scholarly journals Genomic analysis of P elements in natural populations of Drosophila melanogaster

2017 ◽  
Author(s):  
Casey M. Bergman ◽  
Michael G. Nelson ◽  
Vladyslav Bondarenko ◽  
Iryna A. Kozeretska
Keyword(s):  
Drosophila Melanogaster ◽  
Gonadal Dysgenesis ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Read Depth ◽  
North American Population ◽  
Mobile Dna ◽  
Geographic Differences ◽  
Isofemale Strains ◽  
Genomic Basis

AbstractThe Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes in natural populations. Here we compare gonadal dysgenesis phenotypes and genomic P element predictions for isofemale strains obtained from three worldwide populations of D. melanogaster to illuminate the molecular basis of natural variation in cytotype status. We show that the number of predicted P element insertions in genome sequences from isofemale strains is highly correlated across different bioinformatics methods, but the absolute number of insertions per strain is sensitive to method and filtering strategies. Regardless of method used, we find that the number of euchromatic P element insertions predicted per strain varies significantly across populations, with strains from a North American population having fewer P element insertions than strains from populations sampled in Europe or Africa. Despite these geographic differences, numbers of euchromatic P element insertions are not strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in P element insertion numbers across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Additionally, we show that pool-seq samples can uncover population differences in the number of P element insertions observed from isofemale lines, but that efforts to rigorously detect differences in the number of P elements across populations using pool-seq data must properly control for read depth per strain. Our work supports the view that euchromatic P element copy number is not sufficient to explain variation in gonadal dysgenesis across strains of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes.

scholarly journals Genomic analysis ofPelements in natural populations ofDrosophila melanogaster

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3824 ◽  
Author(s):  
Casey M. Bergman ◽  
Shunhua Han ◽  
Michael G. Nelson ◽  
Vladyslav Bondarenko ◽  
Iryna Kozeretska
Keyword(s):  
Gonadal Dysgenesis ◽  
Natural Populations ◽  
Full Length ◽  
Element Content ◽  
Element Abundance ◽  
North American Population ◽  
Mobile Dna ◽  
Geographic Differences ◽  
Isofemale Strains ◽  
Genomic Basis

TheDrosophila melanogaster Ptransposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by thePelement has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in theirPelement composition mate and produce offspring. Despite extensive research on many aspects ofPelement biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations. Here we compare estimates of genomicPelement content with gonadal dysgenesis phenotypes for isofemale strains obtained from three worldwide populations ofD. melanogasterto illuminate the molecular basis of natural variation in cytotype status. We show thatPelement abundance estimated from genome sequences of isofemale strains is highly correlated across different bioinformatics approaches, but that abundance estimates are sensitive to method and filtering strategies as well as incomplete inbreeding of isofemale strains. We find thatPelement content varies significantly across populations, with strains from a North American population having fewerPelements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences inPelement abundance and structure, neither the number ofPelements nor the ratio of full-length to internally-truncated copies is strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation inPelement abundance and structure across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Finally, we confirm that population differences in the abundance and structure ofPelements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. Our work supports the view that genomicPelement content alone is not sufficient to explain variation in gonadal dysgenesis across strains ofD. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences inPelement induced phenotypes.

scholarly journals Phenotypic and genomic analysis of P elements in natural populations of Drosophila melanogaster

2016 ◽  
Author(s):  
I.A. Kozeretska ◽  
V. Bondarenko ◽  
V.I. Shulga ◽  
S.V. Serga ◽  
A.I. Rozhok ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Active Form ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Element Composition ◽  
Strongly Correlated ◽  
Mobile Dna ◽  
P Elements ◽  
The Stability ◽  
Genomic Basis

AbstractThe Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as “P-M hybrid dysgenesis” that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, questions remain about the stability and genomic basis of variation in P-M dysgenesis phenotypes. Here we report the P-M status for a number of populations sampled recently from Ukraine that appear to be undergoing a shift in their P element composition. Gondal dysgenesis assays reveal that Ukrainian populations of D. melanogaster are currently dominated by the P’ cytotype, a cytotype that was previously thought to be rare in nature, suggesting that a new active form of the P element has recently spread in this region. We also compared gondal dysgenesis phenotypes and genomic P element predictions for isofemale strains obtained from three worldwide populations of D. melanogaster in order to guide further work on the molecular basis of differences in cytotype status across populations. We find that the number of euchromatic P elements per strain can vary significantly across populations but that total P element numbers are not strongly correlated with the degree of gondal dysgenesis. Our work shows that rapid changes in cytotype status can occur in natural populations of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes.

scholarly journals Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

2018 ◽  
Author(s):  
Martin Kapun ◽  
Maite G. Barrón ◽  
Fabian Staubach ◽  
Darren J. Obbard ◽  
R. Axel W. Wiberg ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Climate Adaptation ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Short Term ◽  
Dna Viruses ◽  
Local Climate ◽  
Term Evolution ◽  
Spatio Temporal

AbstractGenetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

scholarly journals The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations of Drosophila melanogaster

2019 ◽  
Author(s):  
Alexandre Fournier-Level ◽  
Robert T Good ◽  
Stephen Wilcox ◽  
Rahul V Rane ◽  
Michelle Schiffer ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Management Strategies ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Ecological Factors ◽  
Climate Extremes ◽  
Pest Species ◽  
Different Temperatures ◽  
Considerable Controversy ◽  
Harmful Effects

AbstractImidacloprid, the world’s most utilised insecticide1, has raised considerable controversy due to its harmful effects on non-pest species2–6 and there is increasing evidence showing that insecticides have become the primary selective force in many insect species7–14. The genetic response to insecticides is heterogeneous across population and environment15–17, leading to more complex patterns of genetic variation than previously thought. This motivated the investigation of imidacloprid resistance at different temperatures in natural populations of Drosophila melanogaster originating from four climate extremes replicated across two continents. Population and quantitative genomic analysis, supported by functional tests, demonstrated a polygenic basis to resistance and a major trade-off with thermotolerance. Reduced genetic differentiation at resistance-associated loci indicate enhanced gene flow at these loci. Resistance alleles showed stronger evidence of positive selection in temperate populations compared to tropical populations. Polygenic architecture and ecological factors should be considered when developing sustainable management strategies for both pest and beneficial insects.

scholarly journals Rapid spread of transposable p elements in experimental populations of Drosophila melanogaster.

Genetics ◽  
1989 ◽  
Vol 122 (2) ◽  
pp. 387-396 ◽  
Author(s):  
A G Good ◽  
G A Meister ◽  
H W Brock ◽  
T A Grigliatti ◽  
D A Hickey
Keyword(s):  
Drosophila Melanogaster ◽  
Gonadal Dysgenesis ◽  
Natural Populations ◽  
P Element ◽  
P Elements ◽  
Rapid Spread ◽  
Laboratory Populations ◽  
Experimental Populations

Abstract The invasion of P elements in natural populations of Drosophila melanogaster was modeled by establishing laboratory populations with 1%, 5% and 10% P genomes and monitoring the populations for 20 generations. In one experiment, the ability of flies to either induce or suppress gonadal sterility in different generations was correlated with the amount of P element DNA. In a second experiment, the percentage of genomes that contained P elements, and the distribution of P elements among individual flies was monitored. The ability to induce gonadal dysgenesis increased rapidly each generation. However, the increase in P cytotype lagged behind by five to ten generations. The total amount of P element DNA and the frequency of flies containing P elements increased each generation. The number of P elements within individual genomes decreased initially, but then increased. Finally, the distribution of P elements within the genomes of individuals from later generations varied considerably, and this pattern differed from the parental P strain. These results suggest that the interaction between the assortment and recombination of chromosomal segments, and multiplicative transposition could result in the rapid spread of P elements in natural populations.

The Genetic Architecture of Cold Tolerance in Natural-Populations of Drosophila-Melanogaster and Drosophila-Simulans

1990 ◽  
Vol 38 (2) ◽  
pp. 163 ◽  
Author(s):  
JK Davidson
Keyword(s):  
Drosophila Melanogaster ◽  
Cold Tolerance ◽  
Genetic Architecture ◽  
Population Sample ◽  
Natural Populations ◽  
Diallel Analysis ◽  
Humid Tropics ◽  
Additive Genetic Effects ◽  
Isofemale Strains ◽  
Made In

Genetic analysis of cold tolerance was applied to samples of recently collected isofemale strains of Drosophila melanogaster and D. simulans from natural populations from diverse climates. The temperate zone locality of Melbourne was sampled twice for both species, once in 1986 and again in 1987. In 1987, D. melanogaster collections were also made in the humid tropics at Townsville and the wet/dry tropical locality of Darwin. D. simulans was also collected in Townsville in 1987 but it was not found in Darwin. Diallel analysis was performed for each population sample, so there were seven diallels, each with from 9 to 12 strains which were randomly chosen. Diallel analyses showed that cold tolerance was mainly controlled by additive genetic effects. This pattern was consistent across time, across populations and across species. It is proposed that natural populations of both members of the sibling species have the genetic architecture necessary for adaptive phenotypic response to selection by intermittent periods of low temperature.

scholarly journals Heritability of Two Morphological Characters Within and Among Natural Populations of Drosophila melanogaster

Genetics ◽  
1987 ◽  
Vol 117 (4) ◽  
pp. 727-737
Author(s):  
Jerry A Coyne ◽  
Edward Beecham
Keyword(s):  
Drosophila Melanogaster ◽  
Wing Length ◽  
Genetic Correlations ◽  
Natural Populations ◽  
Morphological Characters ◽  
Correlated Response ◽  
Population Means ◽  
Bristle Number ◽  
Genetic Differentiation Of Populations ◽  
Geographic Differences

ABSTRACT Heritabilities of wing length and abdominal bristle number, as well as genetic correlations between these characters, were determined within and among populations of Drosophila melanogaster in nature. Substantial "natural" heritabilities were found when wild-caught flies from one population were compared to their laboratory-reared offspring. Natural heritabilities of bristle number approximated those derived from laboratory-raised parents and offspring, but wing length heritability was significantly lower in nature than in the laboratory. Among-population heritabilities, estimated by regressing population means of wild-caught flies against those of their laboratory-reared descendants, were close to 0.5. The genetic differentiation of populations was clinal with latitude, and was accompanied by significant geographic differences in the norms of reaction to temperature. These clines are similar to those reported on other continents and in other Drosophila species, and are almost certainly caused by natural selection. Genetic regressions between the characters reveal that the cline in bristle number may be a correlated response to geographic selection on wing length, but not vice versa. Our results indicate that there is a sizable genetic component to phenotypic variation within and among populations of D. melanogaster in nature.

scholarly journals Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

2020 ◽  
Vol 37 (9) ◽  
pp. 2661-2678 ◽  
Author(s):  
Martin Kapun ◽  
Maite G Barrón ◽  
Fabian Staubach ◽  
Darren J Obbard ◽  
R Axel W Wiberg ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Climate Adaptation ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Selective Sweeps ◽  
Short Term ◽  
Dna Viruses ◽  
Local Climate ◽  
Term Evolution

Abstract Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

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