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Convergent Evolution and the Origin of Complex Phenotypes in the Age of Systems Biology

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Polyploid and Hybrid Genomics

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Genetic Rules of Heterosis in Plants

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Molecular Evolution of 18S rDNA in Angiosperms: Implications for Character Weighting in Phylogenetic Analysis

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A large number of tetraploid Arabidopsis thaliana lines, generated by a rapid strategy, reveal high stability of neo-tetraploids during consecutive generations

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Convergent evolution of major histocompatibility complex molecules in humans and New World monkeys

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Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system

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Polyploids as a “model system” for the study of heterosis

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Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

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The Warburg and Crabtree effects: On the origin of cancer cell energy metabolism and of yeast glucose repression

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The Molecular Genetics of Crop Domestication

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Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape

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Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

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Cetaceans on a Molecular Fast Track to Ultrasonic Hearing

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Transcriptomic Shock Generates Evolutionary Novelty in a Newly Formed, Natural Allopolyploid Plant

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Rapid, Repeated, and Clustered Loss of Duplicate Genes in Allopolyploid Plant Populations of Independent Origin

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Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts

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Tetraploidy, aneuploidy and cancer

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Energy metabolism in cancer cells: How to explain the Warburg and Crabtree effects?

inferredcites →https://doi.org/10.1016/j.molp.2015.02.016openalex-snapshot

Making the Bread: Insights from Newly Synthesized Allohexaploid Wheat

inferredcites →https://doi.org/10.1016/j.pbi.2012.01.015openalex-snapshot

Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants

inferredcites →https://doi.org/10.1016/j.pbi.2014.05.008openalex-snapshot

Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

inferredcites →https://doi.org/10.1016/j.pbi.2015.06.003openalex-snapshot

Tracing the evolutionary path to nitrogen-fixing crops

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Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales

inferredcites →https://doi.org/10.1016/j.tibs.2004.11.006openalex-snapshot

Game-theoretical approaches to studying the evolution of biochemical systems

inferredcites →https://doi.org/10.1016/j.tig.2006.02.002openalex-snapshot

How did Saccharomyces evolve to become a good brewer?

inferredcites →https://doi.org/10.1016/j.tig.2006.09.003openalex-snapshot

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon

inferredcites →https://doi.org/10.1016/j.tig.2006.12.006openalex-snapshot

Heterosis: revisiting the magic

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Causes and evolutionary significance of genetic convergence

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Higher-order genetic interactions and their contribution to complex traits

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Unreduced gametes: meiotic mishap or evolutionary mechanism?

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Developmental genetics of floral symmetry evolution

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Molecular mechanisms of polyploidy and hybrid vigor

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Can phylogenetics identify C4 origins and reversals?

inferredcites →https://doi.org/10.1016/j.tree.2012.06.001openalex-snapshot

Experimental evolution

inferredcites →https://doi.org/10.1016/s0168-9525(99)01776-xopenalex-snapshot

Pax 6: mastering eye morphogenesis and eye evolution

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Molecular adaptation of Drosophila melanogaster lysozymes to a digestive function

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Catalytic promiscuity and the evolution of new enzymatic activities

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Enzymes with extra talents: moonlighting functions and catalytic promiscuity

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Yeast genome evolution in the post-genome era

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Recurrent chromosome aberrations in cancer

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Identifying Latent Enzyme Activities: Substrate Ambiguity within Modern Bacterial Sugar Kinases

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Reconstitution of a Defunct Glycolytic Pathway via Recruitment of Ambiguous Sugar Kinases

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Collective dynamics of ‘small-world’ networks

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Adaptive evolution in the stomach lysozymes of foregut fermenters

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Lethality and centrality in protein networks

inferredcites →https://doi.org/10.1038/msb4100170openalex-snapshot

Increased glycolytic flux as an outcome of whole‐genome duplication in yeast

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Evolution, consequences and future of plant and animal domestication

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Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

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Computational systems biology

inferredcites →https://doi.org/10.1038/nature01771openalex-snapshot

Dosage sensitivity and the evolution of gene families in yeast

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Resource competition and social conflict in experimental populations of yeast

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Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

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Finding the missing heritability of complex diseases

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Genome-wide analysis of a long-term evolution experiment with Drosophila

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Genome-wide signatures of convergent evolution in echolocating mammals

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Parallel domestication of the Shattering1 genes in cereals

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A reference genome for common bean and genome-wide analysis of dual domestications

inferredcites →https://doi.org/10.1038/ng.3198openalex-snapshot

Convergent evolution of the genomes of marine mammals

inferredcites →https://doi.org/10.1038/ng.745openalex-snapshot

INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1

inferredcites →https://doi.org/10.1038/ng1181openalex-snapshot

Convergent evolution of gene circuits

inferredcites →https://doi.org/10.1038/nrc1478openalex-snapshot

Why do cancers have high aerobic glycolysis?

inferredcites →https://doi.org/10.1038/nrg3483openalex-snapshot

The genetic causes of convergent evolution

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Genome dynamics during experimental evolution

inferredcites →https://doi.org/10.1038/nrm1276openalex-snapshot

From polyploidy to aneuploidy, genome instability and cancer

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Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change

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Molecular evolution and adaptive radiation: Molecular Evolution and Adaptive Radiation.

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Chromosome doubling of haploid maize seedlings using nitrous oxide gas at the flower primordial stage

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Actinorhizal symbioses and their N2 fixation

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Chromosomal Abnormalities in Cancer

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Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication

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The hearing gene Prestin reunites echolocating bats

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Evidence for an ancient adaptive episode of convergent molecular evolution

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Convergent evolution of metabolic roles in bacterial co-symbionts of insects

inferredcites →https://doi.org/10.1073/pnas.1014138108openalex-snapshot

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

inferredcites →https://doi.org/10.1073/pnas.1101368108openalex-snapshot

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

inferredcites →https://doi.org/10.1073/pnas.1119675109openalex-snapshot

The mystery of missing heritability: Genetic interactions create phantom heritability

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

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Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

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Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

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Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

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Current perspectives and the future of domestication studies

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Storytelling and story testing in domestication

inferredcites →https://doi.org/10.1073/pnas.24.2.56openalex-snapshot

A Cytological Study of Colchicine Effects in the Induction of Polyploidy in Plants

inferredcites →https://doi.org/10.1073/pnas.92.7.2647openalex-snapshot

Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms.

inferredcites →https://doi.org/10.1073/pnas.94.8.3811openalex-snapshot

Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish

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Indeterminism and Natural Selection

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How Have Advances in Comparative Floral Development Influenced Our Understanding of Floral Evolution?

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A novel insight into the cost–benefit model for the evolution of botanical carnivory

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Convergence and Parallelism in Evolution: A Neo-Gouldian Account

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Convergence as Evidence

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Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution

inferredcites →https://doi.org/10.1093/gbe/evt181openalex-snapshot

Massively Convergent Evolution for Ribosomal Protein Gene Content in Plastid and Mitochondrial Genomes

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DOMINANCE OF LINKED FACTORS AS A MEANS OF ACCOUNTING FOR HETEROSIS

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HETEROSIS

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WHAT IS "HETEROSIS"?

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ALTERNATIVE HYPOTHESES OF HYBRID VIGOR

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Induction of Tetraploid Derivatives of Maize Inbred Lines by Nitrous Oxide Gas Treatment

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Cracking the Kranz enigma with systems biology

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Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis

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Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species

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The Role of Mutational Dynamics in Genome Shrinkage

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Disproportional Plastome-Wide Increase of Substitution Rates and Relaxed Purifying Selection in Genes of Carnivorous Lentibulariaceae

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Comparative Genomics as a Time Machine: How Relative Gene Dosage and Metabolic Requirements Shaped the Time-dependent Resolution of Yeast Polyploidy

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Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution

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Detection of convergent and parallel evolution at the amino acid sequence level

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026089openalex-snapshot

The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?

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Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin.

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Scarecrow Plays a Role in Establishing Kranz Anatomy in Maize Leaves

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The small world inside large metabolic networks

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The probability of genetic parallelism and convergence in natural populations

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Differential retention and divergent resolution of duplicate genes following whole-genome duplication

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The discovery of integrated gene networks for autism and related disorders

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Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity

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The Rest of the Iceberg. Legume Diversity and Evolution in a Phylogenetic Context

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Patterns of Sequence Loss and Cytosine Methylation within a Population of Newly Resynthesized Brassica napus Allopolyploids

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AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

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Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network

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Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes[W]

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The Gene Balance Hypothesis: From Classical Genetics to Modern Genomics

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Genomic Changes in Resynthesized Brassica napus and Their Effect on Gene Expression and Phenotype

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Heterosis

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Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints

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Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

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Why, when, and how did yeast evolve alcoholic fermentation?

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THE LOCI OF REPEATED EVOLUTION: A CATALOG OF GENETIC HOTSPOTS OF PHENOTYPIC VARIATION

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The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution

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Homoeologous recombination in allopolyploids: the polyploid ratchet

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Newly synthesized wheat allohexaploids display progenitor‐dependent meiotic stability and aneuploidy but structural genomic additivity

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New grass phylogeny resolves deep evolutionary relationships and discovers C 4 origins

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Mycoheterotrophic germination of Pyrola asarifolia dust seeds reveals convergences with germination in orchids

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Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis

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CONVERGENCE, ADAPTATION, AND CONSTRAINT

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Fermentative lifestyle in yeasts belonging to the Saccharomyces complex

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A roadmap for research on crassulacean acid metabolism ( CAM ) to enhance sustainable food and bioenergy production in a hotter, drier world

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Conservation of fruit dehiscence pathways between L epidium campestre and A rabidopsis thaliana sheds light on the regulation of INDEHISCENT

inferredcites →https://doi.org/10.1111/tpj.12470openalex-snapshot

SCARECROW , SCR ‐ LIKE 23 and SHORT ‐ ROOT control bundle sheath cell fate and function in A rabidopsis thaliana

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Cooperation and Competition in the Evolution of ATP-Producing Pathways

inferredcites →https://doi.org/10.1126/science.1069492openalex-snapshot

Systems Biology: A Brief Overview

inferredcites →https://doi.org/10.1126/science.110.2869.692openalex-snapshot

On the Discovery of the Action of Colchicine on Mitosis in 1889

inferredcites →https://doi.org/10.1126/science.110.2869.692.aopenalex-snapshot

On the Discovery of the Action of Colchicine on Mitosis in 1889

inferredcites →https://doi.org/10.1126/science.1123539openalex-snapshot

Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins

inferredcites →https://doi.org/10.1126/science.1178534openalex-snapshot

The B73 Maize Genome: Complexity, Diversity, and Dynamics

inferredcites →https://doi.org/10.1126/science.1188545openalex-snapshot

Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution

inferredcites →https://doi.org/10.1126/science.1212986openalex-snapshot

The Molecular Diversity of Adaptive Convergence

inferredcites →https://doi.org/10.1126/science.1214449openalex-snapshot

Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

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Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

inferredcites →https://doi.org/10.1126/science.1255274openalex-snapshot

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

inferredcites →https://doi.org/10.1126/science.1260782openalex-snapshot

Erratum for the Report: “Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome” by B. Chalhoub, F. Denoeud, S. Liu, I. A. P. Parkin, H. Tang, X. Wang, J. Chiquet, H. Belcram, C. Tong, B. Samans, M. Corréa, C. Da Silva, J. Just, C. Falentin, C. S. Koh, I. Le Clainche, M.…

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Carnivorous Plants: Phylogeny and Structural Evolution

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The Tragedy of the Commons

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Convergent Domestication of Cereal Crops by Independent Mutations at Corresponding Genetic Loci

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Network Motifs: Simple Building Blocks of Complex Networks

inferredcites →https://doi.org/10.1126/science.7892602openalex-snapshot

Induction of Ectopic Eyes by Targeted Expression of the eyeless Gene in Drosophila

inferredcites →https://doi.org/10.1126/science.7914031openalex-snapshot

Homology of the eyeless Gene of Drosophila to the Small eye Gene in Mice and Aniridia in Humans

inferredcites →https://doi.org/10.1128/aem.61.5.2020-2022.1995openalex-snapshot

Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution

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Photorespiration and the Evolution of C4Photosynthesis

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Nonadditive Gene Expression in Polyploids

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Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

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Molecular Signatures of Natural Selection

inferredcites →https://doi.org/10.1146/annurev.physiol.63.1.359openalex-snapshot

Antifreeze Proteins of Teleost Fishes

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Distinct C4 sub-types and C3 bundle sheath isolation in the Paniceae grasses.

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inferred← citeshttps://doi.org/10.3390/ijms17060938openalex-snapshot

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Peer Review #1 of "Convergent origin of the narrowly lanceolate leaf in the genus Aster—with special reference to an unexpected discovery of a new Aster species from East China (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.6288v0.1/reviews/2openalex-snapshot

Peer Review #2 of "Convergent origin of the narrowly lanceolate leaf in the genus Aster—with special reference to an unexpected discovery of a new Aster species from East China (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.6288v0.2/reviews/1openalex-snapshot

Peer Review #1 of "Convergent origin of the narrowly lanceolate leaf in the genus Aster—with special reference to an unexpected discovery of a new Aster species from East China (v0.2)"

inferred← citeshttps://doi.org/10.7717/peerj.6288openalex-snapshot

Convergent origin of the narrowly lanceolate leaf in the genus Aster —with special reference to an unexpected discovery of a new Aster species from East China

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.