scholarly journals Genomic divergence and adaptive convergence in Drosophila simulans from Evolution Canyon, Israel

2019 ◽  
pp. 201720938 ◽  
Author(s):  
Lin Kang ◽  
Eugenia Rashkovetsky ◽  
Katarzyna Michalak ◽  
Harold R. Garner ◽  
James E. Mahaney ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Drosophila Simulans ◽  
Close Relative ◽  
Evolutionary Divergence ◽  
Selective Sweeps ◽  
Genomic Polymorphism ◽  
Local Adaptations ◽  
Evolution Canyon ◽  
Genomic Regions ◽  
Microclimate Conditions

Biodiversity refugia formed by unique features of the Mediterranean arid landscape, such as the dramatic ecological contrast of “Evolution Canyon,” provide a natural laboratory in which local adaptations to divergent microclimate conditions can be investigated. Significant insights have been provided by studies of Drosophila melanogaster diversifying along the thermal gradient in Evolution Canyon, but a comparative framework to survey adaptive convergence across sister species at the site has been lacking. To fill this void, we present an analysis of genomic polymorphism and evolutionary divergence of Drosophila simulans, a close relative of Drosophila melanogaster with which it co-occurs on both slopes of the canyon. Our results show even deeper interslope divergence in D. simulans than in D. melanogaster, with extensive signatures of selective sweeps present in flies from both slopes but enhanced in the population from the hotter and drier south-facing slope. Interslope divergence was enriched for genes related to electrochemical balance and transmembrane transport, likely in response to increased selection for dehydration resistance on the hotter slope. Both species shared genomic regions that underwent major selective sweeps, but the overall level of adaptive convergence was low, demonstrating no shortage of alternative genomic solutions to cope with the challenges of the microclimate contrast. Mobile elements were a major source of genetic polymorphism and divergence, affecting all parts of the genome, including coding sequences of mating behavior-related genes.

scholarly journals PSEUDOTUMORS AND FITNESS IN DROSOPHILA MELANOGASTER AND DROSOPHILA SIMULANS

Genetics ◽  
1961 ◽  
Vol 46 (8) ◽  
pp. 971-981
Author(s):  
A Di Pasquale ◽  
S Koref-Santibaňez
Keyword(s):  
Drosophila Melanogaster ◽  
Drosophila Simulans

scholarly journals Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Melina Campos ◽  
Luisa D. P. Rona ◽  
Katie Willis ◽  
George K. Christophides ◽  
Robert M. MacCallum
Keyword(s):  
Population Structure ◽  
Anopheles Gambiae ◽  
Malaria Vector ◽  
Mosquito Species ◽  
Gene Clusters ◽  
Selective Sweeps ◽  
Structure Heterogeneity ◽  
Genomic Studies ◽  
Time Required ◽  
Genomic Regions

Abstract Background Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, Anopheles gambiae, other genetic aspects such as selection and adaptation are also important. In the present study, we explore population genetic variation from genome-wide sequencing of 765 An. gambiae and An. coluzzii specimens collected from across Africa. We used t-SNE, a recently popularized dimensionality reduction method, to create a 2D-map of An. gambiae and An. coluzzii genes that reflect their population structure similarities. Results The map allows intuitive navigation among genes distributed throughout the so-called “mainland” and numerous surrounding “island-like” gene clusters. These gene clusters of various sizes correspond predominantly to low recombination genomic regions such as inversions and centromeres, and also to recent selective sweeps. Because this mosquito species complex has been studied extensively, we were able to support our interpretations with previously published findings. Several novel observations and hypotheses are also made, including selective sweeps and a multi-locus selection event in Guinea-Bissau, a known intense hybridization zone between An. gambiae and An. coluzzii. Conclusions Our results present a rich dataset that could be utilized in functional investigations aiming to shed light onto An. gambiae s.l genome evolution and eventual speciation. In addition, the methodology presented here can be used to further characterize other species not so well studied as An. gambiae, shortening the time required to progress from field sampling to the identification of genes and genomic regions under unique evolutionary processes.

scholarly journals Natural variation in fecundity is correlated with species-wide levels of divergence in Caenorhabditis elegans

2021 ◽  
Author(s):  
Gaotian Zhang ◽  
Jake D Mostad ◽  
Erik C Andersen
Keyword(s):  
Life History ◽  
Caenorhabditis Elegans ◽  
Life History Traits ◽  
Life History Trait ◽  
Selective Sweeps ◽  
C Elegans ◽  
Genome Wide ◽  
Genetic Complexity ◽  
Genomic Regions ◽  
Global Population

Abstract Life history traits underlie the fitness of organisms and are under strong natural selection. A new mutation that positively impacts a life history trait will likely increase in frequency and become fixed in a population (e.g. a selective sweep). The identification of the beneficial alleles that underlie selective sweeps provides insights into the mechanisms that occurred during the evolution of a species. In the global population of Caenorhabditis elegans, we previously identified selective sweeps that have drastically reduced chromosomal-scale genetic diversity in the species. Here, we measured the fecundity of 121 wild C. elegans strains, including many recently isolated divergent strains from the Hawaiian islands and found that strains with larger swept genomic regions have significantly higher fecundity than strains without evidence of the recent selective sweeps. We used genome-wide association (GWA) mapping to identify three quantitative trait loci (QTL) underlying the fecundity variation. Additionally, we mapped previous fecundity data from wild C. elegans strains and C. elegans recombinant inbred advanced intercross lines that were grown in various conditions and detected eight QTL using GWA and linkage mappings. These QTL show the genetic complexity of fecundity across this species. Moreover, the haplotype structure in each GWA QTL region revealed correlations with recent selective sweeps in the C. elegans population. North American and European strains had significantly higher fecundity than most strains from Hawaii, a hypothesized origin of the C. elegans species, suggesting that beneficial alleles that caused increased fecundity could underlie the selective sweeps during the worldwide expansion of C. elegans.

scholarly journals Introgression of Drosophila simulans Nuclear Pore Protein 160 in Drosophila melanogaster Alone Does Not Cause Inviability but Does Cause Female Sterility

Genetics ◽  
2010 ◽  
Vol 186 (2) ◽  
pp. 669-676 ◽  
Author(s):  
Kyoichi Sawamura ◽  
Kazunori Maehara ◽  
Shotaro Mashino ◽  
Tatsuo Kagesawa ◽  
Miyuki Kajiwara ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Drosophila Simulans ◽  
Female Sterility ◽  
Nuclear Pore ◽  
Nuclear Pore Protein ◽  
Pore Protein

Effects of Selection at Linked Sites on Patterns of Genetic Variability

2021 ◽  
Vol 52 (1) ◽  
pp. 177-197
Author(s):  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Frequency Distributions ◽  
A Genome ◽  
Demographic Processes ◽  
Dna Sequence Variants ◽  
Genomic Regions ◽  
Functional Components

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

scholarly journals Scanning for Genomic Regions Subject to Selective Sweeps Using SNP-MaP Strategy

2010 ◽  
Vol 8 (4) ◽  
pp. 256-261
Author(s):  
Libin Deng ◽  
Xiaoli Tang ◽  
Wei Chen ◽  
Jiari Lin ◽  
Zhiqing Lai ◽  
...  
Keyword(s):  
Selective Sweeps ◽  
Snp Map ◽  
Genomic Regions

scholarly journals Characterization of the genetic architecture underlying eye size variation within Drosophila melanogaster and Drosophila simulans

2019 ◽  
Author(s):  
Pedro Gaspar ◽  
Saad Arif ◽  
Lauren Sumner-Rooney ◽  
Maike Kittelmann ◽  
Andrew J. Bodey ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Variation ◽  
Size Variation ◽  
Eye Size ◽  
Specific Variation ◽  
Gene Regulatory ◽  
Morphological Differences ◽  
Genomic Regions ◽  
Insect Eye

AbstractThe compound eyes of insects exhibit striking variation in size, reflecting adaptation to different lifestyles and habitats. However, the genetic and developmental bases of variation in insect eye size is poorly understood, which limits our understanding of how these important morphological differences evolve. To address this, we further explored natural variation in eye size within and between four species of the Drosophila melanogaster species subgroup. We found extensive variation in eye size among these species, and flies with larger eyes generally had a shorter inter-ocular distance and vice versa. We then carried out quantitative trait loci (QTL) mapping of intra-specific variation in eye size and inter-ocular distance in both D. melanogaster and D. simulans. This revealed that different genomic regions underlie variation in eye size and inter-ocular distance in both species, which we corroborated by introgression mapping in D. simulans. This suggests that although there is a trade-off between eye size and inter-ocular distance, variation in these two traits is likely to be caused by different genes and so can be genetically decoupled. Finally, although we detected QTL for intra-specific variation in eye size at similar positions in D. melanogaster and D. simulans, we observed differences in eye fate commitment between strains of these two species. This indicates that different developmental mechanisms and therefore, most likely, different genes contribute to eye size variation in these species. Taken together with the results of previous studies, our findings suggest that the gene regulatory network that specifies eye size has evolved at multiple genetic nodes to give rise to natural variation in this trait within and among species.

Relationships within the melanogaster species subgroup of the genus Drosophila ( Sophophora ). I. Inversion polymorphisms in Drosophila melanogaster and Drosophila simulans

1976 ◽  
Vol 193 (1111) ◽  
pp. 137-157 ◽  
Keyword(s):  
Drosophila Melanogaster ◽  
Drosophila Simulans ◽  
Fourth Chromosome ◽  
The Third ◽  
Chromosome Inversions

Drosophila melanogaster from 67 collections have been analysed for their polymorphic inversions. Of the 53 inversions now known in this species 7 are widespread and 43 are endemic. The remaining 3 inversions may be widespread, but if so they are usually very rare. No X or fourth chromosome inversions were found. All the third chromosome inversions were paracentric, while six of the second chromosome inversions were pericentric. No inversions were found in D. simulans , of which 27 collections, from Africa, Europe, Australia and S. America, were studied.

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