scholarly journals Genomic changes under rapid evolution: selection for parasitoid resistance

2014 ◽  
Vol 281 (1779) ◽  
pp. 20132303 ◽  
Author(s):  
Kirsten M. Jalvingh ◽  
Peter L. Chang ◽  
Sergey V. Nuzhdin ◽  
Bregje Wertheim
Keyword(s):  
High Throughput Sequencing ◽  
Rapid Evolution ◽  
Complex Trait ◽  
Selection Response ◽  
Larval Survival ◽  
Major Effect ◽  
Genomic Changes ◽  
Asobara Tabida ◽  
Signature Of Selection ◽  
Segregating Sites

In this study, we characterize changes in the genome during a swift evolutionary adaptation, by combining experimental selection with high-throughput sequencing. We imposed strong experimental selection on an ecologically relevant trait, parasitoid resistance in Drosophila melanogaster against Asobara tabida. Replicated selection lines rapidly evolved towards enhanced immunity. Larval survival after parasitization increased twofold after just five generations of selection. Whole-genome sequencing revealed that the fast and strong selection response in innate immunity produced multiple, highly localized genomic changes. We identified narrow genomic regions carrying a significant signature of selection, which were present across all chromosomes and covered in total less than 5% of the whole D. melanogaster genome. We identified segregating sites with highly significant changes in frequency between control and selection lines that fell within these narrow ‘selected regions’. These segregating sites were associated with 42 genes that constitute possible targets of selection. A region on chromosome 2R was highly enriched in significant segregating sites and may be of major effect on parasitoid defence. The high genetic variability and small linkage blocks in our base population are likely responsible for allowing this complex trait to evolve without causing widespread erosive effects in the genome, even under such a fast and strong selective regime.

scholarly journals An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
João PL Castro ◽  
Michelle N Yancoskie ◽  
Marta Marchini ◽  
Stefanie Belohlavy ◽  
Layla Hiramatsu ◽  
...  
Keyword(s):  
Bone Growth ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Selection Response ◽  
Major Effect ◽  
Selection Experiment ◽  
Genomic Analyses ◽  
Selection Experiments ◽  
Polygenic Adaptation ◽  
History Of

Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

scholarly journals An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

2018 ◽  
Author(s):  
João P. L. Castro ◽  
Michelle N. Yancoskie ◽  
Marta Marchini ◽  
Stefanie Belohlavy ◽  
Marek Kučka ◽  
...  
Keyword(s):  
Bone Growth ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Selection Response ◽  
Major Effect ◽  
Selection Experiment ◽  
Genomic Analyses ◽  
Selection Experiments ◽  
Polygenic Adaptation ◽  
History Of

AbstractEvolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under strong selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicate lines. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci likely to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivation of two limb enhancers of an inhibitor,Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

scholarly journals Advances in understanding the evolution of fungal genome architecture

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 776 ◽  
Author(s):  
Shelby J. Priest ◽  
Vikas Yadav ◽  
Joseph Heitman
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Rapid Evolution ◽  
Genomic Diversity ◽  
Fungal Genome ◽  
Small Scale ◽  
Genomic Changes ◽  
Wide Range ◽  
Domains Of Life ◽  
Fungal Genomes

Diversity within the fungal kingdom is evident from the wide range of morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in long-read sequencing, coupled with the increasing efficiency and decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity and genomic evolution. These studies revealed the presence of both small-scale and large-scale genomic changes. In fungi, research has recently focused on many small-scale changes, such as how hypermutation and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than others. High-throughput sequencing of a diverse set of fungal genomes has also illuminated the frequency, mechanisms, and impacts of large-scale changes, which include chromosome structural variation and changes in chromosome number, such as aneuploidy, polyploidy, and the presence of supernumerary chromosomes. The studies discussed herein have provided great insight into how the architecture of the fungal genome varies within species and across the kingdom and how modern fungi may have evolved from the last common fungal ancestor and might also pave the way for understanding how genomic diversity has evolved in all domains of life.

Statistical Properties of a DNA Sample Under the Finite-Sites Model

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1941-1950 ◽  
Author(s):  
Ziheng Yang
Keyword(s):  
Process Model ◽  
Random Mating ◽  
Major Effect ◽  
Statistical Properties ◽  
Parameter Estimates ◽  
Rate Variation ◽  
Markov Process Model ◽  
D Loop ◽  
Infinite Sites Model ◽  
Segregating Sites

Statistical properties of a DNA sample from a random-mating population of constant size are studied under the finite-sites model. It is assumed that there is no migration and no recombination occurs within the locus. A Markov process model is used for nucleotide substitution, allowing for multiple substitutions at a single site. The evolutionary rates among sites are treated as either constant or variable. The general likelihood calculation using numerical integration involves intensive computation and is feasible for three or four sequences only; it may be used for validating approximate algorithms. Methods are developed to approximate the probability distribution of the number of segregating sites in a random sample of n sequences, with either constant or variable substitution rates across sites. Calculations using parameter estimates obtained for human D-loop mitochondrial DNAs show that among-site rate variation has a major effect on the distribution of the number of segregating sites; the distribution under the finite-sites model with variable rates among sites is quite different from that under the infinite-sites model.

Host defense mechanisms induce genome instability leading to rapid evolution in an opportunistic fungal pathogen

2021 ◽  
Author(s):  
Amanda Smith ◽  
Levi Morran ◽  
Meleah A. Hickman
Keyword(s):  
Fungal Pathogen ◽  
Defense Mechanisms ◽  
Large Scale ◽  
Genome Instability ◽  
Rapid Evolution ◽  
Genomic Changes ◽  
Opportunistic Fungal Pathogen ◽  
Immunocompromised Hosts ◽  
Stressful Environments

The ability to generate genetic variation facilitates rapid adaptation in stressful environments. The opportunistic fungal pathogen Candida albicans frequently undergoes large-scale genomic changes, including aneuploidy and loss-of heterozygosity (LOH), following exposure to host environments. However, the specific host factors inducing C. albicans genome instability remain largely unknown. Here, we leveraged the genetic tractability of nematode hosts to investigate whether innate immune components, including antimicrobial peptides (AMPs) and reactive oxygen species (ROS), induced host-associated C. albicans genome instability. C. albicans associated with immunocompetent hosts carried multiple large-scale genomic changes including LOH, whole chromosome, and segmental aneuploidies. In contrast, C. albicans associated with immunocompromised hosts deficient in AMPs or ROS production had reduced LOH frequencies and fewer, if any, additional genomic changes. To evaluate if extensive host-induced genomic changes had long-term consequences for C. albicans adaptation, we experimentally evolved C. albicans in either immunocompetent or immunocompromised hosts and selected for increased virulence. C. albicans evolved in immunocompetent hosts rapidly increased virulence, but not in immunocompromised hosts. Taken together, this work suggests that host-produced ROS and AMPs induces genotypic plasticity in C. albicans which facilitates rapid evolution.

scholarly journals SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort

2021 ◽  
Vol 9 (10) ◽  
pp. 2145
Author(s):  
Florian Laubscher ◽  
Samuel Cordey ◽  
Alex Friedlaender ◽  
Cecilia Schweblin ◽  
Sarah Noetzlin ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Cohort Analysis ◽  
Rapid Evolution ◽  
Nasopharyngeal Swab ◽  
Bioinformatics Pipeline ◽  
Oncological Patient ◽  
Patient Cohort ◽  
Oncological Patients ◽  
Minority Variants

Background: Oncological patients have a higher risk of prolonged SARS-CoV-2 shedding, which, in turn, can lead to evolutionary mutations and emergence of novel viral variants. The aim of this study was to analyze biological samples of a cohort of oncological patients by deep sequencing to detect any significant viral mutations. Methods: High-throughput sequencing was performed on selected samples from a SARS-CoV-2-positive oncological patient cohort. Analysis of variants and minority variants was performed using a validated bioinformatics pipeline. Results: Among 54 oncological patients, we analyzed 12 samples of 6 patients, either serial nasopharyngeal swab samples or samples from the upper and lower respiratory tracts, by high-throughput sequencing. We identified amino acid changes D614G and P4715L as well as mutations at nucleotide positions 241 and 3037 in all samples. There were no other significant mutations, but we observed intra-host evolution in some minority variants, mainly in the ORF1ab gene. There was no significant mutation identified in the spike region and no minority variants common to several hosts. Conclusions: There was no major and rapid evolution of viral strains in this oncological patient cohort, but there was minority variant evolution, reflecting a dynamic pattern of quasi-species replication.

scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

scholarly journals Rapid selection response to ethanol in S. eubayanus emulates the domestication process under brewing conditions

2020 ◽  
Author(s):  
Wladimir Mardones ◽  
Carlos A. Villarroel ◽  
Valentina Abarca ◽  
Kamila Urbina ◽  
Tomás A. Peña ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Time Course ◽  
De Novo ◽  
Rapid Evolution ◽  
Selection Response ◽  
Diauxic Shift ◽  
Lager Yeast ◽  
Altered Expression ◽  
Domestication Syndrome ◽  
Domestication Process

ABSTRACTAlthough the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (six months) and compared them with evolved controls exposed solely to glucose. Evolved populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all evolved lines, including SNPs, aneuploidies, INDELs, and translocations. In addition, the evolved populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic-off flavors and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in “fast motion” in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.

scholarly journals Repeatable ecological dynamics govern response of experimental community to antibiotic pulse perturbation

2020 ◽  
Author(s):  
Johannes Cairns ◽  
Roosa Jokela ◽  
Lutz Becks ◽  
Ville Mustonen ◽  
Teppo Hiltunen
Keyword(s):  
High Throughput Sequencing ◽  
Rapid Evolution ◽  
Species Traits ◽  
Community Response ◽  
Ecological Community ◽  
Sequencing Data ◽  
Species Sorting ◽  
Adaptive Mutations ◽  
Key Species ◽  
Disturbance Response

AbstractIn an era of pervasive anthropogenic ecological disturbances, there is a pressing need to understand the factors constituting community response and resilience. A detailed understanding of disturbance response needs to go beyond associations and incorporate features of disturbances, species traits, rapid evolution and dispersal. Multispecies microbial communities experiencing antibiotic perturbation represent a key system with important medical dimensions. However, previous microbiome studies on the theme have relied on high-throughput sequencing data from uncultured species without the ability to explicitly account for the role of species traits and immigration. Here we serially passaged a 34-species defined bacterial community through different levels of pulse antibiotic disturbance, manipulating the presence or absence of species immigration. To understand the ecological community response measured by amplicon sequencing, we combined initial trait data measured for each species separately and metagenome sequencing data revealing adaptive mutations during the experiment. We found that the ecological community response was highly repeatable within the experimental treatments, owing to an increasingly strong yet canalized response at increasing antibiotic levels, which could be partly attributed to key species traits (antibiotic susceptibility and growth rate). Increasing antibiotic levels were also coupled with increasing species extinction probability, making species immigration preventing this critical for community resilience. Moreover, we could detect signals of antibiotic resistance evolution occurring within species at the same time scale, leaving evolutionary changes in communities despite recovery at the species compositional level. Together these observations reveal a disturbance response which appears as classic species sorting but is nevertheless accompanied by rapid within-species evolution.

scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

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