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77 results for “Drosophila simulans”
Drosophila simulans template brains
<p>Male and female symmetric averaged templates (11 and 10 brains, respectively) and intersex template brain for <em>Drosophila simulans</em>. Voxel size: (0.461, 0.461, 1) micron.</p>
Drosophila simulans LD results from PLINK for Chromosome X
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and dataset</strong>s: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3R, 3L, and 4.</p>
Drosophila simulans LD results from PLINK for Chromosome 3R
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3L, 4, and X.</p>
Drosophila simulans LD results from PLINK for Chromosome 4
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Wor</strong>k: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3R, 3L, and X.</p>
Drosophila simulans LD results from PLINK for Chromosome 2R
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Wor</strong>k: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 3L, 3R, 4, and X.</p>
Drosophila simulans LD results from PLINK for Chromosome 3L
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3R, 4, and X</p>
Drosophila simulans LD results from PLINK for Chromosome 2L
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2R, 3L, 3R, 4, and X.</p>
Adult Wing images from Drosophila sechellia and D. simulans
<p>These are images of adult wings from two <em>Drosophila</em> species that were dissected by Christian Marier (in the Dworkin lab) and imaged by Ian Dworkin in 2015. Strains were provided by the Wittkopp lab at the University of Michigan. Flies were reared in the Wittkopp lab by Richard Lusk. Adults were stored in 70% ethanol prior to dissection and mounting in 70% glycerol.</p> <p>All images were taken on an Olympus BX-51 microscope on a 4X objective (40X total magnification) and captured with a DP30BW digital camera using Olympus DP controller (V.3,1,1208) software. All images were collected for geometric morphometric analysis.</p> <p>Dsim = <em>Drosophila simulans</em></p> <p>Dsech = <em>Drosophila sechellia</em></p> <p>f VS M is for male and female.</p>
Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies
<p>Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEBxxxx">https://www.ebi.ac.uk/ena/browser/view/</a>PRJEB50024).</p> <p>Transposable Element annotations: we used RepeatMasker 4.1.0 (<a href="http://repeatmasker.org/">http://repeatmasker.org/</a>) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters.</p> <p>Gene annotations: We retrieved gtf files from FlyBase : <a>ftp.flybase.net/genomes/D</a><a>rosophila_melanogaster/dmel_r6,46_FB2022_03/gft/dmel-all-r6.46.gtf.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/gtf/dsim-all-</a><a>r2,02.gtf.gz</a>. The corresponding fasta files were also downloaded from FlyBase: <a>ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/</a><a>fasta</a><a>/dmel-all-</a><a>chromosome-</a><a>r6.46.</a><a>fasta</a><a>.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/</a><a>fasta</a><a>/dsim-all-</a><a>chromosome-</a><a>r2,02.</a><a>fasta</a><a>.gz</a>. We used Liftoff (Shumate and Salzberg, 2020) to lift over gene annotations from the references to our genome assemblies. We used -flank 0.2 and only kept the “gene” and “exon” terms.</p>
P-elements strengthen reproductive isolation within the Drosophila simulans species complex
Determining mechanisms that underlie reproductive isolation is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of reproductive isolation between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause reproductive isolation between PE-containing (P) and PE-lacking (M) lineages of the same species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P-D. simulans father and an M-mother from a sister species exhibit lower F1 female fecundity than crosses involving an M-D. simulans father and an M-sister-species mother. We also find that another TE, I-element, might play a minor role on determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in isolation. --
P-elements strengthen reproductive isolation within the Drosophila simulans species complex
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Drosophila simulans VCF: The set of single nucleotide polymorphisms and insertion/deletions in a population of 170 Drosophila simulans lines.
<p>Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p>
Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade
ABSTRACTSatellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know little about the evolutionary dynamics and molecular mechanisms that shape satDNA distributions in genomes. Here we use high-quality genome assemblies to study evolutionary dynamics of two complex satDNAs, Rsp-like and 1.688 gm/cm3, in Drosophila melanogaster and its three nearest relatives in the simulans clade. We show that large blocks of these repeats are highly dynamic in the heterochromatin, where their genomic location varies across species. We discovered that small blocks of satDNA that are abundant in X chromosome euchromatin are similarly dynamic, with repeats changing in abundance, location, and composition among species. We detail the proliferation of a rare satellite (Rsp-like) across the X chromosome in D. simulans and D. mauritiana. Rsp-like spreads by inserting into existing clusters of the older, more abundant 1.688 satellite, in events that were likely facilitated by microhomology-mediated repair pathways. We show that Rsp-like is abundant on extrachromosomal circular DNA in D. simulans, which may have contributed to its dynamic evolution. Intralocus satDNA expansions via unequal exchange and the movement of higher-order repeats also contribute to the fluidity of the repeat landscape. We find evidence that euchromatic satDNA repeats experience cycles of proliferation and diversification somewhat analogous to bursts of transposable element proliferation. Our study lays a foundation for mechanistic studies of satDNA proliferation and the functional and evolutionary consequences of satDNA movement.
Offspring sex-ratios are stable across the life-course in Drosophila simulans
Within populations, adult sex ratios influence population growth and extinction risk, mating behaviors and parental care. Additionally, sex ratio adjustment can have pronounced effects on individual fitness. Accordingly, it is important that we understand how often, and why, offspring sex ratios deviate from parity. In Drosophila melanogaster, females appear to improve their fitness by producing fewer sons when paired with older males. However, facultative sex ratio adjustment in D. melanogaster is controversial, and our understanding of how sex ratio skew affects fitness is hampered by pronounced sexual conflict in this species. Additionally, it is unclear if maternal age or quality interact with paternal age to influence offspring sex ratios. Here, we test whether offspring sex ratios vary as a function of maternal quality, and maternal and paternal age in Drosophila simulans, a sister species of D. melanogaster that lacks overt sexual conflict. We find that offspring sex ratios are slightly male biased overall, but constant across the female life-course, and independent of female quality, or paternal age. To really understand if, how and when females skew offspring sex ratios, we need studies linking offspring sex ratios to male and female phenotypes that are predicted to shift optimal investment in sons and daughters.
Sexual selection on the genital lobes of male Drosophila simulans
<p class="CxSpFirst">Sexual selection is thought to be responsible for the rapid divergent evolution of male genitalia with several studies detecting multivariate sexual selection on genital form. However, in most cases, selection is only estimated during a single episode of selection, which provides an incomplete view of net selection on genital traits. Here we estimate the strength and form of multivariate selection on the genitalia arch of <i>Drosophila simulans</i> when mating occurs in the absence of a competitor and during sperm competition, in both sperm defence and offense roles (i.e. when mating first and last). We found that the strength of sexual selection on the genital arch was strongest during non-competitive mating and weakest during sperm offense. However, the direction of selection was similar across selection episodes with no evidence for antagonistic selection. Overall, selection was not particularly strong despite genitals clearly evolving rapidly in this species.</p>
Data from: Genome assembly and annotation of a Drosophila simulans strain from Madagascar
Drosophila simulans is a closely relative of the genetic model D. melanogaster. In an effort to improve the genomic resources for D. simulans, we assembled and annotated the genome of a strain originating from Madagascar (M252), the ancestral range of D. simulans. The comparison of the M252 genome to other available D. simulans assemblies confirmed its high quality, but also highlighted genomic regions that are difficult to assemble with NGS data. The annotation of M252 provides a clear improvement with alternative splicing for 52% of the multiple-exon genes, UTRs for 70% of the genes, 225 novel genes and 781 pseudogenes being reported. We anticipate that the M252 genome will be a valuable resource for many research questions.
Paternally inherited P-element copy number affects the magnitude of hybrid dysgenesis in Drosophila simulans and D. melanogaster
<p class="CxSpFirst">Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. <i>P</i>-elements (PEs) in <i>Drosophila</i> are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short and long-read sequenced to infer the number of PEs in the genomes of dozens of isofemale lines from two <i>Drosophila</i> species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M ´ ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species which suggest there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species-specific.</p>
Data from: Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago
Drosophila simulans and D. sechellia are sister species that serve as a model to study the evolution of reproductive isolation. While D. simulans is a human commensal that has spread all over the world, D. sechellia is restricted to the Seychelles archipelago and is found to breed exclusively on the toxic fruit of Morinda citrifolia. We surveyed the relative frequency of males from these two species in a variety of substrates found on five islands of the Seychelles archipelago. We sampled different fruits and found that putative D. simulans can be found in a variety of substrates, including, surprisingly, M. citrifolia. Putative D. sechellia was found preferentially on M. citrifolia fruits, but a small proportion was found in other substrates. Our survey also shows the existence of putative hybrid males in areas where D. simulans is present in Seychelles. The results from this field survey support the hypothesis of current interbreeding between these species in the central islands of Seychelles and open the possibility for fine measurements of admixture between these two Drosophila species to be made.
Data from: Desiccation resistance and mating behavior in laboratory populations of Drosophila simulans originating from the opposing slopes of Lower Nahal Oren (Israel)
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Data from: Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago
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OpenNeuro
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