scholarly journals Hybrid Incompatibilities and Transgressive Gene Expression Between Two Closely Related Subspecies of Drosophila

2020 ◽  
Vol 11 ◽  
Author(s):  
Alwyn C. Go ◽  
Alberto Civetta
Keyword(s):  
Gene Networks ◽  
Sequence Divergence ◽  
Regulatory Elements ◽  
Directional Selection ◽  
Stabilizing Selection ◽  
Sequence Evolution ◽  
Snp Data ◽  
Partial Isolation ◽  
Cascade Effects ◽  
Hybrid Dysfunction

Genome-wide assays of expression between species and their hybrids have identified genes that become either over- or underexpressed relative to the parental species (i.e., transgressive). Transgressive expression in hybrids is of interest because it highlights possible changes in gene regulation linked to hybrid dysfunction. Previous studies in Drosophila that used long-diverged species pairs with complete or nearly complete isolation (i.e., full sterility and partial inviability of hybrids) and high-levels of genome misregulation have found correlations between expression and coding sequence divergence. The work highlighted the possible effects of directional selection driving sequence divergence and transgressive expression. Whether the same is true for taxa at early stages of divergence that have only achieved partial isolation remains untested. Here, we reanalyze previously published genome expression data and available genome sequence reads from a pair of partially isolated subspecies of Drosophila to compare expression and sequence divergence. We find a significant correlation in rates of expression and sequence evolution, but no support for directional selection driving transgressive expression in hybrids. We find that most transgressive genes in hybrids show no differential expression between parental subspecies and used SNP data to explore the role of stabilizing selection through compensatory mutations. We also examine possible misregulation through cascade effects that could be driven by interacting gene networks or co-option of off-target cis-regulatory elements.

scholarly journals Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

scholarly journals Quantitative genetic variability maintained by mutation-stabilizing selection balance: sampling variation and response to subsequent directional selection

1989 ◽  
Vol 54 (1) ◽  
pp. 45-58 ◽  
Author(s):  
Peter D. Keightley ◽  
William G. Hill
Keyword(s):  
Genetic Variance ◽  
Directional Selection ◽  
Quantitative Character ◽  
Stabilizing Selection ◽  
Effective Population ◽  
Selection Responses ◽  
Quantitative Genetic ◽  
Before And After ◽  
Cage Population ◽  
Selection Of

SummaryA model of genetic variation of a quantitative character subject to the simultaneous effects of mutation, selection and drift is investigated. Predictions are obtained for the variance of the genetic variance among independent lines at equilibrium with stabilizing selection. These indicate that the coefficient of variation of the genetic variance among lines is relatively insensitive to the strength of stabilizing selection on the character. The effects on the genetic variance of a change of mode of selection from stabilizing to directional selection are investigated. This is intended to model directional selection of a character in a sample of individuals from a natural or long-established cage population. The pattern of change of variance from directional selection is strongly influenced by the strengths of selection at individual loci in relation to effective population size before and after the change of regime. Patterns of change of variance and selection responses from Monte Carlo simulation are compared to selection responses observed in experiments. These indicate that changes in variance with directional selection are not very different from those due to drift alone in the experiments, and do not necessarily give information on the presence of stabilizing selection or its strength.

Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the α Subunit of CF1 (atpA) and the Proteolipid Subunit of CF0 (atpH)

Genetics ◽  
1987 ◽  
Vol 116 (1) ◽  
pp. 127-139
Author(s):  
Steven R Rodermel ◽  
Lawrence Bogorad
Keyword(s):  
Plastid Genome ◽  
Higher Plants ◽  
Rapid Evolution ◽  
Evolutionary Process ◽  
Nonsynonymous Substitution ◽  
Spatial Arrangement ◽  
Regulatory Elements ◽  
Nucleotide Sequences ◽  
Sequence Evolution ◽  
Α Subunit

ABSTRACT The nucleotide sequences of the maize plastid genes for the α subunit of CF1 (atpA) and the proteolipid subunit of CF 0 (atpH) are presented. The evolution of these genes among higher plants is characterized by a transition mutation bias of about 2:1 and by rates of synonymous and nonsynonymous substitution which are much lower than similar rates for genes from other sources. This is consistent with the notion that the plastid genome is evolving conservatively in primary sequence. Yet, the mode and tempo of sequence evolution of these and other plastid-encoded coupling factor genes are not the same. In particular, higher rates of nonsynonymous substitution in atpE (the gene for the ∊ subunit of CF1) and higher rates of synonymous substitution in atpH in the dicot vs. monocot lineages of higher plants indicate that these sequences are likely subject to different evolutionary constraints in these two lineages. The 5′- and 3′ transcribed flanking regions of atpA and atpH from maize, wheat and tobacco are conserved in size, but contain few putative regulatory elements which are conserved either in their spatial arrangement or sequence complexity. However, these regions likely contain variable numbers of "species-specific" regulatory elements. The present studies thus suggest that the plastid genome is not a passive participant in an evolutionary process governed by a more rapidly changing, readily adaptive, nuclear compartment, but that novel strategies for the coordinate expression of genes in the plastid genome may arise through rapid evolution of the flanking sequences of these genes.

scholarly journals Gene Families, Epistasis and the Amino Acid Preferences of Protein Homologs

2019 ◽  
Vol 15 ◽  
pp. 117693431987048
Author(s):  
Evandro Ferrada
Keyword(s):  
Amino Acid ◽  
Genetic Background ◽  
Sequence Divergence ◽  
Gene Families ◽  
Structure And Function ◽  
Sequence Evolution ◽  
Systematic Analysis ◽  
Fitness Effects ◽  
Computational Work ◽  
And Function

In order to preserve structure and function, proteins tend to preferentially conserve amino acids at particular sites along the sequence. Because mutations can affect structure and function, the question arises whether the preference of a protein site for a particular amino acid varies between protein homologs, and to what extent that variation depends on sequence divergence. Answering these questions can help in the development of models of sequence evolution, as well as provide insights on the dependence of the fitness effects of mutations on the genetic background of sequences, a phenomenon known as epistasis. Here, I comment on recent computational work providing a systematic analysis of the extent to which the amino acid preferences of proteins depend on the background mutations of protein homologs.

Sexual difference in modes of selection on the pleopods of crayfish (Decapoda: Astacoidea) revealed by the allometry of developmentally homologous traits

2003 ◽  
Vol 81 (6) ◽  
pp. 971-978 ◽  
Author(s):  
Naoko Kato ◽  
Tadashi Miyashita
Keyword(s):  
Sexual Difference ◽  
Procambarus Clarkii ◽  
Regression Line ◽  
Directional Selection ◽  
Stabilizing Selection ◽  
Allometric Relationships ◽  
Selective Force ◽  
Developmental Constraints ◽  
Selection Pressures ◽  
Males And Females

Crayfish have five pairs of abdominal limbs called pleopods. In males, the first and second pairs of pleopods are used for transferring spermatophores to the female during copulation. The remaining pleopods in males have no obvious function. Female crayfish use their pleopods to carry eggs. Accordingly, it is expected that the selection pressures that act on the pleopods differ between males and females. To test this hypothesis, we estimated modes of selection on pleopods in two species of crayfish (Procambarus clarkii and Pacifastacus trowbridgii) by comparing allometric relationships in functional and nonfunctional pleopods. Since pleopods are serially homologous traits, developmental constraints on these traits appear to be minimal. The lengths of the first male pleopods, used in copulation, showed lower allometric values and less dispersion around the regression line, suggesting that they have been under stabilizing selection. This likely occurs because the major selective force is the ability of males to copulate with females of various sizes. The pleopods of females showed higher allometric values than pleopods of males without an assigned function. This suggests that the pleopods of females have been under directional selection, most likely because they are longer and can therefore carry more eggs.

scholarly journals The relative impact of evolving pleiotropy and mutational correlation on trait divergence

2019 ◽  
Author(s):  
Jobran Chebib ◽  
Frédéric Guillaume
Keyword(s):  
Stochastic Model ◽  
Directional Selection ◽  
Population Variation ◽  
The Other ◽  
Common Mechanism ◽  
Stabilizing Selection ◽  
Relative Impact ◽  
Relative Importance ◽  
Trait Evolution ◽  
Trait Divergence

AbstractBoth pleiotropic connectivity and mutational correlations can restrict the divergence of traits under directional selection, but it is unknown which is more important in trait evolution. In order to address this question, we create a model that permits within-population variation in both pleiotropic connectivity and mutational correlation, and compare their relative importance to trait evolution. Specifically, we developed an individual-based, stochastic model where mutations can affect whether a locus affects a trait and the extent of mutational correlations in a population. We find that traits can diverge whether there is evolution in pleiotropic connectivity or mutational correlation but when both can evolve then evolution in pleiotropic connectivity is more likely to allow for divergence to occur. The most common genotype found in this case is characterized by having one locus that maintains connectivity to all traits and another that loses connectivity to the traits under stabilizing selection (subfunctionalization). This genotype is favoured because it allows the subfunctionalized locus to accumulate greater effect size alleles, contributing to increasingly divergent trait values in the traits under directional selection without changing the trait values of the other traits (genetic modularization). These results provide evidence that partial subfunctionalization of pleiotropic loci may be a common mechanism of trait divergence under regimes of corridor selection.

scholarly journals An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs

2014 ◽  
Author(s):  
Jesse D Bloom
Keyword(s):  
High Throughput ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Evolutionary Model ◽  
Molecular Data ◽  
Quantitative Model ◽  
Sequence Evolution ◽  
Beta Lactamase ◽  
Evolutionary Models ◽  
High Throughput Experiments

Phylogenetic analyses of molecular data require a quantitative model for how sequences evolve. Traditionally, the details of the site-specific selection that governs sequence evolution are not knowna priori, making it challenging to create evolutionary models that adequately capture the heterogeneity of selection at different sites. However, recent advances in high-throughput experiments have made it possible to quantify the effects of all single mutations on gene function. I have previously shown that such high-throughput experiments can be combined with knowledge of underlying mutation rates to create a parameter-free evolutionary model that describes the phylogeny of influenza nucleoprotein far better than commonly used existing models. Here I extend this work by showing that published experimental data on TEM-1 beta-lactamase (Firnberg et al, 2014) can be combined with a few mutation rate parameters to create an evolutionary model that describes beta-lactamase phylogenies much than most common existing models. This experimentally informed evolutionary model is superior even for homologs that are substantially diverged (about 35% divergence at the protein level) from the TEM-1 parent that was the subject of the experimental study. These results suggest that experimental measurements can inform phylogenetic evolutionary models that are applicable to homologs that span a substantial range of sequence divergence.

scholarly journals Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

2019 ◽  
Author(s):  
Ryan M. Mulqueen ◽  
Brooke A. DeRosa ◽  
Casey A. Thornton ◽  
Zeynep Sayar ◽  
Kristof A. Torkenczy ◽  
...  
Keyword(s):  
Single Cell ◽  
Gene Networks ◽  
Regulatory Gene ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Chromatin Dynamics ◽  
Cell Library ◽  
Fate Decision

AbstractDevelopment is a complex process that requires the precise modulation of regulatory gene networks controlled through dynamic changes in the epigenome. Single-cell-omic technologies provide an avenue for understanding the mechanisms of these processes by capturing the progression of epigenetic cell states during the course of cellular differentiation using in vitro or in vivo models1. However, current single-cell epigenomic methods are limited in the information garnered per individual cell, which in turn limits their ability to measure chromatin dynamics and state shifts. Single-cell combinatorial indexing (sci-) has been applied as a strategy for identifying single-cell-omic originating libraries and removes the necessity of single-cell, single-compartment chemistry2. Here, we report an improved sci-assay for transposase accessible chromatin by sequencing (ATAC-seq), which utilizes the small molecule inhibitor Pitstop 2™ (scip-ATAC-seq)3. We demonstrate that these improvements, which theoretically could be applied to any in situ transposition method for single-cell library preparation, significantly increase the ability of transposase to enter the nucleus and generate highly complex single-cell libraries, without altering biological signal. We applied sci-ATAC-seq and scip-ATAC-seq to characterize the chromatin dynamics of developing forebrain-like organoids, an in vitro model of human corticogenesis4. Using these data, we characterized novel putative regulatory elements, compared the epigenome of the organoid model to human cortex data, generated a high-resolution pseudotemporal map of chromatin accessibility through differentiation, and measured epigenomic changes coinciding with a neurogenic fate decision point. Finally, we combined transcription factor motif accessibility with gene activity (GA) scores to directly observe the dynamics of complex regulatory programs that regulate neurogenesis through developmental pseudotime. Overall, scip-ATAC-seq increases information content per cell and bolsters the potential for future single-cell studies into complex developmental processes.

scholarly journals Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex

2021 ◽  
Author(s):  
Salah E Abdel-Ghany ◽  
Lisa M LaManna ◽  
Zora Svab ◽  
Haleakala E Harroun ◽  
Pal Maliga ◽  
...  
Keyword(s):  
Sequence Divergence ◽  
Sequence Evolution ◽  
Rapid Sequence ◽  
Wide Range ◽  
Functional Consequences ◽  
The Subject ◽  
Genus Silene ◽  
Silene Species ◽  
Protein Sequence Evolution ◽  
Donor Species

The plastid caseinolytic protease (Clp) complex plays essential roles in maintaining protein homeostasis and comprises both plastid-encoded and nuclear-encoded subunits. Despite the Clp complex being retained across green plants with highly conserved protein sequences in most species, examples of extremely accelerated amino acid substitution rates have been identified in numerous angiosperms. The causes of these accelerations have been the subject of extensive speculation but still remain unclear. To distinguish among prevailing hypotheses and begin to understand the functional consequences of rapid sequence divergence in Clp subunits, we used plastome transformation to replace the native clpP1 gene in tobacco (Nicotiana tabacum) with counterparts from another angiosperm genus (Silene) that exhibits a wide range in rates of Clp protein sequence evolution. We found that antibiotic-mediated selection could drive a transgenic clpP1 replacement from a slowly evolving donor species (S. latifolia) to homoplasmy but that clpP1 copies from Silene species with accelerated evolutionary rates remained heteroplasmic, meaning that they could not functionally replace the essential tobacco clpP1 gene. These results suggest that observed cases of rapid Clp sequence evolution are a source of epistatic incompatibilities that must be ameliorated by coevolutionary responses between plastid and nuclear subunits.

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