scholarly journals Evolutionary ecology of natural comammox Nitrospira populations

2020 ◽  
Author(s):  
Alejandro Palomo ◽  
Arnaud Dechesne ◽  
Otto X. Cordero ◽  
Barth F. Smets
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Purifying Selection ◽  
Single Species ◽  
Species Interaction ◽  
Evolutionary Processes ◽  
Sand Filters ◽  
Experimental Systems ◽  
Stable Conditions ◽  
In The Wild

ABSTRACTMicrobial life on Earth commonly occurs in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during last decades, but most studies of evolutionary dynamics are based on single species in isolation or experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammox Nitrospira species, favoured by low ammonium concentrations. Nitrospira species showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. Nitrospira populations were separated by gene flow boundaries, suggesting natural and cohesive populations. They showed low homologous recombination and strong purifying selection, the latest process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. Additionally, we analysed evolutionary processes in populations from different habitats. Interestingly, our results suggest that in comammox Nitrospira these processes are not an intrinsic feature but greatly vary depending on the habitat they inhabit. Compared to other habitats, groundwater fed sand filters impose strong purifying selection and low recombination. Together, this study improves understanding of interactions and evolution of species in the wild, and sheds light on the environmental dependency of evolutionary processes.

scholarly journals Evolutionary Ecology of Natural Comammox Nitrospira Populations

mSystems ◽  
2022 ◽  
Author(s):  
Alejandro Palomo ◽  
Arnaud Dechesne ◽  
Otto X. Cordero ◽  
Barth F. Smets
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Single Species ◽  
Evolutionary Processes ◽  
Ecological Processes ◽  
Interacting Species ◽  
Microbial Species ◽  
Experimental Systems ◽  
Over Time

Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems.

scholarly journals Social transmission in the wild can reduce predation pressure on novel prey signals

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Liisa Hämäläinen ◽  
William Hoppitt ◽  
Hannah M. Rowland ◽  
Johanna Mappes ◽  
Anthony J. Fulford ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Parus Major ◽  
Predation Pressure ◽  
Social Transmission ◽  
Blue Tit ◽  
Cyanistes Caeruleus ◽  
Novel Approach ◽  
Transmission Of Information ◽  
In The Wild ◽  
Animal Communities

AbstractSocial transmission of information is taxonomically widespread and could have profound effects on the ecological and evolutionary dynamics of animal communities. Demonstrating this in the wild, however, has been challenging. Here we show by field experiment that social transmission among predators can shape how selection acts on prey defences. Using artificial prey and a novel approach in statistical analyses of social networks, we find that blue tit (Cyanistes caeruleus) and great tit (Parus major) predators learn about prey defences by watching others. This shifts population preferences rapidly to match changes in prey profitability, and reduces predation pressure from naïve predators. Our results may help resolve how costly prey defences are maintained despite influxes of naïve juvenile predators, and suggest that accounting for social transmission is essential if we are to understand coevolutionary processes.

scholarly journals Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

2019 ◽  
Author(s):  
Kathryn E. Holt ◽  
Florent Lassalle ◽  
Kelly L. Wyres ◽  
Ryan Wick ◽  
Rafal J. Mostowy
Keyword(s):  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Purifying Selection ◽  
Evolutionary Forces ◽  
Polysaccharide Synthesis ◽  
Surface Polysaccharides ◽  
Surface Polysaccharide ◽  
Selective Preservation ◽  
Multiple Species

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormachei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.

scholarly journals Alien Species vs. Native Species: From Community Ecology to Eco-Evolutionary Dynamics

2019 ◽  
Author(s):  
Andersonn Silveira Prestes
Keyword(s):  
Alien Species ◽  
Exotic Species ◽  
Native Species ◽  
Evolutionary Dynamics ◽  
Evolutionary Processes ◽  
Native Communities ◽  
Individualized Approach ◽  
History Of ◽  
Relationship Of ◽  
The Relationship

The establishment and spread of exotic species is a contemporary major concern. Alien species may become invasive in their new habitat, leading to both/either environmental and/or economic impacts. I briefly reviewed the literature in the last decade about the relationship of exotic species and native communities. I identified that professionals usually approach the subject in two main points of view: (1) researchers tend to point out the impacts of alien species on entire communities, evaluating if the relationship is positive, negative or neutral; (2) they focus on the eco-evolutionary processes involved in the introductions, the dynamics of invasion, and individual study cases. When evaluating the response of introductions to entire communities, evidence seems to be ambiguous and may support positive, negative or neutral relationship, especially depending on the scale approached. The unique eco-evolutionary pathways of each introduction may be a great shortcoming in the searching for generalities. On the other hand, advances have been made in understanding the dynamics of invasion on different lineages through a more selective/individualized approach. I suggest that the dynamics of invasion might be studied through a perspective in which different eco-evolutionary processes, levels of organization (from gene to entire communities), the history of the organism(s) and time are taken into account. Individual cases might be compared in attempt to understand how the relationship exotic and native works and in the search for generalities.

scholarly journals In vitrocommunity synergy between bacterial soil isolates can be facilitated by pH stabilisation of the environment

2018 ◽  
Author(s):  
Jakob Herschend ◽  
Klaus Koren ◽  
Henriette L. Røder ◽  
Asker Brejnrod ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Metabolic Activity ◽  
Local Environment ◽  
Single Species ◽  
Species Interaction ◽  
Individual Species ◽  
Community Members ◽  
Community Interactions ◽  
Community Growth ◽  
Over Time

AbstractComposition and development of naturally occurring microbial communities is defined by a complex interplay between the community and the surrounding environment and by interactions between community members. Intriguingly, these interactions can in some cases cause community synergies where the community is able to outperform it single species constituents. However, the underlying mechanisms driving community interactions are often unknown and difficult to identify due to high community complexity. Here we show how pH stabilisation of the environment through the metabolic activity of specific community members acts as a positive inter-species interaction drivingin vitrocommunity synergy in a model consortium of four co-isolated soil bacteria:Microbacterium oxydans,Xanthomonas retroflexus,Stenotrophomonas rhizophilaandPaenibacillus amylolyticus. Using micro-sensor pH measurements to show how individual species change the local pH micro-environment, and how co-cultivation leads to a stabilised pH regime over time. Specifically,in vitroacid production fromPaenibacillus amylolyticusand alkali production primarily fromXanthomonas retroflexuslead to an overall pH stabilisation of the local environment over time, which in turn resulted in enhanced community growth. This specific type of interspecies interaction was found to be highly dependent on media type and media concentration, however similar pH drift from the individual species could be observed across media variants.ImportanceWe show thatin vitrometabolic activity of individual members of a synthetic, co- isolated model community presenting community synergistic growth arises through the inter-species interaction of pH stabilization of the community micro-environment. The observed inter-species interaction is highly media specific and most pronounced under high nutrient availability. This adds to the growing diversity of identified community interactions leading to enhanced community growth.

scholarly journals The evolutionary dynamics of Oropouche Virus (OROV) in South America

2019 ◽  
Author(s):  
Bernardo Gutierrez ◽  
Emma Wise ◽  
Steven Pullan ◽  
Christopher Logue ◽  
Thomas A. Bowden ◽  
...  
Keyword(s):  
Viral Genome ◽  
Amazon Basin ◽  
Evolutionary Dynamics ◽  
Surface Proteins ◽  
Human Populations ◽  
Evolutionary Processes ◽  
Viral Pathogens ◽  
Viral Genomes ◽  
Glycosylation Sites ◽  
Variable Evolutionary Rates

AbstractThe Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these,Oropouche orthobunyavirus(OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.

scholarly journals Divergent and convergent evolution of housekeeping genes in human–pig lineage

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4840 ◽  
Author(s):  
Kai Wei ◽  
Tingting Zhang ◽  
Lei Ma
Keyword(s):  
Active Sites ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Housekeeping Genes ◽  
Neutral Evolution ◽  
Structure Evolution ◽  
Tissue Cell ◽  
Sequencing Data ◽  
Cellular Functions ◽  
Species Specific

Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

scholarly journals Ectothermic telomeres: it's time they came in from the cold

2018 ◽  
Vol 373 (1741) ◽  
pp. 20160449 ◽  
Author(s):  
Mats Olsson ◽  
Erik Wapstra ◽  
Christopher Friesen
Keyword(s):  
Body Temperature ◽  
Life Histories ◽  
Evolutionary Ecology ◽  
Malignant Tumours ◽  
Telomere Attrition ◽  
Specific Effects ◽  
Warm Environment ◽  
Living Things ◽  
Anti Cancer ◽  
In The Wild

We review the evolutionary ecology and genetics of telomeres in taxa that cannot elevate their body temperature to a preferred level through metabolism but do so by basking or seeking out a warm environment. This group of organisms contains all living things on earth, apart from birds and mammals. One reason for our interest in this synthetic group is the argument that high, stable body temperature increases the risk of malignant tumours if long, telomerase-restored telomeres make cells ‘live forever’. If this holds true, ectotherms should have significantly lower cancer frequencies. We discuss to what degree there is support for this ‘anti-cancer’ hypothesis in the current literature. Importantly, we suggest that ectothermic taxa, with variation in somatic telomerase expression across tissue and taxa, may hold the key to understanding ongoing selection and evolution of telomerase dynamics in the wild. We further review endotherm-specific effects of growth on telomeres, effects of autotomy (‘tail dropping’) on telomere attrition, and costs of maintaining sexual displays measured in telomere attrition. Finally, we cover plant ectotherm telomeres and life histories in a separate ‘mini review’. This article is part of the theme issue ‘Understanding diversity in telomere dynamics'.

scholarly journals Eco-evolutionary feedbacks promote fluctuating selection and long-term stability of antagonistic networks

2018 ◽  
Vol 285 (1874) ◽  
pp. 20172596 ◽  
Author(s):  
Cecilia Siliansky de Andreazzi ◽  
Paulo R. Guimarães ◽  
Carlos J. Melián
Keyword(s):  
Temporal Variation ◽  
Evolutionary Dynamics ◽  
Species Interaction ◽  
Fluctuating Selection ◽  
Term Stability ◽  
Long Term Stability ◽  
Interacting Species ◽  
Species Abundances ◽  
Antagonistic Interactions

Studies have shown the potential for rapid adaptation in coevolving populations and that the structure of species interaction networks can modulate the vulnerability of ecological systems to perturbations. Although the feedback loop between population dynamics and coevolution of traits is crucial for understanding long-term stability in ecological assemblages, modelling eco-evolutionary dynamics in species-rich assemblages is still a challenge. We explore how eco-evolutionary feedbacks influence trait evolution and species abundances in 23 empirical antagonistic networks. We show that, if selection due to antagonistic interactions is stronger than other selective pressures, eco-evolutionary feedbacks lead to higher mean species abundances and lower temporal variation in abundances. By contrast, strong selection of antagonistic interactions leads to higher temporal variation of traits and on interaction strengths. Our results present a theoretical link between the study of the species persistence and coevolution in networks of interacting species, pointing out the ways by which coevolution may decrease the vulnerability of species within antagonistic networks to demographic fluctuation.

How Giraffes Work

2021 ◽  
Author(s):  
Graham Mitchell
Keyword(s):  
Single Species ◽  
Free Living ◽  
Factors Affecting ◽  
Normal Functions ◽  
Private Lives ◽  
Social Biology ◽  
Biochemical Systems ◽  
In The Wild ◽  
Physiological And Biochemical ◽  
Biological Milieu

There are few creatures more beautiful, more aloof, and more fascinating than giraffes. Once they were plentiful and filled African landscapes, but in 2016 they were re-classified from “least concern” to “vulnerable” by the International Union for Conservation of Nature. Their survival in the wild is not assured. Much has been written about their private lives, about their behavior, social biology, and ecology, and their history in art and diplomacy. But so far no book has been written about their private lives, their physiology, and their anatomy and biochemistry—in short, the normal functions of a free-living animal in its natural environment—and it is these aspects of their lives that are the focus of this book. The study of a single species could be concise and relatively simply told. In reality it is not. A species never evolves in isolation from the general biological milieu in which it finds itself. Tectonics, astronomical physics, climate, and purely biological factors affecting food and water resources all shape the path of their evolution and all interact with its morphology, its internal physiological and biochemical systems, and the behavior patterns that regulate its daily life. Giraffes are no exception, as is revealed as the story told here unfolds. How do giraffes work? The answers lie in a story filled not only with the internal workings of a unique creature, but with geography, climate changes of great magnitude, and the labors of extraordinary people who put many pieces of the puzzle together.

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