Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

Adaptive Radiation, Ecological Opportunity, and Evolutionary Determinism

(2010) Jonathan B. Losos   AMERICAN NATURALIST

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Changes in Rubisco Kinetics during the Evolution of C4 Photosynthesis in Flaveria (Asteraceae) Are Associated with Positive Selection on Genes Encoding the Enzyme

(2010) Maxim V. Kapralov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cross-species analysis traces adaptation of Rubisco toward optimality in a low-dimensional landscape

(2010) Yonatan Savir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An examination of phylogenetic models of substitution rate variation among lineages

(2009) S. Y.W. Ho   Biology Letters

Gene duplication, transfer, and evolution in the chloroplast genome

(2009) Ai-Sheng Xiong et al.   BIOTECHNOLOGY ADVANCES

Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton

(2009) Satoko Iida et al.   PLoS One

Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses

(2009) Bojian Zhong et al.   PLoS One

Adaptive landscapes and protein evolution

(2009) M. Carneiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

(2009) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

(2008) J Gregory Caporaso et al.   BMC EVOLUTIONARY BIOLOGY

Adaptive evolution of rbcL in Conocephalum (Hepaticae, bryophytes)

(2008) Hidetsugu Miwa et al.   GENE

Assessing Side-Chain Perturbations of the Protein Backbone: A Knowledge-Based Classification of Residue Ramachandran Space

(2008) David B. Dahl et al.   JOURNAL OF MOLECULAR BIOLOGY

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains

(2008) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ohno's Model Revisited: Measuring the Frequency of Potentially Adaptive Mutations under Various Mutational Drifts

(2008) Shimon Bershtein et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary Switch and Genetic Convergence on rbcL following the Evolution of C4 Photosynthesis

(2008) Pascal-Antoine Christin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Directing the evolution of Rubisco and Rubisco activase: first impressions of a new tool for photosynthesis research

(2008) Oliver Mueller-Cajar et al.   PHOTOSYNTHESIS RESEARCH

Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene

(2008) Per Erixon et al.   PLoS One

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

(2008) M. M. Guisinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rooting and Dating Maples (Acer) with an Uncorrelated-Rates Molecular Clock: Implications for North American/Asian Disjunctions

(2008) Susanne S. Renner et al.   SYSTEMATIC BIOLOGY