Population structure and introgression among recently differentiated Drosophila melanogaster populations

Understanding the factors that produce and maintain genetic variation is a central goal of evolutionary biology. Despite a century of genetic analysis, the evolutionary history underlying patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic and phenotypic variation is partitioned across global D. melanogaster populations, and specifically in its putative ancestral range in Subtropical Africa, remains unresolved. Here, we integrate genomic and behavioral analyses to assess patterns of population genetic structure, admixture, mate preference, and genetic incompatibility throughout the range of this model organism. Our analysis includes 174 new accessions from novel and under-sampled regions within Subtropical Africa. We find that while almost all Out of Africa genomes correspond to a single genetic ancestry, different geographic regions within Africa contain multiple distinct ancestries, including the presence of substantial cryptic diversity within Subtropical Africa. We find evidence for significant admixture- and variation in admixture rates-between geographic regions within Africa, as well as between African and non-African lineages. By combining behavioral analysis with population genomics, we demonstrate that female mate choice is highly polymorphic, behavioral types are not monophyletic, and that genomic differences between behavioral types correspond to many regions across the genome. These include regions associated with neurological development, behavior, olfactory perception, and learning. Finally, we discovered that many individual pairs of putative incompatibility loci likely evolved during or after the expansion of D. melanogaster out of Africa. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the distribution of reproductive barriers that are polymorphic within species.

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Geometric Morphology and Population Genomics Provide Insights into the Adaptive Evolution of Apis Cerana in Changbai Mountain

10.21203/rs.3.rs-590369/v1 ◽

2021 ◽

Author(s):

Liu Nannan ◽

Liu Huamiao ◽

Ju Yan ◽

Li Xingan ◽

Li Yang ◽

...

Keyword(s):

Adaptive Evolution ◽

Evolutionary History ◽

Population Genomics ◽

Apis Cerana ◽

Changbai Mountain ◽

Effective Population ◽

Local Adaptations ◽

Geographic Regions ◽

Underlying Mechanisms ◽

Geometric Morphology

Abstract Background: Exploration of adaptive evolution of organisms in response to environmental change will offer us a hint to the evolutionary history of species and the underlying mechanisms of adaptation to local environments, thus guiding future conservation programmes. Before the introduction of Apis mellifera in China, Apis cerana was the only species, which could be reared in captivity to obtain products. Moreover, A. cerana in Changbai Mountain is the only ecotype in such a flora. Result: We investigated the geometric morphological features of A. cerana in Changbai Mountain by analysing 300 wing specimens from 30 populations of A. cerana in 5 geographic regions. A total of 3,859,573 high-quality SNP loci were yielded via the whole-genome resequencing of 130 individuals from 130 A. cerana geographic populations.Conclusion: Corresponding geometric morphology and population genome confirmed the outstanding evolutionary role of the A. cerana population in Changbai Mountain. Genetic differentiation at the subspecies level exists between populations in Changbai Mountain and remaining geographic regions, and a significant reduction in the effective population size and an excessive degree of inbreeding may be responsible for a substantial loss of population genetic diversity. Candidate genes potentially associated with cold environmental adaptations in populations under natural selection were identified, which may represent local adaptations in populations. Our study provided insights into the evolutionary history and adaptive characteristics of A. cerana in Changbai Mountain, as well as the scientific conservation of this population.

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FlyBase: updates to the Drosophila melanogaster knowledge base

Nucleic Acids Research ◽

10.1093/nar/gkaa1026 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D899-D907 ◽

Cited By ~ 1

Author(s):

Aoife Larkin ◽

Steven J Marygold ◽

Giulia Antonazzo ◽

Helen Attrill ◽

Gilberto dos Santos ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Knowledge Base ◽

Fast Track ◽

Model Organism ◽

Disease Models ◽

Online Database ◽

Experimental Tool

Abstract FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays (‘ribbons’) of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.

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MULTIPLE ALLELE APPROACH TO THE STUDY OF GENES IN DROSOPHILA MELANOGASTER THAT ARE INVOLVED IN IMAGINAL DISC DEVELOPMENT

Genetics ◽

10.1093/genetics/89.2.355 ◽

1978 ◽

Vol 89 (2) ◽

pp. 355-370 ◽

Cited By ~ 2

Author(s):

Allen Shearn ◽

Grafton Hersperger ◽

Evelyn Hersperger ◽

Ellen Steward Pentz ◽

Paul Denker

Keyword(s):

Drosophila Melanogaster ◽

Phenotypic Variation ◽

Mutant Allele ◽

Imaginal Disc ◽

Reference Allele ◽

Multiple Allele ◽

Significant Difference ◽

Chromosome Mutations ◽

Cold Sensitive

ABSTRACT The phenotypes of five different lethal mutants of Drosophila melanogaster that have small imaginal discs were analyzed in detail. From these results, we inferred whether or not the observed imaginal disc phenotype resulted exclusively from a primary imaginal disc defect in each mutant. To examine the validity of these inferences, we employed a multiple-allele method. Lethal alleles of the five third-chromosome mutations were identified by screening EMS-treated chromosomes for those which fail to complement with a chromosome containing all five reference mutations. Twenty-four mutants were isolated from 13,197 treated chromosomes. Each of the 24 was then tested for complementation with each of the five reference mutants. There was no significant difference in the mutation frequencies at these five loci. The stage of lethality and the imaginal disc morphology of each mutant allele were compared to those of its reference allele in order to examine the range of defects to be found among lethal alleles of each locus. In addition, hybrids of the alleles were examined for intracistronic complementation. For two of the five loci, we detected no significant phenotypic variation among lethal alleles. We infer that each of the mutant alleles at these two loci cause expression of the null activity phenotype. However, for the three other loci, we did detect significant phenotypic variation among lethal alleles. In fact, one of the mutant alleles at each of these three loci causes no detectable imaginal disc defect. This demonstrates that attempting to assess the developmental role of a gene by studying a single mutant allele may lead to erroneous conclusions. As a byproduct of the mutagenesis procedure, we have isolated two dominant, cold-sensitive mutants.

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Influence of Dopamine on Fluorescent Advanced Glycation End Products Formation Using Drosophila melanogaster

Biomolecules ◽

10.3390/biom11030453 ◽

2021 ◽

Vol 11 (3) ◽

pp. 453

Author(s):

Ana Filošević Vujnović ◽

Katarina Jović ◽

Emanuel Pištan ◽

Rozi Andretić Waldowski

Keyword(s):

Drosophila Melanogaster ◽

Advanced Glycation End Products ◽

Model Organism ◽

Covalent Modification ◽

Advanced Glycation ◽

Biomarkers Of Aging ◽

Glycation End Products ◽

End Products

Non-enzymatic glycation and covalent modification of proteins leads to Advanced Glycation End products (AGEs). AGEs are biomarkers of aging and neurodegenerative disease, and can be induced by impaired neuronal signaling. The objective of this study was to investigate if manipulation of dopamine (DA) in vitro using the model protein, bovine serum albumin (BSA), and in vivo using the model organism Drosophila melanogaster, influences fluorescent AGEs (fAGEs) formation as an indicator of dopamine-induced oxidation events. DA inhibited fAGEs-BSA synthesis in vitro, suggesting an anti-oxidative effect, which was not observed when flies were fed DA. Feeding flies cocaine and methamphetamine led to increased fAGEs formation. Mutants lacking the dopaminergic transporter or the D1-type showed further elevation of fAGEs accumulation, indicating that the long-term perturbation in DA function leads to higher production of fAGEs. To confirm that DA has oxidative properties in vivo, we fed flies antioxidant quercetin (QUE) together with methamphetamine. QUE significantly decreased methamphetamine-induced fAGEs formation suggesting that the perturbation of DA function in vivo leads to increased oxidation. These findings present arguments for the use of fAGEs as a biomarker of DA-associated neurodegenerative changes and for assessment of antioxidant interventions such as QUE treatment.

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A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae

Genetics ◽

10.1093/genetics/165.2.613 ◽

2003 ◽

Vol 165 (2) ◽

pp. 613-621 ◽

Cited By ~ 2

Author(s):

Douglas R Dorer ◽

Jamie A Rudnick ◽

Etsuko N Moriyama ◽

Alan C Christensen

Keyword(s):

Phylogenetic Analysis ◽

Drosophila Melanogaster ◽

Anopheles Gambiae ◽

Evolutionary History ◽

Codon Bias ◽

Good Target ◽

The Family ◽

Genes Encoding ◽

And Function ◽

Gambiae Genome

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

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Quantitative investigation reveals distinct phases in Drosophila sleep

Communications Biology ◽

10.1038/s42003-021-01883-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Xiaochan Xu ◽

Wei Yang ◽

Binghui Tian ◽

Xiuwen Sui ◽

Weilai Chi ◽

...

Keyword(s):

Drosophila Melanogaster ◽

General Pattern ◽

Model Organism ◽

Infrared Camera ◽

Fruit Fly ◽

Genetic Dissection ◽

Power Law Distribution ◽

Quantitative Investigation ◽

Waking Up ◽

Set Up

AbstractThe fruit fly, Drosophila melanogaster, has been used as a model organism for the molecular and genetic dissection of sleeping behaviors. However, most previous studies were based on qualitative or semi-quantitative characterizations. Here we quantified sleep in flies. We set up an assay to continuously track the activity of flies using infrared camera, which monitored the movement of tens of flies simultaneously with high spatial and temporal resolution. We obtained accurate statistics regarding the rest and sleep patterns of single flies. Analysis of our data has revealed a general pattern of rest and sleep: the rest statistics obeyed a power law distribution and the sleep statistics obeyed an exponential distribution. Thus, a resting fly would start to move again with a probability that decreased with the time it has rested, whereas a sleeping fly would wake up with a probability independent of how long it had slept. Resting transits to sleeping at time scales of minutes. Our method allows quantitative investigations of resting and sleeping behaviors and our results provide insights for mechanisms of falling into and waking up from sleep.

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Repeated stress exposure results in a survival–reproduction trade-off in Drosophila melanogaster

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2009.1807 ◽

2009 ◽

Vol 277 (1683) ◽

pp. 963-969 ◽

Cited By ~ 135

Author(s):

Katie E. Marshall ◽

Brent J. Sinclair

Keyword(s):

Drosophila Melanogaster ◽

Model Organism ◽

Intrinsic Rate ◽

Intrinsic Rate Of Increase ◽

Stress Exposure ◽

Trade Off ◽

Repeated Stress ◽

Rate Of Increase ◽

In The Wild ◽

Future Reproduction

While insect cold tolerance has been well studied, the vast majority of work has focused on the effects of a single cold exposure. However, many abiotic environmental stresses, including temperature, fluctuate within an organism's lifespan. Given that organisms may trade-off survival at the cost of future reproduction, we investigated the effects of multiple cold exposures on survival and fertility in the model organism Drosophila melanogaster . We found that multiple cold exposures significantly decreased mortality compared with the same length of exposure in a single sustained bout, but significantly decreased fecundity (as measured by r , the intrinsic rate of increase) as well, owing to a shift in sex ratio. This change was reflected in a long-term decrease in glycogen stores in multiply exposed flies, while a brief effect on triglyceride stores was observed, suggesting flies are reallocating energy stores. Given that many environments are not static, this trade-off indicates that investigating the effects of repeated stress exposure is important for understanding and predicting physiological responses in the wild.

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An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)

Zootaxa ◽

10.11646/zootaxa.4415.1.2 ◽

2018 ◽

Vol 4415 (1) ◽

pp. 45 ◽

Cited By ~ 41

Author(s):

PIOTR GĄSIOREK ◽

DANIEL STEC ◽

WITOLD MOREK ◽

ŁUKASZ MICHALCZYK

Keyword(s):

Dna Sequences ◽

Evolutionary Biology ◽

Model Organism ◽

Laboratory Strain ◽

Sensu Stricto ◽

Nominal Species ◽

28S Rrna ◽

The Family ◽

The 19Th Century ◽

Hypsibius Dujardini

A laboratory strain identified as “Hypsibius dujardini” is one of the best studied tardigrade strains: it is widely used as a model organism in a variety of research projects, ranging from developmental and evolutionary biology through physiology and anatomy to astrobiology. Hypsibius dujardini, originally described from the Île-de-France by Doyère in the first half of the 19th century, is now the nominal species for the superfamily Hypsibioidea. The species was traditionally considered cosmopolitan despite the fact that insufficient, old and sometimes contradictory descriptions and records prevented adequate delineations of similar Hypsibius species. As a consequence, H. dujardini appeared to occur globally, from Norway to Samoa. In this paper, we provide the first integrated taxonomic redescription of H. dujardini. In addition to classic imaging by light microscopy and a comprehensive morphometric dataset, we present scanning electron photomicrographs, and DNA sequences for three nuclear markers (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial marker (COI) that are characterised by various mutation rates. The results of our study reveal that a commercially available strain that is maintained in many laboratories throughout the world, and assumed to represent H. dujardini sensu stricto, represents, in fact, a new species: H. exemplaris sp. nov. Redescribing the nominal taxon for Hypsibiidae, we also redefine the family and amend the definitions of the subfamily Hypsibiinae and the genus Hypsibius. Moreover, we transfer H. arcticus (Murray, 1907) and Hypsibius conifer Mihelčič, 1938 to the genus Ramazzottius since the species exhibit claws and eggs of the Ramazzottius type. Finally, we designate H. fuhrmanni as subjectively invalid because the extremely poor description precludes identifying neotype material.

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Advances in Myeloid-Like Cell Origins and Functions in the Model Organism Drosophila melanogaster

Myeloid Cells in Health and Disease ◽

10.1128/microbiolspec.mchd-0038-2016 ◽

2017 ◽

pp. 59-77 ◽

Cited By ~ 3

Keyword(s):

Drosophila Melanogaster ◽

Model Organism

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Genetic variation in Drosophila melanogaster pathogen susceptibility

Parasitology ◽

10.1017/s0031182006009929 ◽

2006 ◽

Vol 132 (6) ◽

pp. 767-773 ◽

Cited By ~ 53

Author(s):

M. C. TINSLEY ◽

S. BLANFORD ◽

F. M. JIGGINS

Keyword(s):

Biological Control ◽

Drosophila Melanogaster ◽

Genetic Variation ◽

Model Organism ◽

Resistance Evolution ◽

Control Programmes ◽

Host Ecology ◽

Insect Pathogens ◽

Immunological Research ◽

Pathogen Exposure

Genetic variation in susceptibility to pathogens is a central concern both to evolutionary and medical biologists, and for the implementation of biological control programmes. We have investigated the extent of such variation in Drosophila melanogaster, a major model organism for immunological research. We found that within populations, different Drosophila genotypes show wide-ranging variation in their ability to survive infection with the entomopathogenic fungus Beauveria bassiana. Furthermore, striking divergence in susceptibility has occurred between genotypes from temperate and tropical African locations. We hypothesize that this may have been driven by adaptation to local differences in pathogen exposure or host ecology. Genetic variation within populations may be maintained by temporal or spatial variation in the costs and benefits of pathogen defence. Insect pathogens are employed widely as biological control agents and entomopathogenic fungi are currently being developed for reducing malaria transmission by mosquitoes. Our data highlight the need for concern about resistance evolution to these novel biopesticides in vector populations.

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