| ID | Title | Section/Topic | Authors | Keywords |
|---|
| 507 | A bird’s eye view of the systematics of Convolvulaceae: novel insights from nuclear genomic data | Phylogenomics | Simões, Ana Rita; Eserman, Lauren; Zuntini, Alexandre R.; Chatrou, Lars; Utteridge, Timothy; Maurin, Olivier; Rokni, Saba; Roy, Shyamali; Forest, Felix; Baker, William; Stefanovic, Sasa. | Angiosperms353
Convolvulaceae
Cuscuta
phylogenomics
Ipomoea
Target Enrichment |
| 237 | A comprehensive phylogenomic tree of life sheds new light on angiosperm diversification | Phylogenomics | Carruthers, Tom; Zuntini, Alexandre R.; Antonelli, Alexandre; Bellot, Sidonie; Crayn, Darren; Eiserhardt, Wolf L; Forest, Felix; Grace, Olwen; Smith, Stephen; Baker, William. | phylogenomics
Angiosperms
Angiosperms353
macroevolution
Diversification |
| 204 | A First Plastome Phylogeny for Rumex L. (Polygonaceae), with Fossil-Aided Date Calibration | Phylogenomics | Koenemann, Daniel Mark; Kistler, Logan; Burke, Janelle. | RAxML
BEAST
Fossil Calibration
Cenozoic
Plastomics |
| 347 | A genome-wide approach for resolving phylogenetic relationships of subfamily Arbutoideae (Ericaceae) | Phylogenomics | Ramadoss, Niveditha; McElwee-Adame, Alexandra; Parker, V. T.; Gonzalez-Elizondo, Socorro; Litt, Amy; Flores-Renteria, Lluvia. | Arbutoideae
phylogenetics
Arbutus paraphyly |
| 840 | A Hyb-Seq phylogeny of Boechera (Brassicaceae) and related genera | Phylogenomics | Hay, Nikolai; Bailey, C. Donovan; Mandakova, Terezie; Hendriks, Kasper; Pryer, Kathleen; Windham, Michael. | Boechera
Hyb-Seq
phylogenetics
Brassicaceae |
| 102 | Ancient allopolyploidy, early radiation and extensive hybridization have shaped the evolutionary history of the Asian Palmate Group (Araliaceae) | Phylogenomics | Gallego-Narbón, Angélica; Wen, Jun; Valcarcel, Virginia. | Araliaceae
phylogenomics
hybridization
Radiation
ILS |
| 810 | A nuclear phylogenomic overview of Rosaceae | Phylogenomics | Stull, Gregory; Tian, Qin; Liu, Shui-Yin; Fu, Xiao-Gang; Kates, Heather; Folk, Ryan; Guralnick, Robert; Soltis, Pamela; Soltis, Douglas; Yi, Ting-Shuang. | hybridization
phylogenomics
polyploidy
Rosaceae
Rosales
whole genome duplication |
| 85 | An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data | Phylogenomics | Xiang, Qiuyun (Jenny); Du, Zhiyuan; Cheng, Jing; Zhou, Wenbin; Wang, Qing-Feng; Soltis, Douglas; Soltis, Pamela. | phylogenomics
RAD-Seq
Angiosperms353 Hyb-Seq
Cornaceae
Classification
Historical biogeography |
| 904 | A phylogenomic baseline to study the evolution of extreme floral curvature in Centropogon subgenus Centropogon (Campanulaceae) | Phylogenomics | Mansaray, Janet; Frost, Laura; Bedoya, Ana Maria; Lagomarsino, Laura. | |
| 302 | A phylogenomic study of Scutellaria (Lamiaceae) based on chloroplast genomes and 272 nuclear single-copy genes | Phylogenomics | Lee, Yoonkyung; Paton, Alan; Olmstead, Richard; Kim, Sangtae. | Scutellaria
Lamiaceae
Chlroplast genome
Nuclear genome
phylogenomics
Hyb-Seq |
| 1036 | A phylogeny of the evening primrose family (Onagraceae) with a focus on tribe Onagreae using a target enrichment approach | Phylogenomics | Overson, Rick; Johnson, Matthew; Bechen, Lindsey; Kinosian, Sylvia; Douglas, Norman; Fant, Jeremie B; Hoch, Peter; Levin, Rachel; Moore, Michael; Raguso, Robert; Wagner, Warren; Skogen, Krissa; Wickett, Norman. | phylogenomics
HybSeq
Onagraceae
evening primrose
Target Enrichment
systematics
phylogenetics |
| 828 | A tale of two Hyb-Seq probe sets: Comparing the Compositae-1061 probe set with a new probe set targeting 2424 functional genes | Phylogenomics | Gomez, Jorge; Moore, Erika; Burke, John; Mandel, Jennifer. | Asteraceae
Compositae
Hyb-Seq
phylogeny
candidate genes
probe sets |
| 713 | Boreotropical refugia and extensive introgressions explain the revival of north temperate diversity in the New World grapes | Phylogenomics | Nie, Zelong; Hodel, Richard; Ma, Zhiyao; Johnson, Gabriel; Ren, Chen; Meng, Ying; Ickert-Bond, Steffi; Liu, Xiu-Qun; Zimmer, Elizabeth; Wen, Jun. | Boreotropical refugia
New World grapes
temperate radiation
reticulate evolution
phylogenomics
biogeography
Vitis
Vitaceae |
| 166 | Characterization of the entire USDA germplasm collection of Amaranthus | Phylogenomics | Hoffberg, Sandra; Eaton, Deren. | RADseq
crop
collection |
| 676 | Comparative Genomics and Phylogenetic Utility of the Mitochondrial Genome in Apiales | Phylogenomics | Nicolas, Antoine; Earl, Victoria; Hughes, Emily; Molina, Giselle; Scollan, Brianna; Zandel, Stephanie; Plunkett, Gregory. | mitogenome
Apiales
Hydrocotyle
Shotgun Sequencing |
| 303 | Complete chloroplast genomes of seven species of Elsholtzia (Lamiaceae): Comparative and phylogenetic analyses | Phylogenomics | Lee, Yoonkyung; Yun, Narae; Jeon, Yun-Chang; Choi, Sangho; Paik, Jin-Hyub. | Elsholtzia
Lamiaceae
Endemic Species
Chloroplast genome
phylogeny |
| 409 | Completing the angiosperm tree of life - over half-way there | Phylogenomics | Baker, William; PAFTOL, Team. | phylogenomics
Angiosperms353
Open Access
herbariomics
target-capture
Hyb-Seq
Angiosperms
tree of life |
| 603 | Cyto-nuclear Discordance in Adenia | Phylogenomics | Netherland, Michael; Hearn, David. | phylogenomics
Species tree
cytonuclear discordance
introgression |
| 100 | Differential role of climatic niche in colonization and in-situ evolutionary processes of Macaronesian ivies (Hedera L., Araliaceae) | Phylogenomics | Gallego-Narbón, Angélica; Alonso Hernandez, Alejandro; Valcarcel, Virginia; Fernandez-Mazuecos Santa Teresa, Mario. | Hedera
Macaronesia
Climatic niche
phylogenomics
GBS |
| 914 | Dissecting pollinator-driven floral-trait evolution in Agave subg. Manfreda | Phylogenomics | MacNeill, Bryan; McKain, Michael; Ruiz-Sanchez, Eduardo; Rodriguez Contreras, Aaron. | |
| 706 | Dissecting the role of reticulate evolution in the diversification of Prunus (Rosaceae) | Phylogenomics | Hodel, Richard; Zimmer, Elizabeth; Liu, Bin-Bin; Johnson, Gabriel; Potter, Daniel; Wen, Jun. | allopolyploidy
hybridization
phylogenetic network
cytonuclear discord
Hyb-Seq
biogeography |
| 703 | Effects of taxon sampling and shifts in mode of organellar inheritance on Gymnosperm phylogeny | Phylogenomics | Paradiso, Lydia. | gymnosperm
organelle inheritance
taxon sampling
Pinaceae |
| 671 | Environment and geography drive diversification within the Amazon tree, Protium subserratum | Phylogenomics | Misiewicz, Tracy. | Amazon
speciation
Ecological divergence
soils
Tropical biodiversity |
| 553 | Evidence of admixture among hyperdominant rainforest tree species in the Parvifolia clade of Eschweilera | Phylogenomics | Larson, Drew; Vargas, Oscar; Dick, Christopher. | phylogenomics
Lecythidaceae
Ericales
admixture
Neotropics
hybridization
introgression
Tropical biodiversity
targeted sequencing |
| 388 | Evolutionary History of Caryophyllaceae Using DNA sequences | Phylogenomics | Rees, Riley J.; Schenk, John. | phylogeny
Caryophyllaceae
targeted sequencing
Floral Development |
| 212 | Evolution of Asparagus: multiple origins of dioecy and sex chromosomes | Phylogenomics | Bentz, Philip; Carey, Sarah; Harkess, Alex; Leebens-Mack, Jim. | comparative genomics
asparagus
asparagaceae
Monocots
Evolution
Dioecy
sex chromosomes
sex-determination |
| 950 | Evolution of nuclear ribosomal DNA in Asclepias (milkweeds): Patterns of intragenomic polymorphisms and copy number variation | Phylogenomics | Birkenholz, Jude; Fishbein, Mark; Straub, Shannon. | ribosomal DNA
convergent evolution
phylogenomics
gene family |
| 754 | Generation time differences amplify concatenation bias in phylogenetic inference | Phylogenomics | Au, Scarlet; McKenzie, Patrick; Eaton, Deren. | multispecies coalescent (MSC)
concatenation
generation times
phylogenetic inference |
| 294 | Goldenrod herbariomics: Hybrid-sequence capture reveals the phylogeny of Solidago (Asteraceae) | Phylogenomics | Beck, James; McMinn-Sauder, Harper; Stover, Melissa; Lemmon, Alan; Lemmon, Emily; Semple, John. | Anchored Hybrid Enrichment
Chrysoma
herbarium specimens
North America
Solidago
phylogenomics
Oligoneuron
polyploidy |
| 305 | High-molecular-weight DNA extraction for sequencing plant genomes – an optimization of standard methods | Phylogenomics | Kang, Myeongbo; Chanderbali, Andre; Lee, Seungyeon; Soltis, Pamela; Soltis, Douglas; Kim, Sangtae. | DNA extraction
genomic DNA
high molecular weight DNA
plant DNA |
| 79 | Hybridization in Octoploid Fragaria | Phylogenomics | Mortimer, Sebastian; Ashman, Tia-Lynn; Liston, Aaron. | WGS
Fragaria
hybridization |
| 498 | Identifying serpentine adaptation genes by tracing evolutionary-genomic history of Streptanthus, Caulanthus, and their allied genera (Brassicaceae) | Phylogenomics | Daundasekara, Kasuni; Garza, Elyssa; Pepper, Alan. | Brassicaceae
Serpentine
hybridization
phylogenomics
candidate genes |
| 279 | Incorporating Phased Alleles to Reconstruct a Recent and Rapid Radiation in Schiedea (Caryophyllaceae) | Phylogenomics | Loke, Elena; McDonnell, Angela; Moore, Michael; Sakai, Ann; Skogen, Krissa; Wagner, Warren; Weller, Stephen; Weisenberger, Lauren; Wickett, Norman. | Schiedea
Hawaiian Islands
HybSeq
Target Enrichment
Alleles
Incomplete Lineage Sorting
Carophyllaceae
Radiation |
| 432 | Integrating phylogenomic and cytological evidence for the allopolyploid origin of Drosera anglica (Droseraceae) | Phylogenomics | Mohn, Rebekah; Yang, Ya. | polyploid
transcriptome
WGD
carnivorous plant
Caryophyllales |
| 379 | New Plastome Structural Rearrangements Discovered in Core Tillandsioideae (Bromeliaceae) Support recently adopted taxonomy | Phylogenomics | Díaz Contreras Díaz, Daniel David; Vera Paz, Sandra Itzel; Jost, Matthias; Wanke, Stefan; Rossado, Andrés; Hernández Gutiérrez, Rebeca; Salazar, Gerardo; Magallón, Susana; Gouda, Eric; Ramírez Morillo, Ivón; Donadío, Sabina; Granados Mendoza, Carolina. | Phylogenetic informativeness
Inverted repeats (IR)
Gene translocation
Inversions
Ancestral state reconstruction
Evolutionary rate shifts |
| 284 | Nuclear gene-based phylogenomic study resolves Poaceae phylogeny and provides insight to the evolution of C4 photosynthesis | Phylogenomics | Huang, Weichen; Zhang, Lin; Columbus, J. Travis; Hu, Yi; Zhao, Yiyong; Tang, Lin; Guo, Zhenhua; Chen, Wenli; McKain, Michael; Bartlett, Madelaine; Huang, Chien-Hsun; Li, De-zhu; Ge, Song; Ma, Hong. | Poaceae
transcriptome
phylogeny
nuclear gene
photosynthesis |
| 737 | Patterns of Species Diversification in Geissorhiza (Iridaceae): Morphological and Habitat Traits Through Time | Phylogenomics | Eifler, Evan; Karimi, Nisa; Lemmon, Alan; Lemmon, Emily; Givnish, Thomas. | phylogenomics
Iridaceae
Diversification
molecular dating
Psammophory |
| 824 | Phylogenetic analysis of Perennial Endemic North American (PENA) Clade of Apiaceae | Phylogenomics | Odufuwa, Phebian; Smith, James (Jim); Mansfield, Don; Feist, Mary Ann; Darrach, Mark. | phylogenetics
species delimitation
Generic boundaries delineation
Angiosperms353
Geophyte
Lomatium
endemic flora |
| 811 | Phylogenomic analyses based on nuclear and plasmid data yield novel insights into the reticulate evolution of Asarum (Aristolochiaceae) | Phylogenomics | Zuo, Lei; Freudenstein, John. | Asarum
reticulate evolution |
| 473 | Phylogenomics and Evolution of Leaf Volatiles in the California Sages | Phylogenomics | Rose, Jeffrey; Heeg, Luciann; Kriebel, Ricardo; Codina, Audrey; Keefover-Ring, Ken; Sytsma, Kenneth; Drew, Bryan. | essential oil content
Lamiaceae
cytonuclear discordance
California Floristic Province
Salvia
Mediterranean climate |
| 773 | Phylogenomics of Spanish irises, Iris subgenus Xiphium | Phylogenomics | Wilson, Carol. | biodiversity hotspot
Constraint trees
Iris
Iridaceae
mediterranean basin
missing data
nuclear genes
phylogenomics
plastomes
Strait of Gibraltar
targeted enrichment |
| 510 | Phylogenomics of willow (Salix L.) species in Alaska | Phylogenomics | Webb, Campbell O; Burleigh, J Gordon; Ickert-Bond, Steffi. | Salix L.
willow
molecular phylogenetics
Classification
GoFlag 408 |
| 59 | Plastid phylogenomics of the Sansevieria Clade of Dracaena (Asparagaceae) resolves a recent radiation | Phylogenomics | Larridon, Isabel; van Kleinwee, Iris; Shah, Toral; Bauters, Kenneth; Asselman, Pieter; Goetghebeur, Paul; Leliaert, Frederik; Veltjen, Emily. | biogeography
convergent evolution
dated phylogeny
genome skimming
succulent plants |
| 229 | Rampant nuclear-mitochondrial-plastid phylogenomic discordance in globally distributed calcifying microalgae | Phylogenomics | Kao, Tzu-Tong; Wang, Tzu-Haw; Ku, Chuan. | coccolithophore
cytonuclear discordance
heteroplasmy
hybridization
inter-organellar discordance
organelle inheritance
marine phytoplankton
protist |
| 138 | Reconstructing evolutionary relationships in the genus Packera (Asteraceae: Senecioneae) | Phylogenomics | Moore, Erika; Mandel, Jennifer. | chloroplast
nuclear genes
paralogs
phylogenomics
polyploidy |
| 143 | Red gold or corn silk? Detecting economic adulteration in the world’s most expensive spice: saffron | Phylogenomics | Hunter, Elizabeth; Literman, Robert; Handy, Sara. | saffron
genome skimming
adulteration
economic adulteration
genomics |
| 77 | Reference-free and bait-guided phylogenetic inference and species identification in the ginseng genus Panax (Araliaceae) using genome skim data | Phylogenomics | Literman, Robert; Fairbanks, Regina; Liu, Jing; Liu, Bin-Bin; Nie, Zelong; Ren, Chen; Johnson, Gabriel; Wen, Jun; Zimmer, Elizabeth; Hunter, Elizabeth; Handy, Sara. | Panax
ginseng
baits
genome skimming
phylogeny
species identification |
| 866 | Resolving taxonomic uncertainty and clarifying species boundaries in the Cymopterus terebinthinus species complex | Phylogenomics | Taylor, Annie; Smith, James (Jim); Mansfield, Don; Feist, Mary Ann; Buerki, Sven; Darrach, Mark. | phylogenetics
species delimitation
Apiaceae
Angiosperms353
species complex
next generation sequencing |
| 198 | Resolving the reticulate evolutionary history of the New Zealand polyploid-rich genus Azorella (Apiaceae) | Phylogenomics | Ning, Weixuan; Meudt, Heidi; Nicolas, Antoine; Plunkett, Gregory; Lee, William; Tate, Jennifer. | Azorella
Apiaceae
hybridization
Hyb-Seq
whole-genome duplication
phylogenomics
Reticulation
genome skimming |
| 357 | Reticulate evolution as a potential driver of ecological niche adaptation in Quercus. | Phylogenomics | Landis, Henry; Roalson, Eric; Busch, Jeremiah. | quercus
phylogenomics
phylogenetics
Reticulation
adaptation
niche evolution
Evolution |
| 405 | The Australian Angiosperm Tree of Life project | Phylogenomics | Allnutt, Theodore; Barrett, Matthew; Brown, Gillian; Crayn, Darren; Jackson, Chris; Lum, Mabel; McLay, Todd; Murphy, Daniel; Nargar, Katharina; Sauquet, Hervé; Schmidt-Lebuhn, Alexander; Shepherd, Kelly; Simpson, Lalita; Van Dijk, Korjent; Waycott, Michelle. | Australia
target-capture
phylogenomics
Angiosperms |
| 496 | The true blueberries (Vaccinium sect. Cyanococcus) - A first complete phylogenomic hypothesis of diploid taxa and preliminary investigation into polyploids | Phylogenomics | Crowl, Andrew; Fritsch, Peter; Ashrafi, Hamid; Manos, Paul. | Alleles
ericaceae
HybSeq
phylogenomics
polyploidy
Target Enrichment
Vaccinium
hybridization |
| 50 | Trait diversity – a novel phylodiversity measure to investigate eco-evolutionary mechanisms of community assembly | Phylogenomics | Borokini, Israel; Allen, Julie; Smith, Stephen; Guralnick, Robert; Soltis, Pamela; Soltis, Douglas; Laffan, Shawn; Mishler, Brent. | trait diversity |
| 55 | Untying Gordian knots: Unraveling reticulate polyploid plant evolution by RRS genomic data using a large non-model species complex | Phylogenomics | Karbstein, Kevin; Tomasello, Salvatore; Hodac, Ladislav; Wagner, Natascha; Marincek, Pia; Barke, Birthe Hilkka; Pätzold, Claudia; Hörandl, Elvira. | allopolyploidy
apomixis
genome composition
Hyb-Seq
nuclear genes
plastome data
RAD-Seq
Ranunculus auricomus |
| 37 | Whom to trust wehn a microsynteny- and gene-content-based topology differs drastically from sequenced-based trees: Juglandaceae as a test case | Phylogenomics | Renner, Susanne S.; Bai, Wei-Ning; Zhang, Da-Yong. | allopolyploidy
DNA repair
gene-content-based tree
whole-genome duplication
introgression |
| 36 | Whom to trust when a microsynteny-based topology differs drastically from sequence-based phylogenies: the Juglandaceae as a test case | Phylogenomics | Renner, Susanne S.; Bai, Wei-Ning; Zhang, Da-Yong. | Microsynteny
Gene content
allopolyploidy
gene-content-based tree
whole-genome duplication
introgression |
