scholarly journals Selection constrains high rates of satellite DNA mutation in Daphnia pulex

2017 ◽  
Author(s):  
Jullien M. Flynn ◽  
Ian Caldas ◽  
Melania E. Cristescu ◽  
Andrew G. Clark
Keyword(s):  
Satellite Dna ◽  
Related Species ◽  
Rapid Evolution ◽  
Daphnia Pulex ◽  
Selective Constraint ◽  
Mutation Rates ◽  
Stabilizing Selection ◽  
Closely Related Species ◽  
Dna Mutation ◽  
Evolutionary Forces

AbstractA long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated satellite DNA whose composition varies greatly among even closely related species. To elucidate the evolutionary forces governing satellite dynamics, quantification of the rates and patterns of mutations in satellite DNA copy number and tests of its selective neutrality are necessary. Here we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex in addition to six isolates from a non-MA population originating from the same progenitor to both estimate mutation rates of abundances of satellite sequences and evaluate the selective regime acting upon them. We found that mutation rates of individual satellite sequence “kmers” were both high and highly variable, ranging from additions/deletions of 0.29 – 105 copies per generation (reflecting changes of 0.12 - 0.80 percent per generation). Our results also provide evidence that new kmer sequences are often formed from existing ones. The non-MA population isolates showed a signal of either purifying or stabilizing selection, with 33 % lower variation in kmer abundance on average than the MA lines, although the level of selective constraint was not evenly distributed across all kmers. The changes between many pairs of kmers were correlated, and the pattern of correlations was significantly different between the MA lines and the non-MA population. Our study demonstrates that kmer sequences can experience extremely rapid evolution in abundance, which can lead to high levels of divergence in genome-wide satellite DNA composition between closely related species.

scholarly journals The rapid evolution of alternative splicing in plants

2017 ◽  
Author(s):  
Zhihao Ling ◽  
Thomas Brockmöller ◽  
Ian T. Baldwin ◽  
Shuqing Xu
Keyword(s):  
Alternative Splicing ◽  
Related Species ◽  
Donor Site ◽  
Rapid Evolution ◽  
Acceptor Site ◽  
Mrna Levels ◽  
Evolutionary Patterns ◽  
Closely Related Species ◽  
Nonsense Mediated Decay ◽  
Splicing Regulators

AbstractAlternative pre-mRNA splicing (AS) is prevalent among all plants and is involved in many interactions with environmental stresses. However, the evolutionary patterns and underlying mechanisms of AS in plants remain unclear. By analyzing the transcriptomes of six plant species, we revealed that AS diverged rapidly among closely related species, largely due to the gains and losses of AS events among orthologous genes. Furthermore, AS that generates transcripts containing premature termination codons (PTC), although only representing a small fraction of the total AS, are more conserved than those that generate non-PTC containing transcripts, suggesting that AS coupled with nonsense-mediated decay (NMD) might play an important role in regulating mRNA levels post-transcriptionally. With a machine learning approach we analyzed the key determinants of AS to understand the mechanisms underlying its rapid divergence. Among the studied species, the presence/absence of alternative splicing site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5’ donor site and 3’acceptor site, suggesting a relatively conserved AS mechanism. Comparative analysis further demonstrated that variations of the identified AS determinants, mostly are located in introns, significantly contributed to the AS turnover among closely related species in both Solanaceae and Brassicaceae taxa. These new mechanistic insights into the evolution of AS in plants highlight the importance of post-transcriptional regulation in mediating plant-environment interactions.One sentence summaryChanges of intron located splicing regulators contributed to the rapid evolution of alternative splicing in plants.

scholarly journals Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

2019 ◽  
Vol 36 (9) ◽  
pp. 1942-1954 ◽  
Author(s):  
Eddie K H Ho ◽  
Fenner Macrae ◽  
Leigh C Latta ◽  
Maia J Benner ◽  
Cheng Sun ◽  
...  
Keyword(s):  
Daphnia Magna ◽  
Tandem Repeats ◽  
Large Population ◽  
Daphnia Pulex ◽  
Mutation Rates ◽  
Evolutionary Forces ◽  
Repeat Content ◽  
Order Of Magnitude ◽  
Microsatellite Mutation ◽  
Short Time

Abstract Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species, and have rarely been compared across genotypes and populations within a species. Here, we investigate the dynamics of microsatellite mutation over long- and short-time periods by quantifying the starting abundance and mutation rates for microsatellites for six different genotypes of Daphnia magna, an aquatic microcrustacean, collected from three populations (Finland, Germany, and Israel). Using whole-genome sequences of these six starting genotypes, descendent mutation accumulation (MA) lines, and large population controls (non-MA lines), we find each genotype exhibits a distinctive initial microsatellite profile which clusters according to the population-of-origin. During the period of MA, we observe motif-specific, highly variable, and rapid microsatellite mutation rates across genotypes of D. magna, the average of which is order of magnitude greater than the recently reported rate observed in a single genotype of the congener, Daphnia pulex. In our experiment, genotypes with more microsatellites starting out exhibit greater losses and those with fewer microsatellites starting out exhibit greater gains—a context-dependent mutation bias that has not been reported previously. We discuss how genotype-specific mutation rates and spectra, in conjunction with evolutionary forces, can shape both the differential accumulation of repeat content in the genome and the evolution of mutation rates.

scholarly journals Defective satellite DNA clustering into chromocenters underlies hybrid incompatibility in Drosophila

2021 ◽  
Author(s):  
Madhav Jagannathan ◽  
Yukiko M Yamashita
Keyword(s):  
Satellite Dna ◽  
Rapid Evolution ◽  
Dna Binding Proteins ◽  
Dna Repeats ◽  
Hybrid Cells ◽  
Entire Genome ◽  
Closely Related Species ◽  
Hybrid Incompatibility ◽  
Cluster Satellite ◽  
Single Nucleus

Although rapid evolution of pericentromeric satellite DNA repeats is theorized to promote hybrid incompatibility (HI), how divergent repeats affect hybrid cells remains poorly understood. Recently, we demonstrated that sequence-specific DNA-binding proteins cluster satellite DNA from multiple chromosomes into chromocenters, thereby bundling chromosomes to maintain the entire genome in a single nucleus. Here we show that ineffective clustering of divergent satellite DNA in the cells of Drosophila hybrids results in chromocenter disruption, associated micronuclei formation and tissue atrophy. We further demonstrate that previously identified HI factors trigger chromocenter disruption and micronuclei in hybrids, linking their function to a conserved cellular process. Together, we propose a unifying framework that explains how the widely observed satellite DNA divergence between closely related species can cause reproductive isolation.

The Evolutionary Analysis of “Orphans” From the Drosophila Genome Identifies Rapidly Diverging and Incorrectly Annotated Genes

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 589-598 ◽  
Author(s):  
Karl J Schmid ◽  
Charles F Aquadro
Keyword(s):  
Related Species ◽  
Rapid Evolution ◽  
Model Organisms ◽  
Drosophila Genome ◽  
Evolutionary Analysis ◽  
Orphan Genes ◽  
Closely Related Species ◽  
Reading Frame ◽  
Nearly Neutral Mutations ◽  
Neutral Mutations

Abstract In genome projects of eukaryotic model organisms, a large number of novel genes of unknown function and evolutionary history (“orphans”) are being identified. Since many orphans have no known homologs in distant species, it is unclear whether they are restricted to certain taxa or evolve rapidly, either because of a lack of constraints or positive Darwinian selection. Here we use three criteria for the selection of putatively rapidly evolving genes from a single sequence of Drosophila melanogaster. Thirteen candidate genes were chosen from the Adh region on the second chromosome and 1 from the tip of the X chromosome. We succeeded in obtaining sequence from 6 of these in the closely related species D. simulans and D. yakuba. Only 1 of the 6 genes showed a large number of amino acid replacements and in-frame insertions/deletions. A population survey of this gene suggests that its rapid evolution is due to the fixation of many neutral or nearly neutral mutations. Two other genes showed “normal” levels of divergence between species. Four genes had insertions/deletions that destroy the putative reading frame within exons, suggesting that these exons have been incorrectly annotated. The evolutionary analysis of orphan genes in closely related species is useful for the identification of both rapidly evolving and incorrectly annotated genes.

scholarly journals Rapid evolution of the functionally conserved gap gene giant in Drosophila

2021 ◽  
Author(s):  
Wenhan Chang ◽  
Daniel R Matute ◽  
Martin Kreitman
Keyword(s):  
Related Species ◽  
Regulatory Networks ◽  
Driving Forces ◽  
Functional Divergence ◽  
Continuous Process ◽  
Rapid Evolution ◽  
Developmental Outcomes ◽  
Evolutionary Forces ◽  
Gap Gene ◽  
Development Outcomes

Developmental processes in multicellular organisms, and the outcomes they produce, are often evolutionarily conserved. Yet phylogenetic conservation of developmental outcomes is not reflected in functional preservation of the genes regulating these processes, a phenomenon referred to as developmental system drift. Little is known about the evolutionary forces producing change in the molecular details of regulatory genes and their networks while preserving development outcomes. Here we address this void in knowledge by systematically swapping the Drosophila melanogaster coding and noncoding regions of the essential gap gene, giant, a key regulator of embryonic pattern formation, with orthologous sequences drawn from both closely and distantly related species within the genus. Employing sensitized genetic complementation assays, the loss of a transgene's ability to restore viability occurs across phylogeny at every interspecific level of comparison and includes both coding and noncoding changes. Epistasis is present as well -- both between coding and noncoding sequences and, in a dramatic example of change-of-sign epistasis, between the only two coding substitutions separating two very closely related species. A continuous process of functional divergence hidden under conserved phylotypic developmental outcomes requires reconsideration of the prevailing view that the essential genes in conserved regulatory networks are protected from the driving forces of evolutionary change.

scholarly journals Why Aggregate? On the Evolution of Aggregative Multicellularity

2021 ◽  
Author(s):  
Marco La Fortezza ◽  
Kaitlin Schaal ◽  
Gregory J. Velicer
Keyword(s):  
Related Species ◽  
Group Level ◽  
Fruiting Bodies ◽  
Closely Related Species ◽  
Evolutionary Forces ◽  
Selective Pressures ◽  
Open Questions ◽  
Level Function ◽  
The Many ◽  
Microbial Systems

Microbes have evolved many fascinating and complex ways of interacting with conspecifics. Perhaps one of the most interesting is aggregative multicellularity, wherein independent cells come together and adhere to one another in order to form a larger entity. The fundamental benefits of active aggregation into multicellular groups generally remain unclear, and there are many open questions about what selective pressures led to the evolution of this behavior in various eukaryotic and prokaryotic taxa, most notably the dictyostelids and the myxobacteria. Aggregative multicellularity can be partitioned into three main phases: coming together, staying together as a group, and disaggregation. Different selective pressures may have led to adaptations unique to each phase. While aggregative microbial systems generally form elevated multicellular structures such as fruiting bodies, these can vary in complexity and morphology even among closely related species. What evolutionary forces shaped such morphological diversification remains unknown. Strains that are not genetically identical can coaggregate, which can impact group-level function either positively through functional synergy or negatively through harmful exploitation. Such chimerism within aggregates is likely to have played important roles in shaping the evolution of microbial multicellularity. Much further research is needed into the evolutionary forces and processes leading to and shaping the many forms of microbial aggregation.

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