Charles Darwin Meets Ronald Ross: A Population-Genetic Framework for the Evolutionary Dynamics of Malaria

Abstract Spore killing in ascomycetes is a special form of segregation distortion. When a strain with the Killer genotype is crossed to a Sensitive type, spore killing is expressed by asci with only half the number of ascospores as usual, all surviving ascospores being of the Killer type. Using population genetic modeling, this paper explores conditions for invasion of Spore killers and for polymorphism of Killers, Sensitives and Resistants (which neither kill, nor get killed), as found in natural populations. The models show that a population with only Killers and Sensitives can never be stable. The invasion of Killers and stable polymorphism only occur if Killers have some additional advantage during the process of spore killing. This may be due to the effects of local sib competition or some kind of "heterozygous" advantage in the stage of ascospore formation or in the short diploid stage of the life cycle. This form of segregation distortion appears to be essentially different from other, well-investigated forms, and more field data are needed for a better understanding of spore killing.

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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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Genome analysis of the monoclonal marbled crayfish reveals genetic separation over a short evolutionary timescale

Communications Biology ◽

10.1038/s42003-020-01588-8 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Olena Maiakovska ◽

Ranja Andriantsoa ◽

Sina Tönges ◽

Carine Legrand ◽

Julian Gutekunst ◽

...

Keyword(s):

Data Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Population Genetic ◽

Evolutionary Dynamics ◽

Whole Genome Sequencing Data ◽

Freshwater Crayfish ◽

Whole Genome ◽

Size Estimation ◽

Marbled Crayfish

AbstractThe marbled crayfish (Procambarus virginalis) represents a very recently evolved parthenogenetic freshwater crayfish species that has invaded diverse habitats in Europe and in Madagascar. However, population genetic analyses have been hindered by the homogeneous genetic structure of the population and the lack of suitable tools for data analysis. We have used whole-genome sequencing to characterize reference specimens from various known wild populations. In parallel, we established a whole-genome sequencing data analysis pipeline for the population genetic analysis of nearly monoclonal genomes. Our results provide evidence for systematic genetic differences between geographically separated populations and illustrate the emerging differentiation of the marbled crayfish genome. We also used mark-recapture population size estimation in combination with genetic data to model the growth pattern of marbled crayfish populations. Our findings uncover evolutionary dynamics in the marbled crayfish genome over a very short evolutionary timescale and identify the rapid growth of marbled crayfish populations as an important factor for ecological monitoring.

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Legacy parasite collections reveal species-specific population genetic patterns among three species of zoonotic schistosomes (Trematoda: Schistosomatidae)

10.22541/au.163352156.62491828/v1 ◽

2021 ◽

Author(s):

Erika Ebbs ◽

Eric Loker ◽

D'Eldra Malone ◽

Sean Locke ◽

Norm Davis ◽

...

Keyword(s):

Genetic Diversity ◽

Natural History ◽

Population Genetic ◽

Evolutionary Dynamics ◽

Zoonotic Disease ◽

Population History ◽

Effective Size ◽

Temporal Sampling ◽

Species Specific ◽

Host Parasite

Multi-host helminth systems are difficult to study at a population level due to inherent spatial and temporal sampling challenges. Consequently, our understanding of the factors affecting gene flow, genetic drift and effective population size is limited. Population genetic parameters (Ne, Θ, π) are necessary in understanding fundamental processes in host-parasite evolution such as co-evolutionary dynamics, spread of resistance alleles and local adaptation. This study used museum specimens collected over 20-years of three congeneric trematode (Schistosomatidae) species: Trichobilharzia querquedulae, T. physellae, and Trichobilharzia species A . All contribute to the worldwide zoonotic disease cercarial dermatitis (i.e. swimmers Itch). Populations of each species were sampled for two mitochondrial (cox1 and nad4) and one nuclear loci (ITS1) to estimate population genetic structure, genetic diversity, effective size and population history. Significant differences in these measures were revealed among the three congeners. Trichobilharzia querquedulae maintained a well-connected globally diverse metapopulation, with an effective size approximately three times that of the other two species, which were characterized by lower overall genetic diversity and greater population structure, mediated by the definitive duck host. We hypothesize that the species-specific patterns are due to distinctive ecological preferences and migratory behaviors of their respective definitive hosts. This study demonstrates the value of natural history collections to facilitate population genetic studies that would otherwise be infeasible. Applying population genetic data within this comparative congeneric framework allows us to tease apart particular aspects of host-parasite natural history and its influence on microevolutionary patterns within complex helminth systems, including contributions to zoonotic disease.

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Hybridization and rampant mitochondrial introgression among fire salamanders in peninsular Italy

10.1101/258541 ◽

2018 ◽

Author(s):

Roberta Bisconti ◽

Daniele Porretta ◽

Paola Arduino ◽

Giuseppe Nascetti ◽

Daniele Canestrelli

Keyword(s):

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Evolutionary Dynamics ◽

Reticulate Evolution ◽

Secondary Contact ◽

Mitochondrial Introgression ◽

Fire Salamander ◽

Salamandra Salamandra ◽

Fossil Data

ABSTRACTDiscordance between mitochondrial and nuclear patterns of population genetic structure is providing key insights into the eco-evolutionary dynamics between and within species, and their assessment is highly relevant to biodiversity monitoring practices based on DNA barcoding approaches. Here, we investigate the population genetic structure of the fire salamander Salamandra salamandra in peninsular Italy. Both mitochondrial and nuclear markers clearly identified two main population groups. However, nuclear and mitochondrial zones of geographic transition between groups were located 600 km from one another. The overall pattern of genetic variation, together with morphological and fossil data, suggest that a rampant mitochondrial introgression triggered the observed mitonuclear discordance, following a post-glacial secondary contact between lineages. Moreover, at a shallower level of population structure, we observed evidence of asymmetric introgression of nuclear genes between two sub-groups in southern Italy. Our results clearly show the major role played by reticulate evolution in shaping the structure of Salamandra salamandra populations and, together with similar findings in other regions of the species’ range, contribute to identify the fire salamander as a particularly intriguing case to investigate the complexity of mechanisms triggering patterns of mitonuclear discordance in animals.

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Trait Evolution in Microbial Communities

10.1101/2020.12.15.422935 ◽

2020 ◽

Author(s):

Lihong Zhao ◽

Benjamin J Ridenhour ◽

Christopher H Remien

Keyword(s):

Microbial Communities ◽

Population Dynamic ◽

Population Genetic ◽

Evolutionary Dynamics ◽

Relative Fitness ◽

Dynamic Parameters ◽

Population Dynamic Model ◽

Host Health ◽

And Shifts ◽

Over Time

Understanding the evolutionary dynamics of microbial communities is a key step towards the goal of predicting and manipulating microbiomes to promote beneficial states. While interactions within microbiomes and between microbes and their environment collectively determine the community composition and population dynamics, we are often concerned with traits or functions of a microbiome that link more directly to host health. To study how traits of a microbiome are impacted by eco-evolutionary dynamics, we recast a classic resource-mediated population dynamic model into a population genetic framework which incorporates traits. The relative fitness of each group of microbes can be explicitly written in terms of population dynamic parameters, and corresponding evolutionary dynamics emerge. Using several example systems, we demonstrate how natural selection, mutation, and shifts in the environment work together to produce changes in traits over time.

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Population genetics of polymorphism and divergence in rapidly evolving populations

10.1101/2021.06.28.450258 ◽

2021 ◽

Author(s):

Matthew J. Melissa ◽

Benjamin H Good ◽

Daniel S Fisher ◽

Michael M. Desai

Keyword(s):

Traveling Wave ◽

Population Genetic ◽

Evolutionary Dynamics ◽

Frequency Spectra ◽

Fitness Effects ◽

Wide Range ◽

Fixation Probabilities ◽

Wave Models ◽

Traditional Population ◽

Evolving Populations

In rapidly evolving populations, numerous beneficial and deleterious mutations can arise and segregate within a population at the same time. In this regime, evolutionary dynamics cannot be analyzed using traditional population genetic approaches that assume that sites evolve independently. Instead, the dynamics of many loci must be analyzed simultaneously. Recent work has made progress by first analyzing the fitness variation within a population, and then studying how individual lineages interact with this traveling fitness wave. However, these "traveling wave" models have previously been restricted to extreme cases where selection on individual mutations is either much faster or much slower than the typical coalescent timescale T_c. In this work, we show how the traveling wave framework can be extended to intermediate regimes in which the scaled fitness effects of mutations (T_c s) are neither large nor small compared to one. This enables us to describe the dynamics of populations subject to a wide range of fitness effects, and in particular, in cases where it is not immediately clear which mutations are most important in shaping the dynamics and statistics of genetic diversity. We use this approach to derive new expressions for the fixation probabilities and site frequency spectra of mutations as a function of their scaled fitness effects, along with related results for the coalescent timescale T_c and the rate of adaptation or Muller's ratchet. We find that competition between linked mutations can have a dramatic impact on the proportions of neutral and selected polymorphisms, which is not simply summarized by the scaled selection coefficient T_c s. We conclude by discussing the implications of these results for population genetic inferences.

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Adaptation to fragmentation: evolutionary dynamics driven by human influences

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2016.0037 ◽

2017 ◽

Vol 372 (1712) ◽

pp. 20160037 ◽

Cited By ~ 50

Author(s):

Pierre-Olivier Cheptou ◽

Anna L. Hargreaves ◽

Dries Bonte ◽

Hans Jacquemyn

Keyword(s):

Population Genetic ◽

Evolutionary Dynamics ◽

Evolutionary Ecology ◽

Biotic Interactions ◽

Landscape Scale ◽

Adaptive Potential ◽

Demographic Stochasticity ◽

Negative Effects ◽

Major Threat ◽

Dispersal Traits

Fragmentation—the process by which habitats are transformed into smaller patches isolated from each other—has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions. While species have adapted to natural fragmentation, adaptation to anthropogenic fragmentation has received little attention. In this review, we address how and whether organisms might adapt to anthropogenic fragmentation. Drawing on selected case studies and evolutionary ecology models, we show that anthropogenic fragmentation can generate selection on traits at both the patch and landscape scale, and affect the adaptive potential of populations. We suggest that dispersal traits are likely to experience especially strong selection, as dispersal both enables migration among patches and increases the risk of landing in the inhospitable matrix surrounding them. We highlight that suites of associated traits are likely to evolve together. Importantly, we show that adaptation will not necessarily rescue populations from the negative effects of fragmentation, and may even exacerbate them, endangering the entire metapopulation. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.

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Phylogenetics, Genomic Recombination, and NSP2 Polymorphic Patterns of Porcine Reproductive and Respiratory Syndrome Virus in China and the United States in 2014–2018

Journal of Virology ◽

10.1128/jvi.01813-19 ◽

2020 ◽

Vol 94 (6) ◽

Cited By ~ 5

Author(s):

Fang Yu ◽

Yi Yan ◽

Mang Shi ◽

Hai-Zhou Liu ◽

Hong-Liang Zhang ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Hot Spots ◽

Population Genetic ◽

Evolutionary Dynamics ◽

Nonstructural Protein ◽

The United States ◽

Population Genetic Diversity ◽

Recombination Hot Spots ◽

Genomic Recombination

ABSTRACT Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen that affects the pig industry, is a highly genetically diverse RNA virus. However, the phylogenetic and genomic recombination properties of this virus have not been completely elucidated. In this study, comparative analyses of all available genomic sequences of North American (NA)-type PRRSVs (n = 355, including 138 PRRSV genomes sequenced in this study) in China and the United States during 2014–2018 revealed a high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and the GP2 to GP3 regions. Lineage 1 (L1) PRRSV was found to be susceptible to recombination among PRRSVs both in China and the United States. The recombinant major parent between the 1991–2013 data and the 2014–2018 data showed a trend from complex to simple. The major recombination pattern changed from an L8 to L1 backbone during 2014–2018 for Chinese PRRSVs, whereas L1 was always the major backbone for US PRRSVs. Intralineage recombination hot spots were not as concentrated as interlineage recombination hot spots. In the two main clades with differential diversity in L1, NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, NADC34-like PRRSVs have been relatively stable in population genetic diversity for years. Systematic analyses of insertion and deletion (indel) polymorphisms of NSP2 divided PRRSVs into 25 patterns, which could generate novel references for the classification of PRRSVs. The results of this study contribute to a deeper understanding of the recombination of PRRSVs and indicate the need for coordinated epidemiological investigations among countries. IMPORTANCE Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine diseases. However, the phylogenetic and genomic recombination properties of the PRRS virus (PRRSV) have not been completely elucidated. In this study, we systematically compared differences in the lineage distribution, recombination, NSP2 polymorphisms, and evolutionary dynamics between North American (NA)-type PRRSVs in China and in the United States. Strikingly, we found high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and in the GP2 to GP3 region. Also, intralineage recombination hot spots were scattered across the genome between Chinese and US strains. Furthermore, we proposed novel methods based on NSP2 indel patterns for the classification of PRRSVs. Evolutionary dynamics analysis revealed that NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, suggesting that a dominant population may occur and cause an outbreak. Our findings offer important insights into the recombination of PRRSVs and suggest the need for coordinated international epidemiological investigations.

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Darwin in the Clockworks

10.1093/oso/9780198805847.003.0010 ◽

2018 ◽

Author(s):

David D. Nolte

Keyword(s):

Game Theory ◽

New Species ◽

Molecular Evolution ◽

Phase Space ◽

Evolutionary Dynamics ◽

Charles Darwin ◽

Replicator Dynamics ◽

Natural Evolution ◽

Linus Pauling ◽

Gregor Mendel

The preceding chapters established the central role played by families of trajectories in phase space to explain the time evolution of complex systems. This chapter, in turn, uses these ideas to explore the history and development of the theory of natural evolution by Charles Darwin and others. Darwin had many influences, including ideas from Thomas Malthus in the context of economic dynamics. After Darwin, the ideas of evolution matured to encompass broad topics in evolutionary dynamics and the emergence of the idea of fitness landscapes and game theory driving the origin of new species. This chapter shows how the rise of genetics with Gregor Mendel supplied a firm foundation for molecular evolution, leading to the molecular clock of Linus Pauling and the replicator dynamics of Richard Dawkins.

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