4.7 Article

The rate of adaptive molecular evolution in wild and domesticated Saccharomyces cerevisiae populations

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Evolutionary Biology

Changing Population Size in McDonald-Kreitman Style Analyses: Artifactual Correlations and Adaptive Evolution between Humans and Chimpanzees

Vivak Soni et al.

Summary: In the divergence of humans and chimpanzees, the rate of adaptive evolution is found to be negatively correlated with the dissimilarity of amino acid pairs in terms of polarity and volume, as well as the strength of purifying selection. These correlations are not affected by population size contraction.

GENOME BIOLOGY AND EVOLUTION (2022)

Article Genetics & Heredity

Heterogeneity in effective size across the genome: effects on the inverse instantaneous coalescence rate (IICR) and implications for demographic inference under linked selection

Simon Boitard et al.

Summary: This study investigates the consequences of genomic variations in N-e on the genome-wide distribution of coalescence times. The researchers found that linked selection often leads to a spurious apparent decrease in N-e, especially when it involves balancing selection. Additionally, the effect of linked selection can be significantly reduced by population structure. These findings are also relevant to studying other biological processes that generate apparent variations in N-e along the genome.

GENETICS (2022)

Article Biochemistry & Molecular Biology

The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects

Parul Johri et al.

Summary: Current methods for inferring population history assume neutrality, but neglect the effects of direct and background selection. The study shows that background selection can lead to mis-inferences of population growth, especially with increasing strength of purifying selection and density of directly selected sites.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Evolutionary Biology

Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation

Gabriel Schweizer et al.

Summary: The close interaction between pathogens and hosts influences genetic diversity, as seen in the Ustilago maydis pathogen causing corn smut disease, where effector genes are clustered and show higher nonsynonymous adaptive substitutions. The study revealed two partially admixed subpopulations with a recent bottleneck coinciding with maize domestication, highlighting the role of unique genomic regions in pathogen evolution.

GENOME BIOLOGY AND EVOLUTION (2021)

Review Ecology

The Domestication Makeup: Evolution, Survival, and Challenges

Hafiz Ishfaq Ahmad et al.

FRONTIERS IN ECOLOGY AND EVOLUTION (2020)

Review Genetics & Heredity

History and Domestication of Saccharomyces cerevisiae in Bread Baking

Caitlin Lahue et al.

FRONTIERS IN GENETICS (2020)

Article Biochemical Research Methods

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis et al.

BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

Michael Schantz Klausen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

The Impact of Protein Architecture on Adaptive Evolution

Ana Filipa Moutinho et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Biochemistry & Molecular Biology

Evolution of the Yeast Recombination Landscape

Haoxuan Liu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Evolutionary Biology

The genomic determinants of adaptive evolution in a fungal pathogen

Jonathan Grandaubert et al.

EVOLUTION LETTERS (2019)

Article Evolutionary Biology

Genetic Costs of Domestication and Improvement

Brook T. Moyers et al.

JOURNAL OF HEREDITY (2018)

Article Biology

Overestimation of the adaptive substitution rate in fluctuating populations

Marjolaine Rousselle et al.

BIOLOGY LETTERS (2018)

Article Biochemistry & Molecular Biology

Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication

Jean-Luc Legras et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

Vincent Ranwez et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Genetics & Heredity

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

Jia-Xing Yue et al.

NATURE GENETICS (2017)

Review Genetics & Heredity

Evolutionary biology through the lens of budding yeast comparative genomics

Souhir Marsit et al.

NATURE REVIEWS GENETICS (2017)

Article Biochemical Research Methods

UpSetR: an R package for the visualization of intersecting sets and their properties

Jake R. Conway et al.

BIOINFORMATICS (2017)

Article Environmental Sciences

The history of arsenical pesticides and health risks related to the use of Agent Blue

Vladimir Bencko et al.

ANNALS OF AGRICULTURAL AND ENVIRONMENTAL MEDICINE (2017)

Article Biochemistry & Molecular Biology

Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila

David Castellano et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Biochemistry & Molecular Biology

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

Brigida Gallone et al.

Article Biochemistry & Molecular Biology

Independent Origins of Yeast Associated with Coffee and Cacao Fermentation

Catherine L. Ludlow et al.

CURRENT BIOLOGY (2016)

Article Multidisciplinary Sciences

A genomic history of Aboriginal Australia

Anna-Sapfo Malaspinas et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

Vincent Lefort et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemical Research Methods

andi: Fast and accurate estimation of evolutionary distances between closely related genomes

Bernhard Haubold et al.

BIOINFORMATICS (2015)

Review Ecology

Population size and the rate of evolution

Robert Lanfear et al.

TRENDS IN ECOLOGY & EVOLUTION (2014)

Article Biochemistry & Molecular Biology

Bio plus plus : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Laurent Gueguen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Evolutionary Biology

The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes

Toni I. Gossmann et al.

GENOME BIOLOGY AND EVOLUTION (2012)

Review Genetics & Heredity

Adaptive evolution: evaluating empirical support for theoretical predictions

Carrie F. Olson-Manning et al.

NATURE REVIEWS GENETICS (2012)

Review Biology

Bread, beer and wine: Yeast domestication in the Saccharomyces sensu stricto complex

Delphine Sicard et al.

COMPTES RENDUS BIOLOGIES (2011)

Article Genetics & Heredity

Yeast: An Experimental Organism for 21st Century Biology

David Botstein et al.

GENETICS (2011)

Article Biochemical Research Methods

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Peter J. A. Cock et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

Adam Eyre-Walker et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Biochemistry & Molecular Biology

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

Tong Zhou et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Multidisciplinary Sciences

Population genomics of domestic and wild yeasts

Gianni Liti et al.

NATURE (2009)

Review Genetics & Heredity

Effective population size and patterns of molecular evolution and variation

Brian Charlesworth

NATURE REVIEWS GENETICS (2009)

Article Multidisciplinary Sciences

Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact

Melinda A. Zeder

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Review Genetics & Heredity

The distribution of fitness effects of new mutations

Adam Eyre-Walker et al.

NATURE REVIEWS GENETICS (2007)

Article Multidisciplinary Sciences

Plant domestication, a unique opportunity to identify the genetic basis of adaptation

Jeffrey Ross-Ibarra et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Sex increases the efficacy of natural selection in experimental yeast populations

MR Goddard et al.

NATURE (2005)

Article Biochemical Research Methods

Online synonymous codon usage analyses with the ade4 and seqinR packages

D Charif et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Aligning multiple genomic sequences with the threaded blockset aligner

M Blanchette et al.

GENOME RESEARCH (2004)

Article Multidisciplinary Sciences

Fermented beverages of pre- and proto-historic China

PE McGovern et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Review Food Science & Technology

The microbiology of cocoa fermentation and its role in chocolate quality

RF Schwan et al.

CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION (2004)

Review Multidisciplinary Sciences

Evolution, consequences and future of plant and animal domestication

J Diamond

NATURE (2002)

Article Multidisciplinary Sciences

Adaptive protein evolution in Drosophila

NGC Smith et al.

NATURE (2002)