Incompatibility and Interchangeability in Molecular Evolution

The role of mitonuclear incompatibilities in allopatric speciation

(2022) Ronald S. Burton   CELLULAR AND MOLECULAR LIFE SCIENCES

Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex

(2022) Salah E. Abdel-Ghany et al.   PLANT MOLECULAR BIOLOGY

Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms

(2022) Alissa M. Williams et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Recombination resolves the cost of horizontal gene transfer in experimental populations of Helicobacter pylori

(2022) An N. T. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time

(2022) Mateusz Kędzior et al.   Cell Reports

Three problems in the genetics of speciation by selection

(2022) Dolph Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels

(2022) Evan S. Forsythe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution and molecular bases of reproductive isolation

(2022) G Ozan Bozdag et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genomic signatures of mitonuclear coevolution in mammals

(2022) Ryan J Weaver et al.   MOLECULAR BIOLOGY AND EVOLUTION

Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins

(2021) Alexey D. Neverov et al.   PLoS Genetics

Adaptive evolution of hybrid bacteria by horizontal gene transfer

(2021) Jeffrey J. Power et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Complexes Form a Basis for Complex Hybrid Incompatibility

(2021) Krishna B. S. Swamy et al.   Frontiers in Genetics

Inter‐domain horizontal gene transfer of nickel‐binding superoxide dismutase

(2021) K. M. Sutherland et al.   Geobiology

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

(2021) David Sehnal et al.   NUCLEIC ACIDS RESEARCH

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria

(2020) Jessica M. Warren et al.   MITOCHONDRION

Alternative lengthening of telomeres: from molecular mechanisms to therapeutic outlooks

(2020) Jia-Min Zhang et al.   Cell and Bioscience

Cytonuclear Genetic Incompatibilities in Plant Speciation

(2020) Zoé Postel et al.   Plants-Basel

Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects

(2020) Shai Slomka et al.   GENETICS

Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation

(2020) Laura C. Woods et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A hydrophobic ratchet entrenches molecular complexes

(2020) Georg K. A. Hochberg et al.   NATURE

Evolutionary Rate Correlation between Mitochondrial-Encoded and Mitochondria-Associated Nuclear-Encoded Proteins in Insects

(2019) Zhichao Yan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary Changes after Translational Challenges Imposed by Horizontal Gene Transfer

(2019) Stéphanie Bedhomme et al.   Genome Biology and Evolution

Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing

(2018) Hoi Yee Chu et al.   BMC EVOLUTIONARY BIOLOGY

Evaluating genomic signatures of “the large X-effect” during complex speciation

(2018) Daven C. Presgraves   MOLECULAR ECOLOGY

Cytonuclear integration and co-evolution

(2018) Daniel B. Sloan et al.   NATURE REVIEWS GENETICS

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

PRDM9 and Its Role in Genetic Recombination

(2018) Kenneth Paigen et al.   TRENDS IN GENETICS

RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs

(2018) Mark A McClintock et al.   eLife

The Role of Transposable Elements in Speciation

(2018) Antonio Serrato-Capuchina et al.   Genes

Growing old, yet staying young: The role of telomeres in bats’ exceptional longevity

(2018) Nicole M. Foley et al.   Science Advances

Mitochondrial glycolysis in a major lineage of eukaryotes

(2018) Carolina Río Bártulos et al.   Genome Biology and Evolution

Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium

(2017) Seongjun Park et al.   Genome Biology and Evolution

Causes and Consequences of Rapidly Evolving mtDNA in a Plant Lineage

(2017) Justin C. Havird et al.   Genome Biology and Evolution

Function-related replacement of bacterial siderophore pathways

(2017) Hilke Bruns et al.   ISME Journal

Diverse origins of enzymes involved in the biosynthesis of chloroplast peptidoglycan

(2017) Naoki Sato et al.   JOURNAL OF PLANT RESEARCH

The on-again, off-again relationship between mitochondrial genomes and species boundaries

(2017) Daniel B. Sloan et al.   MOLECULAR ECOLOGY

Heterologous Complementation Reveals a Specialized Activity for BacA in the Medicago–Sinorhizobium meliloti Symbiosis

(2017) George C. diCenzo et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs

(2017) Betül Kacar et al.   mBio

Regulation and structure of the heteromeric acetyl-CoA carboxylase

(2016) Matthew J. Salie et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

A Eukaryote without a Mitochondrial Organelle

(2016) Anna Karnkowska et al.   CURRENT BIOLOGY

Plastid–Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae

(2016) Mao-Lun Weng et al.   Genome Biology and Evolution

Evolutionary perspectives of telomerase RNA structure and function

(2016) Joshua D. Podlevsky et al.   RNA Biology

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

(2016) Geoffrey E. Hill   Ecology and Evolution

Recombination-Mediated Telomere Maintenance in Saccharomyces cerevisiae Is Not Dependent on the Shu Complex

(2016) Paula M. van Mourik et al.   PLoS One

Telomerase lost?

(2015) James M. Mason et al.   CHROMOSOMA

Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution

(2015) Justin C. Havird et al.   EVOLUTION

Complementation of Yeast Genes with Human Genes as an Experimental Platform for Functional Testing of Human Genetic Variants

(2015) A. Hamza et al.   GENETICS

Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism

(2015) Walker Pett et al.   Genome Biology and Evolution

tRNA Biology in Mitochondria

(2015) Thalia Salinas-Giegé et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Coordinated Rates of Evolution between Interacting Plastid and Nuclear Genes in Geraniaceae

(2015) Jin Zhang et al.   PLANT CELL

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

(2015) David Roy Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole

(2015) Gordon M. Bennett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria

(2015) Michael W. Gray   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic humanization of yeast genes reveals conserved functions and genetic modularity

(2015) A. H. Kachroo et al.   SCIENCE

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Mitochondrial cytochrome c biogenesis: no longer an enigma

(2015) Shalon E. Babbitt et al.   TRENDS IN BIOCHEMICAL SCIENCES

Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria

(2015) Shimon Bershtein et al.   PLoS Genetics

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis

(2014) Eunyoung Chae et al.   CELL

Hybrid Incompatibility Despite Pleiotropic Constraint in a Sequence-Based Bioenergetic Model of Transcription Factor Binding

(2014) Alexander Y. Tulchinsky et al.   GENETICS

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Natural Variation in Sensitivity to a Loss of Chloroplast Translation in Arabidopsis

(2014) N. Parker et al.   PLANT PHYSIOLOGY

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

(2014) Spiros Papakostas et al.   Nature Communications

Cytonuclear Genomic Interactions and Hybrid Breakdown

(2013) Ronald S. Burton et al.   Annual Review of Ecology Evolution and Systematics

Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis

(2013) Filip Husnik et al.   CELL

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

An Incompatibility between a Mitochondrial tRNA and Its Nuclear-Encoded tRNA Synthetase Compromises Development and Fitness in Drosophila

(2013) Colin D. Meiklejohn et al.   PLoS Genetics

Structural Perspective of Peptidoglycan Biosynthesis and Assembly

(2012) Andrew L. Lovering et al.   Annual Review of Biochemistry

Quantifying Homologous Replacement of Loci between Haloarchaeal Species

(2012) David Williams et al.   Genome Biology and Evolution

High Expression Hampers Horizontal Gene Transfer

(2012) Chungoo Park et al.   Genome Biology and Evolution

Functional Evolution of an Anthocyanin Pathway Enzyme during a Flower Color Transition

(2012) Stacey D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Compensatory Evolution of Ribosomal Proteins in Response to Rapid Divergence of Mitochondrial rRNA

(2012) F. S. Barreto et al.   MOLECULAR BIOLOGY AND EVOLUTION

A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities?

(2012) Ronald S. Burton et al.   MOLECULAR ECOLOGY

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast

(2012) Christian Tagwerker et al.   NUCLEIC ACIDS RESEARCH

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

(2012) J. A. Birchler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conflictual speciation: species formation via genomic conflict

(2012) Bernard Crespi et al.   TRENDS IN ECOLOGY & EVOLUTION

Horizontal gene transfer in the evolution of photosynthetic eukaryotes

(2012) Jinling HUANG et al.   Journal of Systematics and Evolution

Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities

(2012) E. Skippington et al.   Open Biology

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Mitochondrial–Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex

(2011) Naoki Osada et al.   MOLECULAR BIOLOGY AND EVOLUTION

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Biased gene transfer in microbial evolution

(2011) Cheryl P. Andam et al.   NATURE REVIEWS MICROBIOLOGY

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

What are the genomic drivers of the rapid evolution of PRDM9?

(2011) Chris P. Ponting   TRENDS IN GENETICS

Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution

(2010) Marina V Omelchenko et al.   Biology Direct

A Novel Method to Detect Proteins Evolving at Correlated Rates: Identifying New Functional Relationships between Coevolving Proteins

(2010) Nathaniel L. Clark et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

(2010) O. Cohen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rooting the Ribosomal Tree of Life

(2010) G. P. Fournier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Compensatory gene amplification restores fitness after inter-species gene replacements

(2010) Peter A. Lind et al.   MOLECULAR MICROBIOLOGY

The molecular evolutionary basis of species formation

(2010) Daven C. Presgraves   NATURE REVIEWS GENETICS

A single Arabidopsis organellar protein has RNase P activity

(2010) Anthony Gobert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Unique features of animal mitochondrial translation systems

(2010) Kimitsuna WATANABE   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Genomic patterns of pleiotropy and the evolution of complexity

(2010) Z. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybrid incompatibility genes: remnants of a genomic battlefield?

(2010) Norman A. Johnson   TRENDS IN GENETICS

Why do species vary in their rate of molecular evolution?

(2009) L. Bromham   Biology Letters

Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

(2009) A. Monier et al.   GENOME RESEARCH

Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis

(2009) PATRICK J. KEELING   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Subunits of the Plastid ClpPR Protease Complex Have Differential Contributions to Embryogenesis, Plastid Biogenesis, and Plant Development in Arabidopsis

(2009) J. Kim et al.   PLANT CELL

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

(2009) Peter L. Oliver et al.   PLoS Genetics

Incompatibility of Nuclear and Mitochondrial Genomes Causes Hybrid Sterility between Two Yeast Species

(2008) Hsin-Yi Lee et al.   CELL

RNase P without RNA: Identification and Functional Reconstitution of the Human Mitochondrial tRNA Processing Enzyme

(2008) Johann Holzmann et al.   CELL

Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?

(2008) James W. A. Allen et al.   FEBS Journal

Neutrality of Foreign Complex Subunits in an Experimental Model of Lateral Gene Transfer

(2008) A. Wellner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice

(2008) J. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase

(2008) O. Mihola et al.   SCIENCE

Sex chromosomes and speciation in Drosophila

(2008) Daven C. Presgraves   TRENDS IN GENETICS

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality

(2008) Elena Zotenko et al.   PLoS Computational Biology

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

(2007) M. J. Lercher et al.   MOLECULAR BIOLOGY AND EVOLUTION