Research graph
References from Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. Local targets link to admitted publications; unresolved targets remain external evidence.
Use of nuclear genes for phylogeny reconstruction in plants
10.1071/sb03015 · 2004 · External reference
Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV
10.3732/ajb.1400398 · 2014 · External reference
Plastid phylogenomic analysis of green plants: A billion years of evolutionary history
10.1002/ajb2.1048 · 2018 · External reference
Defining coalescent genes: theory meets practice in organelle phylogenomics
10.1093/sysbio/syab053 · 2022 · External reference
Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)
10.3389/fpls.2015.00710 · 2015 · External reference
The biogeography of mitochondrial and nuclear discordance in animals
10.1111/j.1365-294x.2012.05664.x · 2012 · External reference
The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny
10.2307/2399880 · 1995 · External reference
10.1007/978-1-4615-5419-6
10.1007/978-1-4615-5419-6 · 1998 · External reference
Gene tree discordance, phylogenetic inference and the multispecies coalescent
10.1016/j.tree.2009.01.009 · 2009 · External reference
ASTRAL: genome-scale coalescent-based species tree estimation
10.1093/bioinformatics/btu462 · 2014 · External reference
Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes
10.1186/s12862-015-0503-1 · 2015 · External reference
Can plastid genome sequencing be used for species identification in Lauraceae?
10.1093/botlinnean/boab018 · 2021 · External reference
Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots
10.1002/ajb2.1178 · 2018 · External reference
Phylogenetic consequences of cytoplasmic gene flow in plants
1991 · External reference
An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)
10.1111/nph.15386 · 2019 · External reference
Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)
2021 · External reference
What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?
10.1016/j.ympev.2018.10.008 · 2019 · External reference
Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae)
10.2307/2410326 · 1995 · External reference
Causes, consequences and solutions of phylogenetic incongruence
10.1093/bib/bbu015 · 2015 · External reference
Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
10.1016/j.ympev.2017.04.003 · 2017 · External reference
Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages
10.1002/ajb2.1468 · 2020 · External reference
A statistical approach for distinguishing hybridization and incomplete lineage sorting
10.1086/600082 · 2009 · External reference
A comprehensive phylogenomic platform for exploring the angiosperm tree of life
10.1093/sysbio/syab035 · 2022 · External reference
A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering
10.1093/sysbio/syy086 · 2019 · External reference
Illumina sequencing library preparation for highly multiplexed target capture and sequencing
10.1101/pdb.prot5448 · 2010 · External reference
Practical considerations for plant phylogenomics
10.1002/aps3.1038 · 2018 · External reference
Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics
10.3732/ajb.1100335 · 2012 · External reference
Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline
10.1111/bij.12642 · 2016 · External reference
The treasure vault can be opened: large-scale genome skimming works well using herbarium and silica gel dried material
10.3390/plants9040432 · 2020 · External reference
Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics
10.1186/s13007-019-0534-5 · 2020 · External reference
Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms
2017 · External reference
Out of sight, out of mind: widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal
10.1093/sysbio/syaa049 · 2021 · External reference
Resolving recalcitrant clades in the Pantropical Ochnaceae: insights from comparative phylogenomics of plastome and nuclear genomic data derived from targeted sequencing
10.3389/fpls.2021.638650 · 2021 · External reference
Phylogeny and classification of the subfamily Rubioideae (Rubiaceae)
10.1007/bf00985458 · 2000 · External reference
Conflicting phylogenetic signals in genomic data of the coffee family (Rubiaceae)
10.1111/jse.12566 · 2020 · External reference
Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)
10.3389/fpls.2022.967456 · 2022 · External reference
Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny
10.3732/ajb.1700255 · 2017 · External reference
Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes
10.1002/ajb2.1697 · 2021 · External reference
A rapid DNA isolation procedure for small quantities of fresh leaf tissue
1987 · External reference
Unresolved reference
External reference
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
10.1093/bioinformatics/bts199 · 2012 · External reference
NOVOWrap: An automated solution for plastid genome assembly and structure standardization
10.1111/1755-0998.13410 · 2021 · External reference
NOVOPlasty: de novo assembly of organelle genomes from whole genome data
2017 · External reference
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
10.1089/cmb.2012.0021 · 2012 · External reference
Mauve: multiple alignment of conserved genomic sequence with rearrangements
10.1101/gr.2289704 · 2004 · External reference
Reordering contigs of draft genomes using the Mauve Aligner
10.1093/bioinformatics/btp356 · 2009 · External reference
GeSeq—versatile and accurate annotation of organelle genomes
10.1093/nar/gkx391 · 2017 · External reference
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement
10.1371/journal.pone.0011147 · 2010 · External reference
Do alignment and trimming methods matter for phylogenomic (UCE) analyses?
10.1093/sysbio/syaa064 · 2020 · External reference
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
10.1371/journal.pbio.3001007 · 2020 · External reference
Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference
10.1093/sysbio/syv033 · 2015 · External reference
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
10.1093/bioinformatics/btp348 · 2009 · External reference
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
10.1186/1471-2148-10-210 · 2010 · External reference
The root of the mammalian tree inferred from whole mitochondrial genomes
10.1016/s1055-7903(03)00057-5 · 2003 · External reference
Phylogenomics and the reconstruction of the tree of life
10.1038/nrg1603 · 2005 · External reference
RY-coding and non-homogeneous models can ameliorate the maximum-likelihood inferences from nucleotide sequence data with parallel compositional heterogeneity
10.4137/ebo.s9017 · 2012 · External reference
From algae to angiosperms—inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
10.1186/1471-2148-14-23 · 2014 · External reference
Data types and the phylogeny of Neoaves
10.3390/birds2010001 · 2021 · External reference
IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
10.1093/molbev/msaa015 · 2020 · External reference
10.1109/gce.2010.5676129
10.1109/gce.2010.5676129 · External reference
ModelFinder: fast model selection for accurate phylogenetic estimates
10.1038/nmeth.4285 · 2017 · External reference
UFBoot2: improving the ultrafast bootstrap approximation
10.1093/molbev/msx281 · 2018 · External reference
Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere
10.1038/s41467-022-28917-1 · 2022 · External reference
DendroPy: a Python library for phylogenetic computing
10.1093/bioinformatics/btq228 · 2010 · External reference
Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows
2021 · External reference
A phylogeny of Urophylleae (Rubiaceae) based on rps16 intron data
2008 · External reference
The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms
10.1111/j.1467-7652.2007.00245.x · 2007 · External reference
Deep phylogenetic incongruence in the angiosperm clade Rosidae
10.1016/j.ympev.2014.11.003 · 2015 · External reference
A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily
10.1111/jse.12745 · 2021 · External reference
A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae
10.1016/j.ympev.2022.107545 · 2022 · External reference
Timetree of Rubiaceae—phylogeny and dating the family, subfamilies and tribes
10.1086/599077 · 2009 · External reference
Rare and enigmatic genera (Dunnia, Schizocolea, Colletoecema), sisters to species-rich clades: phylogeny and aspects of conservation biology in the coffee family
10.1016/j.ympev.2008.04.006 · 2008 · External reference
A revised time tree of the asterids: establishing a temporal framework for evolutionary studies of the coffee family (Rubiaceae)
10.1371/journal.pone.0126690 · 2015 · External reference
Phylogenetic affinity of an enigmatic Rubiaceae from the Seychelles revealing a recent biogeographic link with Central Africa: gen. nov. Seychellea and trib. nov. Seychelleeae
10.1016/j.ympev.2019.106685 · 2020 · External reference
Why are most organelle genomes transmitted maternally?
10.1002/bies.201400110 · 2015 · External reference
Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes
10.1111/nph.12431 · 2013 · External reference
Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations
10.1038/s41598-021-81988-w · 2021 · External reference
Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus
10.1016/j.ympev.2014.07.014 · 2014 · External reference
Phylogeny of Anthospermeae of the coffee family inferred using clock and nonclock models
10.1086/703353 · 2019 · External reference
Contentious relationships in phylogenomic studies can be driven by a handful of genes
10.1038/s41559-017-0126 · 2017 · External reference
Evolutionary relationships in the Spermacoceae alliance (Rubiaceae) using information from six molecular loci: insights into systematic affinities of Neohymenopogon and Mouretia
10.1002/tax.583009 · 2009 · External reference
Phylogenetic affinities of Myrioneuron and Cyanoneuron, generic limits of the tribe Argostemmateae and description of a new Asian tribe, Cyanoneuroneae (Rubiaceae)
10.12705/642.2 · 2015 · External reference
Molecular-based assessments of tribal and generic limits and relationships in Rubiaceae (Gentianales): Polyphyly of Pomazoteae and paraphyly of Ophiorrhizeae and Ophiorrhiza
10.1002/tax.12023 · 2019 · External reference
A revision of the genus Mouretia (Rubiaceae)
10.1111/j.1756-1051.1997.tb00298.x · 1997 · External reference
The rps16 intron and the phylogeny of Rubioideae (Rubiaceae)
10.1007/bf00985737 · 1999 · External reference
Deep divergences in the coffee family and the systematic position of Acranthera
10.1007/s00606-008-0138-4 · 2009 · External reference
Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels
10.1016/s1055-7903(02)00240-3 · 2002 · External reference
Phylogenomic resolution of the phylogeny of laurasiatherian mammals: exploring phylogenetic signals within coding and noncoding sequences
10.1093/gbe/evx147 · 2017 · External reference
Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution
10.1186/s12864-017-4319-9 · 2017 · External reference
Genome-scale profiling reveals noncoding loci carry higher proportions of concordant data
10.1093/molbev/msab026 · 2021 · External reference
Evolution and trends in the Psychotrieae alliance (Rubiaceae)—A rarely reported evolutionary change of many-seeded carpels from one-seeded carpels
10.1016/j.ympev.2008.03.034 · 2008 · External reference
A supermatrix approach provides a comprehensive genus-level phylogeny for Gentianales
10.1111/jse.12192 · 2016 · External reference
Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae)
10.1002/tax.562006 · 2007 · External reference
Role of the Qinghai-Tibetan Plateau uplift in the Northern Hemisphere disjunction: evidence from two herbaceous genera of Rubiaceae
10.1038/s41598-017-13543-5 · 2017 · External reference
Phylogeny, character evolution and spatiotemporal diversification of the species-rich and world-wide distributed tribe Rubieae (Rubiaceae)
10.1371/journal.pone.0207615 · 2018 · External reference
Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
10.1016/j.ympev.2019.05.022 · 2019 · External reference
Taxon sampling and the accuracy of phylogenetic analyses
2008 · External reference
Resolving difficult phylogenetic questions: why more sequences are not enough
10.1371/journal.pbio.1000602 · 2011 · External reference
Phylogenomics—principles, opportunities and pitfalls of big-data phylogenetics
10.1111/syen.12406 · 2020 · External reference
Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition
10.1093/oxfordjournals.molbev.a026286 · 2000 · External reference
Magic bullets and golden rules: data sampling in molecular phylogenetics
10.1016/j.zool.2005.09.006 · 2005 · External reference
The roles of protein structure, taxon sampling, and model complexity in phylogenomics: a case study focused on early animal divergences
10.3390/biophysica1020008 · 2021 · External reference
Relative benefits of amino-acid, codon, degeneracy, DNA, and purine-pyrimidine character coding for phylogenetic analyses of exons
10.1111/jse.12233 · 2017 · External reference
Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions
10.1093/sysbio/syt109 · 2014 · External reference
Resolving the systematic positions of enigmatic taxa: manipulating the chloroplast genome data of Saxifragales
10.1016/j.ympev.2018.04.033 · 2018 · External reference
Plastome structure and phylogenetic relationships of Styracaceae (Ericales)
10.1186/s12862-021-01827-4 · 2021 · External reference
The effects of partitioning on phylogenetic inference
10.1093/molbev/msv026 · 2015 · External reference
10.1007/978-1-62703-995-6_1
10.1007/978-1-62703-995-6_1 · 2014 · External reference
Chloroplast genomes of Rubiaceae: comparative genomics and molecular phylogeny in subfamily Ixoroideae
10.1371/journal.pone.0232295 · 2020 · External reference
Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution
10.1186/s12870-022-03480-5 · 2022 · External reference
Complete chloroplast genomes of Leptodermis scabrida complex: Comparative genomic analyses and phylogenetic relationships
10.1016/j.gene.2021.145715 · 2021 · External reference
The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family
10.1093/aob/mcu050 · 2014 · External reference
Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
10.1111/jse.12179 · 2015 · External reference
Plastid genome evolution in the early-diverging legume subfamily Cercidoideae (Fabaceae)
2018 · External reference
Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera
1994 · External reference
The dynamic history of plastid genomes in the Campanulaceae sensu lato is unique among angiosperms
10.1073/pnas.1403363111 · 2014 · External reference
Passiflora plastome sequencing reveals widespread genomic rearrangements
10.1111/jse.12425 · 2019 · External reference
Two distinct plastid genome configurations and unprecedented intraspecies length variation in the accD coding region in Medicago truncatula
10.1093/dnares/dsu007 · 2014 · External reference
Mitochondrion-to-plastid DNA transfer: it happens
10.1111/nph.12704 · 2014 · External reference
Foreign plastid sequences in plant mitochondria are frequently acquired via mitochondrion-to-mitochondrion horizontal transfer
10.1038/srep43402 · 2017 · External reference
Taxonomic revision of Cruckshanksia and Oreopolus (Rubiaceae: Hedyotideae)
10.2307/2399989 · 1996 · External reference
Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the Broomrape family
10.1105/tpc.113.113373 · 2013 · External reference
Plastome evolution in hemiparasitic Mistletoes
10.1093/gbe/evv165 · 2015 · External reference
Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii
10.1073/pnas.91.21.9794 · 1994 · External reference
The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates
10.1186/1471-2148-8-130 · 2008 · External reference
The chloroplast genome of Utricularia reniformis sheds light on the evolution of the ndh gene complex of terrestrial carnivorous plants from the Lentibulariaceae Family
10.1371/journal.pone.0165176 · 2016 · External reference
A new carnivorous plant lineage (Triantha) with a unique sticky-inflorescence trap
10.1073/pnas.2022724118 · 2021 · External reference
The plastid genome of Najas flexilis: adaptation to submersed environments is accompanied by the complete loss of the ndh complex in an aquatic angiosperm
10.1371/journal.pone.0068591 · 2013 · External reference
Genome sequencing of the endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) reveals potential mechanisms of evolutionary specialization
10.1016/j.isci.2020.101124 · 2020 · External reference
The complete plastome sequences of seven species in Gentiana sect. Kudoa (Gentianaceae): insights into plastid gene loss and molecular evolution
10.3389/fpls.2018.00493 · 2018 · External reference
Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)
10.1007/s11103-011-9753-5 · 2011 · External reference
Seven new complete plastome sequences reveal rampant independent loss of the ndh gene family across orchids and associated instability of the inverted repeat/small single-copy region boundaries
10.1371/journal.pone.0142215 · 2015 · External reference
Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences
10.1186/s12870-022-03529-5 · 2022 · External reference
Insights into chloroplast genome evolution across Opuntioideae (Cactaceae) reveals robust yet sometimes conflicting phylogenetic topologies
10.3389/fpls.2020.00729 · 2020 · External reference
Plastid ndh genes in plant evolution
10.1016/j.plaphy.2010.04.009 · 2010 · External reference