scholarly journals The role of multilevel selection in host microbiome evolution

2019 ◽  
Vol 116 (41) ◽  
pp. 20591-20597 ◽  
Author(s):  
Simon van Vliet ◽  
Michael Doebeli
Keyword(s):  
Generation Time ◽  
Evolutionary Dynamics ◽  
Horizontal Transmission ◽  
Multilevel Selection ◽  
Microbiome Composition ◽  
Active Debate ◽  
Multilevel Selection Theory ◽  
Verbal Arguments ◽  
Host Generation

Animals are associated with a microbiome that can affect their reproductive success. It is, therefore, important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial, and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here, we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared with the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.

scholarly journals The role of multilevel selection in host microbiome evolution

2019 ◽  
Author(s):  
Simon van Vliet ◽  
Michael Doebeli
Keyword(s):  
Generation Time ◽  
Evolutionary Dynamics ◽  
Horizontal Transmission ◽  
Multilevel Selection ◽  
Microbiome Composition ◽  
Active Debate ◽  
Multilevel Selection Theory ◽  
Verbal Arguments ◽  
Host Generation

Animals are associated with a microbiome that can affect their reproductive success. It is therefore important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared to the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.

scholarly journals Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guillermo Velo-Antón ◽  
André Lourenço ◽  
Pedro Galán ◽  
Alfredo Nicieza ◽  
Pedro Tarroso
Keyword(s):  
Contact Zone ◽  
Environmental Heterogeneity ◽  
Evolutionary Dynamics ◽  
Morphological Differentiation ◽  
Phenotypic Traits ◽  
Hybrid Zones ◽  
Landscape Resistance ◽  
Phenotypic Differentiation ◽  
Contact Zones

AbstractExplicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.

scholarly journals Kin and group selection are both flawed but useful data analysis tools

2019 ◽  
Author(s):  
jeff smith ◽  
R. Fredrik Inglis
Keyword(s):  
Empirical Research ◽  
Social Evolution ◽  
Multilevel Selection ◽  
Selection Theory ◽  
Fitness Effects ◽  
Data Driven Approach ◽  
Biological Interpretation ◽  
Multilevel Selection Theory ◽  
Microbial Systems ◽  
Analytical Tools

AbstractFor understanding the evolution of social behavior in microbes, mathematical theory can aid empirical research but is often only used as a qualitative heuristic. How to properly formulate social evolution theory has also been contentious. Here we evaluate kin and multilevel selection theory as tools for analyzing microbial data. We reanalyze published datasets that share a common experimental design and evaluate these theories in terms of data visualization, statistical performance, biological interpretation, and quantitative comparison across systems. We find that the canonical formulations of both kin and multilevel selection are almost always poor analytical tools because they use statistical regressions that are poorly specified for the strong selection and nonadditive fitness effects common in microbial systems. Analyzing both individual and group fitness outcomes helps clarify the biology of selection. We also identify analytical practices in empirical research that suggest how theory might better handle the challenges of microbial data. A quantitative, data-driven approach thus shows how kin and multilevel selection theory both have substantial room for improvement as tools for understanding social evolution in all branches of life.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

Modulation of instinal microbiom in the formation and progression of ulterative colitis.

2020 ◽  
Vol 75 (6) ◽  
pp. 577-584
Author(s):  
G. R. Bikbavova ◽  
M. A. Livzan
Keyword(s):  
Ulcerative Colitis ◽  
Short Chain Fatty Acids ◽  
Intestinal Wall ◽  
Intestinal Microbiome ◽  
Industrial Society ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Available Information ◽  
Post Industrial

In recent decades, an increase in the incidence of ulcerative colitis has been observed throughout the world. The purpose of this review is to generalize the available information on the influence of environmental factors and intestinal microbiome on the occurrence and development of ulcerative colitis, the role of bacteria metabolism products in the pathogenesis of the disease. Studied literature, we came to the conclusion that lifestyle in the era of post-industrial society has a significant impact on the microbial composition of the intestine and leads to changes in its diversity in patients suffering from ulcerative colitis. The changes include a decrease in the number of residential flora with anti-inflammatory activity, which synthesize short-chain fatty acids, and an increase in the number of potentially pathogenic and pathogenic microorganisms. Within the phylums Firmicutes and Proteobacteria, the proportional ratio changes. The combination of aggression factors (deterioration of the intestinal microbiome composition, the presence of aggressive intestinal metabolites) leads to intestinal mucosa permeability disfunction, impairing its barrier function. Food and bacterial agents can penetrate deeper layers of the intestinal wall through mucosal defects, which then stimulate the development of inflammatory and immune responses.

The role of biotic interactions in invasion ecology: theories and hypotheses.

2020 ◽  
pp. 26-44
Author(s):  
Cang Hui ◽  
◽  
Pietro Landi ◽  
Guillaume Latombe ◽  
◽  
...  
Keyword(s):  
Native Species ◽  
Evolutionary Dynamics ◽  
Biotic Interactions ◽  
Evolutionary Games ◽  
Invasion Ecology ◽  
Ecological Communities ◽  
Dynamic Interactions ◽  
Ecological Fitting ◽  
And Function

Changes in biotic interactions in the native and invaded range can enable a non-native species to establish and spread in novel environments. Invasive non-native species can in turn generate impacts in recipient systems partly through the changes they impose on biotic interactions; these interactions can lead to altered ecosystem processes in the recipient systems. This chapter reviews models, theories and hypotheses on how invasion performance and impact of introduced species in recipient ecosystems can be conjectured according to biotic interactions between native and non-native species. It starts by exploring the nature of biotic interactions as ensembles of ecological and evolutionary games between individuals of both the same and different groups. This allows us to categorize biotic interactions as direct and indirect (i.e. those involving more than two species) that emerge from both coevolution and ecological fitting during community assembly and invasion. We then introduce conceptual models that can reveal the ecological and evolutionary dynamics between interacting non-native and resident species in ecological networks and communities. Moving from such theoretical grounding, we review 20 hypotheses that have been proposed in invasion ecology to explain the invasion performance of a single non-native species, and seven hypotheses relating to the creation and function of assemblages of non-native species within recipient ecosystems. We argue that, although biotic interactions are ubiquitous and quintessential to the assessment of invasion performance, they are nonetheless difficult to detect and measure due to strength dependency on sampling scales and population densities, as well as the non-equilibrium transient dynamics of ecological communities and networks. We therefore call for coordinated efforts in invasion science and beyond, to devise and review approaches that can rapidly map out the entire web of dynamic interactions in a recipient ecosystem.

scholarly journals Role of the intestinal microbiome in colorectal cancer surgery outcomes

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Lelde Lauka ◽  
Elisa Reitano ◽  
Maria Clotilde Carra ◽  
Federica Gaiani ◽  
Paschalis Gavriilidis ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Surgery ◽  
Intestinal Microbiome ◽  
Colorectal Cancer Surgery ◽  
Microbiome Composition ◽  
Cancer Specific Mortality ◽  
Surgery Outcomes ◽  
Disease Free

Abstract Objectives Growing evidence supports the role of the intestinal microbiome in the carcinogenesis of colorectal cancers, but its impact on colorectal cancer surgery outcomes is not clearly defined. This systematic review aimed to analyze the association between intestinal microbiome composition and postoperative complication and survival following colorectal cancer surgery. Methods A systematic review was conducted according to the 2009 PRISMA guidelines. Two independent reviewers searched the literature in a systematic manner through online databases, including Medline, Scopus, Embase, Cochrane Oral Health Group Specialized Register, ProQuest Dissertations and Theses Database, and Google Scholar. Human studies investigating the association between the intestinal microbiome and the short-term (anastomotic leakage, surgical site infection, postoperative ileus) and long-term outcomes (cancer-specific mortality, overall and disease-free survival) of colorectal cancer surgery were selected. Patients with any stage of colorectal cancer were included. The Newcastle-Ottawa scale for case-control and cohort studies was used for the quality assessment of the selected articles. Results Overall, 8 studies (7 cohort studies and 1 case-control) published between 2014 and 2018 were included. Only one study focused on short-term surgical outcomes, showing that anastomotic leakage is associated with low microbial diversity and abundance of Lachnospiraceae and Bacteroidaceae families in the non-cancerous resection lines of the stapled anastomoses of colorectal cancer patients. The other 7 studies focused on long-term oncological outcomes, including survival and cancer recurrence. The majority of the studies (5/8) found that a higher level of Fusobacterium nucleatum adherent to the tumor tissue is associated with worse oncological outcomes, in particular, increased cancer-specific mortality, decreased median and overall survival, disease-free and cancer-specific survival rates. Also a high abundance of Bacteroides fragilis was found to be linked to worse outcomes, whereas the relative abundance of the Prevotella-co-abundance group (CAG), the Bacteroides CAG, and the pathogen CAG as well as Faecalibacterium prausnitzii appeared to be associated with better survival. Conclusions Based on the limited available evidence, microbiome composition may be associated with colorectal cancer surgery outcomes. Further studies are needed to elucidate the role of the intestinal microbiome as a prognostic factor in colorectal cancer surgery and its possible clinical implications.

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