The Role of Plasticity and Adaptation in the Incipient Speciation of a Fire Salamander Population

Phenotypic plasticity and local adaptation via genetic change are two major mechanisms of response to dynamic environmental conditions. These mechanisms are not mutually exclusive, since genetic change can establish similar phenotypes to plasticity. This connection between both mechanisms raises the question of how much of the variation observed between species or populations is plastic and how much of it is genetic. In this study, we used a structured population of fire salamanders (Salamandra salamandra), in which two subpopulations differ in terms of physiology, genetics, mate-, and habitat preferences. Our goal was to identify candidate genes for differential habitat adaptation in this system, and to explore the degree of plasticity compared to local adaptation. We therefore performed a reciprocal transfer experiment of stream- and pond-originated salamander larvae and analyzed changes in morphology and transcriptomic profile (using species-specific microarrays). We observed that stream- and pond-originated individuals diverge in morphology and gene expression. For instance, pond-originated larvae have larger gills, likely to cope with oxygen-poor ponds. When transferred to streams, pond-originated larvae showed a high degree of plasticity, resembling the morphology and gene expression of stream-originated larvae (reversion); however the same was not found for stream-originated larvae when transferred to ponds, where the expression of genes related to reduction-oxidation processes was increased, possibly to cope with environmental stress. The lack of symmetrical responses between transplanted animals highlights the fact that the adaptations are not fully plastic and that some level of local adaptation has already occurred in this population. This study illuminates the process by which phenotypic plasticity allows local adaptation to new environments and its potential role in the pathway of incipient speciation.

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Genetic assimilation of ancestral plasticity during parallel adaptation

10.1101/2021.11.30.470425 ◽

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.

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The Catenulida flatworm can express genes from its microbiome or from the DNA it ingests

Scientific Reports ◽

10.1038/s41598-019-55659-w ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Marcos Trindade Rosa ◽

Elgion L. S. Loreto

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity ◽

Reporter Gene ◽

Gfp Expression ◽

Naked Dna ◽

Expression Of Genes ◽

Potential Sources ◽

Foreign Genes

AbstractStenostomum are tiny planarians of the phylum Platyhelminthes that reproduce asexually. We transfected these worms using plasmids containing a gfp reporter gene. Here we show that they can express genes present in plasmids carried by bacteria and those that are encoded by naked DNA, such as plasmids or PCR fragments, transfected by electroporation; they can also express genes taken up during feeding. The microbiome associated with worm maintenance was evaluated, and the results indicated that when a plasmid is maintained in the microbiome, gfp gene expression is stable. When genes originate from naked DNA or bacteria not maintained in the microbiome, GFP expression is transient. Therefore, changes in the microbiome can modify the ability of worms to express foreign genes. In stable GFP-expressing worms, NSG showed that the gfp gene was maintained in the plasmid and was not integrated into the chromosome. These results suggest that, at least for some organisms such as flatworms, the expression of genes provided by the microbiome or the environment can be considered among the potential sources of phenotypic plasticity, which can have implications for evolvability.

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Phenotypic plasticity

10.1093/oso/9780198797500.003.0005 ◽

2018 ◽

Author(s):

Karen D. Williams ◽

Marla B. Sokolowski

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity ◽

Environmental Change ◽

Behavioral Plasticity ◽

Behavioral Flexibility ◽

Insect Behavior ◽

Behavioral Variability ◽

Gene By Environment Interactions ◽

Affect Gene Expression

Why is there so much variation in insect behavior? This chapter will address the sources of behavioral variability, with a particular focus on phenotypic plasticity. Variation in social, nutritional, and seasonal environmental contexts during development and adulthood can give rise to phenotypic plasticity. To delve into mechanism underlying behavioral flexibility in insects, examples of polyphenisms, a type of phenotypic plasticity, will be discussed. Selected examples reveal that environmental change can affect gene expression, which in turn can affect behavioral plasticity. These changes in gene expression together with gene-by-environment interactions are discussed to illuminate our understanding of insect behavioral plasticity.

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Impact of Environmental Stressors on Gene Expression in the Embryo of the Italian Wall Lizard

Applied Sciences ◽

10.3390/app11114723 ◽

2021 ◽

Vol 11 (11) ◽

pp. 4723

Author(s):

Rosaria Scudiero ◽

Chiara Maria Motta ◽

Palma Simoniello

Keyword(s):

Gene Expression ◽

Protein Interactions ◽

Membrane Trafficking ◽

Translational Regulation ◽

Cellular Protection ◽

Terrestrial Vertebrate ◽

Expression Of Genes ◽

Stress Changes ◽

Probable Consequence ◽

The Impact

The cleidoic eggs of oviparous reptiles are protected from the external environment by membranes and a parchment shell permeable to water and dissolved molecules. As a consequence, not only physical but also chemical insults can reach the developing embryos, interfering with gene expression. This review provides information on the impact of the exposure to cadmium contamination or thermal stress on gene expression during the development of Italian wall lizards of the genus Podarcis. The results obtained by transcriptomic analysis, although not exhaustive, allowed to identify some stress-reactive genes and, consequently, the molecular pathways in which these genes are involved. Cadmium-responsive genes encode proteins involved in cellular protection, metabolism and proliferation, membrane trafficking, protein interactions, neuronal transmission and plasticity, immune response, and transcription regulatory factors. Cold stress changes the expression of genes involved in transcriptional/translational regulation and chromatin remodeling and inhibits the transcription of a histone methyltransferase with the probable consequence of modifying the epigenetic control of DNA. These findings provide transcriptome-level evidence of how terrestrial vertebrate embryos cope with stress, giving a key to use in population survival and environmental change studies. A better understanding of the genes contributing to stress tolerance in vertebrates would facilitate methodologies and applications aimed at improving resistance to unfavourable environments.

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Transversal gene expression panel to evaluate intestinal health in broiler chickens in different challenging conditions

Scientific Reports ◽

10.1038/s41598-021-85872-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

L. Criado-Mesas ◽

N. Abdelli ◽

A. Noce ◽

M. Farré ◽

J. F. Pérez ◽

...

Keyword(s):

Gene Expression ◽

Immune Response ◽

Barrier Function ◽

Nutrient Transport ◽

Gene Expression Pattern ◽

Vaccine Dose ◽

Special Focus ◽

Intestinal Health ◽

Barrier Failure ◽

Expression Of Genes

AbstractThere is a high interest on gut health in poultry with special focus on consequences of the intestinal diseases, such as coccidiosis and C. perfringens-induced necrotic enteritis (NE). We developed a custom gene expression panel, which could provide a snapshot of gene expression variation under challenging conditions. Ileum gene expression studies were performed through high throughput reverse transcription quantitative real-time polymerase chain reaction. A deep review on the bibliography was done and genes related to intestinal health were selected for barrier function, immune response, oxidation, digestive hormones, nutrient transport, and metabolism. The panel was firstly tested by using a nutritional/Clostridium perfringens model of intestinal barrier failure (induced using commercial reused litter and wheat-based diets without exogenous supplementation of enzymes) and the consistency of results was evaluated by another experiment under a coccidiosis challenge (orally gavaged with a commercial coccidiosis vaccine, 90× vaccine dose). Growth traits and intestinal morphological analysis were performed to check the gut barrier failure occurrence. Results of ileum gene expression showed a higher expression in genes involved in barrier function and nutrient transport in chickens raised in healthy conditions, while genes involved in immune response presented higher expression in C.perfringens-challenged birds. On the other hand, the Eimeria challenge also altered the expression of genes related to barrier function and metabolism, and increased the expression of genes related to immune response and oxidative stress. The panel developed in the current study gives us an overview of genes and pathways involved in broiler response to pathogen challenge. It also allows us to deep into the study of differences in gene expression pattern and magnitude of responses under either a coccidial vaccine or a NE.

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Selection of reference genes for gene expression analysis in Liriodendron hybrids’ somatic embryogenesis and germinative tissues

Scientific Reports ◽

10.1038/s41598-021-84518-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tingting Li ◽

Weigao Yuan ◽

Shuai Qiu ◽

Jisen Shi

Keyword(s):

Gene Expression ◽

Somatic Embryogenesis ◽

Reference Genes ◽

Gene Selection ◽

Elongation Factor ◽

Reverse Transcription Pcr ◽

Expression Of Genes ◽

Suitable Reference ◽

Functional Analyses ◽

Elongation Factor 1

AbstractThe differential expression of genes is crucial for plant somatic embryogenesis (SE), and the accurate quantification of gene expression levels relies on choosing appropriate reference genes. To select the most suitable reference genes for SE studies, 10 commonly used reference genes were examined in synchronized somatic embryogenic and subsequent germinative cultures of Liriodendron hybrids by using quantitative real-time reverse transcription PCR. Four popular normalization algorithms: geNorm, NormFinder, Bestkeeper and Delta-Ct were used to select and validate the suitable reference genes. The results showed that elongation factor 1-gamma, histone H1 linker protein, glyceraldehyde-3-phosphate dehydrogenase and α-tubulin were suitable for SE tissues, while elongation factor 1-gamma and actin were best for the germinative organ tissues. Our work will benefit future studies of gene expression and functional analyses of SE in Liriodendron hybrids. It is also serves as a guide of reference gene selection in early embryonic gene expression analyses for other woody plant species.

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Controllability of Boolean networks with intermittent disturbances

Modern Physics Letters B ◽

10.1142/s0217984920503091 ◽

2020 ◽

Vol 34 (28) ◽

pp. 2050309

Author(s):

Tao You ◽

Hailun Zhang ◽

Mingyu Yang ◽

Xiao Wang ◽

Yangming Guo

Keyword(s):

Gene Expression ◽

Boolean Network ◽

Boolean Networks ◽

Genetic Mutations ◽

Intermittent Control ◽

Mathematical Tool ◽

Pulse Control ◽

Expression Of Genes ◽

Complicated Process ◽

Living Being

In biological systems, gene expression is an important subject. In order to clarify the specific process of gene expression, mathematical tools are needed to simulate the process. The Boolean network (BN) is a good mathematical tool. In this paper, we study a Boolean network with intermittent perturbations. This is of great significance for studying genetic mutations in bioengineering. The expression of genes in the internal system of a living being is a very complicated process, and it is clear that the process is trans-ageal for humans. Through the intermittent control and pulse control of the BN, we can obtain the trajectory of gene expression better and faster, which will provide a very important theoretical basis for our next research.

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Integrating metabolomics and targeted gene expression to uncover potential biomarkers of fungal/oomycetes-associated disease susceptibility in grapevine

Scientific Reports ◽

10.1038/s41598-020-72781-2 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Marisa Maia ◽

António E. N. Ferreira ◽

Rui Nascimento ◽

Filipa Monteiro ◽

Francisco Traquete ◽

...

Keyword(s):

Gene Expression ◽

Plant Defence ◽

Breeding Programs ◽

Analysis Group ◽

Expression Of Genes ◽

Leucoanthocyanidin Reductase ◽

Defence Responses ◽

Targeted Gene Expression ◽

Plant Defence Responses ◽

First Time

Abstract Vitis vinifera, one of the most cultivated fruit crops, is susceptible to several diseases particularly caused by fungus and oomycete pathogens. In contrast, other Vitis species (American, Asian) display different degrees of tolerance/resistance to these pathogens, being widely used in breeding programs to introgress resistance traits in elite V. vinifera cultivars. Secondary metabolites are important players in plant defence responses. Therefore, the characterization of the metabolic profiles associated with disease resistance and susceptibility traits in grapevine is a promising approach to identify trait-related biomarkers. In this work, the leaf metabolic composition of eleven Vitis genotypes was analysed using an untargeted metabolomics approach. A total of 190 putative metabolites were found to discriminate resistant/partial resistant from susceptible genotypes. The biological relevance of discriminative compounds was assessed by pathway analysis. Several compounds were selected as promising biomarkers and the expression of genes coding for enzymes associated with their metabolic pathways was analysed. Reference genes for these grapevine genotypes were established for normalisation of candidate gene expression. The leucoanthocyanidin reductase 2 gene (LAR2) presented a significant increase of expression in susceptible genotypes, in accordance with catechin accumulation in this analysis group. Up to our knowledge this is the first time that metabolic constitutive biomarkers are proposed, opening new insights into plant selection on breeding programs.

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Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽

10.3390/genes12010082 ◽

2021 ◽

Vol 12 (1) ◽

pp. 82

Author(s):

Yunxiao Wei ◽

Guoliang Li ◽

Shujiang Zhang ◽

Shifan Zhang ◽

Hui Zhang ◽

...

Keyword(s):

Gene Expression ◽

Brassica Napus ◽

Differentially Expressed Genes ◽

Expression Patterns ◽

Female Parent ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Transcriptional Changes ◽

Aa Genome ◽

High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

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