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Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

https://doi.org/10.1101/774018
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Outgoing claims: the papers this work cites, builds on, or argues with.

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More than euglossines: the diverse pollinators and floral scents of Zygopetalinae orchids
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Draft Genome Sequence of the Endophytic Bacterium Enterobacter spp. MR1, Isolated from Drought Tolerant Plant (Butea monosperma)
inferredcites →https://doi.org/10.1016/j.molp.2014.12.011openalex-snapshot
The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb
inferredcites →https://doi.org/10.1016/j.ympev.2007.12.008openalex-snapshot
Dealing with incongruence in the quest for the species tree: A case study from the orchid genus Satyrium
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Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA results
inferredcites →https://doi.org/10.1016/j.ympev.2015.11.019openalex-snapshot
Sex and the Catasetinae (Darwin’s favourite orchids)
inferredcites →https://doi.org/10.1016/j.ympev.2017.02.006openalex-snapshot
A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
inferredcites →https://doi.org/10.1016/j.ympev.2018.05.031openalex-snapshot
Australasian orchid biogeography at continental scale: Molecular phylogenetic insights from the Sun Orchids (Thelymitra, Orchidaceae)
inferredcites →https://doi.org/10.1016/j.ympev.2018.06.041openalex-snapshot
From tree tops to the ground: Reversals to terrestrial habit in Galeandra orchids (Epidendroideae: Catasetinae)
inferredcites →https://doi.org/10.1016/j.ympev.2018.07.014openalex-snapshot
Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex
inferredcites →https://doi.org/10.1016/j.ympev.2019.106540openalex-snapshot
Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes
inferredcites →https://doi.org/10.1016/j.ympev.2019.106672openalex-snapshot
Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data
inferredcites →https://doi.org/10.1038/nature06039openalex-snapshot
Dating the origin of the Orchidaceae from a fossil orchid with its pollinator
inferredcites →https://doi.org/10.1038/nature23897openalex-snapshot
The Apostasia genome and the evolution of orchids
inferredcites →https://doi.org/10.1038/ng.3149openalex-snapshot
The genome sequence of the orchid Phalaenopsis equestris
inferredcites →https://doi.org/10.1038/s41467-018-03423-5openalex-snapshot
The Gastrodia elata genome provides insights into plant adaptation to heterotrophy
inferredcites →https://doi.org/10.1038/s41598-017-04261-zopenalex-snapshot
Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics
inferredcites →https://doi.org/10.1038/s41598-017-12300-yopenalex-snapshot
Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwin’s Favourite Orchids
inferredcites →https://doi.org/10.1038/s41598-019-40055-1openalex-snapshot
Asymmetric paralog evolution between the “cryptic” gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4
inferredcites →https://doi.org/10.1038/s41598-019-40144-1openalex-snapshot
Genomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencing
inferredcites →https://doi.org/10.1038/srep19029openalex-snapshot
The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution
inferredcites →https://doi.org/10.1086/697997openalex-snapshot
The Natural History of Cirrhaea and the Pollination System of Stanhopeinae (Orchidaceae)
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/aob/mci090openalex-snapshot
Pseudocopulatory Pollination in Lepanthes (Orchidaceae: Pleurothallidinae) by Fungus Gnats
inferredcites →https://doi.org/10.1093/aob/mcl191openalex-snapshot
Evolutionary and Morphometric Implications of Morphological Variation Among Flowers Within an Inflorescence: A Case-Study Using European Orchids
inferredcites →https://doi.org/10.1093/aob/mcp004openalex-snapshot
Molecular phylogenetics and the evolution of fruit and leaf morphology of Dichaea (Orchidaceae: Zygopetalinae)
inferredcites →https://doi.org/10.1093/aob/mcp190openalex-snapshot
Orchid biology: from Linnaeus via Darwin to the 21st century
inferredcites →https://doi.org/10.1093/aob/mcu253openalex-snapshot
Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification
inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot
HyPhy: hypothesis testing using phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr507openalex-snapshot
FLASH: fast length adjustment of short reads to improve genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/botlinnean/box087openalex-snapshot
Pollination of Trichosalpinx (Orchidaceae: Pleurothallidinae) by biting midges (Diptera: Ceratopogonidae)
inferredcites →https://doi.org/10.1093/botlinnean/box096openalex-snapshot
Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample
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/nar/gkx391openalex-snapshot
GeSeq – versatile and accurate annotation of organelle genomes
inferredcites →https://doi.org/10.1093/oso/9780198507123.001.0001openalex-snapshot
Genera Orchidacearum
inferredcites →https://doi.org/10.1093/oso/9780198507130.001.0001openalex-snapshot
Genera Orchidacearum
inferredcites →https://doi.org/10.1093/sysbio/syaa013openalex-snapshot
Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae
inferredcites →https://doi.org/10.1093/sysbio/syv070openalex-snapshot
Rumbling Orchids: How To Assess Divergent Evolution Between Chloroplast Endosymbionts and the Nuclear Host
inferredcites →https://doi.org/10.1093/sysbio/syx050openalex-snapshot
Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics
inferredcites →https://doi.org/10.1098/rspb.2015.1553openalex-snapshot
Orchid phylogenomics and multiple drivers of their extraordinary diversification
inferredcites →https://doi.org/10.1111/boj.12234openalex-snapshot
An updated classification of Orchidaceae
inferredcites →https://doi.org/10.1111/boj.12299openalex-snapshot
Phylogenetics of Eulophiinae (Orchidaceae: Epidendroideae): evolutionary patterns and implications for generic delimitation
inferredcites →https://doi.org/10.1111/j.1095-8312.2010.01440.xopenalex-snapshot
Phylogeny, diversification patterns and historical biogeography of euglossine orchid bees (Hymenoptera: Apidae)
inferredcites →https://doi.org/10.1111/j.1095-8339.1985.tb01015.xopenalex-snapshot
Stem structure and its bearing on the systematics of Pleurothallidinae (Orchidaceae)
inferredcites →https://doi.org/10.1111/j.1095-8339.2011.01200.xopenalex-snapshot
Phylogenetic analysis of Chloraeinae (Orchidaceae) based on plastid and nuclear DNA sequences
inferredcites →https://doi.org/10.1111/jbi.12726openalex-snapshot
Biogeographical diversification of mainland Asian Dendrobium (Orchidaceae) and its implications for the historical dynamics of evergreen broad‐leaved forests
inferredcites →https://doi.org/10.1111/nph.13106openalex-snapshot
The velamen protects photosynthetic orchid roots against UV ‐ B damage, and a large dated phylogeny implies multiple gains and losses of this function during the C enozoic
inferredcites →https://doi.org/10.1111/nph.13855openalex-snapshot
Disentangling visual and olfactory signals in mushroom‐mimicking Dracula orchids using realistic three‐dimensional printed flowers
inferredcites →https://doi.org/10.1111/nph.14629openalex-snapshot
Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot
inferredcites →https://doi.org/10.1111/pbi.12936openalex-snapshot
Chromosome‐level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding
inferredcites →https://doi.org/10.1126/science.1209175openalex-snapshot
Asynchronous Diversification in a Specialized Plant-Pollinator Mutualism
inferredcites →https://doi.org/10.11646/phytotaxa.246.1.3openalex-snapshot
Subtribal relationships in Cymbidieae (Epidendroideae, Orchidaceae) reveal a new subtribe, Dipodiinae, based on plastid and nuclear coding DNA
inferredcites →https://doi.org/10.11646/phytotaxa.272.1.1openalex-snapshot
Phylogenetic reassessment of Specklinia and its allied genera in the Pleurothallidinae (Orchidaceae)
inferredcites →https://doi.org/10.11646/phytotaxa.340.2.2openalex-snapshot
Genus-level taxonomical changes in the Lepanthes affinity (Orchidaceae, Pleurothallidinae)
inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
inferredcites →https://doi.org/10.1186/1745-6150-8-3openalex-snapshot
Next-generation phylogenomics
inferredcites →https://doi.org/10.1186/s12870-017-1160-xopenalex-snapshot
Phylogenetics of subtribe Orchidinae s.l. (Orchidaceae; Orchidoideae) based on seven markers (plastid matK, psaB, rbcL, trnL-F, trnH-psba, and nuclear nrITS, Xdh): implications for generic delimitation
inferredcites →https://doi.org/10.1186/s13059-020-02154-5openalex-snapshot
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
inferredcites →https://doi.org/10.1371/journal.pone.0099016openalex-snapshot
Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications
inferredcites →https://doi.org/10.1371/journal.pone.0185056openalex-snapshot
BBMerge – Accurate paired shotgun read merging via overlap
inferredcites →https://doi.org/10.15517/lank.v11i1.18310openalex-snapshot
Two new species of Teagueia (Orchidaceae: Pleurothallidinae) from East-Central Ecuador
inferredcites →https://doi.org/10.15517/lank.v11i3.18275openalex-snapshot
Mating systems in the Pleurothallidinae (Orchidaceae): evolutionary and systematic implications
inferredcites →https://doi.org/10.15517/lank.v13i3.14425openalex-snapshot
Generic and Subtribal relationShipS in neotropical cymbidieae (orchidaceae) baSed on matK/ycf1 plaStid data
inferredcites →https://doi.org/10.15517/lank.v16i2.26008openalex-snapshot
Genera Pleurothallidinarum: an updated phylogenetic overview of Pleurothallidinae
inferredcites →https://doi.org/10.15517/lank.v5i2.19799openalex-snapshot
Generic Relationships of Zygopetalinae (Orchidaceae: Cymbidieae): Combined Molecular Evidence
inferredcites →https://doi.org/10.2307/2807055openalex-snapshot
Icones Pleurothallidinarum VII. Systematics of Platystele (Orchidaceae).
inferredcites →https://doi.org/10.2307/3558390openalex-snapshot
Phylogenetic relationships in Pleurothallidinae (Orchidaceae): combined evidence from nuclear and plastid DNA sequences
inferredcites →https://doi.org/10.2307/4119796openalex-snapshot
Phytochemical Ecology, Phytochemical Society Symposia Series no. 8
inferredcites →https://doi.org/10.3100/hpib.v21iss2.2016.n4openalex-snapshot
Phylogenetic Reassessment of Acianthera (Orchidaceae: Pleurothallidinae)
inferredcites →https://doi.org/10.3389/fpls.2017.00715openalex-snapshot
The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots
inferredcites →https://doi.org/10.3389/fpls.2019.01328openalex-snapshot
The Origin and Diversification of the Hyperdiverse Flora in the Chocó Biogeographic Region
inferredcites →https://doi.org/10.3390/ijms19030716openalex-snapshot
Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution
inferredcites →https://doi.org/10.3732/ajb.1100334openalex-snapshot
Strategies for transcriptome analysis in nonmodel plants
inferredcites →https://doi.org/10.3732/ajb.90.5.777openalex-snapshot
Phylogenetics of Cranichideae with emphasis on Spiranthinae (Orchidaceae, Orchidoideae): evidence from plastid and nuclear DNA sequences
inferredcites →https://doi.org/10.3732/apps.1400042openalex-snapshot
Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics
inferredcites →https://doi.org/10.7717/peerj.167openalex-snapshot
Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology
inferredcites →https://doi.org/10.7717/peerj.2017openalex-snapshot
The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ajb2.1702openalex-snapshot
Hundreds of nuclear and plastid loci yield novel insights into orchid relationships
inferred← citeshttps://doi.org/10.1093/aob/mcac021openalex-snapshot
Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids
inferred← citeshttps://doi.org/10.1093/botlinnean/boad019openalex-snapshot
The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)
inferred← citeshttps://doi.org/10.1093/hr/uhac220openalex-snapshot
Advances and prospects of orchid research and industrialization
inferred← citeshttps://doi.org/10.1111/jipb.13415openalex-snapshot
Phylogenomics and the flowering plant tree of life
inferred← citeshttps://doi.org/10.1111/jipb.13462openalex-snapshot
Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
inferred← citeshttps://doi.org/10.1111/jipb.13609openalex-snapshot
Nuclear phylogenomics of angiosperms and insights into their relationships and evolution
inferred← citeshttps://doi.org/10.1111/nph.18904openalex-snapshot
Fossil berries reveal global radiation of the nightshade family by the early Cenozoic
inferred← citeshttps://doi.org/10.3389/fpls.2023.1219354openalex-snapshot
Plastid phylogenomics clarifies broad-level relationships in Bulbophyllum (Orchidaceae) and provides insights into range evolution of Australasian section Adelopetalum
inferred← citeshttps://doi.org/10.3389/fpls.2024.1388537openalex-snapshot
Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genus Dipodium and provides insights into plastid gene degeneration
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