scholarly journals Genomic Variation in Natural Populations ofDrosophila melanogaster

Genetics ◽  
2012 ◽  
Vol 192 (2) ◽  
pp. 533-598 ◽  
Author(s):  
Charles H. Langley ◽  
Kristian Stevens ◽  
Charis Cardeno ◽  
Yuh Chwen G. Lee ◽  
Daniel R. Schrider ◽  
...  
Keyword(s):  
Natural Populations ◽  
Genomic Variation

scholarly journals A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes

2020 ◽  
Author(s):  
Mehmet Göktay ◽  
Andrea Fulgione ◽  
Angela M Hancock
Keyword(s):  
North America ◽  
Defense Response ◽  
Balancing Selection ◽  
Natural Populations ◽  
Housekeeping Genes ◽  
Intermediate Frequency ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Structural Variants ◽  
Defense Response Genes

Abstract Genomic variation in the model plant Arabidopsis thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single-nucleotide polymorphisms. Conversely, structural variation has been largely ignored in spite of its potential to dramatically affect phenotype. Here, we identify 155,440 indels and structural variants ranging in size from 1 bp to 10 kb, including presence/absence variants (PAVs), inversions, and tandem duplications in 1,301 A. thaliana natural accessions from Morocco, Madeira, Europe, Asia, and North America. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes, and we find that PAVs are concentrated in defense-related genes (R-genes, secondary metabolites) and F-box genes. This implies the presence of a “core” genome underlying basic cellular processes and a “flexible” genome that includes genes that may be important in spatially or temporally varying selection. Further, we find an excess of intermediate frequency PAVs in defense response genes in nearly all populations studied, consistent with a history of balancing selection on this class of genes. Finally, we find that PAVs in genes involved in the cold requirement for flowering (vernalization) and drought response are strongly associated with temperature at the sites of origin.

scholarly journals Population differentiation and structural variation in the genome of Manduca sexta across the United States

2020 ◽  
Author(s):  
Andrew J. Mongue ◽  
Akito Y. Kawahara
Keyword(s):  
Manduca Sexta ◽  
Sex Chromosome ◽  
Natural Habitat ◽  
Natural Populations ◽  
The United States ◽  
Genomic Variation ◽  
The Other ◽  
Z Chromosome ◽  
Scientific Disciplines ◽  
Two Populations

AbstractMany species that are extensively studied in the laboratory are less well characterized in their natural habitat, and laboratory strains represent only a small fraction of the variation in a species’ genome. Here we investigate genomic variation in three natural populations of an agricultural pest and a model insect for many scientific disciplines, the tobacco hornworm (Manduca sexta). We show that hornworms from Arizona, Kansas, and North Carolina are genetically distinct, with Arizona being particularly differentiated from the other two populations. Specifically, two segregating inversions and a potential pseudogene are found only in the Arizona population. One inversion on the Z chromosome may enhance adaptive evolution of the sex chromosome, while the significance of the other, autosomal inversion remains unclear. The pseudogene may be involved in the exploitation of a novel hostplant in Arizona, but functional genetic assays will be required to confirm this hypothesis. Nevertheless, our results reveal undiscovered natural variation and provide useful genomic data for a model insect species.

scholarly journals Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1240
Author(s):  
Jia Guo ◽  
Patrick J. Brown ◽  
Albert L. Rayburn ◽  
Carolyn J. Butts-Wilmsmeyer ◽  
Arvid Boe ◽  
...  
Keyword(s):  
Abiotic Stress Tolerance ◽  
Natural Populations ◽  
Genomic Variation ◽  
Biofuel Production ◽  
Breeding Value ◽  
Grass Species ◽  
Gene Pools ◽  
Ploidy Levels ◽  
Geographical Factors ◽  
Prairie Cordgrass

Prairie cordgrass (Spartina pectinata Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedicated bioenergy crop for sustainable cellulosic biofuel production. However, as with many other undomesticated grass species, little information is known about the genetic diversity or population structure of prairie cordgrass natural populations as compared to their ecotypic and geographic adaptation in North America. In this study, we sampled and characterized a total of 96 prairie cordgrass natural populations with 9315 high quality SNPs from a genotyping-by-sequencing (GBS) approach. The natural populations were collected from putative remnant prairie sites throughout the Midwest and Eastern USA, which are the major habitats for prairie cordgrass. Partitioning of genetic variance using SNP marker data revealed significant variance among and within populations. Two potential gene pools were identified as being associated with ploidy levels, geographical separation, and climatic separation. Geographical factors such as longitude and altitude, and environmental factors such as annual temperature, annual precipitation, temperature of the warmest month, precipitation of the wettest month, precipitation of Spring, and precipitation of the wettest month are important in affecting the intraspecific distribution of prairie cordgrass. The divergence of prairie cordgrass natural populations also provides opportunities to increase breeding value of prairie cordgrass as a bioenergy and conservation crop.

scholarly journals Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast

2019 ◽  
Vol 36 (9) ◽  
pp. 1975-1989 ◽  
Author(s):  
Sergio Tusso ◽  
Bart P S Nieuwenhuis ◽  
Fritz J Sedlazeck ◽  
John W Davey ◽  
Daniel C Jeffares ◽  
...  
Keyword(s):  
Single Molecule ◽  
Phenotypic Variation ◽  
Natural Populations ◽  
Strand Break ◽  
Transgressive Segregation ◽  
Genomic Variation ◽  
Population History ◽  
Structural Genomic ◽  
History Of ◽  
Reproductive Compatibility

Abstract Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20–60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.

scholarly journals Evolution as an ecosystem process: insights from genomics

Genome ◽  
2018 ◽  
Vol 61 (4) ◽  
pp. 298-309 ◽  
Author(s):  
Blake Matthews ◽  
Rebecca J. Best ◽  
Philine G.D. Feulner ◽  
Anita Narwani ◽  
Romana Limberger
Keyword(s):  
Evolutionary Dynamics ◽  
Genome Structure ◽  
Natural Populations ◽  
Genomic Variation ◽  
Ecosystem Dynamics ◽  
Genomic Diversity ◽  
Ecosystem Change ◽  
Ecosystem Process ◽  
Integrative Research ◽  
Genomic Studies

Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems.

scholarly journals Sardines at a junction: seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

2021 ◽  
Author(s):  
Aglaia Antoniou ◽  
Tereza Manousaki ◽  
Francisco Ramírez ◽  
Alessia Cariani ◽  
Rita Cannas ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Dynamic Equilibrium ◽  
Natural Populations ◽  
Spatial Dimension ◽  
Western Mediterranean ◽  
Genomic Variation ◽  
Entire Genome ◽  
Outlier Loci ◽  
Genomic Approach ◽  
Nw Mediterranean

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while new can be asked. Such questions include how different local environments influence both adaptive and neutral genomic variation within and among populations, providing insights not only into local adaptation of natural populations, but also into their responses to global change and the exploitation-induced evolution. Here, under a seascape genomic approach, ddRAD genomic data were used along with environmental information to uncover the underlying processes (migration, selection) shaping European sardines (Sardina pilchardus) of the Western Mediterranean and adjacent Atlantic waters. This information can be relevant to the (re)definition of fishery stocks, and their short-term adaptive potential. We found that studied sardine samples form two clusters, detected using both neutral and adaptive (outlier) loci suggesting that natural selection and local adaptation play a key role in driving genetic change among the Atlantic and the Mediterranean sardines. Temperature and especially the trend in the number of days with sea surface temperature (SST) above 19oC was crucial at all levels of population structuring with implications on species’ key biological processes, especially reproduction. Our findings provide evidence for a dynamic equilibrium where population structure is maintained by physical and biological factors under the opposing influences of migration and selection. Given its dynamic nature, such a system postulates a continuous monitoring under a seascape genomic approach that can benefit by incorporating a temporal as well as a more detailed spatial dimension.

scholarly journals Ancestral admixture is the main determinant of global biodiversity in fission yeast

2018 ◽  
Author(s):  
Sergio Tusso ◽  
Bart P.S. Nieuwenhuis ◽  
Fritz J. Sedlazeck ◽  
John W. Davey ◽  
Daniel Jeffares ◽  
...  
Keyword(s):  
Single Molecule ◽  
Phenotypic Variation ◽  
Natural Populations ◽  
Strand Break ◽  
Transgressive Segregation ◽  
Genomic Variation ◽  
Population History ◽  
Structural Genomic ◽  
History Of ◽  
Reproductive Compatibility

Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization occurred ~20 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency and position of structural genomic variation (SV) using nanopore and single-molecule real time sequencing, discovering over 800 SVs. Despite being associated with double-strand break initiation points, SV exerted overall little influence on the introgression landscape or on reproductive compatibility that exist between strains. In contrast, we find strongly increased statistical linkage between ancestral populations that is consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.

scholarly journals Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaojuan Wang ◽  
Hua Rao ◽  
Jianxiang Ma ◽  
Xiaodan Chen ◽  
Guanglin Li ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Local Adaptation ◽  
Molecular Mechanisms ◽  
Natural Populations ◽  
Northern China ◽  
Genomic Variation ◽  
Forward Genetics ◽  
Local Adaptations ◽  
Salt Cress ◽  
Eutrema Salsugineum

Eutrema salsugineum has long been used as the model for examining salt and other abiotic stress in plants. In addition to the forward genetics approaches widely used in the lab, natural variations undoubtedly will provide a rich genetic resource for studying molecular mechanisms underlying the stress tolerance and local adaptation of this species. We used 90 resequencing whole genomes of natural populations of this species across its Asian and North American distributions to detect the selection signals for genes involved in salt and other stresses at the species-range level and local distribution. We detected selection signals for genes involved in salt and other abiotic tolerance at the species level. In addition, several cold-induced and defense genes showed selection signals due to local adaptation in North America-NE Russia or northern China, respectively. These variations and findings provide valuable resources for further deciphering genetic mechanisms underlying the stress tolerance and local adaptations of this model species.

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