| ID | Title | Section/Topic | Authors | Keywords |
|---|
| 639 | Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
Log in to add this item to your schedule | Phylogenomics | Kates, Heather; Johnson, Matthew; Gardner, Elliot; Zerega, Nyree; Wickett, Norman. | Targeted Sequence Capture
Hyb-Seq
heterozygosity
allelic sequence data
Phylogenomics methods |
| 744 | A phylogenomics pipeline for identifying crop wild relatives: an example from the Dioscorea yams, a major pantropical crop
Log in to add this item to your schedule | Phylogenomics | Soto Gomez, Marybel; Viruel, Juan ; Kantar , Michael; Wilkin, Paul; Graham, Sean. | Phylogenomics methods
Nuclear monocot phylogenomics
Hyb-Seq
Dioscoreaceae
Dioscoreales
low-copy nuclear loci |
| 740 | Assessing the reticulate history of white oaks (Quercus) using hundreds of nuclear loci
Log in to add this item to your schedule | Phylogenomics | Crowl, Andrew; McVay, John; Hipp, Andrew; Manos, Paul. | Quercus
Hybridization
Oaks
SNAQ
Introgression
gene flow
HybSeq |
| 626 | Capsi-conundrum: Resolving Relationships within Capsiceae (Solanaceae)
Log in to add this item to your schedule | Phylogenomics | Sanbonmatsu , Katie K; Mukai, Maya; Spalink, Daniel; Bohs, Lynn Allison. | Capsicum
Solanaceae
Lycianthes
Capsiceae
Phylogenomics
Phylogenetics
genealogical discordance
Incomplete Lineage Sorting
concordance
Evolution
MrBayes
BUCKy |
| 280 | Characterizing gene-tree conflict and systematic error in plastome-inferred phylogenies
Log in to add this item to your schedule | Phylogenomics | Walker, Joseph; Stull, Gregory; Walker-Hale, Nathanael; Vargas, Oscar M; Larson, Drew. | Chloroplast genome
plastome
angiosperms
Genomic conflict
gene tree conflict
Systematic error
Phylogenomics
rpoC2 |
| 111 | Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics
Log in to add this item to your schedule | Phylogenomics | Chau, John; Olmstead, Richard. | hybrid enrichment
single-copy nuclear genes
PPR genes
Buddleja
Scrophulariaceae
Lamiales |
| 809 | Designing and testing a kit to enrich phylogenetically informative exons for all angiosperms
Log in to add this item to your schedule | Phylogenomics | Wickett, 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 |
| 482 | Detecting Hybridization in Hawaiian Cyrtandra (Gesneriaceae) Using Genome-wide Data
Log in to add this item to your schedule | Phylogenomics | Kleinkopf, Jospeh; Wagner, Warren; Roalson, Eric. | Cyrtandra
Gesneriaceae
Hawaii
Hyb-Seq
Hybridization |
| 484 | Developing tools to capture loci of two distant clades of Melastomataceae
Log in to add this item to your schedule | Phylogenomics | Amarasinghe, Prabha; Jantzen, Johanna; Soltis, Douglas; Soltis, Pamela S.; Cellinese, Nico. | Memecylon
Tibouchina
Melastomataceae
target enrichment
HybPiper |
| 459 | Differential Decay of an Ancient Mitochondrial Insertion in the Plastid Genomes of Paspalum (Poaceae)
Log in to add this item to your schedule | Phylogenomics | Burke, Sean; Ungerer, Mark; Duvall, M. | Poaceae
Paspalum
mtDNA
ptDNA
molecular evolution
inserts
Next generation sequencing
Grasses |
| 135 | Difficulties in the Inference of Ancient Whole-Genome Duplications
Log in to add this item to your schedule | Phylogenomics | Song, Michael; Rothfels, Carl; Igic, Boris. | Polyploidy
whole genome duplication
ks plot |
| 130 | Elucidating the Multiple Independent Whole Genomes Duplication Events in the Brassicales
Log in to add this item to your schedule | Phylogenomics | Brose, 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 |
| 414 | Embracing gene tree conflict to inform species relationships: An example in the clade Caryophyllales
Log in to add this item to your schedule | Phylogenomics | Walker, Joseph; Brown, Joseph; Smith, Stephen. | Phylogenomics
gene tree conflict
Caryophyllales
supermatrix
Coalescent |
| 738 | Evolution and Historical Biogeography of Asteraceae using Hyb-Seq Data
Log in to add this item to your schedule | Phylogenomics | Mandel, Jennifer; Siniscalchi, Carolina; Thapa, Ramhari; Dikow, Rebecca; Watson, Linda E; Funk, Vicki. | Compositae
Phylogenomics
Biogeography
Hyb-Seq
Sunflower |
| 376 | Evolutionary origins of cultivated sweetpotato and relationships in the Batatas complex
Log in to add this item to your schedule | Phylogenomics | Eserman, Lauren; Leebens-Mack, Jim. | sweetpotato
Ipomoea
Phylogenomics
Crop wild relatives |
| 240 | Evolution of function and structure in the leucine-rich repeat gene family in flowering plants
Log in to add this item to your schedule | Phylogenomics | Gallagher, Joseph; Man, Jarrett; Bartlett, Madelaine. | leucine-rich repeat
molecular evolution
Phylogenomics |
| 191 | Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments
Log in to add this item to your schedule | Phylogenomics | Wang, 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 |
| 185 | Extensive gene tree discordance in Malpighiales not explained by incomplete lineage sorting and gene tree estimation error
Log in to add this item to your schedule | Phylogenomics | Cai, 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 |
| 823 | Genomic patterns of gene flow and divergence in the genus Antirrhinum
Log in to add this item to your schedule | Phylogenomics | Duran Castillo , Mario Saturnino; Hudson, Andrew; Twyford, Alex. | Speciation
Phylogenetics
Hybridization
Antirrhinum |
| 583 | Hunting the treasure of Cape Oxalis diversity
Log in to add this item to your schedule | Phylogenomics | Zeisek, Vojtěch; Oberlander, Kenneth; Dreyer, Leanne; Schmickl, Roswitha; Schneeweiss, Hanna. | Phylogenomics
Phylogenetics
biodiversity
Taxonomy
Evolution
Oxalis
HTS
South Africa
Greater Cape Floristic Region |
| 239 | Massive polyploidization but no obvious role for polyploids in the radiation of southern African Oxalis L.: insights from phylogenomics and cytogenetics
Log in to add this item to your schedule | Phylogenomics | Schmickl, 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 |
| 574 | Milkweed Phylogenomics: Assessing Incomplete Lineage Sorting and Intergenomic Discordance
Log in to add this item to your schedule | Phylogenomics | Fishbein, 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 |
| 248 | Monocot plastid phylogenomics, timeline, and the power of multi-gene analyses
Log in to add this item to your schedule | Phylogenomics | Givnish, 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 |
| 183 | Nested phylogenetic conflicts and deep phylogenomics in plants
Log in to add this item to your schedule | Phylogenomics | Smith, Stephen; Brown, Joseph; Walker, Joseph. | Phylogenomics
land plants
Phylogenetics
heterogeneity
conflict |
| 258 | Origin(s) of a hybrid: History of allopolyploid Brassica napus using genome-wide data
Log in to add this item to your schedule | Phylogenomics | An, Hong; Gaynor, Michelle; Gebken, Sarah; Qi, Xinshuai; Barker, Michael; Pires, Joseph Chris. | Brassica
Phylogenomics |
| 597 | Phylogenomic analyses reveal extensive gene flow within the magic flowers (Achimenes)
Log in to add this item to your schedule | Phylogenomics | Roberts, Wade; Roalson, Eric. | Achimenes
Gesneriaceae
Hybridization
Introgression
Phylogenomics
transcriptomics |
| 837 | Phylogenomic Analysis of Polyploidy in “Reedy” Arundinoids (Poaceae)
Log in to add this item to your schedule | Phylogenomics | Teisher, Jordan; McKain, Michael; Kellogg, Elizabeth. | Phragmites australis
Arundo donax
Grass
Evolution |
| 862 | Phylogenomic analysis of the wheat tribe Triticeae (Poaceae) based on chloroplast and nuclear data acquired using a Hyb-Seq approach
Log in to add this item to your schedule | Phylogenomics | Mason-Gamer, Roberta; White, Dawson. | Poaceae
Gramineae
target enrichment |
| 416 | Phylogenomics of Aesculus L. (Sapindaceae) inferred from RAD-seq data – insights into biogeography and evolution of the genus
Log in to add this item to your schedule | Phylogenomics | Du, Zhiyuan; Xiang, Jenny; Harris, AJ. | Aesculus
RAD-seq
intercontinental disjunction
Niche Evolution
Biogeography |
| 521 | Phylogenomics of Nyssa from single copy genes and Fluidgim sequencing – insights into biogeography and character evolution
Log in to add this item to your schedule | Phylogenomics | Zhou, Wenbin; Xiang, Jenny; Wen, Jun. | eastern Asia-eastern North American disjunction
Nyssa
Fluidigm sequencing
Ancestral character estimation
Biogeography |
| 957 | Phylogenomics subgenus Hermodactyloides, a small lineage of bulbous Iris that are mostly narrow endemics
Log in to add this item to your schedule | Phylogenomics | Wilson, Carol; Freyman, Will. | Biogeography
Endemism
genome skimming
Iris
Iridaceae
Targeted Sequence Capture
Next generation sequencing |
| 260 | Physcraper: automatic updating of phylogenies
Log in to add this item to your schedule | Phylogenomics | Kandziora, Martha; McTavish, Emily Jane. | Phylogenetics
workflow
automatic updating
python
Senecioneae
Asteraceae |
| 460 | Plastome phylogenomics and characterization of rare genomic changes in plastome groups 1 and 2 Poeae (Pooideae; Poaceae)
Log in to add this item to your schedule | Phylogenomics | Orton, Lauren; Burke, Sean; Duvall, M. | chloroplast
plastome
Plastid
Poeae
Pooideae
Poaceae
Phylogenomics |
| 348 | REPHINE: REcursive PHylogenetic INferencE
Log in to add this item to your schedule | Phylogenomics | Miller, Joe. | Phylogenetics
DNA alignments |
| 778 | Resolving Relationships in Leucaena through Reference Guided and de novo Transcriptomics
Log in to add this item to your schedule | Phylogenomics | Abair, Alexander; Nageswara-Rao, Madhugiri; Dugas, Diana; Hughes, Colin; Bailey, Donovan. | Leucaena
Leguminosae
Polyploid
phylogeny
Genomics
transcriptomics
Hybridization
orthology
paralogy |
| 719 | Resolving the Phylogeny and Understanding the Molecular Evolution of Rapidly Diversifying South American Pitcher Plants Heliamphora(Sarraceniaceae)
Log in to add this item to your schedule | Phylogenomics | Liu, Sukuan; Smith, Stacey D.. | Carnivorous Plants
Evolution
RNA-Seq
Phylogenetics |
| 498 | Seed plant phylogeny inferred from integrated analyses of morphological and molecular data
Log in to add this item to your schedule | Phylogenomics | Mathews, 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 |
| 850 | Target-enrichment phylogenomics improves the resolution of legume lineages at generic, tribal, and subfamily levels
Log in to add this item to your schedule | Phylogenomics | Vatanparast, Mohammad; Egan, Ashley. | Sequence capture
Hyb-Seq
Fabaceae
Systematics |
| 794 | Testing for the Monophyly of the Mentzelia Section Bartonia (Loasaceae) Pinnatisect-Leaved Species with Genome Skimming
Log in to add this item to your schedule | Phylogenomics | Schenk, John; Kelly, Khadijah. | phylogeny
Phylogenomics
genome skimming
Cytonuclear discordance
Mentzelia
Loasaceae
Incomplete Lineage Sorting
Next generation sequencing
convergent evolution |
| 846 | Testing the monophyly of bryophytes using expanded genome and transcriptome sampling
Log in to add this item to your schedule | Phylogenomics | Wickett, 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 |
| 607 | The Evolutionary and Ecological Roles of Illinois Listed Endangered and Threatened Grasses
Log in to add this item to your schedule | Phylogenomics | Pischl, Phyllis; Duvall, M. | Poaceae
Endangered Species
Phylogenomics |
