The past decade has witnessed a tremendous increase in interest in polyploidy, which may partly be related to the development of new powerful genetic and genomic tools. These have provided numerous insights into mainly genetic and genomic consequences of polyploidy, dramatically improving our understanding of the dynamics of the polyploidization process and its importance as a mechanism in animal evolution. In contrast, several other aspects of polyploidization, such as physiology, ecology and development, have received considerably less attention. Our aim is not to make an exhaustive review of current knowledge about animal polyploidy, but rather to thoroughly elaborate on some very fundamental questions which still remain open or even neglected. In particular, we show that properties of new polyploid lineages largely depend upon the proximate way in which they arose, but the evolutionary pathways to polyploidy are often unresolved. To help researchers orientate amongst the number of pathways to polyploidy, we provide an extensive review of particular scenarios proposed in distinct animal taxa. We discuss how polyploidy relates to hybridization, particularly with respect to asexuality, and elaborate on whether clonal triploids may help to overcome the constraints of aneuploidy, thereby serving as a triploid bridge towards the establishment of new polyploid species. We further show that in most animal asexual complexes clonal lineages may become established only under one ploidy level (usually either di- or triploidy), and that it is rather rare to see the coexistence of successful clones of different ploidies. We discuss why the rate of polyploidization is higher in some taxa than in others, and what tools we have to evaluate the rate of polyploidization. Finally, we review some of the immediate physiological and developmental effects of polyploidy which are related to the genome size/cell size relation and show how studies of polyploidy may enhance the study of macroecology and developmental biology. See also the sister article focusing on plants by Weiss-Schneeweiss et al. in this themed issue.

• MeSH
• aneuploidie MeSH
• délka genomu MeSH
• diploidie MeSH
• ekosystém MeSH
• fenotyp MeSH
• fylogeneze MeSH
• hybridizace genetická MeSH
• molekulární evoluce * MeSH
• polyploidie * MeSH
• velikost buněčného jádra MeSH
• velikost buňky MeSH
• vznik druhů (genetika) MeSH
• žáby klasifikace   genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

• MeSH
• biologická evoluce MeSH
• biologie MeSH
• inteligence MeSH
• myšlení MeSH
• vývoj člověka MeSH

• Konspekt
• Biologické vědy
• NLK Obory
• biologie
• přírodní vědy

BACKGROUND: In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs). RESULTS: We sequenced genes encoding Toll-like receptor 4 (Tlr4) and 7 (Tlr7), two of the key bacterial- and viral-sensing receptors of innate immunity, across 23 species within the subfamily Murinae. Although we have shown that the phylogeny of both Tlr genes is largely congruent with the phylogeny of rodents based on a comparably sized non-immune sequence dataset, we also identified several potentially important discrepancies. The sequence analyses revealed that major parts of both Tlrs are evolving under strong purifying selection, likely due to functional constraints. Yet, also several signatures of positive selection have been found in both genes, with more intense signal in the bacterial-sensing Tlr4 than in the viral-sensing Tlr7. 92% and 100% of sites evolving under positive selection in Tlr4 and Tlr7, respectively, were located in the extracellular domain. Directly in the Ligand-Binding Region (LBR) of TLR4 we identified two rapidly evolving amino acid residues and one site under positive selection, all three likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In contrast, all putative sites of LBRTLR7 involved in the detection of viral nucleic acids were highly conserved across rodents. Interspecific differences in the predicted 3D-structure of the LBR of both Tlrs were not related to phylogenetic history, while analyses of protein charges clearly discriminated Rattini and Murini clades. CONCLUSIONS: In consequence of the constraints given by the receptor protein function purifying selection has been a dominant force in evolution of Tlrs. Nevertheless, our results show that episodic diversifying parasite-mediated selection has shaped the present species-specific variability in rodent Tlrs. The intensity of diversifying selection was higher in Tlr4 than in Tlr7, presumably due to structural properties of their ligands.

• MeSH
• druhová specificita MeSH
• fylogeneze MeSH
• molekulární evoluce * MeSH
• Murinae klasifikace   genetika   imunologie   MeSH
• přirozená imunita MeSH
• terciární struktura proteinů MeSH
• toll-like receptor 4 chemie   genetika   imunologie   MeSH
• toll-like receptor 7 chemie   genetika   imunologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Prediction methods have become an integral part of biomedical and biotechnological research. However, their clinical interpretations are largely based on biochemical or molecular data, but not clinical data. Here, we focus on improving the reliability and clinical applicability of prediction algorithms. We assembled and curated two large non-overlapping large databases of clinical phenotypes. These phenotypes were caused by missense variations in 44 and 63 genes associated with Mendelian diseases. We used these databases to establish and validate the model, allowing us to improve the predictions obtained from EVmutation, SNAP2 and PoPMuSiC 2.1. The predictions of clinical effects suffered from a lack of specificity, which appears to be the common constraint of all recently used prediction methods, although predictions mediated by these methods are associated with nearly absolute sensitivity. We introduced evidence-based tailoring of the default settings of the prediction methods; this tailoring substantially improved the prediction outcomes. Additionally, the comparisons of the clinically observed and theoretical variations led to the identification of large previously unreported pools of variations that were under negative selection during molecular evolution. The evolutionary variation analysis approach described here is the first to enable the highly specific identification of likely disease-causing missense variations that have not yet been associated with any clinical phenotype.

• MeSH
• algoritmy MeSH
• ektodysplasiny genetika   MeSH
• fenotyp MeSH
• genetická variace MeSH
• genetické nemoci vrozené genetika   MeSH
• genomika MeSH
• glukosa-6-fosfátdehydrogenasa genetika   MeSH
• hemoglobiny genetika   MeSH
• hepatocytární jaderný faktor 4 genetika   MeSH
• lidé MeSH
• missense mutace MeSH
• modely genetické * MeSH
• molekulární evoluce MeSH
• mutace * MeSH
• pravděpodobnostní funkce MeSH
• proteomika MeSH
• tyrosinfosfatasa nereceptorového typu 11 genetika   MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Phylogenetic studies typically demonstrate lower evolutionary ages of clones, relative to their sexual ancestors. This has often been attributed to heightened extinction risk of asexual organisms. We previously criticized such interpretations and demonstrated that the life span of clones is ultimately limited by neutral drift depending on the rate at which new clones are spawned into an asexual community of a finite size. Therefore, it is important to investigate whether the natural rates of such influxes are sufficiently high to account for the relative ephemerality of clones without assuming their increased extinction rate. I applied the neutral clonal turnover model to phylogenies of polyploid asexual ferns and simulated the coalescent trees over a wide range of demographic structures and sampling schemes. On parameterizing the model with biologically relevant estimates of population sizes and plant polyploidization rates, simulated clonal assemblages appeared younger than their sexual counterparts even in the absence of selection against clones. Therefore, differences observed between the ages of sexual and clonal lineages may be explained by the neutral clonal turnover. Researchers should consider the possibility that natural clones may get lost by neutral drift before their fate could eventually be affected by any long-term constraints of asexuality.

• MeSH
• modely genetické * MeSH
• molekulární evoluce * MeSH
• nepohlavní rozmnožování genetika   MeSH
• polyploidie MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The gut microbiome of primates, including humans, is reported to closely follow host evolutionary history, with gut microbiome composition being specific to the genetic background of its primate host. However, the comparative models used to date have mainly included a limited set of closely related primates. To further understand the forces that shape the primate gut microbiome, with reference to human populations, we expanded the comparative analysis of variation among gut microbiome compositions and their primate hosts, including 9 different primate species and 4 human groups characterized by a diverse set of subsistence patterns (n = 448 samples). The results show that the taxonomic composition of the human gut microbiome, at the genus level, exhibits increased compositional plasticity. Specifically, we show unexpected similarities between African Old World monkeys that rely on eclectic foraging and human populations engaging in nonindustrial subsistence patterns; these similarities transcend host phylogenetic constraints. Thus, instead of following evolutionary trends that would make their microbiomes more similar to that of conspecifics or more phylogenetically similar apes, gut microbiome composition in humans from nonindustrial populations resembles that of generalist cercopithecine monkeys. We also document that wild cercopithecine monkeys with eclectic diets and humans following nonindustrial subsistence patterns harbor high gut microbiome diversity that is not only higher than that seen in humans engaging in industrialized lifestyles but also higher compared to wild primates that typically consume fiber-rich diets.IMPORTANCE The results of this study indicate a discordance between gut microbiome composition and evolutionary history in primates, calling into question previous notions about host genetic control of the primate gut microbiome. Microbiome similarities between humans consuming nonindustrialized diets and monkeys characterized by subsisting on eclectic, omnivorous diets also raise questions about the ecological and nutritional drivers shaping the human gut microbiome. Moreover, a more detailed understanding of the factors associated with gut microbiome plasticity in primates offers a framework to understand why humans following industrialized lifestyles have deviated from states thought to reflect human evolutionary history. The results also provide perspectives for developing therapeutic dietary manipulations that can reset configurations of the gut microbiome to potentially improve human health.

• MeSH
• Bacteria klasifikace   izolace a purifikace   MeSH
• dieta * MeSH
• feces mikrobiologie   MeSH
• fylogeneze MeSH
• genetická variace * MeSH
• lidé MeSH
• molekulární evoluce * MeSH
• primáti mikrobiologie   MeSH
• RNA ribozomální 16S genetika   MeSH
• střevní mikroflóra * MeSH
• životní styl MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH

Gene duplication plays an important role in the origin of evolutionary novelties, but the mechanisms responsible for the retention and functional divergence of the duplicated copy are not fully understood. The α-globin genes provide an example of a gene family with different numbers of gene duplicates among rodents. Whereas Rattus and Peromyscus each have three adult α-globin genes (HBA-T1, HBA-T2 and HBA-T3), Mus has only two copies. High rates of amino acid evolution in the independently derived HBA-T3 genes of Peromyscus and Rattus have been attributed to positive selection. Using RACE PCR, reverse transcription-PCR (RT-PCR) and RNA-seq, we show that another rodent, the bank vole Clethrionomys glareolus, possesses three transcriptionally active α-globin genes. The bank vole HBA-T3 gene is distinguished from each HBA-T1 and HBA-T2 by 20 amino acids and is transcribed 23- and 4-fold lower than HBA-T1 and HBA-T2, respectively. Polypeptides corresponding to all three genes are detected by electrophoresis, demonstrating that the translated products of HBA-T3 are present in adult erythrocytes. Patterns of codon substitution and the presence of low-frequency null alleles suggest a postduplication relaxation of purifying selection on bank vole HBA-T3.

• MeSH
• alfa-globiny genetika   MeSH
• Arvicolinae genetika   MeSH
• Bayesova věta MeSH
• DNA primery genetika   MeSH
• druhová specificita MeSH
• duplicitní geny genetika   MeSH
• elektroforéza MeSH
• erytrocyty metabolismus   MeSH
• fylogeneze * MeSH
• genetická variace * MeSH
• klonování DNA MeSH
• modely genetické MeSH
• molekulární sekvence - údaje MeSH
• polymerázová řetězová reakce s reverzní transkripcí MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza RNA MeSH
• selekce (genetika) * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• biologická evoluce MeSH
• biologie MeSH
• ekologie MeSH

• Konspekt
• Biologické vědy
• NLK Obory
• biologie
• environmentální vědy

The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA-protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.

• MeSH
• biologická evoluce * MeSH
• fylogeneze MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH

Positive selection acting on Toll-like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host-pathogen molecular co-adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study, we provide evidence of phenotypic variability in the avian TLR4 ligand-binding region (LBR), the direct interface between host and pathogen molecular structures. We show that 55 passerine species vary substantially in the distribution of electrostatic potential on the surface of the receptor, and based on these distinct patterns, we identified four species clusters. Seven of the 34 evolutionarily nonconservative and positively selected residues correspond topologically to sites previously identified as being important for lipopolysaccharide, lipid IVa or MD-2 binding. Five of these positions codetermine the identity of the charge clusters. Groups of species that host-related communities of pathogens were predicted to cluster based on their TLR4 LBR charge. Despite some evidence for convergence among taxa, there were no clear associations between the TLR4 LBR charge distribution and any of the general ecological characteristics compared (migration, latitudinal distribution and diet). Closely related species, however, mostly belonged to the same surface charge cluster indicating that phylogenetic constraints are key determinants shaping TLR4 adaptive evolution. Our results suggest that host innate immune evolution is consistent with Fahrenholz's rule on the cospeciation of hosts and their parasites.

• MeSH
• glykolipidy chemie   genetika   MeSH
• interakce hostitele a patogenu genetika   MeSH
• konformace proteinů MeSH
• ligandy MeSH
• lipid A analogy a deriváty   chemie   genetika   MeSH
• lipopolysacharidy chemie   genetika   MeSH
• lymfocytární antigen 96 chemie   genetika   MeSH
• mikrobiota genetika   MeSH
• molekulární evoluce * MeSH
• molekulární modely MeSH
• přirozená imunita genetika   MeSH
• ptáci genetika   parazitologie   MeSH
• sekvenční analýza DNA MeSH
• selekce (genetika) * genetika   MeSH
• statická elektřina MeSH
• toll-like receptor 4 chemie   genetika   MeSH
• vazba proteinů MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH