The roles of sexual selection and sexual conflict in shaping patterns of genome and transcriptome variation

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(7), С. 981 - 993

Опубликована: Март 23, 2023

Язык: Английский

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Sex-biased gene expression at single-cell resolution: cause and consequence of sexual dimorphism

Evolution Letters, Год журнала: 2023, Номер 7(3), С. 148 - 156

Опубликована: Апрель 14, 2023

Gene expression differences between males and females are thought to be key for the evolution of sexual dimorphism, sex-biased genes often used study molecular footprint sex-specific selection. However, gene is measured from complex aggregations diverse cell types, making it difficult distinguish sex in that due regulatory rewiring within similar types those simply a consequence developmental cell-type abundance. To determine role versus underlying expression, we use single-cell transcriptomic data multiple somatic reproductive tissues male female guppies, species exhibits extensive phenotypic dimorphism. Our analysis at resolution demonstrates nonisometric scaling populations each tissue heterogeneity abundance sexes can influence inferred patterns by increasing both false-positive false-negative rates. Moreover, show that, bulk level, subset product significantly confound coding-sequence evolution. Taken together, our results offer unique insight into effects allometry cellular on perceived highlight power RNA-sequencing distinguishing result change stem abundance, hence rather than cause

Язык: Английский

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On the Decoupling of Evolutionary Changes in mRNA and Protein Levels

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(8)

Опубликована: Июль 27, 2023

Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein closer target natural selection but typically measured as amount mRNA. broad assumption that mRNA levels are good proxies for has been undermined by a number studies reporting moderate or weak correlations between two measures species. One biological explanation this discrepancy there compensatory evolution level regulation translation. However, we do not understand evolutionary conditions necessary occur nor expected strength correlation levels. Here, develop theoretical model coevolution investigate dynamics over time. We find widespread when stabilizing on level; observation held true variety regulatory pathways. When under directional selection, translation rate same were negatively correlated positively genes. These findings help results from comparative potentially enable researchers disentangle statistical hypotheses mismatch transcriptomic proteomic data.

Язык: Английский

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Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Фев. 5, 2024

Abstract Chemosensory tissues exhibit significant between-species variability, yet the evolution of gene expression and cell types underlying this diversity remain poorly understood. To address these questions, we conducted transcriptomic analyses five chemosensory from six Drosophila species integrated findings with single-cell datasets. While stabilizing selection predominantly shapes transcriptomes, thousands genes in each tissue have evolved differences. Genes that changed one often multiple other but at different past epochs are more likely to be type-specific than unchanged genes. Notably, chemosensory-related undergone widespread changes, numerous species-specific gains/losses including novel chemoreceptors patterns. Sex differences also pervasive, a D. melanogaster- specific excess male-biased sensory muscle cells its forelegs. Together, our provide new insights for understanding evolutionary changes both global individual levels.

Язык: Английский

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Macroevolutionary divergence of gene expression driven by selection on protein abundance

Science, Год журнала: 2025, Номер 387(6738), С. 1063 - 1068

Опубликована: Март 6, 2025

The regulation of messenger RNA (mRNA) and protein abundances is well-studied, but less known about the evolutionary processes shaping their relationship. To address this, we derived a new phylogenetic model applied it to multispecies mammalian data. Our analyses reveal (i) strong stabilizing selection on over macroevolutionary time, (ii) mutations affecting mRNA minimally impact abundances, (iii) evolve under align with (iv) adapt faster than owing greater mutational opportunity. These conclusions are supported by comparisons parameters independent functional genomic By decomposing selective influences mRNA-protein dynamics, our approach provides framework for discovering rules that drive divergence in gene expression.

Язык: Английский

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DNA-based molecular classifiers for the profiling of gene expression signatures

Journal of Nanobiotechnology, Год журнала: 2024, Номер 22(1)

Опубликована: Апрель 17, 2024

Abstract Although gene expression signatures offer tremendous potential in diseases diagnostic and prognostic, but massive caused challenges for experimental detection computational analysis clinical setting. Here, we introduce a universal DNA-based molecular classifier profiling generating immediate outcomes. The begins with feature transformation, modular programmable strategy was used to capture relative relationships of low-concentration RNAs convert them general coding inputs. Then, competitive inhibition the DNA catalytic reaction enables strict weight assignment different inputs according their importance, followed by summation, annihilation reporting accurately implement mathematical model classifier. We validated entire workflow utilizing miRNA levels diagnosis hepatocellular carcinoma (HCC) samples an accuracy 85.7%. results demonstrate provides solution explore correlation between patterns disease diagnostics, monitoring, prognosis, supports personalized healthcare primary care.

Язык: Английский

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Fourth Report on Chicken Genes and Chromosomes 2022

Cytogenetic and Genome Research, Год журнала: 2022, Номер 162(8-9), С. 405 - 528

Опубликована: Янв. 1, 2022

none

Язык: Английский

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Lineage-resolved analysis of embryonic gene expression evolution inC. elegansandC. briggsae

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 6, 2024

Abstract What constraints govern the evolution of gene expression patterns across development remains a fundamental question evolutionary biology. The advent single-cell sequencing opens possibility learning these by systematically profiling homologous cells different organisms. nematode C. elegans is well-studied model for embryonic development, and its invariant lineage that conserved with other Caenorhabditis species makes it an ideal to directly compare between progenitor terminal cell types evolution. We have measured spatiotemporal divergence embryogenesis collecting, annotating, comparing transcriptomes progenitors types, using dataset comprising >200,000 >190,000 briggsae cells. find high level similarity in programs despite tens millions years divergence, consistent their developmental lineages. Even still, thousands genes show cell-type specific patterns, are enriched categories involved environmental response behavior. Comparing degree conservation reveals certain such as neurons, diverged more than others intestine body wall muscle. Taken together, this work identifies likely on provides powerful resource addressing diverse questions.

Язык: Английский

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Constraints on the optimization of gene product diversity

Molecular Systems Biology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 10, 2025

Abstract RNA and proteins can have diverse isoforms due to post-transcriptional post-translational modifications. A fundamental question is whether these are mostly beneficial or the result of noisy molecular processes. To assess plausibility explanations, we developed mathematical models depicting different regulatory architectures investigated isoform evolution under multiple population genetic regimes. We found that factors beyond selection, such as effective size number cis -acting loci, significantly influence evolutionary outcomes. sub-optimal phenotypes more likely evolve when populations small and/or -loci large. also discovered opposing selection on - trans loci constrain adaptation, leading a non-monotonic relationship between optimization. More generally, our provide quantitative framework for developing statistical tests analyze empirical data; demonstration this, analyzed A-to-I editing levels in coleoids be largely consistent with non-adaptive explanations.

Язык: Английский

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Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution

Genome Biology and Evolution, Год журнала: 2023, Номер 15(12)

Опубликована: Ноя. 24, 2023

Abstract Phylogenetic comparative methods are increasingly used to test hypotheses about the evolutionary processes that drive divergence in gene expression among species. However, it is unknown whether distributional assumptions of phylogenetic models designed for quantitative phenotypic traits realistic data and importantly, reliability conclusions studies may depend on well described by chosen model. To evaluate this, we first fit several trait evolution 8 previously published datasets, comprising a total 54,774 genes with 145,927 unique gene–tissue combinations. Using developed approach, then assessed how best model set an absolute (not just relative) sense. First, find Ornstein–Uhlenbeck models, which values constrained around optimum, were preferred 66% Second, 61% combinations, best-fit was found perform well; rest be performing poorly at least one statistics examined. Third, when simple do not well, this appears typically consequence failing fully account heterogeneity rate evolution. We advocate assessment performance should become routine component studies; doing so can improve inferences inspire development novel models.

Язык: Английский

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