| ID | Title | Section/Topic | Authors | Keywords |
|---|
| 186 | Adding to the Pantry of the FDA Reference Standard Library, GenometrakrCP
Log in to add this item to your schedule | Phylogenomics | Hunter, Elizabeth Sage; Literman, Robert; Zhang, Ning; Ott, Brittany; Wen, Jun; Greenbaum, Alexandra; Hsu, Erica; Handy, Sara. | database
botanicals
genomics
chloroplasts
plant identifcation
DNA |
| 316 | A genomic perspective to the biogeography of the Caribbean spurge Euphorbia tithymaloides
Log in to add this item to your schedule | Phylogenomics | Medina-Rodriguez, Max D.; Maya Lastra, Carlos Alonso; Cacho, N. Ivalu. | ring species
Euphorbia
RADseq
phylogenetic analysis
population genetic structure |
| 812 | Analysis of Global Vaccinium Species during an Undergraduate Course in Phylogenetics
Log in to add this item to your schedule | Phylogenomics | Yocca, Alan. | phylogenetics
Undergraduate research
Ancestral State reconstruction |
| 756 | A new approach using targeted sequence capture for phylogenomic studies across Cactaceae
Log in to add this item to your schedule | Phylogenomics | Acha, Serena; Acha, Serena; Majure, Lucas. | Cacti
Opuntia
Hyb-Seq
Neotropics
Target enrichment |
| 877 | A new tool for measuring phylogenetic distance metrics for investigating genealogical variation
Log in to add this item to your schedule | Phylogenomics | Au, Scarlet; McKenzie, Patrick; Eaton, Deren. | phylogenomics
distance metrics
Python
toytree |
| 559 | A phylogenomics approach to resolving one of the world’s most diverse, tropical angiosperm radiations: Melastomataceae
Log in to add this item to your schedule | Phylogenomics | Bacci, Lucas; Cellinese, Nico; Michelangeli, Fabian; Judd, Walter; Reginato, Marcelo; Majure, Lucas. | Comparative Phylogenetics
Neotropics
Paleotropics
radiation |
| 390 | A population perspective on plastome degradation in the mycoheterotrophic Corallorhiza maculata species complex
Log in to add this item to your schedule | Phylogenomics | Thixton, Hana; Santee, Mathilda Viola; Freudenstein, John; Barrett, Craig. | Orchidaceae
parasite
mycoheterotrophy
floral morphology
pseudogene |
| 415 | Chloroplast genomes of two species of Epidendrum (Orchidaceae, Laeliinae): developing resources for evolutionary studies in a mega-diverse genus
Log in to add this item to your schedule | Phylogenomics | Meza-Lazaro, Rubi N.; Cabrera, Lidia I.; Granados Mendoza, Carolina; Hágsater, Eric; Magallon, Susana; Salazar, Gerardo. | coding DNA
Epidendrum
gene loss
Neotropics
non-coding DNA
Orchidaceae
phylogenomics
Plastome |
| 520 | Conflicting phylogenomic signals reveal ongoing hybridization and introgression in limestone Begonia diversification (sect. Coelocentrum, Begoniaceae)
Log in to add this item to your schedule | Phylogenomics | Tseng, Yu-Hsin; Kidner, Catherine; Hsieh, Chia-Lun; Xu, Wei-Bin; Peng, Ching-I; Yan, Liu; Chung, Kuo-Fang. | Begonia
Hyb-Seq
Plastome
Limestone
hybridization
Introgression
radiation
phylogenomics |
| 592 | Custom-made or universal? The use of target capture to bridge macro- and microevolutionary processes in tillandsioid bromeliads (Tillandsia spp), a Neotropical rapid radiation
Log in to add this item to your schedule | Phylogenomics | Yardeni, Gil; de la Harpe, Marylaure; Barfuss, Michael; Till, Walter; Crego, Clara Groot; Rivera, Norma; Viruel, Juan; Paris, Margot; Hess, Jaqueline; Kroemer, Thorsten; Lexer, Christian; Paun, Ovidiu; LeRoy, Thibault. | Bromeliaceae
Angiosperms353
targeted sequencing
target capture
evolutionary radiation
Tillandsia
population genetic structure
phylogenomics |
| 625 | Damage in Antique DNA from Herbarium Specimens: Harmful Rust or Healthy Patina?
Log in to add this item to your schedule | Phylogenomics | Johnson, Matthew; Audi, Lauren; Zerega, Nyree; Gardner, Elliot M.. | target capture
Herbariomics
Artocarpus
bioinformatics |
| 970 | Designing Rubiaceae-specific probes for targeted sequence capture in-silico
Log in to add this item to your schedule | Phylogenomics | Ball, Laymon; Lagomarsino, Laura. | target capture
Rubiaceae
Probe design |
| 484 | Determining the timing of colonization of Pueraria montana using 3RAD data and the new tool, superBPP
Log in to add this item to your schedule | Phylogenomics | Hoffberg, Sandra; Mauricio, Rodney; Eaton, Deren. | colonization
dated phylogeny
BPP
RADseq
clonal reproduction
invasive plants |
| 411 | Diversification in the Perennial Endemic North American Clade of Apiaceae – How far are we from completion?
Log in to add this item to your schedule | Phylogenomics | Odufuwa, Phebian; Smith, James; Mansfield, Donald; Feist, Mary Ann; Darrach, Mark; Downie, Stephen; Plunkett, Gregory. | Apiaceae
PENA
convergent evolution
NGS
phylogenetic framework
species delimitation
generic circumscription |
| 825 | Diversification of Kohleria (Gesneriaceae)
Log in to add this item to your schedule | Phylogenomics | Hansen, Kimberly; Clavijo, Laura; Zuluaga, Alejandro; Roalson, Eric. | Gesneriaceae
Kohleria
Andes Mountains
high throughput sequencing |
| 1040 | Evaluating taxonomic circumscription in the Dudleya cymosa (Crassulaceae) species complex using high-throughput sequencing with an emphasis on rare and potentially undescribed subspecies in Southern California
Log in to add this item to your schedule | Phylogenomics | Hasenstab-Lehman, Kristen; Guilliams, C. Matt; Elvin, Mark; McCabe, Stephen; Yost, Jenn. | conservation
Dudleya
phylogenomics
ddRAD-seq
Crassulaceae |
| 547 | Evolution of Cardamine (Brassicaceae) perennials in Southwestern Asia and their phylogenetic relationships to related European polyploid species complexes
Log in to add this item to your schedule | Phylogenomics | Kantor, Adam; Kučera, Jaromír; Šlenker, Marek; Perný, Marián; Breidy, Joêlle; Marhold, Karol; Slovák, Marek; Zozomová-Lihová, Judita. | endemism
Cardamine
Southwestern Asia
Hyb-Seq
Morphometrics |
| 1102 | Evolution of gene families in Solanales
Log in to add this item to your schedule | Phylogenomics | Ganju, Anish; Rosales, Maribel; Gupta, Ishaan; Gowda, Vinita. | polyploidy
Solanaceae
Convolvulaceae
gene families
Reconciliation
phylogenetic trees |
| 250 | Finding the limits of Piper amalago L., a widespread Neotropical shrub
Log in to add this item to your schedule | Phylogenomics | Hastings, Cara; Bornstein, Allan; Davidson, Chris; Smith, James. | phylogenomics
Neotropical speciation
species complex
species delimitation
Angiosperms353 |
| 493 | Genome-enabled systematics in the tribe Brassiceae
Log in to add this item to your schedule | Phylogenomics | Thomas, Shawn; Pires, Chris. | phylogenomics
genome evolution
Brassicaceae
divergence time estimation |
| 658 | Hogtie: A Reference-Free Tool for Identifying Introgression in Plant Genomes
Log in to add this item to your schedule | Phylogenomics | Cohen, Rachel; Eaton, Deren. | modeling
phylogenetics
K-mer
HGT
Introgression
transcriptomics |
| 276 | Hyb-Seq resolves relationships among Cirsium, a recently radiated group of Compositae in North America
Log in to add this item to your schedule | Phylogenomics | Ackerfield, Jennifer; Siniscalchi, Carol; Mandel, Jennifer. | Compositae
Cirsium
Hyb-Seq
phylogenomics |
| 1097 | Hybrid speciation in Senecio (Asteraceae, Senecioneae) from the Andes: insights from phylogenomics
Log in to add this item to your schedule | Phylogenomics | Salomon, Luciana; Kandziora, Martha; Gorospe, Juan Manuel; Gorospe, Juan Manuel; Fer, Tomas; Kolar, Filip; Sklenar, Petr; Schmickl, Roswitha. | Andes
evolutionary radiation
hybridization
paralogy
Senecio |
| 346 | Implausibly strong gene tree discordance in a radiating plant group that seems to lack hybrids and neopolyploids? A case study of high-Andean Loricaria (Asteraceae)
Log in to add this item to your schedule | Phylogenomics | Kandziora, Martha; Gorospe, Juan Manuel; Gorospe, Juan Manuel; Sklenar, Petr; Fer, Tomas; Kolar, Filip; Schmickl, Roswitha. | |
| 578 | In-silico identification of low-copy nuclear loci for your plant group of interest, based on published target capture probe sets and genomes
Log in to add this item to your schedule | Phylogenomics | Scheunert, Agnes; Lautenschlager, Ulrich; Oberprieler, Christoph. | phylogenomics
target capture
in-silico loci selection
low-copy nuclear loci
CompCOS loci
shell script
Compositae
Leucanthemum |
| 265 | Inverted repeat region expansion and evolutionary dynamics of Annonaceae plastid genomes
Log in to add this item to your schedule | Phylogenomics | Jo, Sangjin; Kim, Young-Kee; Jansen, Robert; Kim, Ki-Joong. | Annonaceae
inversion
inverted repeat (IR)
nucleotide substitution rates
Plastome |
| 376 | Is lack of phylogenetic resolution the hallmark of alpine radiation? Insights from the afro-alpine giants inDendrosenecio (Senecioneae, Asteraceae)
Log in to add this item to your schedule | Phylogenomics | Gizaw, Abel; Gorospe, Juan Manuel; Gorospe, Juan Manuel; Kandziora, Martha; Chala, Desalegn; Gustafsson, Lovisa; Zinaw, Abush; Salomón, Luciana; Eilu, Gerald; Brochmann, Christian; Kolar, Filip; Schmickl, Roswitha. | afro-alpine
phylogenomics |
| 1025 | Is one gene enough to determine parental genome dosage in polyploid species?
Log in to add this item to your schedule | Phylogenomics | Myint, Sarah; Grusz, Amanda. | Genome skimming
Undergraduate research
Pteridaceae
allopolyploid
Myriopteris yavapensis |
| 1022 | Mahonia vs. Berberis unloaded: Generic delimitation and revised infrafamilial classification of Berberidaceae based on plastid phylogenomics
Log in to add this item to your schedule | Phylogenomics | Hsieh, Chia-Lun; Yu, Chih-Chieh; Huang, Yu-Lan; Chung, Kuo-Fang. | Alloberberis
Bongardieae tri. nov.
Jeffersonieae tri. nov
molecular dating
Moranothamnus
Plastome
tribal delimitation |
| 115 | Mitochondrial phylogenomics of mycoheterotrophic Ericaceae and parasitic Cuscuta
Log in to add this item to your schedule | Phylogenomics | Lin, Qianshi; Stefanovic, Sasa. | mitochondrial genome
mycoheterotrophic plants
parasitic plants
horizontal gene transfer
Ericaceae
Cuscuta
Convolvulaceae |
| 899 | Molecular phylogenetics of Vaccinium
Log in to add this item to your schedule | Phylogenomics | Barash, Andrew; Bukhari, Daaren; Karthikeyan, Akshitha; Mitchell, Allison; Niemiec, Ashlin; Radgens, Gabe; Schneider, Jared; Sharpe, Sydney; Srinivasan, Vidhula; Xenos, Christina; Yocca, Alan; McKain, Michael; Edger, Patrick. | Vaccinium
phylogenetics |
| 781 | New perspectives on the evolution of plant breeding systems in the radiation of Hawaiian Schiedea (Caryophyllaceae)
Log in to add this item to your schedule | Phylogenomics | McDonnell, Angela; Loke, Elena; Moore, Michael; Sakai, Ann; Weller, Stephen; Wagner, Warren; Skogen, Krissa; Weisenberger, Lauren; Wickett, Norman. | Genome Assembly
Genome Duplication
transcriptomics
Targeted enrichment
Probe design
Hawaiian Islands
Breeding system |
| 273 | Next-generation phylogenomics of the genus Erica (Ericaceae) in the Cape Floristic Region, South Africa
Log in to add this item to your schedule | Phylogenomics | Musker, Seth. | phylogenomics
target capture
Targeted Sequencing of 353 Genes
Genotyping-by-Sequencing
Cape Floristic Region
Ericaceae
diversification
Speciation |
| 958 | Patterns of Species Diversification in Geissorhiza (Iridaceae): Phylogeny, Biogeography, and Vulnerability in the Cape Floristic Region
Log in to add this item to your schedule | Phylogenomics | Eifler, Evan; Karimi, Nisa; Lemmon, Alan R.; Lemmon, Emily M.; Givnish, Thomas. | phylogenomics
Iridaceae
Cape Floristic Region
diversification
Speciation
biogeography
Trait evolution
Mimicry |
| 1032 | Phasing Polyploid Alleles from Target Enrichment Data
Log in to add this item to your schedule | Phylogenomics | Crowl, Andrew; Tiley, George; Manos, Paul; Sessa, Emily; Solis-Lemus, Claudia; Yoder, Anne; Burleigh, Gordon. | Alleles
Hyb-Seq
Target enrichment
Phasing
Polyploids
bioinformatics
hybridization
Phylogenetic Networks |
| 1051 | Phylogenetic relationships of Mexican species of Cladocolea Tiegh. and Struthanthus Mart. (Loranthaceae)
Log in to add this item to your schedule | Phylogenomics | Galván-González, Luis Gil; Cerros-Tlatilpa, Rosa; Espejo-Serna, Adolfo; Steinmann, Victor; Ocampo, Gilberto; Miguel-Vázquez, Mónica I.. | Loranthaceae
Psittacanthinae
mistletoe
hemiparasite
ParasiticPlant |
| 702 | Phylogenetic relationships of the strawberry subtribe Fragariinae (Rosaceae, Potentilleae) inferred from whole genome sequences
Log in to add this item to your schedule | Phylogenomics | Allen, Geraldine; Liston, Aaron; Eriksson, Torsten. | Fragariinae
Fragaria
phylogenomics
Rosaceae
hybridization
polyploidy
whole genome sequencing |
| 990 | Phylogenetic relationships within the Jarava-Pappostipa clade (Pooideae; Stipeae) with emphasis on the population genomics of Jarava neaei
Log in to add this item to your schedule | Phylogenomics | Morello, Santiago; Sassone, Agostina; Sede, Silvana; Giussani, Liliana; Starr, Julian. | ddRADseq
Patagonia
species delimitation
phylogenomics
Stipeae |
| 544 | Phylogenetics and evolution of the model grass genus Brachypodium based on different sources of genomic and cytogenetic data
Log in to add this item to your schedule | Phylogenomics | Decena Rodriguez, Maria Angeles; Sancho, Rubén; Inda Aramendia, Luis Angel; Pérez-Collazos, Ernesto; Catalan, Pilar. | Brachypodium perennials
cytogenetics
genome skimming
phylogenomics
plastomes
polyploids
progenitor subgenomes
rDNA 35S and 5S loci |
| 545 | Phylogenetic signal, abundance and characterization of the repeteome of the temperate Loliinae grasses
Log in to add this item to your schedule | Phylogenomics | Moreno Aguilar, María Fernanda; Sanchez Rodriguez, Aminael; Arnelas Seco, Itziar; Catalan, Pilar. | repetitive DNA
Loliinae grasses
Genome skimming
Repeat explorer
phylogenomics
phylogenetic signal |
| 218 | Phylogenomic analysis of New Zealand polyploid Azorella (Apiaceae)
Log in to add this item to your schedule | Phylogenomics | Ning, Weixuan; Meudt, Heidi; Nicolas, Antoine; Plunkett, Gregory; Tate, Jennifer. | Azorella
Angiosperm353
phylogenomic
genomic size variation
polyploidy |
| 153 | Phylogenomic analysis of the centric diatom order Thalassiosirales based on genome and transcriptome data
Log in to add this item to your schedule | Phylogenomics | Roberts, Wade; Alverson, Andrew. | Diatoms
Genome skimming
Transcriptome
phylogenomics
Genome Assembly |
| 269 | Phylogenomic relationships in Nicotiana benthamiana: insights into the origin of the N. benthamiana lab variant
Log in to add this item to your schedule | Phylogenomics | Cauz-Santos, Luiz Augusto; Dodsworth, Steven; Jakob, Aljaž; Samuel, Rosabelle; Paun, Ovidiu; Chase, Mark. | Nicotiana benthamiana
model organism
phylogenomics
RADseq |
| 822 | Phylogenomics of a clade of temperate North American milkweeds based on extensive sampling of individuals within species
Log in to add this item to your schedule | Phylogenomics | Straub, Shannon; Wagner, Carl; Boutte, Julien; Fishbein, Mark. | Asclepias
Apocynaceae
Hyb-Seq
species tree
milkweed
phylogenomics
low-copy nuclear loci
Plastome
incomplete lineage sorting
Introgression |
| 699 | Phylogenomics of Fagaceae: evolutionary correlates of a pollination shift
Log in to add this item to your schedule | Phylogenomics | Gardner, Elliot M.; Arifiani, Deby; Pereira, Joan; Garner, Mira; Worcester, Lindsey; Hahn, Marlene; Manos, Paul; Cannon, Charles; Hipp, Andrew. | phylogenomics
Fagaceae
HybSeq
pollination
Systematics
oaks
supertrees
Quercus
Lithocarpus
Castanopsis |
| 515 | Phylogenomics with Hyb-Seq Unravels Korean Hosta Evolution
Log in to add this item to your schedule | Phylogenomics | Yoo, Mi-Jeong; Lee, Byoung-Yoon; Kim, Sangtae; Lim, Chae Eun. | phylogenomics
Korean Hosta
Hyb-Seq
Targeted enrichment
divergence time estimation |
| 919 | PickMe! A coalescent-based tool for taxa selection for phylogenomics
Log in to add this item to your schedule | Phylogenomics | Rusinko, Joseph; Yu, Cai; Allison, Doherty; Katherine, Thompson; Boutte, Julien; Fishbein, Mark; Straub, Shannon. | taxa selection
milkweed
species tree |
| 519 | Plastid genomes provide resolution and support for phylogenetic relationships in Zinniinae (Asteraceae; Heliantheae)
Log in to add this item to your schedule | Phylogenomics | Skibicki, Sam; Barrett, Craig. | phylogenomics
Asteraceae
Herbariomics
Plastid genomes
Zinniinae |
| 569 | Plastome phylogenetics within the South American garlics (tribe Leucocoryneae, Allioideae, Amaryllidaceae)
Log in to add this item to your schedule | Phylogenomics | Sassone, Agostina; Blattner, Frank. | Alliaceae
chloroplast
phylogenomics
whole genome shotgun (WGS) |
| 1114 | PURC2: an updated pipeline for processing amplicon sequence data from hybrids and polyploids
Log in to add this item to your schedule | Phylogenomics | Schafran, Peter; Li, Fay-Wei; Rothfels, Carl. | polyploid
Hybrids
PacBio
phylogenetics
bioinformatics |
| 651 | Rampant ongoing chloroplast capture revealed by Sarracenia plastome phylogeny
Log in to add this item to your schedule | Phylogenomics | Baldwin, Ethan. | chloroplast
Plastome
carnivorous plant
hybridization |
| 792 | Reconstructing a plastid phylogeny of the Dipsacales from off-target Angiosperms353 Hyb-Seq data
Log in to add this item to your schedule | Phylogenomics | Lerner, Ariel; Lee, Aaron; Gilman, Ian S.; Srivastav, Mansa; Donoghue, Michael; Clement, Wendy. | |
| 281 | Reconstructing evolutionary relationships in the genus Packera (Asteraceae: Senecioneae)
Log in to add this item to your schedule | Phylogenomics | Moore, Erika; Mandel, Jennifer. | phylogenomics
Systematics
Compositae
HybPiper
Phyluce |
| 637 | Repeat contribution to genome size ups and downs in the sunflower family
Log in to add this item to your schedule | Phylogenomics | Pascual-Díaz, Joan Pere; Vitales, Daniel; Kovarik, Ales; Garnatje, Teresa; Rodriguez, Roi; Garcia, Sonia. | Asteraceae
Repeatome
phylogenomics
transposable elements
chloroplast DNA
genome size |
| 440 | Resolving Relationships in Mentzelia Section Bartonia (Loasaceae) in the Face of Cytonuclear Discordance
Log in to add this item to your schedule | Phylogenomics | Moore, Abigail; Schenk, John. | plastid genome
cytonuclear discordance
Genome skimming
genomics
hybridization
incongruence
Loasaceae
Mentzelia
phylogenomics
species tree |
| 538 | Canceled Resolving the backbone relationships of Poplars and Willows using plastid genome phylogenetic analysis
Log in to add this item to your schedule | Phylogenomics | Gambhir, Diksha; Sanderson, Brian; Ma, Tao; Percy, Diana; Cronk, Quentin; Olson, Matt. | Salicaceae
phylogeny
gene flow
hybridization |
| 380 | Species delimitation in the Leucanthemum atratum-group (Compositae, Anthemideae) based on Genotyping-by-Sequencing data
Log in to add this item to your schedule | Phylogenomics | Dorfner, Marco; Ott, Tankred; Bergmann, Stephan; Vogt, Robert; Oberprieler, Christoph. | polyploidy
Taxonomy
Asteraceae
Europe
Alps
Apennine
GBS |
| 868 | SuperBPP: a new method for inferring large-scale time-calibrated species trees
Log in to add this item to your schedule | Phylogenomics | Maya Lastra, Carlos Alonso; Hoffberg, Sandra; Landis, Henry; Eaton, Deren; Landis, Michael. | multispecies coalescent model
Divergence time
species tree |
| 602 | Targeted enrichment of Angiosperms353 in the Dipsacales highlights nodes of conflict and clarity
Log in to add this item to your schedule | Phylogenomics | Lee, Aaron; Gilman, Ian S.; Srivastav, Mansa; Lerner, Ariel; Donoghue, Michael; Clement, Wendy. | Zabelia
Heptacodium
Angiosperms353
gene tree conflict
cytonuclear discordance |
| 818 | The phylogenetic distribution of sex-determining genomic regions in Amaranthus identified from a new reference-free GWAS approach
Log in to add this item to your schedule | Phylogenomics | Dzurlic, Jasmina; Eaton, Deren; Cohen, Rachel. | Dioecy
GWAS
k-mers
evolution of sex
Amaranthus |
| 266 | Two contrasting modes of plastome evolution from photosynthetic and mycoheterotrophic vanilloid orchids (Vanilloideae, Orchidaceae)
Log in to add this item to your schedule | Phylogenomics | Kim, Young-kee; Jo, Sangjin; Kwak, Myounghai; Kim, Ki-Joong. | Orchidaceae
Vanilloideae
phylogenomics
Plastome
gene loss
substitution rates |
| 185 | Utilizing botanical big data to look for tiny toxic components
Log in to add this item to your schedule | Phylogenomics | Hunter, Elizabeth Sage; Literman, Robert; Handy, Sara. | Digitalis
genomics
plant identification
DNA
bioinformatics
botanicals |
| 260 | Whence came these plants most foul? Phylogenomics and biogeography of Orchidantha (Lowiaceae)
Log in to add this item to your schedule | Phylogenomics | Niissalo, Matti A.; Gardner, Elliot M.; Khew, Gillian S.; Šída, Otakar; Leong-Škorničková, Jana. | biogeography
genomics
Herbaceous
HybSeq
Lowiaceae
Orchidantha
Zingiberales |
| 875 | Wide hybridization followed by aneuploidy explains the origin of the apple tribe
Log in to add this item to your schedule | Phylogenomics | Hodel, Richard; Zimmer, Elizabeth; Wen, Jun. | Cytonuclear discord
Ancient hybridization
Reticulate Evolution
Amygdaloideae
Rosaceae |
