scholarly journals Detecting Signatures Of Selection In Regulatory Variation

2021 ◽  
Author(s):  
Peter D Price ◽  
Daniela H Palmer Droguett ◽  
Jessica A Taylor ◽  
Dong W Kim ◽  
Elsie S Place ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Phenotypic Diversity ◽  
Sequence Evolution ◽  
Simulation Studies ◽  
Consensus Model ◽  
Tissue Composition ◽  
Regulatory Evolution ◽  
Regulatory Variation ◽  
Phylogenetic Methods ◽  
Signatures Of Selection

A substantial amount of phenotypic diversity results from changes in gene regulation. Understanding how regulatory diversity evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of regulatory evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene regulation are subject to biases that can lead to false signatures of selection. In this review, we first outline the main approaches for describing regulatory evolution and their inherent biases. Next, we bridge the gap between the fields of comparative phylogenetic methods and transcriptomics to reinforce the main pitfalls of inferring regulatory selection and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of regulatory variation and identifying major, unanswered questions in disentangling how selection acts on the transcriptome.

scholarly journals Coexpression reveals conserved mechanisms of transcriptional cell identity

2020 ◽  
Author(s):  
Megan Crow ◽  
Hamsini Suresh ◽  
John Lee ◽  
Jesse Gillis
Keyword(s):  
Gene Regulation ◽  
Cell Types ◽  
Regulatory Evolution ◽  
Closely Related Species ◽  
Cell Identity ◽  
Gene Coexpression ◽  
Evolution Of Gene Regulation ◽  
Orthology Prediction ◽  
Species Specific ◽  
Coexpression Networks

ABSTRACTWhat makes a mouse a mouse, and not a hamster? The answer lies in the genome, and more specifically, in differences in gene regulation between the two organisms: where and when each gene is expressed. To quantify differences, a typical study will either compare functional genomics data from homologous tissues, limiting the approach to closely related species; or compare gene repertoires, limiting the resolution of the analysis to gross correlations between phenotypes and gene family size. As an alternative, gene coexpression networks provide a basis for studying the evolution of gene regulation without these constraints. By incorporating data from hundreds of independent experiments, meta-analytic coexpression networks reflect the convergent output of species-specific transcriptional regulation.In this work, we develop a measure of regulatory evolution based on gene coexpression. Comparing data from 14 species, we quantify the conservation of coexpression patterns 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-specificity. Strikingly, we uncover deeply conserved patterns of gradient-like expression across cell types from both the animal and plant kingdoms. These results suggest that ancient genes contribute to transcriptional cell identity through mechanisms that are independent of duplication and divergence.

scholarly journals Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for the Evolution of Gene Expression

2019 ◽  
Author(s):  
Elisa Buchberger ◽  
Micael Reis ◽  
Ting-Hsuan Lu ◽  
Nico Posnien
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Evolutionary Biology ◽  
Expression Data ◽  
Regulatory Evolution ◽  
Specific Expression ◽  
Genome Wide ◽  
Key Driver ◽  
Context Dependent ◽  
Genome Wide Expression

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic variation. An exceptional contribution of cis-regulatory evolution has for instance been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and developmental stage-specific expression. We argue that the regulatory context must be considered when studying evolution of gene expression.

scholarly journals Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape

2016 ◽  
Author(s):  
Marco Trizzino ◽  
YoSon Park ◽  
Marcia Holsbach-Beltrame ◽  
Katherine Aracena ◽  
Katelyn Mika ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Phenotypic Diversity ◽  
Regulatory Element ◽  
Critical Role ◽  
Primary Source ◽  
Primate Species ◽  
Rna Seq ◽  
Cell Type Specificity ◽  
Regulatory Landscape

AbstractGene regulation plays a critical role in the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species. We performed ChlP-seq for two histone modifications and RNA-seq to profile cis-regulatory element (CRE) activity and gene expression. The primate regulatory landscape is largely conserved across the lineage. Conserved CRE function is associated with sequence conservation, proximity to coding genes, cell type specificity of CRE function, and transcription factor binding. Newly evolved CREs are enriched in immune response and neurodevelopmental functions, while conserved CREs bind master regulators. Transposable elements (TEs) are the primary source of novelty in primate gene regulation. Newly evolved CREs are enriched in young TEs that affect gene expression. However, only 17% of conserved CREs overlap a TE, suggesting that target gene expression is under strong selection. Finally, we identified specific genomic features driving the functional recruitment of newly inserted TEs.

scholarly journals Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information

2020 ◽  
Author(s):  
M.E. López ◽  
M.I. Cádiz ◽  
E.B. Rondeau ◽  
B.F. Koop ◽  
J.M. Yáñez
Keyword(s):  
Disease Resistance ◽  
Coho Salmon ◽  
Phenotypic Diversity ◽  
Oncorhynchus Kisutch ◽  
Culture Conditions ◽  
Selection Signatures ◽  
Breeding Programs ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
Signatures Of Selection

AbstractAnimal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection known as selection signatures or selective sweeps have been traced in the genomes of many animal livestock species by exploiting variations in linkage disequilibrium patterns and/or reduction of genetic diversity.Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subject to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn that have been previously associated with body weight in Atlantic salmon or sec24d and robo1 that have been associated with disease resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.

scholarly journals Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies

2021 ◽  
Author(s):  
R Axel W Wiberg ◽  
Jeremias N Brand ◽  
Lukas Schaerer
Keyword(s):  
Sexual Selection ◽  
Sequence Evolution ◽  
Model Species ◽  
Free Living ◽  
Molecular Sequence ◽  
Functional Annotations ◽  
Genome Wide ◽  
Large Genus ◽  
Signatures Of Selection ◽  
Efficiency Of Selection

Sexual selection is expected to drive the evolution of many striking behaviours and morphologies, leaving signatures of selection at loci underlying these phenotypes. However, relatively few studies have contrasted molecular sequence evolution at such loci across lineages that differ in their sexual selection context. Our comparative genomics study of Macrostomum, a large genus of free-living simultaneously hermaphroditic flatworms, takes advantage of functional annotations from the model species, M. lignano, and transcriptome assemblies of 97 congeners. We compare molecular sequence evolution in species with contrasting sperm morphologies, which are strongly associated with multiple convergent shifts in the mating strategy and thus reflect the sexual selection context in Macrostomum. The sperm of most reciprocally mating species carry lateral bristles, likely functioning as anchoring mechanisms against post-copulatory sperm removal. Hypodermically mating species lack these bristles, potentially as adaptations to a different environment experienced by hypodermic sperm. We document faster molecular sequence evolution in reproduction-related, compared to ubiquitously-expressed, genes across all sperm morphologies, consistent with more intense selection acting on the former. Furthermore, we observed faster molecular sequence evolution in species with hypodermic sperm morphologies, in both reproduction-related and ubiquitously-expressed genes. These genome-wide patterns suggest that shifts to hypodermic mating reduce the efficiency of selection, possibly due to higher selfing rates in hypodermically mating species. Moreover, we find little evidence for convergent amino acid changes across species. We provide the first comprehensive comparative analysis of molecular sequence evolution in a group of simultaneously hermaphroditic animals, across well-replicated contrasts of lineages with divergent sperm morphologies.

scholarly journals Unraveling cis and trans regulatory evolution during cotton domestication

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Ying Bao ◽  
Guanjing Hu ◽  
Corrinne E. Grover ◽  
Justin Conover ◽  
Daojun Yuan ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Sequence Evolution ◽  
Regulatory Evolution ◽  
Evolutionary Diversification ◽  
Regulatory Changes ◽  
Genome Wide ◽  
Network Properties ◽  
High Level ◽  
Cis And Trans ◽  
Allotetraploid Cotton

AbstractCis and trans regulatory divergence underlies phenotypic and evolutionary diversification. Relatively little is understood about the complexity of regulatory evolution accompanying crop domestication, particularly for polyploid plants. Here, we compare the fiber transcriptomes between wild and domesticated cotton (Gossypium hirsutum) and their reciprocal F1 hybrids, revealing genome-wide (~15%) and often compensatory cis and trans regulatory changes under divergence and domestication. The high level of trans evolution (54%–64%) observed is likely enabled by genomic redundancy following polyploidy. Our results reveal that regulatory variation is significantly associated with sequence evolution, inheritance of parental expression patterns, co-expression gene network properties, and genomic loci responsible for domestication traits. With respect to regulatory evolution, the two subgenomes of allotetraploid cotton are often uncoupled. Overall, our work underscores the complexity of regulatory evolution during fiber domestication and may facilitate new approaches for improving cotton and other polyploid plants.

scholarly journals GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes

2019 ◽  
Author(s):  
Daniel J. Wilson ◽  
Keyword(s):  
Cold Shock ◽  
Protein A ◽  
Protein Coding ◽  
Dead Box ◽  
Phylogenetic Methods ◽  
Coalescent Simulations ◽  
Genome Wide ◽  
Very Large Datasets ◽  
Signature Of Selection ◽  
Signatures Of Selection

ABSTRACTThe dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters such as dN/dS, but analysing very large datasets poses a major statistical challenge. Here I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: (i) it is fast no matter how large the sample size and (ii) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well-estimated even when genomegaMap’s simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in M. tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.

The Infancy of Solar-Type Stars and its Relevance for the Origin of Life

1997 ◽  
Vol 161 ◽  
pp. 267-282 ◽  
Author(s):  
Thierry Montmerle
Keyword(s):  
Main Sequence ◽  
Solar Nebula ◽  
Circumstellar Disks ◽  
T Tauri Stars ◽  
Necessary Condition ◽  
Sequence Evolution ◽  
T Tauri ◽  
Solar Type ◽  
Optical Domain ◽  
The Origin Of Life

AbstractFor life to develop, planets are a necessary condition. Likewise, for planets to form, stars must be surrounded by circumstellar disks, at least some time during their pre-main sequence evolution. Much progress has been made recently in the study of young solar-like stars. In the optical domain, these stars are known as «T Tauri stars». A significant number show IR excess, and other phenomena indirectly suggesting the presence of circumstellar disks. The current wisdom is that there is an evolutionary sequence from protostars to T Tauri stars. This sequence is characterized by the initial presence of disks, with lifetimes ~ 1-10 Myr after the intial collapse of a dense envelope having given birth to a star. While they are present, about 30% of the disks have masses larger than the minimum solar nebula. Their disappearance may correspond to the growth of dust grains, followed by planetesimal and planet formation, but this is not yet demonstrated.

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