Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia

AbstractWe lack a thorough understanding of the origin and maintenance of standing genetic variation that enables rapid evolutionary responses of natural populations. Whole genome sequencing of a resurrected Daphnia population shows that standing genetic variation in over 500 genes follows an evolutionary trajectory that parallels the pronounced and rapid adaptive evolution of multiple traits in response to predator-driven natural selection and its subsequent relaxation. Genetic variation carried by only five founding individuals from the regional genotype pool is shown to suffice at enabling the observed evolution. Our results provide insight on how natural populations can acquire the genomic variation, through colonization by a few regional genotypes, that fuels rapid evolution in response to strong selection pressures. While these evolutionary responses in our study population involved hundreds of genes, we observed no evidence of genetic erosion.

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Acquired variation outweighs inherited variation in whole genome analysis of methotrexate polyglutamate accumulation in leukemia

Blood ◽

10.1182/blood-2008-07-172106 ◽

2009 ◽

Vol 113 (19) ◽

pp. 4512-4520 ◽

Cited By ~ 38

Author(s):

Deborah French ◽

Wenjian Yang ◽

Cheng Cheng ◽

Susana C. Raimondi ◽

Charles G. Mullighan ◽

...

Keyword(s):

Gene Expression ◽

Genetic Variation ◽

Copy Number Variation ◽

Cell Lines ◽

Copy Number ◽

Genomic Variation ◽

Leukemia Cells ◽

Whole Genome ◽

Chromosome 18 ◽

Number Variation

Abstract Methotrexate polyglutamates (MTXPGs) determine in vivo efficacy in acute lymphoblastic leukemia (ALL). MTXPG accumulation differs by leukemic subtypes, but genomic determinants of MTXPG variation in ALL remain unclear. We analyzed 3 types of whole genome variation: leukemia cell gene expression and somatic copy number variation, and inherited single nucleotide polymorphism (SNP) genotypes and determined their association with MTXPGs in leukemia cells. Seven genes (FHOD3, IMPA2, ME2, RASSF4, SLC39A6, SMAD2, and SMAD4) displayed all 3 types of genomic variation associated with MTXPGs (P < .05 for gene expression, P < .01 for copy number variation and SNPs): 6 on chromosome 18 and 1 on chromosome 10. Increased chromosome 18 (P = .002) or 10 (P = .036) copy number was associated with MTXPGs even after adjusting for ALL subtype. The expression of the top 7 genes in leukemia cells accounted for more variation in MTXPGs (46%) than did the expression of the top 7 genes in normal HapMap cell lines (20%). The top 7 inherited SNPs in patients accounted for approximately the same degree of variation (17%) in MTXPGs as did the top 7 SNP genotypes in HapMap cell lines (20%). We conclude that acquired genetic variation in leukemia cells has a stronger influence on MTXPG accumulation than inherited genetic variation.

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Cryptic genetic variation underpins rapid adaptation to ocean acidification

10.1101/700526 ◽

2019 ◽

Cited By ~ 2

Author(s):

M. C. Bitter ◽

L. Kapsenberg ◽

J.-P. Gattuso ◽

C. A. Pfister

Keyword(s):

Climate Change ◽

Genetic Variation ◽

Natural Populations ◽

Future Climate Change ◽

Rapid Adaptation ◽

Larval Size ◽

Larval Population ◽

Cryptic Genetic Variation ◽

Standing Variation ◽

Seawater Ph

AbstractGlobal climate change has intensified the need to assess the capacity for natural populations to adapt to abrupt shifts in the environment. Reductions in seawater pH constitute a conspicuous stressor associated with increasing atmospheric carbon dioxide that is affecting ecosystems throughout the world’s oceans. Here, we quantify the phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the marine mussel, Mytilus galloprovincialis. We reared a genetically diverse larval population in ambient and extreme low pH conditions (pHT 8.1 and 7.4) and tracked changes in the larval size and allele frequency distributions through settlement. Additionally, we separated larvae by size to link a fitness-related trait to its underlying genetic background in each treatment. Both phenotypic and genetic data show that M. galloprovincialis can evolve in response to a decrease in seawater pH. This process is polygenic and characterized by genotype-environment interactions, suggesting the role of cryptic genetic variation in adaptation to future climate change. Holistically, this work provides insight into the processes underpinning rapid evolution, and demonstrates the importance of maintaining standing variation within natural populations to bolster species’ adaptive capacity as global change progresses.

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Understanding and using quantitative genetic variation

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0203 ◽

2010 ◽

Vol 365 (1537) ◽

pp. 73-85 ◽

Cited By ~ 169

Author(s):

William G. Hill

Keyword(s):

Genetic Variation ◽

Complex Traits ◽

Natural Populations ◽

Multiple Traits ◽

Individual Gene ◽

Term Selection ◽

Laboratory Selection ◽

Gene Level ◽

Breeding Programmes ◽

The Individual

Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. Its basis is in statistical models and methodology, albeit based on many strong assumptions. While these are formally unrealistic, methods work. Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. Hence, new methods of prediction of merit in breeding programmes are again based on essentially numerical methods, but incorporating genomic information. Long-term selection responses are revealed in laboratory selection experiments, and prospects for continued genetic improvement are high. There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. Methods based on summary statistics and predictions rather than at the individual gene level seem likely to prevail for some time yet.

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Quantitative genetic basis of floral design in a natural plant population

10.1101/2020.11.06.371831 ◽

2020 ◽

Author(s):

Juannan Zhou ◽

Charles B. Fenste ◽

Richard J. Reynolds

Keyword(s):

Genetic Variation ◽

Genetic Parameters ◽

Mixed Model ◽

Linear Mixed Model ◽

Genetic Correlations ◽

Natural Populations ◽

Plant Evolution ◽

Floral Traits ◽

Floral Trait ◽

Evolutionary Trajectory

AbstractThe amount of genetic variation of floral traits and the degree to which they are genetically correlated are important parameters for the study of plant evolution. Estimates of these parameters can reveal the effect of historical selection relative to neutral processes such as mutation and drift, and allow us to predict the short-term evolutionary trajectory of a population under various selective regimes. Here, we assess the heritability and genetic correlation of the floral design of a native N. American tetraploid plant, Silene stellata (Caryophyllaceae), in a natural population. Specifically, we use a linear mixed model to estimate the genetic parameters based on a genealogy reconstructed from highly variable molecular markers. Overall, we found significant heritabilities in five out of nine studied traits. The level of heritability was intermediate (0.027 – 0.441). Interestingly, the floral trait showing the highest level of genetic variation was previously shown to be under strong sexually conflicting selection, which may serve as a mechanism for maintaining the observed genetic variation. Additionally, we also found prevalent positive genetic correlations between floral traits. Our results suggest that S. stellata is capable of responding to phenotypic selection on its floral design, while the abundant positive genetic correlations could also constrain the evolutionary trajectories to certain directions. Furthermore, this study demonstrates the utility and feasibility of marker-based approaches for estimating genetic parameters in natural populations.

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Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

PeerJ ◽

10.7717/peerj.9293 ◽

2020 ◽

Vol 8 ◽

pp. e9293

Author(s):

Xiulin Wan ◽

Xinhui Li ◽

Todd Osmundson ◽

Chunling Li ◽

He Yan

Keyword(s):

Antibiotic Resistance ◽

Genetic Variation ◽

Genome Sequence ◽

Resistance Genes ◽

Genomic Variation ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Broad Host Range ◽

Whole Genome ◽

Resistance Determinants

Background Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Glässer’s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen. Methods The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1—a plasmid observed in ST328—to confer antibiotic resistance. Results The ST328 genome contained a novel Tn6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6’)-Ie-aph(2”)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13–91.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors (gigP, malQ, and gmhA) and drug resistance genes (norA, bacA, ksgA, and bcr) in G. parasuis were identified. Resistance determinants (sul2, aph(3”)-Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Conclusions Our comparative genomic analysis of worldwide G. parasuis isolates provides valuable insight into the emergence and transmission of G. parasuis in the swine industry. The result suggests the importance of transposon-related and/or plasmid-related gene variations in the evolution of G. parasuis.

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The evolutionary plasticity of chromosome metabolism allows adaptation to DNA replication stress

10.1101/770859 ◽

2019 ◽

Cited By ~ 1

Author(s):

Marco Fumasoni ◽

Andrew W. Murray

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Replication ◽

Natural Populations ◽

Replication Stress ◽

Dna Damage Checkpoint ◽

Whole Genome ◽

Replication Forks ◽

Evolutionary Trajectory ◽

Chromatid Cohesion ◽

Dna Replication Stress

AbstractChromosome metabolism is defined by the pathways that collectively maintain the genome, including chromosome replication, repair and segregation. Because aspects of these pathways are conserved, chromosome metabolism is considered resistant to evolutionary change. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, successive mutations. Whole-genome sequencing and testing candidate mutations revealed adaptive changes in three aspects of chromosome metabolism: DNA replication, DNA damage checkpoint and sister chromatid cohesion. Although no gene was mutated in every population, the same pathways were sequentially altered, defining a functionally reproducible evolutionary trajectory. We propose that this evolutionary plasticity of chromosome metabolism has important implications for genome evolution in natural populations and cancer.

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Standing genetic variation fuels rapid adaptation to ocean acidification

Nature Communications ◽

10.1038/s41467-019-13767-1 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 14

Author(s):

M. C. Bitter ◽

L. Kapsenberg ◽

J.-P. Gattuso ◽

C. A. Pfister

Keyword(s):

Genetic Variation ◽

Global Change ◽

Global Climate ◽

Shell Growth ◽

Natural Populations ◽

Rapid Adaptation ◽

Shell Size ◽

Larval Population ◽

Standing Variation ◽

Seawater Ph

AbstractGlobal climate change has intensified the need to assess the capacity for natural populations to adapt to abrupt shifts in the environment. Reductions in seawater pH constitute a conspicuous global change stressor that is affecting marine ecosystems globally. Here, we quantify the phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the Mediterranean mussel, Mytilus galloprovincialis. We reared a genetically diverse larval population in two pH treatments (pHT 8.1 and 7.4) and tracked changes in the shell-size distribution and genetic variation through settlement. Additionally, we identified differences in the signatures of selection on shell growth in each pH environment. Both phenotypic and genetic data show that standing variation can facilitate adaptation to declines in seawater pH. This work provides insight into the processes underpinning rapid evolution, and demonstrates the importance of maintaining variation within natural populations to bolster species’ adaptive capacity as global change progresses.

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