scholarly journals Transposable element dynamics are consistent across the Drosophila phylogeny, despite drastically differing content

2019 ◽  
Author(s):  
Tom Hill
Keyword(s):  
Drosophila Melanogaster ◽  
Related Species ◽  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Low Frequency ◽  
Fitness Costs ◽  
Closely Related Species ◽  
Drosophila Phylogeny ◽  
Turn Over ◽  
Insertion Frequency

AbstractBackgroundThe evolutionary dynamics of transposable elements (TEs) vary across the tree of life and even between closely related species with similar ecologies. In Drosophila, most of the focus on TE dynamics has been completed in Drosophila melanogaster and the overall pattern indicates that TEs show an excess of low frequency insertions, consistent with their frequent turn over and high fitness cost in the genome. Outside of D. melanogaster, insertions in the species Drosophila algonquin, suggests that this situation may not be universal, even within Drosophila. Here we test whether the pattern observed in D. melanogaster is similar across five Drosophila species that share a common ancestor more than fifty million years ago.ResultsFor the most part, TE family and order insertion frequency patterns are broadly conserved between species, supporting the idea that TEs have invaded species recently, are mostly costly and dynamics are conserved in orthologous regions of the host genomeConclusionsMost TEs retain similar activities and fitness costs across the Drosophila phylogeny, suggesting little evidence of drift in the dynamics of TEs across the phylogeny, and that most TEs have invaded species recently.

scholarly journals Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny

2018 ◽  
Vol 35 (4) ◽  
pp. 925-941 ◽  
Author(s):  
Kevin H -C Wei ◽  
Sarah E Lower ◽  
Ian V Caldas ◽  
Trevor J S Sless ◽  
Daniel A Barbash ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Rapid Evolution ◽  
Single Mutation ◽  
Closely Related Species ◽  
Interspecific Differences ◽  
Limited Sampling ◽  
Drosophila Phylogeny ◽  
Males And Females ◽  
Species Specific ◽  
Turn Over

Abstract Simple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through nonallelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly. However, limited sampling has prevented detailed understanding of their evolutionary dynamics. Here, we characterize simple satellites from whole-genome sequences generated from males and females of nine Drosophila species, spanning 40 Ma of evolution. We show that PCR-free library preparation and postsequencing GC-correction better capture satellite quantities than conventional methods. We find that over half of the 207 simple satellites identified are species-specific, consistent with previous descriptions of their rapid evolution. Based on a maximum parsimony framework, we determined that most interspecific differences are due to lineage-specific gains. Simple satellites gained within a species are typically a single mutation away from abundant existing satellites, suggesting that they likely emerge from existing satellites, especially in the genomes of satellite-rich species. Interestingly, unlike most of the other lineages which experience various degrees of gains, the lineage leading up to the satellite-poor D. pseudoobscura and D. persimilis appears to be recalcitrant to gains, providing a counterpoint to the notion that simple satellites are universally rapidly evolving.

Locomotion is not influenced by denticle number in larvae of the fruit fly Drosophila melanogaster

2005 ◽  
Vol 83 (2) ◽  
pp. 368-371 ◽  
Author(s):  
Mark J Fitzpatrick ◽  
Evelyn Szewczyk
Keyword(s):  
Drosophila Melanogaster ◽  
Related Species ◽  
Natural Variation ◽  
Fruit Fly ◽  
Fruit Flies ◽  
Negative Effects ◽  
Closely Related Species ◽  
Locomotory Performance ◽  
Locomotion Speed

Denticles are small projections on the underside of larval fruit flies that are used to grip the substrate while crawling. Previous studies have shown that (i) there is natural variation in denticle number and pattern between Drosophila melanogaster (Meigen, 1830) and several closely related species and (ii) mutations affecting denticle morphology have negative effects on locomotory performance. We hypothesized that there would be a correlation between denticle number and locomotory performance within populations of D. melanogaster. Despite finding considerable variation in denticle number, we found no correlation between denticle number and three measurements of larval locomotion: speed, acceleration, and absolute turning rate.

scholarly journals Comparative transcriptomics of the venoms of continental and insular radiations of West African cones

2020 ◽  
Vol 287 (1929) ◽  
pp. 20200794
Author(s):  
Samuel Abalde ◽  
Manuel J. Tenorio ◽  
Carlos M. L. Afonso ◽  
Rafael Zardoya
Keyword(s):  
Related Species ◽  
Common Ancestor ◽  
West African ◽  
Generic Level ◽  
Closely Related Species ◽  
Functional Convergence ◽  
Venom Glands ◽  
Phylogenetic Framework ◽  
The Common ◽  
Secreted Peptides

The transcriptomes of the venom glands of 13 closely related species of vermivorous cones endemic to West Africa from genera Africonus and Varioconus were sequenced and venom repertoires compared within a phylogenetic framework using one Kalloconus species as outgroup. The total number of conotoxin precursors per species varied between 108 and 221. Individuals of the same species shared about one-fourth of the total conotoxin precursors. The number of common sequences was drastically reduced in the pairwise comparisons between closely related species, and the phylogenetical signal was totally eroded at the inter-generic level (no sequence was identified as shared derived), due to the intrinsic high variability of these secreted peptides. A common set of four conotoxin precursor superfamilies (T, O1, O2 and M) was expanded in all studied cone species, and thus, they are considered the basic venom toolkit for hunting and defense in the West African vermivorous cone snails. Maximum-likelihood ancestral character reconstructions inferred shared conotoxin precursors preferentially at internal nodes close to the tips of the phylogeny (between individuals and between closely related species) as well as in the common ancestor of Varioconus . Besides the common toolkit, the two genera showed significantly distinct catalogues of conotoxin precursors in terms of type of superfamilies present and the abundance of members per superfamily, but had similar relative expression levels indicating functional convergence. Differential expression comparisons between vermivorous and piscivorous cones highlighted the importance of the A and S superfamilies for fish hunting and defense.

scholarly journals Lack of underdominance in a naturally occurring pericentric inversion in Drosophila melanogaster and its implications for chromosome evolution.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 791-802
Author(s):  
J A Coyne ◽  
S Aulard ◽  
A Berry
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Genetic Drift ◽  
Related Species ◽  
Pericentric Inversion ◽  
Chromosome Evolution ◽  
Natural Populations ◽  
Crossing Over ◽  
Closely Related Species ◽  
Naturally Occurring

Abstract In(2LR)PL is a large pericentric inversion polymorphic in populations of Drosophila melanogaster on two Indian Ocean islands. This polymorphism is puzzling: because crossing over in female heterokaryotypes produces inviable zygotes, such inversions are thought to be underdominant and should be quickly eliminated from populations. The observed fixation for such inversions among related species has led to the idea that genetic drift can cause chromosome evolution in opposition to natural selection. We found, however, that In(2LR)PL is not underdominant for fertility, as heterokaryotypic females produce perfectly viable eggs. Genetic analysis shows that the lack of underdominance results from the nearly complete absence of crossing over in the inverted region. This phenomenon is probably caused by mechanical and not genetic factors, because crossing over is not suppressed in In(2LR)PL homokaryotypes. Our observations do not support the idea that the fixation of pericentric inversions among closely related species implies the action of genetic drift overcoming strong natural selection in very small populations. If chromosome arrangements vary in their underdominance, it is those with the least disadvantage as heterozygotes, like In(2LR)PL, that will be polymorphic or fixed in natural populations.

scholarly journals The Loci of Behavioral Evolution: Evidence That Fas2 and tilB Underlie Differences in Pupation Site Choice Behavior between Drosophila melanogaster and D. simulans

2019 ◽  
Vol 37 (3) ◽  
pp. 864-880
Author(s):  
Alison Pischedda ◽  
Michael P Shahandeh ◽  
Thomas L Turner
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Related Species ◽  
Choice Behavior ◽  
Genetic Basis ◽  
Association Studies ◽  
Single Gene ◽  
Closely Related Species ◽  
Environmentally Sensitive ◽  
Pupation Site

Abstract The behaviors of closely related species can be remarkably different, and these differences have important ecological and evolutionary consequences. Although the recent boom in genotype–phenotype studies has led to a greater understanding of the genetic architecture and evolution of a variety of traits, studies identifying the genetic basis of behaviors are, comparatively, still lacking. This is likely because they are complex and environmentally sensitive phenotypes, making them difficult to measure reliably for association studies. The Drosophila species complex holds promise for addressing these challenges, as the behaviors of closely related species can be readily assayed in a common environment. Here, we investigate the genetic basis of an evolved behavioral difference, pupation site choice, between Drosophila melanogaster and D. simulans. In this study, we demonstrate a significant contribution of the X chromosome to the difference in pupation site choice behavior between these species. Using a panel of X-chromosome deficiencies, we screened the majority of the X chromosome for causal loci and identified two regions associated with this X-effect. We then collect gene disruption and RNAi data supporting a single gene that affects pupation behavior within each region: Fas2 and tilB. Finally, we show that differences in tilB expression correlate with the differences in pupation site choice behavior between species. This evidence associating two genes with differences in a complex, environmentally sensitive behavior represents the first step toward a functional and evolutionary understanding of this behavioral divergence.

scholarly journals Recent Insights into Mechanisms of Genome Size Change in Plants

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Corrinne E. Grover ◽  
Jonathan F. Wendel
Keyword(s):  
Genome Size ◽  
Related Species ◽  
Evolutionary Dynamics ◽  
Higher Order ◽  
Size Change ◽  
Closely Related Species ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Recent Developments

Genome sizes vary considerably across all eukaryotes and even among closely related species. The genesis and evolutionary dynamics of that variation have generated considerable interest, as have the patterns of variation themselves. Here we review recent developments in our understanding of genome size evolution in plants, drawing attention to the higher order processes that can influence the mechanisms generating changing genome size.

scholarly journals Evolutionary dynamics of circular RNAs in primates

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Gabriela Santos-Rodriguez ◽  
Irina Voineagu ◽  
Robert James Weatheritt
Keyword(s):  
Related Species ◽  
Evolutionary Dynamics ◽  
Expression Profiles ◽  
Primate Evolution ◽  
Circular Rnas ◽  
Species Identity ◽  
Closely Related Species ◽  
Tissue Specific ◽  
Organ Type ◽  
Species Specific

Many primate genes produce circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. By comparing to species-specific circRNAs, we identified that the downstream intron of the conserved circRNAs display a dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

scholarly journals Evolutionary dynamics of circular RNAs in primates

2021 ◽  
Author(s):  
Gabriela Santos-Rodriguez ◽  
Irina Voineagu ◽  
Robert James Weatheritt
Keyword(s):  
Related Species ◽  
Evolutionary Dynamics ◽  
Expression Profiles ◽  
Primate Evolution ◽  
Circular Rnas ◽  
Species Identity ◽  
Closely Related Species ◽  
Tissue Specific ◽  
Comparative Analyses ◽  
Organ Type

Many primate genes produce noncoding circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. These circRNAs are defined by an extended downstream intron that has shown dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

scholarly journals Comparative sequence analysis of a gene-dense region among closely related species of Drosophila melanogaster

2004 ◽  
Vol 79 (6) ◽  
pp. 351-359 ◽  
Author(s):  
Yoshihiro Kawahara ◽  
Takashi Matsuo ◽  
Masafumi Nozawa ◽  
Tadasu Shin-I ◽  
Yuji Kohara ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Sequence Analysis ◽  
Related Species ◽  
Comparative Sequence Analysis ◽  
Dense Region ◽  
Closely Related Species ◽  
Comparative Sequence

scholarly journals Telomeric TART elements target the piRNA machinery in Drosophila

PLoS Biology ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. e3000689
Author(s):  
Christopher E. Ellison ◽  
Meenakshi S. Kagda ◽  
Weihuan Cao
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Related Species ◽  
Nuclear Export ◽  
Small Rnas ◽  
Critical Role ◽  
Closely Related Species ◽  
Factor Gene ◽  
Antagonistic Coevolution ◽  
Copy Numbers

Coevolution between transposable elements (TEs) and their hosts can be antagonistic, where TEs evolve to avoid silencing and the host responds by reestablishing TE suppression, or mutualistic, where TEs are co-opted to benefit their host. The TART-A TE functions as an important component of Drosophila telomeres but has also reportedly inserted into the Drosophila melanogaster nuclear export factor gene nxf2. We find that, rather than inserting into nxf2, TART-A has actually captured a portion of nxf2 sequence. We show that TART-A produces abundant Piwi-interacting small RNAs (piRNAs), some of which are antisense to the nxf2 transcript, and that the TART-like region of nxf2 is evolving rapidly. Furthermore, in D. melanogaster, TART-A is present at higher copy numbers, and nxf2 shows reduced expression, compared to the closely related species Drosophila simulans. We propose that capturing nxf2 sequence allowed TART-A to target the nxf2 gene for piRNA-mediated repression and that these 2 elements are engaged in antagonistic coevolution despite the fact that TART-A is serving a critical role for its host genome.

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