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Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies

https://doi.org/10.1007/s00239-017-9792-x

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

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Complete Sequence of the Maize Chloroplast Genome: Gene Content, Hotspots of Divergence and Fine Tuning of Genetic Information by Transcript Editing

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Metabolic Rate, Generation Time, and the Rate of Molecular Evolution in Birds

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HyPhy: Hypothesis Testing Using Phylogenies

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Use of Chloroplast DNA Rearrangements in Reconstructing Plant Phylogeny

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The Plastid Genomes of Flowering Plants

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Plastid Genomes of Seed Plants

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Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants

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Vicia faba chloroplast DNA has only one set of ribosomal RNA genes as shown by partial denaturation mapping and R-loop analysis

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Genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution

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Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements

inferredcites →https://doi.org/10.1007/bf00365763openalex-snapshot

The site of deletion of the inverted repeat in pea chloroplast DNA contains duplicated gene fragments

inferredcites →https://doi.org/10.1007/s00239-002-2333-yopenalex-snapshot

Nucleotide Substitution Rates in Legume Chloroplast DNA Depend on the Presence of the Inverted Repeat

inferredcites →https://doi.org/10.1007/s00239-002-2395-0openalex-snapshot

Broad-Scale Analysis Contradicts the Theory That Generation Time Affects Molecular Evolutionary Rates in Plants

inferredcites →https://doi.org/10.1007/s00239-008-9086-4openalex-snapshot

Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes

inferredcites →https://doi.org/10.1007/s00239-008-9180-7openalex-snapshot

Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions

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Evolutionary Rates in Veronica L. (Plantaginaceae): Disentangling the Influence of Life History and Breeding System

inferredcites →https://doi.org/10.1007/s00239-009-9317-3openalex-snapshot

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

inferredcites →https://doi.org/10.1007/s11103-011-9753-5openalex-snapshot

Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)

inferredcites →https://doi.org/10.1007/s11295-012-0573-9openalex-snapshot

Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing

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The neutral theory of molecular evolution

inferredcites →https://doi.org/10.1016/j.sajb.2013.05.001openalex-snapshot

Reconstructing the deep-branching relationships of the papilionoid legumes

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Somatic deleterious mutation rate in a woody plant: estimation from phenotypic data

inferredcites →https://doi.org/10.1038/scientificamerican1179-98openalex-snapshot

The Neutral Theory of Molecular Evolution

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Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions and accelerated rate of evolution in clpP

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Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement

inferredcites →https://doi.org/10.1073/pnas.0709121104openalex-snapshot

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

inferredcites →https://doi.org/10.1073/pnas.0806759105openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1403363111openalex-snapshot

The dynamic history of plastid genomes in the Campanulaceae sensu lato is unique among angiosperms

inferredcites →https://doi.org/10.1073/pnas.78.9.5533openalex-snapshot

Rearrangements in the chloroplast genomes of mung bean and pea

inferredcites →https://doi.org/10.1073/pnas.82.6.1741openalex-snapshot

Evidence for higher rates of nucleotide substitution in rodents than in man.

inferredcites →https://doi.org/10.1073/pnas.84.24.9054openalex-snapshot

Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.

inferredcites →https://doi.org/10.1073/pnas.89.16.7844openalex-snapshot

Extensive variation in evolutionary rate of rbcL gene sequences among seed plants.

inferredcites →https://doi.org/10.1073/pnas.90.22.10676openalex-snapshot

An examination of the generation-time effect on molecular evolution.

inferredcites →https://doi.org/10.1073/pnas.90.9.4087openalex-snapshot

Body size, metabolic rate, generation time, and the molecular clock.

inferredcites →https://doi.org/10.1073/pnas.93.19.10274openalex-snapshot

Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.

inferredcites →https://doi.org/10.1073/pnas.94.11.5722openalex-snapshot

Molecular evolution of angiosperm mitochondrial introns and exons

inferredcites →https://doi.org/10.1074/jbc.m309212200openalex-snapshot

Clp Protease Complexes from Photosynthetic and Non-photosynthetic Plastids and Mitochondria of Plants, Their Predicted Three-dimensional Structures, and Functional Implications

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Evolutionary Rates Analysis of Leguminosae Implicates a Rapid Diversification of Lineages during the Tertiary

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A Rapid Bootstrap Algorithm for the RAxML Web Servers

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inferredcites →https://doi.org/10.1093/aob/mcw065openalex-snapshot

Variable presence of the inverted repeat and plastome stability inErodium

inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot

APE: Analyses of Phylogenetics and Evolution in R language

inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot

HyPhy: hypothesis testing using phylogenies

inferredcites →https://doi.org/10.1093/bioinformatics/btm468openalex-snapshot

CREx: inferring genomic rearrangements based on common intervals

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Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene

inferredcites →https://doi.org/10.1093/gbe/evv125openalex-snapshot

Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion

inferredcites →https://doi.org/10.1093/gbe/evw033openalex-snapshot

Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity

inferredcites →https://doi.org/10.1093/gbe/evw115openalex-snapshot

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

inferredcites →https://doi.org/10.1093/gbe/evw167openalex-snapshot

Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content

inferredcites →https://doi.org/10.1093/genetics/130.3.677openalex-snapshot

Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes.

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The Complete Chloroplast Genome Sequence of Pelargonium × hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants

inferredcites →https://doi.org/10.1093/molbev/msm036openalex-snapshot

Gene Relocations within Chloroplast Genomes of Jasminum and Menodora (Oleaceae) Are Due to Multiple, Overlapping Inversions

inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot

PAML 4: Phylogenetic Analysis by Maximum Likelihood

inferredcites →https://doi.org/10.1093/molbev/msq229openalex-snapshot

Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

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

inferredcites →https://doi.org/10.1093/molbev/mst257openalex-snapshot

Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025781openalex-snapshot

Correlated rates of synonymous site evolution across plant genomes

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040605openalex-snapshot

Chloroplast DNA evolves slowly in the palm family (Arecaceae).

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Rate of rbc L gene sequence evolution and species diversification in flowering plants (angiosperms)

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EVOLUTIONARY ANALYSIS OF THE LARGE SUBUNIT OF CARBOXYLASE ( rbcL ) NUCLEOTIDE SEQUENCE AMONG THE GRASSES (GRAMINEAE)

inferredcites →https://doi.org/10.1111/j.1558-5646.1990.tb05207.xopenalex-snapshot

EVOLUTIONARY SIGNIFICANCE OF THE LOSS OF THE CHLOROPLAST‐DNA INVERTED REPEAT IN THE LEGUMINOSAE SUBFAMILY PAPILIONOIDEAE

inferredcites →https://doi.org/10.1111/jse.12179openalex-snapshot

Plastid genome sequences of legumes reveal parallel inversions and multiple losses ofrps16in papilionoids

inferredcites →https://doi.org/10.1111/nph.13743openalex-snapshot

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

inferredcites →https://doi.org/10.1111/nph.14375openalex-snapshot

Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes

inferredcites →https://doi.org/10.1111/pbi.12141openalex-snapshot

Highly rearranged and size‐variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers

inferredcites →https://doi.org/10.1111/pbi.12179openalex-snapshot

Evolutionary and biotechnology implications of plastid genome variation in the inverted‐repeat‐lacking clade of legumes

inferredcites →https://doi.org/10.1126/science.1118884openalex-snapshot

Mutation Pressure and the Evolution of Organelle Genomic Architecture

inferredcites →https://doi.org/10.1126/science.1163197openalex-snapshot

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

inferredcites →https://doi.org/10.1126/science.3082006openalex-snapshot

Rates of DNA Sequence Evolution Differ Between Taxonomic Groups

inferredcites →https://doi.org/10.1146/annurev.ecolsys.37.091305.110215openalex-snapshot

Some Evolutionary Consequences of Being a Tree

inferredcites →https://doi.org/10.1186/1471-2148-12-8openalex-snapshot

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

inferredcites →https://doi.org/10.1186/1471-2148-4-27openalex-snapshot

Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes

inferredcites →https://doi.org/10.1186/1471-2148-6-36openalex-snapshot

A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects.

inferredcites →https://doi.org/10.1186/1471-2148-8-130openalex-snapshot

The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates

inferredcites →https://doi.org/10.1186/1471-2164-8-174openalex-snapshot

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inferredcites →https://doi.org/10.1186/1471-2229-8-70openalex-snapshot

Complete nucleotide sequence of the Cryptomeria japonicaD. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

inferredcites →https://doi.org/10.1186/s12862-014-0228-6openalex-snapshot

Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

inferredcites →https://doi.org/10.1186/s12862-014-0268-yopenalex-snapshot

Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome

inferredcites →https://doi.org/10.1186/s13059-014-0542-8openalex-snapshot

K r /K c but not d N /d S correlates positively with body mass in birds, raising implications for inferring lineage-specific selection

inferredcites →https://doi.org/10.12705/622.8openalex-snapshot

Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species–rich clades

inferredcites →https://doi.org/10.1371/journal.pbio.1001241openalex-snapshot

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

inferredcites →https://doi.org/10.1371/journal.pone.0005297openalex-snapshot

Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses

inferredcites →https://doi.org/10.1371/journal.pone.0079685openalex-snapshot

Balanced Gene Losses, Duplications and Intensive Rearrangements Led to an Unusual Regularly Sized Genome in Arbutus unedo Chloroplasts

inferredcites →https://doi.org/10.1371/journal.pone.0125768openalex-snapshot

The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

inferredcites →https://doi.org/10.2307/2409416openalex-snapshot

Evolutionary Significance of the Loss of the Chloroplast-DNA Inverted Repeat in the Leguminosae Subfamily Papilionoideae

inferredcites →https://doi.org/10.2307/2409569openalex-snapshot

Evolutionary Analysis of the Large Subunit of Carboxylase (rbcL) Nucleotide Sequence Among the Grasses (Gramineae)

inferredcites →https://doi.org/10.3732/ajb.1200380openalex-snapshot

Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early‐branching lineages

inferredcites →https://doi.org/10.3732/ajb.1500184openalex-snapshot

Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

inferredcites →https://doi.org/10.3732/ajb.91.11.1846openalex-snapshot

A phylogeny of legumes (Leguminosae) based on analysis of the plastid mat K gene resolves many well‐supported subclades within the family

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Plastid-Nuclear Coevolution of Ribosomal Protein Genes in Papilionoid Legumes

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Nucleotide substitution rates of diatom plastid encoded protein genes are positively correlated with genome architecture

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Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent

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inferred← citeshttps://doi.org/10.3390/genes14101914openalex-snapshot

Comparative Plastid Genome and Phylogenomic Analyses of Potamogeton Species

inferred← citeshttps://doi.org/10.3390/ijms221910485openalex-snapshot

Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes

inferred← citeshttps://doi.org/10.3390/ijms24043606openalex-snapshot

Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

inferred← citeshttps://doi.org/10.3390/plants12122231openalex-snapshot

Pueraria montana Population Structure and Genetic Diversity Based on Chloroplast Genome Data

inferred← citeshttps://doi.org/10.6084/m9.figshare.16620913openalex-snapshot

Additional file 1 of Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

inferred← citeshttps://doi.org/10.6084/m9.figshare.16620916openalex-snapshot

Additional file 2 of Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

inferred← citeshttps://doi.org/10.6084/m9.figshare.23606857openalex-snapshot

Additional file 1 of The complete chloroplast genome of Ulmus mianzhuensis with insights into structural variations, adaptive evolution, and phylogenetic relationships of Ulmus (Ulmaceae)

inferred← citeshttps://doi.org/10.64898/2026.05.22.727288openalex-snapshot

Coordinated Evolutionary Rates in Oxidative Phosphorylation Complexes of Papilionoid Legumes: Cytonuclear Coevolution and Relaxed Selection

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