Pseudofinder: detection of pseudogenes in prokaryotic genomes

Prokaryotic genomes are generally gene dense and encode relatively few pseudogenes, or nonfunctional/inactivated remnants of genes. However, in certain contexts, such as recent ecological shifts or extreme population bottlenecks (such as those experienced by symbionts and pathogens), pseudogenes can quickly accumulate and form a substantial fraction of the genome. Identification of pseudogenes is, thus, a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis. With Pseudofinder's multi-pronged, reference-based approach, we demonstrate its capacity to detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes, which can have only one or a few inactivating mutations. Additionally, Pseudofinder can detect intact genes undergoing relaxed selection, which may indicate incipient pseudogene formation. Implementation of Pseudofinder in annotation pipelines will not only clarify the functional potential of sequenced microbes, but will also generate novel insights and hypotheses regarding the evolutionary dynamics of bacterial and archaeal genomes.

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Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

10.1101/709832 ◽

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.

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Daphnia as a Model for Eco-evolutionary Dynamics

10.1093/oso/9780190620271.003.0016 ◽

2018 ◽

pp. 403-424

Author(s):

Matthew R. Walsh ◽

Michelle Packer ◽

Shannon Beston ◽

Collin Funkhouser ◽

Michael Gillis ◽

...

Keyword(s):

Life History ◽

Evolutionary Dynamics ◽

Model Organism ◽

Life History Evolution ◽

Ecological Processes ◽

Evolutionary Forces ◽

Evolutionary Changes ◽

History Evolution ◽

Ecological Importance ◽

The Many

Much research has shown that variation in ecological processes can drive rapid evolutionary changes over periods of years to decades. Such contemporary adaptation sets the stage for evolution to have reciprocal impacts on the properties of populations, communities, and ecosystems, with ongoing interactions between ecological and evolutionary forces. The importance and generality of these eco-evolutionary dynamics are largely unknown. In this chapter, we promote the use of water fleas (Daphnia sp.) as a model organism in the exploration of eco-evolutionary interactions in nature. The many characteristics of Daphnia that make them suitable for laboratory study in conjunction with their well-known ecological importance in lakes, position Daphnia to contribute new and important insights into eco-evolutionary dynamics. We first review the influence of key environmental stressors in Daphnia evolution. We then highlight recent work documenting the pathway from life history evolution to ecology using Daphnia as a model. This review demonstrates that much is known about the influence of ecology on Daphnia life history evolution, while research exploring the genomic basis of adaptation as well as the influence of Daphnia life history traits on ecological processes is beginning to accumulate.

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Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds

Genome Biology and Evolution ◽

10.1093/gbe/evz154 ◽

2019 ◽

Vol 11 (8) ◽

pp. 2376-2390 ◽

Cited By ~ 13

Author(s):

Luohao Xu ◽

Simon Yung Wa Sin ◽

Phil Grayson ◽

Scott V Edwards ◽

Timothy B Sackton

Keyword(s):

Sex Chromosomes ◽

Evolutionary Dynamics ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Z Chromosome ◽

Recombination Suppression ◽

Evolutionary Forces ◽

Genomic Level ◽

Standard Models ◽

Pseudoautosomal Regions

Abstract Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.

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Evolutionary dynamics of human and avian metapneumoviruses

Journal of General Virology ◽

10.1099/vir.0.2008/006957-0 ◽

2008 ◽

Vol 89 (12) ◽

pp. 2933-2942 ◽

Cited By ~ 67

Author(s):

Miranda de Graaf ◽

Albert D. M. E. Osterhaus ◽

Ron A. M. Fouchier ◽

Edward C. Holmes

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Recent Common Ancestor ◽

Human Populations ◽

Population Bottlenecks ◽

Genetic Lineages ◽

The Past ◽

Most Recent Common Ancestor ◽

Large Sets ◽

Respiratory Tract Illnesses

Human (HMPV) and avian (AMPV) metapneumoviruses are closely related viruses that cause respiratory tract illnesses in humans and birds, respectively. Although HMPV was first discovered in 2001, retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV was first isolated in the 1970s, and can be classified into four subgroups, A–D. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has emerged from AMPV-C upon zoonosis. Presently, at least four genetic lineages of HMPV circulate in human populations – A1, A2, B1 and B2 – of which lineages A and B are antigenically distinct. We used a Bayesian Markov Chain Monte Carlo (MCMC) framework to determine the evolutionary and epidemiological dynamics of HMPV and AMPV-C. The rates of nucleotide substitution, relative genetic diversity and time to the most recent common ancestor (TMRCA) were estimated using large sets of sequences of the nucleoprotein, the fusion protein and attachment protein genes. The sampled genetic diversity of HMPV was found to have arisen within the past 119–133 years, with consistent results across all three genes, while the TMRCA for HMPV and AMPV-C was estimated to have existed around 200 years ago. The relative genetic diversity observed in the four HMPV lineages was low, most likely reflecting continual population bottlenecks, with only limited evidence for positive selection.

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Increased pollination specialization did not increase corolla shape constraints in Antillean plants

10.1101/041533 ◽

2016 ◽

Cited By ~ 1

Author(s):

Simon Joly ◽

François Lambert ◽

Hermine Alexandre ◽

Julien Clavel ◽

Étienne Léveillé-Bourret ◽

...

Keyword(s):

Structural Variation ◽

Reproductive Organs ◽

Evolutionary Constraints ◽

Evolutionary Models ◽

Relaxed Selection ◽

Generalist Species ◽

Evolutionary Forces ◽

Pollination Strategy ◽

Effective Pollinators ◽

Generalist Pollination

AbstractFlowers show important structural variation as reproductive organs but the evolutionary forces underlying this diversity are still poorly understood. In animal-pollinated species, flower shape is strongly fashioned by selection imposed by pollinators, which is expected to vary according to guilds of effective pollinators. Using the Antillean subtribe Gesneriinae (Gesneriaceae), we tested the hypothesis that pollination specialists pollinated by one functional type of pollinator have maintained more similar corolla shapes through time due to stronger selection constraints compared to species with more generalist pollination strategies. Using geometric morphometrics and evolutionary models, we showed that the corolla of hummingbird specialists, bat specialists, and species with a mixed-pollination strategy (pollinated by hummingbirds and bats; thus a more generalist strategy) have distinct shapes and that these shapes have evolved under evolutionary constraints. However, we did not find support for smaller disparity in corolla shape for hummingbird specialists compared to more generalist species. This could be because the corolla shape of more generalist species in subtribe Gesneriinae, which has evolved multiple times, is finely adapted to be effectively pollinated by both bats and hummingbirds. These results suggest that pollination generalization is not necessarily associated with relaxed selection constraints.

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Evolutionary dynamics of sex chromosomes of paleognathous birds

10.1101/295089 ◽

2018 ◽

Cited By ~ 3

Author(s):

Luohao Xu ◽

Simon Yung Wa Sin ◽

Phil Grayson ◽

Scott V. Edwards ◽

Timothy B. Sackton

Keyword(s):

Sex Chromosomes ◽

Evolutionary Dynamics ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Z Chromosome ◽

Recombination Suppression ◽

Evolutionary Forces ◽

Genomic Level ◽

Standard Models ◽

Pseudoautosomal Regions

AbstractStandard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large non-degenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over more than 100 MY, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analysed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions or DRs), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in DRs for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.

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Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

10.1101/210955 ◽

2017 ◽

Cited By ~ 10

Author(s):

Nandita R. Garud ◽

Benjamin H. Good ◽

Oskar Hallatschek ◽

Katherine S. Pollard

Keyword(s):

Evolutionary Dynamics ◽

Purifying Selection ◽

Gut Bacteria ◽

Fundamental Limits ◽

Evolutionary Forces ◽

Standard Population ◽

Evolutionary Changes ◽

Or Gene ◽

Adult Twins ◽

Long Timescales

AbstractGut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in ∼30 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over ∼6 month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps are seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.

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Evolution with a seed bank: the population genetic consequences of microbial dormancy

10.1101/156356 ◽

2017 ◽

Author(s):

WR Shoemaker ◽

JT Lennon

Keyword(s):

Seed Bank ◽

Population Genetic ◽

Evolutionary Dynamics ◽

Phenotypic Diversity ◽

Seed Banks ◽

Hedging Strategy ◽

Term Survival ◽

Evolutionary Forces ◽

Growth And Reproduction

ABSTRACTDormancy is a bet-hedging strategy that allows organisms to persist through conditions that are sub-optimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long-term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence microbial evolutionary dynamics.

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The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

10.1101/726158 ◽

2019 ◽

Author(s):

Tanita Wein ◽

Tal Dagan

Keyword(s):

Genetic Diversity ◽

Genetic Drift ◽

Evolutionary Dynamics ◽

Natural Populations ◽

Population Bottleneck ◽

Population Bottlenecks ◽

High Genetic Diversity ◽

Temperature Regimes ◽

Consequent Reduction ◽

History Of

AbstractPopulation bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to genetic drift following population bottlenecks. We evolved Escherichia coli populations under three different population bottlenecks (small, medium, large) in two temperature regimes (37°C and 20°C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity in all bottleneck sizes, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of the evolvability in bacteria; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

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Robust detection of natural selection using a probabilistic model of tree imbalance

10.1101/2021.05.12.443797 ◽

2021 ◽

Author(s):

Enes Dilber ◽

Jonathan Terhorst

Keyword(s):

Natural Selection ◽

Open Source Software ◽

Probabilistic Model ◽

Simulated Data ◽

Population Expansion ◽

Effective Population ◽

Robust Detection ◽

Evolutionary Forces ◽

Tree Topologies ◽

Neutrality Tests

Neutrality tests such as Tajima's D and Fay and Wu's H are standard implements in the population genetics toolbox. One of their most common uses is to scan the genome for signals of natural selection. However, it is well understood that deviance measures like D and H are confounded by other evolutionary forces---in particular, population expansion---that may be unrelated to selection. Because they are not model-based, it is not clear how to deconfound these statistics in a principled way. In this paper we derive new likelihood-based methods for detecting natural selection which are robust to confounding by fluctuations in effective population size. At the core of our method is a novel probabilistic model of tree imbalance, which generalizes Kingman's coalescent to allow certain aberrant tree topologies to arise more frequently than is expected under neutrality. We derive a frequency spectrum-based estimator which can be used in place of D, and also extend to the case where genealogies are first estimated. We benchmark our methods on real and simulated data, and provide an open source software implementation.

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