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Phylogenomics

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IDTitleSection/TopicAuthorsKeywords
639Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
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PhylogenomicsKates, Heather; Johnson, Matthew; Gardner, Elliot; Zerega, Nyree; Wickett, Norman.Targeted Sequence Capture
Hyb-Seq
heterozygosity
allelic sequence data
Phylogenomics methods
744A phylogenomics pipeline for identifying crop wild relatives: an example from the Dioscorea yams, a major pantropical crop
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PhylogenomicsSoto Gomez, Marybel; Viruel, Juan ; Kantar , Michael; Wilkin, Paul; Graham, Sean.Phylogenomics methods
Nuclear monocot phylogenomics
Hyb-Seq
Dioscoreaceae
Dioscoreales
low-copy nuclear loci
740Assessing the reticulate history of white oaks (Quercus) using hundreds of nuclear loci
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PhylogenomicsCrowl, Andrew; McVay, John; Hipp, Andrew; Manos, Paul.Quercus
Hybridization
Oaks
SNAQ
Introgression
gene flow
HybSeq
626Capsi-conundrum: Resolving Relationships within Capsiceae (Solanaceae)
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PhylogenomicsSanbonmatsu , Katie K; Mukai, Maya; Spalink, Daniel; Bohs, Lynn Allison.Capsicum
Solanaceae
Lycianthes
Capsiceae
Phylogenomics
Phylogenetics
genealogical discordance
Incomplete Lineage Sorting
concordance
Evolution
MrBayes
BUCKy
280Characterizing gene-tree conflict and systematic error in plastome-inferred phylogenies
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PhylogenomicsWalker, Joseph; Stull, Gregory; Walker-Hale, Nathanael; Vargas, Oscar M; Larson, Drew.Chloroplast genome
plastome
angiosperms
Genomic conflict
gene tree conflict
Systematic error
Phylogenomics
rpoC2
111Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics
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PhylogenomicsChau, John; Olmstead, Richard.hybrid enrichment
single-copy nuclear genes
PPR genes
Buddleja
Scrophulariaceae
Lamiales
809Designing and testing a kit to enrich phylogenetically informative exons for all angiosperms
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PhylogenomicsWickett, Norman; Johnson, Matthew; Botigue, Laura; Devault, Alison; Dodsworth, Stephen; Forest, Felix; Kim, Jan; Leebens-Mack, Jim; Soltis, Douglas; Soltis, Pamela S.; Baker, William J.; Pokorny, Lisa.HybSeq
HybPiper
Sequence capture
Machine Learning
single-copy nuclear genes
482Detecting Hybridization in Hawaiian Cyrtandra (Gesneriaceae) Using Genome-wide Data
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PhylogenomicsKleinkopf, Jospeh; Wagner, Warren; Roalson, Eric.Cyrtandra
Gesneriaceae
Hawaii
Hyb-Seq
Hybridization
484Developing tools to capture loci of two distant clades of Melastomataceae
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PhylogenomicsAmarasinghe, Prabha; Jantzen, Johanna; Soltis, Douglas; Soltis, Pamela S.; Cellinese, Nico.Memecylon
Tibouchina
Melastomataceae
target enrichment
HybPiper
459Differential Decay of an Ancient Mitochondrial Insertion in the Plastid Genomes of Paspalum (Poaceae)
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PhylogenomicsBurke, Sean; Ungerer, Mark; Duvall, M.Poaceae
Paspalum
mtDNA
ptDNA
molecular evolution
inserts
Next generation sequencing
Grasses
135Difficulties in the Inference of Ancient Whole-Genome Duplications
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PhylogenomicsSong, Michael; Rothfels, Carl; Igic, Boris.Polyploidy
whole genome duplication
ks plot
130Elucidating the Multiple Independent Whole Genomes Duplication Events in the Brassicales
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PhylogenomicsBrose, Julia; Mabry, Makenzie; Dismukes, Wade; Beric, Aleksandra; Washburn, Jacob; Edger, Patrick; Hall, Jocelyn; McKain, Michael; Al-Shehbaz, Ihsan; Harkess, Alex; Schranz, M. Eric; Conant, Gavin; Pires, Joseph Chris.Brassicales
whole chloroplast
Phylogenomics
414Embracing gene tree conflict to inform species relationships: An example in the clade Caryophyllales
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PhylogenomicsWalker, Joseph; Brown, Joseph; Smith, Stephen.Phylogenomics
gene tree conflict
Caryophyllales
supermatrix
Coalescent
738Evolution and Historical Biogeography of Asteraceae using Hyb-Seq Data
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PhylogenomicsMandel, Jennifer; Siniscalchi, Carolina; Thapa, Ramhari; Dikow, Rebecca; Watson, Linda E; Funk, Vicki.Compositae
Phylogenomics
Biogeography
Hyb-Seq
Sunflower
376Evolutionary origins of cultivated sweetpotato and relationships in the Batatas complex
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PhylogenomicsEserman, Lauren; Leebens-Mack, Jim.sweetpotato
Ipomoea
Phylogenomics
Crop wild relatives
240Evolution of function and structure in the leucine-rich repeat gene family in flowering plants
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PhylogenomicsGallagher, Joseph; Man, Jarrett; Bartlett, Madelaine.leucine-rich repeat
molecular evolution
Phylogenomics
191Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments
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PhylogenomicsWang, Ning; Yang, Ya; Moore, Michael J.; Brockington, Samuel; Walker, Joseph; Brown, Joseph; Eggli, Urs; Majure, Lucas; Smith, Stephen.gene tree conflict
gene duplication
molecular evolution
paleopolyploidy
Portulacineae
stress adaptation
185Extensive gene tree discordance in Malpighiales not explained by incomplete lineage sorting and gene tree estimation error
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PhylogenomicsCai, Liming; Xi, Zhenxiang; Lemmon, Emily; Lemmon, Alan; Mast, Austin; Buddenhagen, Christopher; Liu, Liang; Davis, Charles.Anchored hybrid enrichment
Subsampling
Gene tree-species tree conflict
Hybridization
Rapid radiation
Coalescent method
823Genomic patterns of gene flow and divergence in the genus Antirrhinum
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PhylogenomicsDuran Castillo , Mario Saturnino; Hudson, Andrew; Twyford, Alex.Speciation
Phylogenetics
Hybridization
Antirrhinum
583Hunting the treasure of Cape Oxalis diversity
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PhylogenomicsZeisek, Vojtěch; Oberlander, Kenneth; Dreyer, Leanne; Schmickl, Roswitha.Phylogenomics
Phylogenetics
biodiversity
Taxonomy
Evolution
Oxalis
HTS
South Africa
Greater Cape Floristic Region
239Massive polyploidization but no obvious role for polyploids in the radiation of southern African Oxalis L.: insights from phylogenomics and cytogenetics
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PhylogenomicsSchmickl, Roswitha; Oberlander, Kenneth; Zeisek, Vojtěch; Liston, Aaron; Schneeweiss, Hanna; Záveská, Eliška; Emshwiller, Eve; Dreyer, Leanne; Suda, Jan.radiation
whole genome duplication
Hyb-Seq
Greater Cape Floristic Region
574Milkweed Phylogenomics: Assessing Incomplete Lineage Sorting and Intergenomic Discordance
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PhylogenomicsFishbein, Mark; Straub, Shannon; Boutte, Julien; Weitemeier, Kevin A.; Cronn, Richard; Liston, Aaron.Phylogenomics
Phylogenetics
nuclear genes
target enrichment
HybSeq
Incomplete Lineage Sorting
milkweed
Asclepias
Apocynaceae
248Monocot plastid phylogenomics, timeline, and the power of multi-gene analyses
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PhylogenomicsGivnish, Thomas J; Zuluaga-Trochez, Alejandro; Spalink, Daniel; Graham, Sean; Barrett, Craig; Soto Gomez, Marybel; Lam, Vivienne; Saarela, Jeffery; Sass, Chodon; LIma, Danilo; Leebens-Mack, Jim; Pires, Joseph Chris; Zomlefer, Wendy; Gandolfo, Maria A; Davis, Jerrold; Stevenson, Dennis; Specht, Chelsea.Commelinids
partitioned maximum likelihood
net rates of species diversification
mycoheterotrophy
183Nested phylogenetic conflicts and deep phylogenomics in plants
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PhylogenomicsSmith, Stephen; Brown, Joseph; Walker, Joseph.Phylogenomics
land plants
Phylogenetics
heterogeneity
conflict
258Origin(s) of a hybrid: History of allopolyploid Brassica napus using genome-wide data
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PhylogenomicsAn, Hong; Gaynor, Michelle; Gebken, Sarah; Qi, Xinshuai; Barker, Michael; Pires, Joseph Chris.Brassica
Phylogenomics
597Phylogenomic analyses reveal extensive gene flow within the magic flowers (Achimenes)
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PhylogenomicsRoberts, Wade; Roalson, Eric.Achimenes
Gesneriaceae
Hybridization
Introgression
Phylogenomics
transcriptomics
837Phylogenomic Analysis of Polyploidy in “Reedy” Arundinoids (Poaceae)
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PhylogenomicsTeisher, Jordan; McKain, Michael; Kellogg, Elizabeth.Phragmites australis
Arundo donax
Grass
Evolution
862Phylogenomic analysis of the wheat tribe Triticeae (Poaceae) based on chloroplast and nuclear data acquired using a Hyb-Seq approach
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PhylogenomicsMason-Gamer, Roberta; White, Dawson.Poaceae
Gramineae
target enrichment
416Phylogenomics of Aesculus L. (Sapindaceae) inferred from RAD-seq data – insights into biogeography and evolution of the genus
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PhylogenomicsDu, Zhiyuan; Xiang, Jenny; Harris, AJ.Aesculus
RAD-seq
intercontinental disjunction
Niche Evolution
Biogeography
521Phylogenomics of Nyssa from single copy genes and Fluidgim sequencing – insights into biogeography and character evolution
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PhylogenomicsZhou, Wenbin; Xiang, Jenny; Wen, Jun.eastern Asia-eastern North American disjunction
Nyssa
Fluidigm sequencing
Ancestral character estimation
Biogeography
957Phylogenomics subgenus Hermodactyloides, a small lineage of bulbous Iris that are mostly narrow endemics
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PhylogenomicsWilson, Carol; Freyman, Will.Biogeography
Endemism
genome skimming
Iris
Iridaceae
Targeted Sequence Capture
Next generation sequencing
260Physcraper: automatic updating of phylogenies
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PhylogenomicsKandziora, Martha; McTavish, Emily Jane.Phylogenetics
workflow
automatic updating
python
Senecioneae
Asteraceae
460Plastome phylogenomics and characterization of rare genomic changes in plastome groups 1 and 2 Poeae (Pooideae; Poaceae)
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PhylogenomicsOrton, Lauren; Burke, Sean; Duvall, M.chloroplast
plastome
Plastid
Poeae
Pooideae
Poaceae
Phylogenomics
348REPHINE: REcursive PHylogenetic INferencE
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PhylogenomicsMiller, Joe.Phylogenetics
DNA alignments
778Resolving Relationships in Leucaena through Reference Guided and de novo Transcriptomics
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PhylogenomicsAbair, Alexander; Nageswara-Rao, Madhugiri; Dugas, Diana; Hughes, Colin; Bailey, Donovan.Leucaena
Leguminosae
Polyploid
phylogeny
Genomics
transcriptomics
Hybridization
orthology
paralogy
719Resolving the Phylogeny and Understanding the Molecular Evolution of Rapidly Diversifying South American Pitcher Plants Heliamphora(Sarraceniaceae)
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PhylogenomicsLiu, Sukuan; Smith, Stacey D..Carnivorous Plants
Evolution
RNA-Seq
Phylogenetics
498Seed plant phylogeny inferred from integrated analyses of morphological and molecular data
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PhylogenomicsMathews, Sarah; Campbell, Christopher; Cronn, Richard; Gernandt, David; Graham, Sean; Hansen, Kimberly; Holman, Garth; G.Kelch, Dean; Lam, Vivienne; Li, Jianhua; Liston, Aaron; Little, Damon; Mapes, Gene; Mei, Wenbin; Moore, Abigail; Nagalingum, Nathalie; Parks, Matthew; Peery, Rhiannon; Rai, Hardeep; Raubeson, Linda; Ross, Gregory; Rothwell, Gar; Ruhsam, Markus; Ryberg, Patricia E.; Schwarzbach, Andrea; Stevenson, Dennis; Stockey, Ruth; Yang, Yong.seed plant
phylogeny
fossils
molecules
morphology
850Target-enrichment phylogenomics improves the resolution of legume lineages at generic, tribal, and subfamily levels
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PhylogenomicsVatanparast, Mohammad; Egan, Ashley.Sequence capture
Hyb-Seq
Fabaceae
Systematics
794Testing for the Monophyly of the Mentzelia Section Bartonia (Loasaceae) Pinnatisect-Leaved Species with Genome Skimming
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PhylogenomicsSchenk, John; Kelly, Khadijah.phylogeny
Phylogenomics
genome skimming
Cytonuclear discordance
Mentzelia
Loasaceae
Incomplete Lineage Sorting
Next generation sequencing
convergent evolution
846Testing the monophyly of bryophytes using expanded genome and transcriptome sampling
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PhylogenomicsWickett, Norman; Parks, Matthew; Johnson, Matthew; Mirarab, Siavash; Mai, Uyen; Peter, Szovenyi; Kirbis, Alexander; Waller, Manuel; Neubauer, Anna.Bryophytes
land plants
gene tree conflict
gene genealogy interrogation
single-copy nuclear genes
607The Evolutionary and Ecological Roles of Illinois Listed Endangered and Threatened Grasses
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PhylogenomicsPischl, Phyllis; Duvall, M.Poaceae
Endangered Species
Phylogenomics

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