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 classification isolation & purification MeSH
- Diet * MeSH
- Feces microbiology MeSH
- Phylogeny MeSH
- Genetic Variation * MeSH
- Humans MeSH
- Evolution, Molecular * MeSH
- Primates microbiology MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Gastrointestinal Microbiome * MeSH
- Life Style MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Comparative Study MeSH
... Other Limiting Materials 98 Sensory Capacities and Environmental Cues 99 Adaptive Suites 100 Design Constraints ... ... Competitive Exclusion 248 -- Balance Between Intraspecific and Interspecific Competition 249 -- Evolutionary ... ... 304 -- “Prudent” Predation and Optimal Yield 312 -- Selected Experiments and Observations 313 -- Evolutionary ... ... Phylogeny and the Modem Comparative Method 338 -- Phylogenetically Independent Contrasts 340 -- Evolutionary ... ... Numbers, and Biomass 358 Energy Flow and Ecological Energetics 359 Secondary Succession 363 -- Evolutionary ...
6th ed. xv, 512 s.
Adaptive responses are probably the most effective long-term responses of populations to climate change, but they require sufficient evolutionary potential upon which selection can act. This requires high genetic variance for the traits under selection and low antagonizing genetic covariances between the different traits. Evolutionary potential estimates are still scarce for long-lived, clonal plants, although these species are predicted to dominate the landscape with climate change. We studied the evolutionary potential of a perennial grass, Festuca rubra, in western Norway, in two controlled environments corresponding to extreme environments in natural populations: cold-dry and warm-wet, the latter being consistent with the climatic predictions for the country. We estimated genetic variances, covariances, selection gradients and response to selection for a wide range of growth, resource acquisition and physiological traits, and compared their estimates between the environments. We showed that the evolutionary potential of F. rubra is high in both environments, and genetic covariances define one main direction along which selection can act with relatively few constraints to selection. The observed response to selection at present is not sufficient to produce genotypes adapted to the predicted climate change under a simple, space for time substitution model. However, the current populations contain genotypes which are pre-adapted to the new climate, especially for growth and resource acquisition traits. Overall, these results suggest that the present populations of the long-lived clonal plant may have sufficient evolutionary potential to withstand long-term climate changes through adaptive responses.
- MeSH
- Biological Evolution * MeSH
- Ecosystem MeSH
- Festuca genetics physiology MeSH
- Climate Change * MeSH
- Selection, Genetic MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Norway MeSH
The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.
- MeSH
- Arabidopsis genetics physiology MeSH
- Brassica genetics physiology MeSH
- Brassicaceae genetics physiology MeSH
- Phylogeny MeSH
- Genome, Chloroplast genetics MeSH
- Genome, Plant genetics MeSH
- Evolution, Molecular * MeSH
- Polyploidy MeSH
- Sequence Analysis, DNA MeSH
- Genetic Speciation MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Blastocystis is the most prevalent microbial eukaryote in the human and animal gut, yet its role as commensal or parasite is still under debate. Blastocystis has clearly undergone evolutionary adaptation to the gut environment and possesses minimal cellular compartmentalization, reduced anaerobic mitochondria, no flagella, and no reported peroxisomes. To address this poorly understood evolutionary transition, we have taken a multi-disciplinary approach to characterize Proteromonas lacertae, the closest canonical stramenopile relative of Blastocystis. Genomic data reveal an abundance of unique genes in P. lacertae but also reductive evolution of the genomic complement in Blastocystis. Comparative genomic analysis sheds light on flagellar evolution, including 37 new candidate components implicated with mastigonemes, the stramenopile morphological hallmark. The P. lacertae membrane-trafficking system (MTS) complement is only slightly more canonical than that of Blastocystis, but notably, we identified that both organisms encode the complete enigmatic endocytic TSET complex, a first for the entire stramenopile lineage. Investigation also details the modulation of mitochondrial composition and metabolism in both P. lacertae and Blastocystis. Unexpectedly, we identify in P. lacertae the most reduced peroxisome-derived organelle reported to date, which leads us to speculate on a mechanism of constraint guiding the dynamics of peroxisome-mitochondrion reductive evolution on the path to anaerobiosis. Overall, these analyses provide a launching point to investigate organellar evolution and reveal in detail the evolutionary path that Blastocystis has taken from a canonical flagellated protist to the hyper-divergent and hyper-prevalent animal and human gut microbe.
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
- Aneuploidy MeSH
- Genome Size MeSH
- Diploidy MeSH
- Ecosystem MeSH
- Phenotype MeSH
- Phylogeny MeSH
- Hybridization, Genetic MeSH
- Evolution, Molecular * MeSH
- Polyploidy * MeSH
- Cell Nucleus Size MeSH
- Cell Size MeSH
- Genetic Speciation MeSH
- Anura classification genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
... However, like all our other features, intelligence is a product of evolutionary change. ... ... study of primates, our closest non-human relatives, giving strong impetus to the case for an \'evolutionary ... ... -- Further reading -- How to reconstruct evolutionary history -- Linnean taxomony -- Evolution -- Evolutionary ... ... taxomony: cladistics -- Molecular taxomony -- 11 imate and human evolutionary relationships -- Inventing ... ... -- 45 -- The traditional story of animal learning -- Individual learning channelled by genetic constraints ...
ix, 266 s. : il. ; 24 cm
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
- Models, Genetic * MeSH
- Evolution, Molecular * MeSH
- Reproduction, Asexual genetics MeSH
- Polyploidy MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
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
- Species Specificity MeSH
- Phylogeny MeSH
- Evolution, Molecular * MeSH
- Murinae classification genetics immunology MeSH
- Immunity, Innate MeSH
- Protein Structure, Tertiary MeSH
- Toll-Like Receptor 4 chemistry genetics immunology MeSH
- Toll-Like Receptor 7 chemistry genetics immunology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't 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
- Algorithms MeSH
- Ectodysplasins genetics MeSH
- Phenotype MeSH
- Genetic Variation MeSH
- Genetic Diseases, Inborn genetics MeSH
- Genomics MeSH
- Glucosephosphate Dehydrogenase genetics MeSH
- Hemoglobins genetics MeSH
- Hepatocyte Nuclear Factor 4 genetics MeSH
- Humans MeSH
- Mutation, Missense MeSH
- Models, Genetic * MeSH
- Evolution, Molecular MeSH
- Mutation * MeSH
- Likelihood Functions MeSH
- Proteomics MeSH
- Protein Tyrosine Phosphatase, Non-Receptor Type 11 genetics MeSH
- Computational Biology methods MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
