4.6 Article

Environment-dependent pleiotropic effects of mutations on the maximum growth rate r and carrying capacity K of population growth

期刊

PLOS BIOLOGY
卷 17, 期 1, 页码 -

出版社

PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pbio.3000121

关键词

-

资金

  1. U.S. National Institutes of Health [GM103232, GM120093]

向作者/读者索取更多资源

Maximum growth rate per individual (r) and carrying capacity (K) are key life-history traits that together characterize the density-dependent population growth and therefore are crucial parameters of many ecological and evolutionary theories such as r/K selection. Although r and K are generally thought to correlate inversely, both r/K tradeoffs and trade-ups have been observed. Nonetheless, neither the conditions under which each of these relationships occur nor the causes of these relationships are fully understood. Here, we address these questions using yeast as a model system. We estimated r and K using the growth curves of over 7,000 yeast recombinants in nine environments and found that the r-K correlation among genotypes changes from 0.53 to -0.52 with the rise of environment quality, measured by the mean r of all genotypes in the environment. We respectively mapped quantitative trait loci (QTLs) for r and K in each environment. Many QTLs simultaneously influence r and K, but the directions of their effects are environment dependent such that QTLs tend to show concordant effects on the two traits in poor environments but antagonistic effects in rich environments. We propose that these contrasting trends are generated by the relative impacts of two factors-the tradeoff between the speed and efficiency of ATP production and the energetic cost of cell maintenance relative to reproduction-and demonstrate an agreement between model predictions and empirical observations. These results reveal and explain the complex environment dependency of the r-K relationship, which bears on many ecological and evolutionary phenomena and has biomedical implications.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.6
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Letter Multidisciplinary Sciences

Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes

Haoxuan Liu, Jianzhi Zhang

NATURE COMMUNICATIONS (2022)

Article Multidisciplinary Sciences

Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms

Piaopiao Chen, Agnes H. Michel, Jianzhi Zhang

Summary: Epistasis can lead to drastically different phenotypic consequences of the same mutation in different individuals. Gene essentiality changes tend to occur concordantly among components of the same protein complex or metabolic pathway and among a group of over 100 mitochondrial proteins, revealing molecular machines or functional modules as units of gene essentiality variation.

NATURE COMMUNICATIONS (2022)

Article Genetics & Heredity

Evaluation of methods for estimating coalescence times using ancestral recombination graphs

Debora Y. C. Brandt, Xinzhu Wei, Yun Deng, Andrew H. Vaughn, Rasmus Nielsen

Summary: This study compared the estimates of coalescence times from three ancestral recombination graph inference programs using standard neutral coalescent simulations. The results showed that ARGweaver had the most accurate estimates at each locus, while Relate was often more accurate than tsinfer+tsdate. However, all three methods tended to overestimate small coalescence times and underestimate large ones. The posterior distribution of ARGweaver was closer to the expected distribution compared to Relate, but it sacrificed scalability.

GENETICS (2022)

Article Biochemistry & Molecular Biology

Is the Mutation Rate Lower in Genomic Regions of Stronger Selective Constraints?

Haoxuan Liu, Jianzhi Zhang

Summary: This study challenges the theory that mutations are blind to their consequences by finding that the plant Arabidopsis thaliana has lower mutation rates in genomic regions where mutations are more likely to be deleterious. However, further analysis of mutational data from baker's yeast and humans does not support this finding. The study also suggests that the extra mutations detected in Arabidopsis may be sequencing errors.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

Article Multidisciplinary Sciences

Synonymous mutations in representative yeast genes are mostly strongly non-neutral

Xukang Shen, Siliang Song, Chuan Li, Jianzhi Zhang

Summary: Synonymous mutations in protein-coding genes are not neutral and often result in reduced fitness and disturbed mRNA expression levels. Non-synonymous mutations have greater fitness variations across environments, which may explain the lower substitution rates compared to synonymous mutations.

NATURE (2022)

Review Genetics & Heredity

What Has Genomics Taught An Evolutionary Biologist?

Jianzhi Zhang

Summary: Genomics, a interdisciplinary field of biology, has revolutionized various subdisciplines of life sciences by providing large amount of data, introducing high-throughput technologies, and offering new approaches to biology. In this review, the author describes what they have learned from genomics, mainly focusing on variation, interaction, and selection, which are central topics in evolutionary biology. The author expects that the most important contributions of genomics to evolutionary biology in the future will include providing genome sequences of almost all known species on Earth, facilitating high-throughput phenotyping of natural variants and mutants, and assisting in the determination of causality in evolutionary processes using experimental evolution.

GENOMICS PROTEOMICS & BIOINFORMATICS (2023)

Article Multidisciplinary Sciences

Contraception ends the genetic maintenance of human same-sex sexual behavior

Siliang Song, Jianzhi Zhang

Summary: Because human same-sex sexual behavior is heritable and leads to fewer offspring, it is puzzling why these alleles have not been purged. The antagonistic pleiotropy hypothesis suggests that these alleles benefit individuals performing opposite-sex sexual behavior. However, our analysis of the UK Biobank data shows that having more sexual partners no longer predicts more offspring, and same-sex behavior is genetically negatively correlated with the number of offspring, indicating a loss of genetic maintenance in modern societies.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)

Article Multidisciplinary Sciences

Chance promoter activities illuminate the origins of eukaryotic intergenic transcriptions

Haiqing Xu, Chuan Li, Chuan Xu, Jianzhi Zhang

Summary: The functional significance of pervasive intergenic transcription from eukaryotic genomes is debated. This study shows that only a small fraction (1-5%) of yeast intergenic transcription is unrelated to chance promoter activity or neighboring gene expression.

NATURE COMMUNICATIONS (2023)

Correction Multidisciplinary Sciences

The rate and molecular spectrum of mutation are selectively maintained in yeast (vol 12, 4044, 2021)

Haoxuan Liu, Jianzhi Zhang

NATURE COMMUNICATIONS (2023)

Article Biology

The lingering effects of Neanderthal introgression on human complex traits

Xinzhu Wei, Christopher R. Robles, Ali Pazokitoroudi, Andrea Ganna, Alexander Gusev, Arun Durvasula, Steven Gazal, Po-Ru Loh, David Reich, Sriram Sankararaman

Summary: Through analyzing the genetic data of 300,000 individuals and 96 distinct phenotypes, it is found that the genetic variants introduced from interbreeding with Neanderthals have a modest contribution to complex human traits. However, these introgressed variants tend to be depleted compared to modern human variants, possibly due to purifying selection. The significant associations between introgressed Neanderthal variants and phenotypes are likely driven by nearby modern human variants rather than the introgressed variants themselves.
Article Biochemistry & Molecular Biology

On the Decoupling of Evolutionary Changes in mRNA and Protein Levels

Daohan Jiang, Alexander L. Cope, Jianzhi Zhang, Matt Pennell

Summary: Variation in gene expression across lineages plays a crucial role in explaining phenotypic variation and adaptation. However, the assumption that mRNA levels can accurately represent protein levels has been challenged by studies showing weak correlations between the two measures across species. This discrepancy might be due to compensatory evolution between mRNA levels and translation regulation, but the conditions and strength of the correlation are still not well understood. A theoretical model of the coevolution of mRNA and protein levels reveals that compensatory evolution is common with stabilizing selection on protein levels, while under directional selection, mRNA levels and translation rates show negative correlations across lineages but positive correlations across genes. These findings offer insights into comparative studies of gene expression and provide a framework to distinguish biological and statistical hypotheses for the transcriptomic-proteomic mismatch.

MOLECULAR BIOLOGY AND EVOLUTION (2023)

Article Biology

Genomic estimates of mutation and substitution rates contradict the evolutionary speed hypothesis of the latitudinal diversity gradient

Haoxuan Liu, Mengyi Sun, Jianzhi Zhang

Summary: The latitudinal diversity gradient (LDG) is the decrease in biodiversity from the equator to the poles. Previous studies have suggested that this gradient is driven by differences in nucleotide mutation and substitution rates related to temperature. However, analysis of genomic data does not support this hypothesis. Instead, there is a significant negative association between the nonsynonymous substitution rate and temperature, indicating that the demand for protein stability at higher temperatures leads to a higher fraction of detrimental mutations.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2023)

Article Genetics & Heredity

Effective fitness under fluctuating selection with genetic drift

Siliang Song, Jianzhi Zhang

Summary: The natural environment fluctuates, affecting the fitness of organisms. The commonly used measure of geometric mean fitness may be misleading due to genetic drift. In this study, a new measure called effective fitness is proposed, which captures the overall effect of fluctuating selection more accurately by considering average expected allele frequency change caused by selection.

G3-GENES GENOMES GENETICS (2023)

Article Multidisciplinary Sciences

Transcriptomic analysis reveals the rareness of genetic assimilation of gene expression in environmental adaptations

Piaopiao Chen, Jianzhi Zhang

Summary: This study analyzed transcriptomic data from multiple species and found that genetic assimilation of environment-induced gene expression is not common, with most genes retaining their expression plasticity after organisms adapt to new environments.

SCIENCE ADVANCES (2023)

Biographical-Item Ecology

Masatoshi Nei (1931-2023)

Jianzhi Zhang, Sudhir Kumar

Summary: He is an evolutionary geneticist who revolutionized evolutionary biology through powerful statistical methods in molecular research.

NATURE ECOLOGY & EVOLUTION (2023)

暂无数据