scholarly journals Parallel evolution of gene expression between trophic specialists despite divergent genotypes and morphologies

2018 ◽  
Vol 2 (2) ◽  
pp. 62-75 ◽  
Author(s):  
Joseph A. McGirr ◽  
Christopher H. Martin
Keyword(s):  
Gene Expression ◽  
Parallel Evolution

scholarly journals Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
María José Rivas ◽  
María Saura ◽  
Andrés Pérez-Figueroa ◽  
Marina Panova ◽  
Tomas Johansson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Sequence ◽  
Population Genomics ◽  
Parallel Evolution ◽  
Ecological Adaptation

scholarly journals Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

2012 ◽  
Vol 22 (3) ◽  
pp. 650-669 ◽  
Author(s):  
Tereza Manousaki ◽  
Pincelli M. Hull ◽  
Henrik Kusche ◽  
Gonzalo Machado-Schiaffino ◽  
Paolo Franchini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Parallel Evolution ◽  
Ecological Divergence ◽  
Cichlid Fishes ◽  
Adaptive Radiations ◽  
Differential Gene

scholarly journals Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 400 ◽  
Author(s):  
Alexandre Rêgo ◽  
Samridhi Chaturvedi ◽  
Amy Springer ◽  
Alexandra M. Lish ◽  
Caroline L. Barton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Allele Frequency ◽  
Development Time ◽  
Callosobruchus Maculatus ◽  
Parallel Evolution ◽  
Frequency Change ◽  
Multiple Traits ◽  
Population Genomic ◽  
Performance Traits ◽  
Frequency Changes

Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.

scholarly journals Evolution of Gene Expression and Splicing in Parallel Cold-Adapted Fly Populations

2019 ◽  
Author(s):  
Yuheng Huang ◽  
Justin B. Lack ◽  
Grant T. Hoppel ◽  
John E. Pool
Keyword(s):  
Gene Expression ◽  
Adaptive Evolution ◽  
Parallel Evolution ◽  
Population Variation ◽  
Regulatory Evolution ◽  
Cold Adapted ◽  
Mitochondrial Functions ◽  
Expression Evolution ◽  
Gene Regulatory ◽  
Trans Regulation

AbstractChanges in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find significant although somewhat limited evidence for parallel expression evolution between them, and less evidence for parallel splicing evolution. We find that genes with mitochondrial functions are particularly enriched among candidates for adaptive expression evolution. We also develop a method to estimate cis-versus trans-encoded contributions to expression or splicing differences that does not rely on the presence of fixed differences between parental strains. Applying this method, we infer important roles of both cis-and trans-regulation among our putatively adaptive expression and splicing differences. The apparent contributions of cis-versus trans-regulation to adaptive evolution vary substantially among population pairs, with an Ethiopian pair showing pervasive trans-effects, suggesting that basic characteristics of regulatory evolution may depend on biological context. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.

scholarly journals Parallel Evolution of Opsin Gene Expression in African Cichlid Fishes

2010 ◽  
Vol 27 (12) ◽  
pp. 2839-2854 ◽  
Author(s):  
K. E. O'Quin ◽  
C. M. Hofmann ◽  
H. A. Hofmann ◽  
K. L. Carleton
Keyword(s):  
Gene Expression ◽  
Parallel Evolution ◽  
Opsin Gene ◽  
Cichlid Fishes ◽  
African Cichlid

scholarly journals Rapid parallel adaptation despite gene flow in silent crickets

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiao Zhang ◽  
Jack G. Rayner ◽  
Mark Blaxter ◽  
Nathan W. Bailey
Keyword(s):  
Gene Expression ◽  
Gene Flow ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
De Novo ◽  
Parallel Evolution ◽  
De Novo Mutation ◽  
Genome Scans ◽  
Wing Structures ◽  
In The Wild

AbstractGene flow is predicted to impede parallel adaptation via de novo mutation, because it can introduce pre-existing adaptive alleles from population to population. We test this using Hawaiian crickets (Teleogryllus oceanicus) in which ‘flatwing’ males that lack sound-producing wing structures recently arose and spread under selection from an acoustically-orienting parasitoid. Morphometric and genetic comparisons identify distinct flatwing phenotypes in populations on three islands, localized to different loci. Nevertheless, we detect strong, recent and ongoing gene flow among the populations. Using genome scans and gene expression analysis we find that parallel evolution of flatwing on different islands is associated with shared genomic hotspots of adaptation that contain the gene doublesex, but the form of selection differs among islands and corresponds to known flatwing demographics in the wild. We thus show how parallel adaptation can occur on contemporary timescales despite gene flow, indicating that it could be less constrained than previously appreciated.

scholarly journals Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weed Monochoria vaginalis

2021 ◽  
Author(s):  
Shinji Tanigaki ◽  
Akira Uchino ◽  
Shigenori Okawa ◽  
Chikako Miura ◽  
Kenshiro Hamamura ◽  
...  
Keyword(s):  
Gene Expression ◽  
Herbicide Resistance ◽  
Parallel Evolution ◽  
Agricultural Weed

scholarly journals Genetic assimilation of ancestral plasticity during parallel adaptation

2021 ◽  
Author(s):  
Daniel Wood ◽  
Jon A Holmberg ◽  
Owen Gregory Osborne ◽  
Andrew J Helmsetter ◽  
Luke T Dunning ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
General Pattern ◽  
Parallel Evolution ◽  
Genetic Assimilation ◽  
Ancestral Gene ◽  
Expression Levels ◽  
Degree Of Convergence ◽  
High Degree ◽  
Gene Expression Levels

Phenotypic plasticity in ancestral populations is hypothesised to facilitate adaptation, but evidence supporting its contribution is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel genetic and phenotypic adaptive changes has not been explored. The most general finding is that nearly all ancestral gene expression plasticity is reversed following adaptation, but this is usually examined transcriptome-wide rather than focused on the genes directly involved in adaptation. We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared to ancestral, zinc-sensitive plants. Our experiments show that reinforcement of ancestral plasticity plays an influential role in the evolution of plasticity in derived populations and, surprisingly, one third of constitutive differences between ecotypes are the result of genetic assimilation of ancestral plasticity. Ancestral plasticity also increases the chance that genes are recruited repeatedly during adaptation. However, despite a high degree of convergence in gene expression levels between independently adapted lineages, genes with ancestral plasticity are as likely to have similar expression levels in adapted populations as genes without. Overall, these results demonstrate that ancestral plasticity does play an important role in adaptive parallel evolution, particularly via genetic assimilation across evolutionary replicates.

scholarly journals Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)

2021 ◽  
Author(s):  
Aglaia Szukala ◽  
Jessica Lovegrove-Walsh ◽  
Hirzi Luqman ◽  
Simone Fior ◽  
Thomas Mahteson Wolfe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Parallel Evolution ◽  
Functional Enrichment ◽  
Adaptive Traits ◽  
Modern Biology ◽  
Divergent Gene ◽  
Multiple Routes ◽  
Demographic Modelling ◽  
Differential Gene ◽  
Different Populations

Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution - the independent evolution of similar phenotypes in different populations - provides a powerful framework to explore this question. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae) and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling confirm the previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying adaptation of each replicate ecotype pair, with a strikingly low amount of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by divergent gene expression are the same across ecotype pairs, in strong contrast to the non-shared genetic basis. The remarkable redundancy of differential gene expression indicates that diverged adaptive traits are highly polygenic. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.

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