Evolutionary Dynamics in the RNA Bacteriophage Qβ Depends on the Pattern of Change in Selective Pressures

The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qβ) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qβ, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways.

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Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Nature Communications ◽

10.1038/s41467-021-20958-2 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

H. De Kort ◽

J. G. Prunier ◽

S. Ducatez ◽

O. Honnay ◽

M. Baguette ◽

...

Keyword(s):

Genetic Diversity ◽

Life History ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Peripheral Populations ◽

Plant Dispersal ◽

Weak Support ◽

Animal Populations ◽

Plant Groups ◽

Conservation Genetic

AbstractUnderstanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

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Molecular Evolutionary Dynamics of Respiratory Syncytial Virus Group A in Recurrent Epidemics in Coastal Kenya

Journal of Virology ◽

10.1128/jvi.03105-15 ◽

2016 ◽

Vol 90 (10) ◽

pp. 4990-5002 ◽

Cited By ~ 19

Author(s):

James R. Otieno ◽

Charles N. Agoti ◽

Caroline W. Gitahi ◽

Ann Bett ◽

Mwanajuma Ngama ◽

...

Keyword(s):

Genetic Diversity ◽

Respiratory Syncytial Virus ◽

Time Scales ◽

Evolutionary Dynamics ◽

Nucleotide Substitutions ◽

High Genetic Diversity ◽

Data Set ◽

New Variant ◽

Syncytial Virus ◽

Highest Posterior Density

ABSTRACTThe characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing the efficiency of preexisting immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000 to 2012) in Kilifi (n= 649), Kenya, and contemporaneous sequences (n= 1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%), and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2 and then GA2 by ON1. Within these genotypes, there was considerable variation in potentialN-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi data set was estimated at 3.58 × 10−3(95% highest posterior density interval = 3.04 to 4.16) nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences. Our findings highlight ongoing genetic evolution and high diversity of circulating RSV-A strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics.IMPORTANCEThe mechanisms underlying recurrent epidemics of RSV are poorly understood. We observe high genetic diversity in circulating strains within and between epidemics in both local and global settings. On longer time scales (∼7 years) there is sequential replacement of genotypes, whereas on shorter time scales (one epidemic to the next or within epidemics) there is a high turnover of variants within genotypes. Further, this genetic diversity is predicted to be associated with variation in antigenic profiles. These observations provide an explanation for recurrent RSV epidemics and have potential implications on the long-term effectiveness of vaccines.

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Phylogeography of post-Pleistocene population expansion in Dasyscyphella longistipitata (Leotiomycetes, Helotiales), an endemic fungal symbiont of Fagus crenata in Japan

MycoKeys ◽

10.3897/mycokeys.65.48409 ◽

2020 ◽

Vol 65 ◽

pp. 1-24

Author(s):

Jaime Gasca-Pineda ◽

Patricia Velez ◽

Tsuyoshi Hosoya

Keyword(s):

Genetic Diversity ◽

Environmental Changes ◽

Continuous Distribution ◽

Population Expansion ◽

Fagus Crenata ◽

High Genetic Diversity ◽

Environmental Suitability ◽

The Japanese Archipelago ◽

The Last Glacial Maximum ◽

The Last Glacial

During the Last Glacial Maximum (LGM), drastic environmental changes modified the topology of the Japanese Archipelago, impacting species distributions. An example is Fagus crenata, which has a present continuous distribution throughout Japan. However, by the end of the LGM it was restricted to southern refugia. Similarly, Dasyscyphella longistipitata (Leotiomycetes, Helotiales, Lachnaceae) occurs strictly on cupules of F. crenata, sharing currently an identical distribution. As the effects of the LGM remain poorly understood for saprobiotic microfungal species, herein we identified past structuring forces that shaped the current genetic diversity within D. longistipitata in relation to its host using a phylogeographic approach. We inferred present and past potential distributions through species distribution modeling, identifying environmental suitability areas in mid-southern Japan from which subsequent colonizations occurred. Our findings suggest that current high genetic diversity and lack of genetic structure within D. longistipitata are the result of recent multiple re-colonization events after the LGM.

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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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Genetic diversity and conservation of the endemic tuco-tuco Ctenomys ibicuiensis (Rodentia: Ctenomyidae)

Journal of Mammalogy ◽

10.1093/jmammal/gyaa119 ◽

2020 ◽

Author(s):

Mayara Delagnelo Medeiros ◽

Daniel Galiano ◽

Bruno Busnello Kubiak ◽

Paula Angélica Roratto ◽

Thales Renato Ochotorena de Freitas

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Environmental Changes ◽

Isolation By Distance ◽

Conservation Status ◽

Significant Risk ◽

Structured Populations ◽

Small Range ◽

High Genetic Diversity ◽

Landscape Modification

Abstract Endemic, small range species are susceptible to environmental changes and landscape modification. Understanding genetic diversity and distributional patterns is important for implementation of effective conservation measures. In this context, genetic diversity was evaluated to update the conservation status of an endemic tuco-tuco, Ctenomys ibicuiensis. Phylogeographic and population genetic analyses of mitochondrial DNA and microsatellite loci were carried out using 46 individuals sampled across the species’ distribution. Ctenomys ibicuiensis presented moderate to high genetic diversity and highly structured populations with low levels of gene flow and isolation by distance. Anthropogenic landscape changes threaten this restricted-range tuco-tuco. Considering its limited geographic distribution and highly structured populations with low gene flow, we consider C. ibicuiensis to be at significant risk of extinction.

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Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting (Emberiza jankowskii)

PeerJ ◽

10.7717/peerj.2917 ◽

2017 ◽

Vol 5 ◽

pp. e2917 ◽

Cited By ~ 2

Author(s):

Dan Li ◽

Keping Sun ◽

Yunjiao Zhao ◽

Aiqing Lin ◽

Shi Li ◽

...

Keyword(s):

Genetic Diversity ◽

Major Histocompatibility Complex ◽

Mhc Class Ii ◽

Nucleotide Diversity ◽

Environmental Changes ◽

Major Histocompatibility ◽

High Genetic Diversity ◽

Exon 2 ◽

Histocompatibility Complex ◽

Segregating Sites

Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size. Many historically significant populations are no longer present in previously populated regions, with only three breeding populations present in Inner Mongolia (i.e., the Aolunhua, Gahaitu and Lubei557 populations). Efforts focused on facilitating the conservation of the Rufous-backed Bunting (Emberiza jankowskii) are becoming increasingly important. However, the genetic diversity ofE. jankowskiihas not been investigated. In the present study, polymorphism in exon 2 of the MHCIIB ofE. jankowskiiwas investigated. This polymorphism was subsequently compared with a related species, the Meadow Bunting (Emberiza cioides). A total of 1.59 alleles/individual were detected inE. jankowskiiand 1.73 alleles/individual were identified inE.cioides. The maximum number of alleles per individual from the threeE. jankowskiipopulations suggest the existence of at least three functional loci, while the maximum number of alleles per individual from the threeE. cioidespopulations suggest the presence of at least four functional loci. Two of the alleles were shared between theE. jankowskiiandE. cioides. Among the 12 unique alleles identified inE. jankowskii, 10.17 segregating sites per allele were detected, and the nucleotide diversity was 0.1865. Among the 17 unique alleles identified inE. cioides, eight segregating sites per allele were detected, and the nucleotide diversity was 0.1667. Overall, compared to other passerine birds, a relatively low level of MHC polymorphism was revealed inE. jankowskii, which was similar to that inE. cioides. Positive selection was detected by PAML/SLAC/FEL analyses in the region encoding the peptide-binding region in both species, and no recombination was detected. Phylogenetic analysis showed that the alleles fromE. jankowskiiandE. cioidesbelong to the same clade and the two species shared similar alleles, suggesting the occurrence of a trans-species polymorphism between the twoEmberizaspecies.

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Characterization of Lebanese Germplasm of Snake Melon (Cucumis melo subsp. melo var. flexuosus) Using Morphological Traits and SSR Markers

Agronomy ◽

10.3390/agronomy10091293 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1293

Author(s):

Joe Merheb ◽

Magdalena Pawełkowicz ◽

Ferdinando Branca ◽

Hanna Bolibok-Brągoszewska ◽

Agnieszka Skarzyńska ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Skin Color ◽

Cucumis Melo ◽

Environmental Changes ◽

Phenotypic Variability ◽

Morphological Variability ◽

Color Pattern ◽

High Genetic Diversity ◽

Improvement Programs

Snake melon (Cucumis melo subsp. melo L. var. flexuosus (L.) Naudin) is an ancient and traditional crop in the Mediterranean region. Nevertheless, there has been poor interest in assessing snake melon germplasm where its genetic resources have not been surveyed before despite their potential in adaptation to environmental changes. In this study, we assess the genetic diversity of snake melon landraces collected from different Lebanese regions at both morphological and molecular levels. Morphological characterization using a set of 18 descriptors revealed an important phenotypic variability among the landraces studied. Principle component analysis indicated that fruit hair and its consistency, fruit size, and skin color pattern were good criteria for discriminating among landraces. Based on the scatter plot diagram, landraces of snake melon formed five different groups with one being defined as typical var. flexuosus. Ten simple sequence repeat (SSR) markers were used for the molecular characterization. Fifty-six different alleles were detected, with an average of 5.6 alleles per locus. Polymorphism information content of SSR markers ranged from 0.06 to 0.84 (average 0.38). Cluster analysis based on molecular markers showed high genetic diversity and divided the landraces into five distinct genetic groups, confirming thereby the morphological variability. Findings of this study indicate a significant diversity for the Lebanese snake melon germplasm that must be further conserved and considered in improvement programs of this ancient crop.

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The Ecology of Bacterial Genes and the Survival of the New

International Journal of Evolutionary Biology ◽

10.1155/2012/394026 ◽

2012 ◽

Vol 2012 ◽

pp. 1-14 ◽

Cited By ~ 17

Author(s):

M. Pilar Francino

Keyword(s):

Evolutionary Dynamics ◽

Environmental Changes ◽

Gene Families ◽

Relative Importance ◽

Gene Duplications ◽

Bacterial Genomes ◽

Selective Pressures ◽

Different Types ◽

Bacterial Genes ◽

Gains And Losses

Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.

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Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

10.1101/016493 ◽

2015 ◽

Author(s):

Emiliano Trucchi ◽

Benoit Facon ◽

Paolo Gratton ◽

Emiliano Mori ◽

Nils Chr. Stenseth ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Leading Edge ◽

High Genetic Diversity ◽

Hystrix Cristata ◽

The North ◽

Fundamental Information ◽

Genome Wide ◽

Crested Porcupine ◽

Species Specific

AbstractStudying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.

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

Genome Biology and Evolution ◽

10.1093/gbe/evz243 ◽

2019 ◽

Author(s):

Tanita Wein ◽

Tal Dagan

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Natural Populations ◽

Population Bottleneck ◽

Population Bottlenecks ◽

High Genetic Diversity ◽

Temperature Regimes ◽

Consequent Reduction ◽

History Of

Abstract Population 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 population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (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 regardless the bottleneck size, 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 bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

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