scholarly journals Quantifying Parallel Evolution

2020 ◽  
Author(s):  
William R. Shoemaker ◽  
Jay T. Lennon
Keyword(s):  
Dimensionality Reduction ◽  
Evolutionary Dynamics ◽  
Parallel Evolution ◽  
Temporal Patterns ◽  
Tree Of Life ◽  
Microbial Populations ◽  
Gene Level ◽  
Evolutionary Trajectories

AbstractParallel evolution is consistently observed across the tree of life. However, the degree of parallelism between replicate populations in evolution experiments is rarely quantified at the gene level. Here we examine parallel evolution as the degree of covariance between replicate populations, providing a justification for the use of dimensionality reduction. We examine the extent that signals of gene-level covariance can be inferred in microbial evolve-and-resequence evolution experiments, finding that deviations from parallelism are difficult to quantify at a given point in time. However, this low statistical signal means that covariance between replicate populations is unlikely to interfere with the ability to detect divergent evolutionary trajectories for populations in different environments. Finally, we find evidence suggesting that temporal patterns of parallelism are comparatively easier to detect and that these patterns may reflect the evolutionary dynamics of microbial populations.

scholarly journals Chaos and the (un)predictability of evolution in a changing environment

2017 ◽  
Author(s):  
Artur Rego-Costa ◽  
Florence Débarre ◽  
Luis-Miguel Chevin
Keyword(s):  
Evolutionary Dynamics ◽  
Initial Conditions ◽  
Strong Dependence ◽  
Environmental Stochasticity ◽  
Phenotypic Evolution ◽  
Evolutionary System ◽  
Chaotic Oscillations ◽  
Changing Environment ◽  
Environmental Forcing ◽  
Evolutionary Trajectories

Among the factors that may reduce the predictability of evolution, chaos, characterized by a strong dependence on initial conditions, has received much less attention than randomness due to genetic drift or environmental stochasticity. It was recently shown that chaos in phenotypic evolution arises commonly under frequency-dependent selection caused by competitive interactions mediated by many traits. This result has been used to argue that chaos should often make evolutionary dynamics unpredictable. However, populations also evolve largely in response to external changing environments, and such environmental forcing is likely to influence the outcome of evolution in systems prone to chaos. We investigate how a changing environment causing oscillations of an optimal phenotype interacts with the internal dynamics of an eco-evolutionary system that would be chaotic in a constant environment. We show that strong environmental forcing can improve the predictability of evolution, by reducing the probability of chaos arising, and by dampening the magnitude of chaotic oscillations. In contrast, weak forcing can increase the probability of chaos, but it also causes evolutionary trajectories to track the environment more closely. Overall, our results indicate that, although chaos may occur in evolution, it does not necessarily undermine its predictability.

scholarly journals Convergent Evolution of Elongate Forms in Craniates and of Locomotion in Elongate Squamate Reptiles

2020 ◽  
Vol 60 (1) ◽  
pp. 190-201 ◽  
Author(s):  
Philip J Bergmann ◽  
Sara D W Mann ◽  
Gen Morinaga ◽  
Elyse S Freitas ◽  
Cameron D Siler
Keyword(s):  
Convergent Evolution ◽  
Evolutionary Dynamics ◽  
Tree Of Life ◽  
Locomotor Performance ◽  
Vertebral Number ◽  
Body Form ◽  
Squamate Reptiles ◽  
Remote Locations ◽  
Caudal Vertebrae ◽  
Vertebral Shape

Abstract Synopsis Elongate, snake- or eel-like, body forms have evolved convergently many times in most major lineages of vertebrates. Despite studies of various clades with elongate species, we still lack an understanding of their evolutionary dynamics and distribution on the vertebrate tree of life. We also do not know whether this convergence in body form coincides with convergence at other biological levels. Here, we present the first craniate-wide analysis of how many times elongate body forms have evolved, as well as rates of its evolution and reversion to a non-elongate form. We then focus on five convergently elongate squamate species and test if they converged in vertebral number and shape, as well as their locomotor performance and kinematics. We compared each elongate species to closely related quadrupedal species and determined whether the direction of vertebral or locomotor change matched in each case. The five lineages examined are obscure species from remote locations, providing a valuable glimpse into their biology. They are the skink lizards Brachymeles lukbani, Lerista praepedita, and Isopachys anguinoides, the basal squamate Dibamus novaeguineae, and the basal snake Malayotyphlops cf. ruficaudus. Our results support convergence among these species in the number of trunk and caudal vertebrae, but not vertebral shape. We also find that the elongate species are relatively slower than their limbed counterparts and move with lower frequency and higher amplitude body undulations, with the exception of Isopachys. This is among the first evidence of locomotor convergence across distantly related, elongate species.

scholarly journals Mortality and coexistence time both cause changes in predator-prey co-evolutionary dynamics

2020 ◽  
Author(s):  
Thomas Scheuerl ◽  
Veijo Kaitala
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Process ◽  
Mortality Rates ◽  
Predator Prey ◽  
Ecological Changes ◽  
Evolutionary Changes ◽  
Predation Efficiency ◽  
Evolutionary Trajectories ◽  
Predator Defence ◽  
Transfer Interval

AbstractAll organisms are sensitive to the abiotic environment, and in multispecies communities a deteriorating environment increasing mortality and limiting coexistence time can cause ecological changes. When interaction within the community is changed this can impact co-evolutionary processes. Here we use a mathematical model to predict ecological and evolutionary changes in a simple predator-prey community under different mortality rates and times of coexistence, both controlled by various transfer volume and transfer interval. In the simulated bacteria-ciliate system, we find species densities to be surprisingly robust under changed mortality rates and times both species coexist, resulting in stable densities. Confirming a theoretical prediction however, the evolution of anti-predator defence in the bacteria and evolution of predation efficiency in ciliates relax under high mortalities and limited times both partners interact. In contrast, evolutionary trajectories intensify when global mortalities are low, and the predator-prey community has more time for close interaction. These results provide testable hypotheses for future studies of predator-prey systems and we hope this work will help to bridge the gap in our knowledge how ecological and evolutionary process together shape composition of microbial communities.

scholarly journals Tell Me Where You’ve Been and I’ll Tell You How You’ll Evolve

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Marco Fumasoni
Keyword(s):  
High Temperatures ◽  
Adaptive Evolution ◽  
Experimental Evolution ◽  
Evolutionary Biology ◽  
Genetic Basis ◽  
Microbial Populations ◽  
Evolutionary Processes ◽  
Link Type ◽  
Selection Experiments ◽  
Evolutionary Trajectories

ABSTRACT The reproducibility of adaptive evolution is a long-standing debate in evolutionary biology. Kempher et al. (M. L. Kempher, X. Tao, R. Song, B. Wu, et al., mBio 11:e00569-20, 2020, https://doi.org/10.1128/mBio.00569-20) used experimental evolution to investigate the effect of previous evolutionary trajectories on the ability of microbial populations to adapt to high temperatures. Despite the divergence caused by adaptation to previous environments, all populations reproducibly converged on similar final levels of fitness. Nevertheless, the genetic basis of adaptation depended on past selection experiments, reinforcing the idea that previous adaptation can dictate the trajectories of later evolutionary processes.

scholarly journals Parallel evolution of influenza across multiple spatiotemporal scales

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Katherine S Xue ◽  
Terry Stevens-Ayers ◽  
Angela P Campbell ◽  
Janet A Englund ◽  
Steven A Pergam ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
De Novo ◽  
Parallel Evolution ◽  
Global Scale ◽  
De Novo Mutations ◽  
Small Set ◽  
Spatiotemporal Scales ◽  
H3n2 Influenza ◽  
Multiple Patients

Viral variants that arise in the global influenza population begin as de novo mutations in single infected hosts, but the evolutionary dynamics that transform within-host variation to global genetic diversity are poorly understood. Here, we demonstrate that influenza evolution within infected humans recapitulates many evolutionary dynamics observed at the global scale. We deep-sequence longitudinal samples from four immunocompromised patients with long-term H3N2 influenza infections. We find parallel evolution across three scales: within individual patients, in different patients in our study, and in the global influenza population. In hemagglutinin, a small set of mutations arises independently in multiple patients. These same mutations emerge repeatedly within single patients and compete with one another, providing a vivid clinical example of clonal interference. Many of these recurrent within-host mutations also reach a high global frequency in the decade following the patient infections. Our results demonstrate surprising concordance in evolutionary dynamics across multiple spatiotemporal scales.

scholarly journals Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history

PLoS Biology ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. e3001010
Author(s):  
Eva Bons ◽  
Christine Leemann ◽  
Karin J. Metzner ◽  
Roland R. Regoes
Keyword(s):  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Large Population ◽  
Parallel Evolution ◽  
Cell Types ◽  
Drug Pressure ◽  
Evolutionary Paths ◽  
The Impact ◽  
Hiv 1

An often-returning question for not only HIV-1, but also other organisms, is how predictable evolutionary paths are. The environment, mutational history, and random processes can all impact the exact evolutionary paths, but to which extent these factors contribute to the evolutionary dynamics of a particular system is an open question. Especially in a virus like HIV-1, with a large mutation rate and large population sizes, evolution is expected to be highly predictable if the impact of environment and history is low, and evolution is not neutral. We investigated the effect of environment and mutational history by analyzing sequences from a long-term evolution experiment, in which HIV-1 was passaged on 2 different cell types in 8 independent evolutionary lines and 8 derived lines, 4 of which involved a switch of the environment. The experiments lasted for 240–300 passages, corresponding to approximately 400–600 generations or almost 3 years. The sequences show signs of extensive parallel evolution—the majority of mutations that are shared between independent lines appear in both cell types, but we also find that both environment and mutational history significantly impact the evolutionary paths. We conclude that HIV-1 evolution is robust to small changes in the environment, similar to a transmission event in the absence of an immune response or drug pressure. We also find that the fitness landscape of HIV-1 is largely smooth, although we find some evidence for both positive and negative epistatic interactions between mutations.

scholarly journals DISSEQT—DIStribution-based modeling of SEQuence space Time dynamics†

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
R Henningsson ◽  
G Moratorio ◽  
A V Bordería ◽  
M Vignuzzi ◽  
M Fontes
Keyword(s):  
Sequence Space ◽  
Rna Virus ◽  
Population Based ◽  
Space Time ◽  
Fitness Landscapes ◽  
Microbial Populations ◽  
Dynamic Nature ◽  
Time Dynamics ◽  
Low Dimension ◽  
Evolutionary Trajectories

Abstract Rapidly evolving microbes are a challenge to model because of the volatile, complex, and dynamic nature of their populations. We developed the DISSEQT pipeline (DIStribution-based SEQuence space Time dynamics) for analyzing, visualizing, and predicting the evolution of heterogeneous biological populations in multidimensional genetic space, suited for population-based modeling of deep sequencing and high-throughput data. The pipeline is openly available on GitHub (https://github.com/rasmushenningsson/DISSEQT.jl, accessed 23 June 2019) and Synapse (https://www.synapse.org/#!Synapse: syn11425758, accessed 23 June 2019), covering the entire workflow from read alignment to visualization of results. Our pipeline is centered around robust dimension and model reduction algorithms for analysis of genotypic data with additional capabilities for including phenotypic features to explore dynamic genotype–phenotype maps. We illustrate its utility and capacity with examples from evolving RNA virus populations, which present one of the highest degrees of genetic heterogeneity within a given population found in nature. Using our pipeline, we empirically reconstruct the evolutionary trajectories of evolving populations in sequence space and genotype–phenotype fitness landscapes. We show that while sequence space is vastly multidimensional, the relevant genetic space of evolving microbial populations is of intrinsically low dimension. In addition, evolutionary trajectories of these populations can be faithfully monitored to identify the key minority genotypes contributing most to evolution. Finally, we show that empirical fitness landscapes, when reconstructed to include minority variants, can predict phenotype from genotype with high accuracy.

A Study of Feature Selection and Dimensionality Reduction Methods for Classification-Based Phishing Detection System

2021 ◽  
Vol 11 (1) ◽  
pp. 1-35
Author(s):  
Amit Singh ◽  
Abhishek Tiwari
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Dimensionality Reduction ◽  
Detection System ◽  
Parallel Evolution ◽  
Feature Selection Method ◽  
Sensitive Information ◽  
Selection Methods ◽  
Survey Paper ◽  
Reduction Methods

Phishing was introduced in 1996, and now phishing is the biggest cybercrime challenge. Phishing is an abstract way to deceive users over the internet. Purpose of phishers is to extract the sensitive information of the user. Researchers have been working on solutions of phishing problem, but the parallel evolution of cybercrime techniques have made it a tough nut to crack. Recently, machine learning-based solutions are widely adopted to tackle the menace of phishing. This survey paper studies various feature selection method and dimensionality reduction methods and sees how they perform with machine learning-based classifier. The selection of features is vital for developing a good performance machine learning model. This work is comparing three broad categories of feature selection methods, namely filter, wrapper, and embedded feature selection methods, to reduce the dimensionality of data. The effectiveness of these methods has been assessed on several machine learning classifiers using k-fold cross-validation score, accuracy, precision, recall, and time.

Ecological Opportunities, Communities, and Evolution

2017 ◽  
Author(s):  
Mark A. McPeek
Keyword(s):  
Climate Change ◽  
Community Structure ◽  
Community Ecology ◽  
Local Community ◽  
Evolutionary Dynamics ◽  
Evolutionary Adaptation ◽  
Regional Patterns ◽  
Interacting Species ◽  
Evolutionary Trajectories ◽  
Regional Community

This book investigates how local and regional patterns of community structure develop across space and through time by focusing on the theoretical interrelationships among community ecology, evolutionary adaptation, dispersal, and speciation and extinction. It discusses the purely ecological dynamics of interacting species in different community modules, how species in simple community modules evolve to adapt to one another, and how speciation and biogeographic mixing of taxa influence local community structure. It also examines community mixing due to climate change and how regional community structure is shaped by the ecological and evolutionary dynamics of species across a metacommunity. This introduction provides an overview of the evolutionary trajectories of various species in the context of ecological opportunity and community ecology, aggregated taxa in the trophic web, types of species found in a community, sources of biodiversity in a community, and the dynamics of natural selection, coevolution, and community structure.

scholarly journals LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life

2016 ◽  
Vol 8 (11) ◽  
pp. 3301-3322 ◽  
Author(s):  
Atma M. Ivancevic ◽  
R. Daniel Kortschak ◽  
Terry Bertozzi ◽  
David L. Adelson
Keyword(s):  
Evolutionary Dynamics ◽  
Tree Of Life
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