the rationality of our conjecture, though differences for certain plant groups require further investigation. Our study provides a novel way to reveal the cause of the Cambrian explosion and the origin time of species branches through existing genome sequences. Full article

Tusavirus 1 of species Protoparvovirus incertum 1 (family Parvoviridae) was first identified in humans and later in small ruminants (caprine and ovine). This study reports the full-length coding sequences (~4400–4600 nt) of three novel tusavirus-related protoparvoviruses from ovine (“misavirus”, PV540792), for the first time bovine (“sisavirus”, PV540793) and subsequently from caprine (“gisavirus” PV540850/51) fecal samples, using next-generation sequencing (NGS) and PCR techniques. Their NS1, VP1 and VP2 proteins shared 61–63% amino acid identities with each other and with tusaviruses, suggesting these three viruses belong to three novel species in the genus Protoparvovirus. Phylogenetic analyses placed them with tusaviruses on a separate main branch, implying a shared origin among these most likely ruminant protoparvoviruses. A small-scale epidemiological investigation on 318 ruminant enteric samples using novel generic NS1 primers found misavirus in 14/51 (27.5%) ovine and sisavirus in 19/203 (9.4%) bovine samples from multiple Hungarian farms. Tusavirus was present in 5/51 (9.8%) ovine and 15/62 (24.2%) caprine samples, all from one farm. The highest prevalences for all three viruses were found in animals aged 2–12 months, though sporadic cases were also found in other age groups. Partial NS and VP sequence-based phylogenetic trees showed virus-specific lineages for misa-, sisa-, gisa- and tusaviruses, with various strains forming sub-lineages. These findings suggest the presence of multiple genotypes and/or members of additional species, which was supported by a VP sequence-based hierarchical cluster analysis. The study’s viruses were mostly phylogenetically separated by host; however, two bovine sisavirus strains with diverse phylogenetic localizations in the NS (belonging to bovine sisaviruses) and VP1 trees (distantly related to ovine misaviruses) could indicate previous (interspecies?) recombination events. Full article

A new method of macroevolutionary analysis—high-resolution phylogenetics, integrating both morphological and molecular traits—has revealed well-supported evidence of complexity-based processes generating and controlling biodiversity. A novel technique of using evolutionary rates following a strict morphological clock, at least approximately, may allow detailed information on speciation and extinction events across geologic time. Branching series of minimally monophyletic genera are used to characterize in detail the branching lineage of the widely distributed moss family Streptotrichaceae. A strict morphological clock is calibrated by timing of genera new to recently exposed islands, molecular scaling against fossil taxa, and fossil evidence of the origin of the modern bryoflora. The numbers of genera generated in each 22-million-year interval are similar, while only one genus is inferred as extinct. The general outline of the phylogeny is tadpole-shaped because cumulative extinction is less than cumulative speciation, thus sustaining the family over vast time spans. Extant species per genus increase significantly over time, not through the proliferation of secondary descendants (i.e., more than four species per ancestral node), but through the selective preservation of lineages via extinction. Ancient traits are preserved throughout the lineage. It is hypothesized that descendant species are protected from coeval competition through bursts of speciation. This study supports a complexity-based explanation of the interaction of major evolutionary processes resulting in sustainability. Full article

Krameropteris is an extinct fern genus found in mid-Cretaceous Myanmar amber, assigned to the Dennstaedtiaceae, with only one previously described species, i.e., K. resinatus. This study describes a new species, K. calophyllum, also preserved in Myanmar amber. The new species is characterized by branched venation with free veinlets terminating in thickened tips, multicellular hairs along the pinnule margins, and submarginal or medial exindusiate sori at the ends of veinlets. Its sporangia are polypod-type, producing trilete spores. This new species represents the second record of an extinct fern genus of the early-diverging Dennstaedtiaceae lineage found in Myanmar amber. Krameropteris calophyllum differs from K. resinatus in its pinnule epidermal characteristics and spore morphology, with the latter exhibiting a conspicuously ornamented perine, covered with sparse tubercles and ridges. The new species provides insights into potential herbivory interactions and the relationship between mid-Cretaceous polypod ferns and the smallest mite ever recorded. These findings suggest that Dennstaedtiaceae exhibited species-level diversity by the mid-Cretaceous, indicating an earlier origin of the family, potentially as early as the Early Jurassic, consistent with recent DNA-based time divergence estimates. Full article

Stick and leaf insects are a group among the Insecta that are famous for their extraordinary mimicry ability. Since the establishment of the Phasmatodea, their internal classification has been constantly revised. Mitochondrial genes as molecular markers have been widely used for species classification, but the phylogenetic relationships within the Phasmatodea remain to be thoroughly discussed. In the present study, five mitogenomes of Phasmatodea ranging from 15,746 bp to 16,747 bp in length were sequenced. Bayesian inference (BI) and maximum likelihood (ML) analyses were carried out based on a 13 PCGs data matrix (nt123) and a combined matrix of 13 PCGs and two rRNA genes (nt123_rRNA). The present study supports the conclusion that Phylliidae was the basal group of Neophasmatodea and confirms the monophyly of Lonchodinae and Necrosciinae, but it shows that Lonchodidae was polyphyletic. A sister group of Bacillidae and Pseudophasmatidae was also recovered. The phylogenetic tree based on the nt_123 dataset showed higher node support values. The construction of a divergent time tree in this study supported the conclusion that extant Phasmatodea originated in the Jurassic (170 Mya) and most lineages diverged after the Cretaceous–Paleogene extinction event. To explore whether the mitochondrial genes of Phraortes liaoningensis collected from high latitudes where low temperatures occur for eight months of the year are under selection pressure, this study used the branch-site model and the branch model to analyze the selection pressure on the 13 mitochondria protein-coding genes (PCGs). We found that both ND2 and ND4L of Ph. liaoningensis exhibited positive selection sites using the branch-site model. This study shows that a low-temperature environment causes mitochondrial genes to be selected to meet the energy requirements for survival. Full article

Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism’s energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed. Full article

The potato is one of the most important food crops in the world. Improving the efficiency of potato breeding is of great importance for solving the global food problem. Today, researchers distinguish between six potato cytoplasm types: A, M, P, T, W, D. In the current study, the complete chloroplast genomes of Solanum tuberosum accessions with five out of the six major cytoplasmic genome types were sequenced (T-, W-, D-, A-, and P-genomes). A comparative analysis of the plastomes in potato accessions with different cytoplasm types was carried out for the first time. The time of origin of the different cytoplasm types was estimated. The presence of two main groups of chloroplast genomes among cultivated potato was confirmed. Based on the phylogenetic analysis of the complete plastome sequences, five main evolutionary branches of chloroplast genomes can be distinguished within the Petota section. Samples with A- and P- cytoplasm formed isolated and distant groups within a large and polymorphic group of samples with M-type cytoplasm, suggesting that A and P genomes arose independently. The findings suggest that the diversity of the T-genome in S. tuberosum Group Tuberosum could be initially low due to a bottle neck already existing at the origin of the Chilean clade. Differences in the rbcL gene sequence may be one of the factors causing differences in economically important traits in species with A and T-type cytoplasm. The data obtained will contribute to the development of methods for molecular marking of cytoplasm types and increase knowledge about the evolution and diversity of potato. Full article

Schisandra chinensis (Turcz.) Baill. is an important medicinal plant in northeast China. Cutting propagation is an effective method for the rapid propagation of many tree species. This research aimed to determine a suitable growing medium and appropriate root hormone type, concentration and treatment time through the utilization of different substrates and hormones to treat one-year-old branches of S. chinensis. The optimal treatment achieved a rooting rate of 60% with 225 ppm ABT and 75 ppm NAA for 2.5 h. The substrate of vermiculite/perlite = 1:1 (urea+potassium) was beneficial to the adventitious root formation, which reached 79%. The adventitious root primordium of S. chinensis originated from the junction of the xylem and cambium. ABT and NAA treatments altered the peak timing of POD, PPO and IAAO in S. chinensis cuttings. During the adventitious root formation of S. chinensis cuttings, the high endogenous IAA concentration promoted the occurrence of adventitious roots in the early stage and the lower endogenous IAA and GA₃ concentrations promoted the elongation and growth of adventitious roots in the later period. Low ABA and ZR concentrations enabled adventitious root formation and elongation. An efficient cutting propagation system would enable the mass propagation of S. chinensis seedlings. Full article

Endodontic and periodontal disease are conditions of infectious origin that can lead to tooth loss or develop into systemic hyperinflammation, which may be associated with a wide variety of diseases, including cardiovascular. Endodontic and periodontal treatment often relies on antibiotics. Since new antimicrobial resistances are a major threat, the use of standard antibiotics is not recommended when the infection is only local. Antimicrobial peptides were recently demonstrated to be valid alternatives for dental treatments. The antimicrobial peptide M33D is a tetrabranched peptide active against Gram-negative and Gram-positive bacteria. It has a long life, unusual for peptides, because its branched form provides resistance to proteases. Here the efficacy of M33D and of its analog M33i/l as antibiotics for local use in dentistry was evaluated. M33D and M33i/l were active against reference strains and multidrug-resistant clinical isolates of Gram-negative and Gram-positive species. Their minimum inhibitory concentration against different strains of dental interest was between 0.4 and 6.0 μM. Both peptides acted rapidly on bacteria, impairing membrane function. They also disrupted biofilm effectively. Disinfection of the root canal is crucial for endodontic treatments. M33D and M33i/l reduced E. faecalis colonies to one-twentieth in a dentin slices model reproducing root canal irrigation. They both captured and neutralized lipopolysaccharide (LPS), a bacterial toxin responsible for inflammation. The release of IL-1β and TNFα by LPS-stimulated murine macrophages was reduced by both peptides. Human cardiac fibroblasts respond to different insults with the release of proinflammatory cytokines, and consequently, they are considered directly involved in atherogenic cardiovascular processes, including those triggered by infections. The presence of M33D and M33i/l at MIC concentration reduced IL6 release from LPS- stimulated human cardiac fibroblasts, hence proving to be promising in preventing bacteria-induced atherogenesis. The two peptides showed low toxicity to mammalian cells, with an EC50 one order of magnitude higher than the average MIC and low hemolytic activity. The development of antimicrobial peptides for dental irrigations and medication is a very promising new field of research that will provide tools to fight dental infections and their severe consequences, while at the same time protecting standard antibiotics from new outbreaks of antimicrobial resistance. Full article

Orchardgrass (Dactylis glomerata L.) is a species in the Gramineae family that is highly important economically and valued for its role in ecology. However, the phylogeny and taxonomy of D. glomerata are still controversial based on current morphological and molecular evidence. The study of chloroplast (cp) genomes has developed into a powerful tool to develop molecular markers for related species and reveal the relationships between plant evolution and phylogenetics. In this study, we conducted comparative genomic analyses and phylogenetic inferences on 14 cp genomes of D. glomerata originating from the Mediterranean and Eurasia. The genome size ranged from 134,375 bp to 134,993 bp and exhibited synteny of gene organization and order. A total of 129–131 genes were identified, including 85–87 protein coding genes, 38 tRNA genes and 8 rRNA genes. The cp sequences were highly conserved, and key sequence variations were detected at the junctions of inverted repeats (IRs)/small single–copy (SSC) regions. Moreover, nine highly variable regions were identified among the subspecies based on a sequence divergence analysis. A total of 285 RNA editing sites were detected that were relevant to 52 genes, where rpoB exhibited the most abundant RNA editing sites. The phylogenetic analysis revealed that all Dactylis subspecies clustered into a monophyletic group and most branches provided a high support bootstrap. The main divergence time of D. glomerata was dated to the Miocene era, and this could have been due to changes in the climate. These findings will provide useful insights for further studies on phylogeny, the identification of subspecies and the development of hypotheses for the evolutionary history of the genus Dactylis and of the Gramineae family. Full article

To further understand the origin and evolution of Patellogastropoda, we determined the mitochondrial genome sequence of Cellana toreuma, and compared its mitogenome characteristics with the other four limpets of Nacellidae. The ratio of Ka and Ks indicated that these Nacellidae species were suffering a purifying selection, with exception of the atp6 gene. The gene sequence is basically consistent among families, while there are great differences among Lottidae species. According to the mitogenome sequences of selected gastropod species, we reconstructed a new phylogenetic tree with two methods. The data complement the mitogenome database of limpets and is a favorable research tool for the phylogenetic analysis of Gastropoda. It is found that there is a long-branch attraction (LBA) artefact in the family Lottiidae of Patellogastropoda. Therefore, the Patellogastropoda was separated by Heterobranchia, and Lottiidae is located at the root of the whole phylogenetic tree. Furthermore, we constructed the divergence time tree according to the Bayesian method and discussed the internal historical dynamics, and divergence differences among the main lineages of 12 Patellogastropoda under an uncorrelated relaxed molecular clock. In turn, we made a more comprehensive discussion on the divergence time of limpets at the molecular level. Full article

Santalum (Santalaceae, sandalwood) is a hemiparasitic genus that includes approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of phylogenetic relationships will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. The Santalum chloroplast genome contains typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 110 unique genes. The whole set of ndh genes and the infA gene were found to lose their functions. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Branch-model-based selection analyses showed that the Santalum species were under widespread purifying selection. Our phylogenomic assessment provides an improved resolution to the phylogenetic relationships of Santalum compared to the past analyses. Our divergence time analysis showed that the crown age of Santalum was 8.46 Mya (million years ago), the first divergence occurred around 6.97 Mya, and diversification was completed approximately 1 Mya. By sequencing the 11 Santalum species chloroplast genomes, we identified the variations in the Santalum chloroplast genomes. Using the chloroplast genome sequences, phylogeny and divergence time analyses discovered that the Santalum species were likely to originate due to radiation evolution, and most speciation events occurred less than 1 Mya. Full article

Branched fatty acid esters of hydroxy fatty acids (FAHFAs) are endogenous lipids reported to have antidiabetic and anti-inflammatory effects. Since skeletal muscle is a major target for insulin, the aim of this study is to explore for the first time the influence of several FAHFAs in C2C12 myoblasts and in skeletal muscle phenotype in mice. Here, we show that eleven FAHFAs belonging to different families inhibit C2C12 myoblast proliferation. In addition, all FAHFAs decreased mitochondrial cytochrome c oxidase activity without affecting reactive oxygen species production and the mitochondrial network. During C2C12 myoblasts differentiation, we found that two of the most active lipids, 9-PAHPA and 9-OAHPA, did not significantly affect the fusion index and the expression of myosin heavy chains. However, we found that three months’ intake of 9-PAHPA or 9-OAHPA in mice increased the expression of more oxidative myosin in skeletal muscle without affecting skeletal muscle mass, number, and mean fiber area, mitochondrial activity, and oxidative stress parameters. In conclusion, our study indicated that the eleven FAHFAs tested decreased the proliferation rate of C2C12 myoblasts, probably through the inhibition of mitochondrial activity. In addition, we found that 9-PAHPA or 9-OAHPA supplementation in mice induced a switch toward a more oxidative contractile phenotype of skeletal muscle. These data suggest that the increase in insulin sensitivity previously described for these two FAHFAs is of muscular origin. Full article

Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium in molecular plant breeding. The aim of this study was the identification of single nucleotide polymorphisms (SNPs) and SilicoDArT markers associated with yield traits and morphological features in maize. Plant material constituted inbred lines. The field experiment with inbred lines was established on 10 m² plots in a set of complete random blocks in three replicates. We observed 22 quantitative traits. Association mapping was performed in this study using a method based on the mixed linear model with the population structure estimated by eigenanalysis (principal component analysis applied to all markers) and modeled by random effects. As a result of mapping, 969 markers (346 SNPs and 623 SilocoDArT) were selected from 49,911 identified polymorphic molecular markers, which were significantly associated with the analyzed morphological features and yield structure traits. Markers associated with five or six traits were selected during further analyses, including SilicoDArT 4591115 (anthocyanin coloration of anthers, length of main axis above the highest lateral branch, cob length, number of grains per cob, weight of fresh grains per cob and weight of fresh grains per cob at 15% moisture), SilicoDArT 7059939 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, time of silk emergence—50% of flowering plants, anthocyanin coloration of anthers and cob diameter), SilicoDArT 5587991 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, anthocyanin coloration of anthers, curvature of lateral branches and number of rows of grain). The two genetic similarity dendrograms between the inbred lines were constructed based on all significant SNPs and SilicoDArT markers. On both dendrograms lines clustered according to the kernel structure (flint, dent) and origin. The selected markers may be useful in predicting hybrid formulas in a heterosis culture. The present study demonstrated that molecular SNP and Silico DArT markers could be used in this species to group lines in terms of origin and lines with incomplete origin data. They can also be useful in maize in predicting the hybrid formula and can find applications in the selection of parental components for heterosis crossings. Full article

The use of fully-mechanized operations, normally targeted at coniferous species, has also been on the rise in mixed-species and continuous-cover forests comprised of a strong share of deciduous species. With special form characteristics (complex crowns, large-diameter branches, forks and sweeps, high wood density, etc.), deciduous trees can lead to wide-ranging harvesting productivities, often divergent from those originally derived from coniferous species. Due to the importance and growing interest in mechanizing operations in close-to-nature mixedwood and deciduous stands, obtaining insight on harvesting productivity in large-diameter deciduous trees was of interest. This study located in Bavaria, Germany, monitored four harvesters (two wheeled and two tracked machines) operated in four distinct harvest blocks (case studies), all of which had a high percentage of large-diameter European beech and oak trees. Harvesting productivity and volume recovery was assessed and quantified. Based on the field inventory of European beech and oak trees and continuous time-and-motion study, average harvesting productivity ranged from 29 to 43 m³/PMH₀ (productive machine hours without delay), whereas volume recovery fluctuated between 73% and 85% for trees that were completely felled and processed by machines. Because of the rather limited sample size and the variable conditions between case studies, results should only be used as general orientation on the performance of the tested machines and additional research is suggested to further understand the influence of tree form characteristics on impediments to mechanized processing. Full article