Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions

Papakostas, Spiros; Vøllestad, Leif Asbjørn; Bruneaux, Matthieu; Aykanat, Tutku; Vanoverbeke, Joost; Ning, Man; Primmer, Craig R.; Leder, Erica H.

doi:10.1038/ncomms5071

Cited by 89 publications

(82 citation statements)

References 71 publications

(129 reference statements)

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“…We used one‐way best hits zebrafish orthologs to estimate pleiotropy for differentially expressed genes based on their number of associated GO biological processes, PPIs, and developmental stages when they are known to be expressed (Papakostas et al. ). We again used GO Consortium resources (Ashburner et al.…”

Section: Methodsmentioning

confidence: 99%

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

McGirr

Martin

2018

Evolution Letters

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Parallel evolution of gene expression commonly underlies convergent niche specialization, but parallel changes in expression could also underlie divergent specialization. We investigated divergence in gene expression and whole‐genome genetic variation across three sympatric Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist and two derived specialists adapted to novel niches: a scale‐eating and a snail‐eating pupfish. We sampled total mRNA from all three species at two early developmental stages and compared gene expression with whole‐genome genetic differentiation among all three species in 42 resequenced genomes. Eighty percent of genes that were differentially expressed between snail‐eaters and generalists were up or down regulated in the same direction between scale‐eaters and generalists; however, there were no fixed variants shared between species underlying these parallel changes in expression. Genes showing parallel evolution of expression were enriched for effects on metabolic processes, whereas genes showing divergent expression were enriched for effects on cranial skeleton development and pigment biosynthesis, reflecting the most divergent phenotypes observed between specialist species. Our findings reveal that even divergent niche specialists may exhibit convergent adaptation to higher trophic levels through shared genetic pathways. This counterintuitive result suggests that parallel evolution in gene expression can accompany divergent ecological speciation during adaptive radiation.

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Section: Methodsmentioning

confidence: 99%

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

McGirr

Martin

2018

Evolution Letters

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“…Consequently, differences in patterns of G Â E variation will influence the ability of populations to evolve new adaptive responses following introduction or in situ environmental challenges. In addition, a better understanding of the genetic architectures underlying reaction norms, such as the effects of modularity versus pleiotropy of regulatory pathways [118], will better inform models of constraint on plasticity evolution in natural populations [67,119].…”

Section: (B) Plasticity and Evolutionary Potentialmentioning

confidence: 99%

Invasions and extinctions through the looking glass of evolutionary ecology

Colautti

Alexander

Dlugosch

et al. 2017

Phil. Trans. R. Soc. B

116

102

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One contribution of 18 to a theme issue 'Human influences on evolution, and the ecological and societal consequences'. Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift. Endangered species are less likely to benefit from admixture, which offsets mutation load but also reduces fitness when populations are locally adapted. Invading species generally experience more benign environments with fewer natural enemies, which increases fitness directly and also indirectly by masking inbreeding depression. Adaptive phenotypic plasticity can maintain fitness in novel environments but is more likely to evolve in invasive species encountering variable habitats and to be compromised by demographic factors in endangered species. Placed in an eco-evolutionary context, these differences affect the breadth of the ecological niche, which arises as an emergent property of antagonistic selection and genetic constraints. Comparative studies of invasions and extinctions that apply an eco-evolutionary perspective could provide new insights into the environmental and genetic basis of ecological success in novel environments and improve efforts to preserve global biodiversity.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

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“…were used for further analysis in the Chipster open source platform (version 1.4). 20 The arrays were normalized using the quantile method. 23 Probes with missing values and probes that varied least across all observations were filtered away based on the coefficient of variation value 0.2, leaving 18 256 probes for further analyses.…”

Section: Rna Sample Preparation and Array Hybridizationmentioning

confidence: 99%

Spatial Variation in Transcript and Protein Abundance of Atlantic Salmon during Feeding Migration in the Baltic Sea

Kanerva

Vehmas

Nikinmaa

et al. 2014

Environ. Sci. Technol.

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The fitness and reproductive output of fishes can be affected by environmental disturbances. In this study, transcriptomics and label-free proteomics were combined to investigate Atlantic salmon (Salmo salar) sampled from three different field locations within the Baltic Sea (Baltic Main Basin (BMB), Gulf of Finland (GoF), and Bothnian Sea (BS)) during marine migration. The expression of several stress related mRNAs and proteins of xenobiotic metabolism, oxidative stress, DNA damage, and cell death were increased in salmon from GoF compared to salmon from BMB or BS. Respiratory electron chain and ATP synthesis related gene ontology-categories were upregulated in GoF salmon, whereas those associated with RNA processing and synthesis, translation, and protein folding decreased. Differences were seen also in metabolism and immune function related gene expression. Comparisons of the transcriptomic and proteomic profiles between salmon from GoF and salmon from BMB or BS suggest environmental stressors, especially exposure to contaminants, as a main explanation for differences. Salmon feeding in GoF are thus “disturbed by hazardous substances”. The results may also be applied in evaluating the conditions of pelagic ecosystems in the different parts of Baltic Sea.

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Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions

Cited by 89 publications

References 71 publications

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

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

Invasions and extinctions through the looking glass of evolutionary ecology

Spatial Variation in Transcript and Protein Abundance of Atlantic Salmon during Feeding Migration in the Baltic Sea

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