| ID | Title | Section/Topic | Authors | Keywords |
|---|
| 644 | Amount of hybridization differs with varying gene tree lengths in reference aligned RADseq data | Phylogenomics | Hoffberg, Sandra; Eaton, Deren. | Gene tree discordance
hybridization
simulated sequence data
RADSeq
network analysis
Phylogenetics |
| 749 | A new (old) approach to genotype-based phylogenomic inference within species, with an example from the saguaro cactus (Carnegiea gigantea) | Phylogenomics | Sanderson, Michael; Burquez, Alberto; Copetti, Dario; McMahon, Michelle; Zeng, Yichao; Wojciechowski, Martin. | |
| 551 | A new extant cyanobacterial lineage that diverged from Gloeobacterover 1.4 billion years | Phylogenomics | Rahmatpour, Nasim; Hauser, Duncan; Nelson, Jessica; Villarreal Aguilar, Juan Carlos; Ho, Ming-Yang; Li, Fay-Wei. | photosynthesis
Cyanobacteria |
| 324 | A new nuclear phylogeny unravels fast-moving radiations in the Theaceae | Phylogenomics | Yan, Yujing. | Target Enrichment
Hybpiper
Theeae
Camellia
Incomplete lineage sorting
NGS filtering strategies |
| 277 | A target capture approach for exploring the drivers and constraints of adaptive radiation in tillandsioid bromeliads (Tillandsia spp) | Phylogenomics | Yardeni, Gil; Hess, Jaqueline; de La Harpe, Marylaure; Barfuss, Michael H. J.; Viruel, Juan; Paris, Margot; Groot Crego, Clara; Till, Walter; Leroy, Thibault; Paun, Ovidiu; Lexer, Christian. | Bromeliaceae
Targeted sequencing
Tillandsia
population genomics
phylogenomics
adaptive radiation |
| 500 | Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis | Phylogenomics | Gaynor, Michelle; Fu, Chaonan; Gao, Lianming; Lu, Li-Min; Soltis, Douglas; Soltis, Pamela. | Diapensiaceae
Angiosperm353
climatic niche
ecological niche modelling |
| 727 | Chloroplast phylogenomics and character evolution of Eastern Asian Astragalus (Leguminosae) – tackling the phylogenetic structure of the largest genus of flowering plants in Asia | Phylogenomics | SU, CHUN; Duan, Lei; Chang, Zhaoyang; Wen, Jun. | Astragalus
Chloroplast Genome
East Asia
trichome |
| 143 | Consensus and discordance in next-generation phylogenetic analyses of Daucus | Phylogenomics | Spooner, David; Ruess, Holly; Ellison, Shelby; Senalik, Douglas; Simon, Philipp. | carrot
phylogenomics
resequencing
SNPs
phylogenetic discordance |
| 810 | Dispelling the Mirage of C4 Driven Drought Tolerance in Poaceae: A Phylogenomic Study | Phylogenomics | Nissenbaum, Matthew; Burke, Sean; Orton, Lauren; Holthuijzen, Wieteke; Duvall, M. | photosynthesis
C4 photosynthesis
Drought
drought tolerance
Ancestral character state reconstruction |
| 865 | Extract and annotate genes from raw RNA-seq reads: kakapo | Phylogenomics | Ramanauskas, Karolis; Igić, Boris; Igić, Boris; Igić, Boris; Igić, Boris. | SRA
RNA-seq
self-incompatibility
gene family evolution
evolution |
| 347 | Genome sequence for the purple-flowered Andean shrub Iochroma cyaneum (Solanaceae) | Phylogenomics | Strickler, Susan; Gates, Daniel; Powell, Adrian; Hauser, Duncan; Vilela, Julianne; Hu, Alice; Li, Fay-Wei; Mueller, Lukas; Smith, Stacey. | Iochroma
genome assembly
phylogenomics |
| 405 | Genotyping-by-sequencing reveals the impact of climatic niche on the successful colonization of Madeira by ivies (Hedera L., Araliaceae) | Phylogenomics | Alonso, Alejandro; Coca, Marina; Monjas, David; Gallego-Narbón, Angélica ; Fernández-Mazuecos, Mario; Valcarcel, Virginia. | Hedera
GBS
Macaronesia
climatic niche |
| 283 | How well does an angiosperm-wide vs. a family-specific targeted sequencing probe kit unravel relationships in the pantropical Ochnaceae | Phylogenomics | Shah, Toral; Schneider, Julio; Zizka, Georg; Maurin, Olivier; Baker, William J.; Forest, Félix; Brewer, Grace E.; Savolainen, Vincent; Darbyshire, Iain; Larridon, Isabel. | Ochnaceae
missing data
probe kit
Targeted sequencing
phylogenetic informativeness
Coalescence |
| 642 | Improved and automated marker recovery from targeted capture data | Phylogenomics | Ortiz, Edgardo M.; Schaefer, Hanno. | target capture
enrichment
Angiosperms353
assembly
alignment |
| 692 | Molecular assessment of the Azorella multifida complex and its diversification within humid upper Andean habitats | Phylogenomics | Nicolas, Antoine; Alfaro, Bryan; Babio, Lucas; Ferraro, Justin; Franklin, Sean; Nair, Harikrishnan; Plunkett, Gregory. | Azorella
Páramos
Jalca
Andes
Species Complex |
| 367 | Molecular identification and phylogenomic resolution of Aloe vera and relatives using customised nuclear target enrichment | Phylogenomics | Woudstra, Yannick; Viruel, Juan; Howard, Caroline; Rønsted, Nina; Grace, Olwen. | target capture
Targeted sequencing
next-generation sequencing
ASTRAL
Aloe ferox
Aloe arborescens
herbarium specimens
Aloiampelos
Xanthorrhoeaceae
phylogeny
phylogenomics
Systematics
DNA barcoding
Aloe barbadensis |
| 386 | Museomics unveil the phylogeny and biogeography of the neglected Juan Fernandez archipelago Megalachne and Podophorus endemic grasses and their connection with relict Pampean-Ventanian fescues | Phylogenomics | Moreno Aguilar, Maria Fernanda; Arnelas Seco, Itziar; Sanchez Rodriguez, Aminael; Viruel, Juan; Catalan, Pilar. | ancestral range reconstruction
endemic Loliinae gasses
Fernandezian clade
genome skimming
phylogenomics
taxonomically neglected species |
| 873 | Novel Phylogenomics in Geissorhiza (Iridaceae): Preliminary results from the Cape Floristic Region | Phylogenomics | Eifler, Evan; Lemmon, Alan; Lemmon, Emily; Givnish, Thomas. | phylogenomics
Biogeography
Systematics
character evolution |
| 640 | Nuclear phylogenomic analysis resolves the backbone of Prunus and identifies lineages impacted by frequent reticulate evolution | Phylogenomics | Hodel, Richard; Zimmer, Elizabeth; Wen, Jun. | allopolyploidy
hybridization
reticulate evolution
gene tree discord
transcriptome
plastome |
| 174 | Phylogenomic analysis of New Zealand polyploid Azorella (Apiaceae) | Phylogenomics | Ning, Weixuan; Meudt, Heidi; Nicolas, Antoine; Plunkett, Gregory; Tate, Jennifer. | phylogenomics
Target Enrichment
polyploidy
Azorella
phylogeny
genome size |
| 216 | Phylogenomic data reveals hard polytomies in the large genus Solanum (Solanaceae) | Phylogenomics | Gagnon, Edeline; Hilgenhof, Rebecca; Orejuela, Andrés; Sablok, Gaurav; Aubriot, Xavier; Giacomin, Leandro; Gouvêa, Yuri; Bohs, Lynn; Dodsworth, Steven; Maurin, Olivier; Forest, Félix; Poczai, Péter; Knapp, Sandra; Särkinen, Tiina. | Solanaceae
PAFTOL
Solanales |
| 661 | Phylogenomics, floral evolution, and formation of an ornamented ring species-complex in the Bay Area Clade of Calochortus (Liliaceae) | Phylogenomics | Givnish, Thomas; Lemmon, Alan; Lemmon, Emily; Specht, Chelsea; Eifler, Evan; Karimi, Nisa. | historical biogeography
phylogenomics
California Floristic Province
convergence |
| 807 | Phylogenomics, reticulate evolution, historical biogeography, shifts in climatic niche, and parallel adaptive radiations in floral syndrome in the genus Calochortus (Liliaceae) | Phylogenomics | Karimi, Nisa; Lemmon, Alan; Lemmon, Emily; Hernandez, Adriana; Eifler, Evan; Strickler, Susan; Specht, Chelsea; Givnish, Thomas. | |
| 745 | Phylogenomics of Aralia sect. Aralia (Araliaceae): insights into its species delimitations and diversification in eastern Asia | Phylogenomics | Liu, Jing; Ren, Chen; Wen, Jun. | Araliaceae
Aralia
Biogeography
phylogenomics
eastern Asian - North American disjunction |
| 890 | Phylogenomics of Hamamelis and Castanea with 353 Angiosperm genes and RAD-seq data – A proposed approach for cleaning the paralogs | Phylogenomics | Zhou, Wenbin; Zhou, Wenbin; Soghigian, John; Xiang, Jenny. | Target Enrichment
Angiosperm 353
Paralogs
heterozygousity |
| 889 | Phylogenomics of the Blue- and White-Fruited Dogwoods of Cornus L. - Insights into the Evolution of Eastern Asian-Eastern North American Disjunct Clades | Phylogenomics | Lindelof, Kira; Zhou, Wenbin; Zhou, Wenbin; Xiang, Jenny. | Cornus
eastern Asian-eastern North American disjunction
RAD-seq
Biogeography
ecological niche and morphospace |
| 831 | Phylogenomics of the genus Hosta: Disentangling the impact of an ancient polyploid event on phylogeny resolution | Phylogenomics | Lewis, Michelle; Blakely, Sarah; McKain, Michael. | chloroplast
target capture
Angiosperm353
Hosta
Agavoideae
polyploidy |
| 793 | Phylogeny and multiple independent whole-genome duplication events in the Brassicales | Phylogenomics | Mabry, Makenzie; Pires, Joseph. | phylogenomics
Brassicales
polyploidy
Genomes
Whole-genome duplication
Brassicaceae
Cleomaceae |
| 221 | Phylotranscriptomics of the Petunieae clade of Solanaceae | Phylogenomics | Wheeler, Lucas C.; Walker, Joseph F. ; Ng, Julienne; Deanna, Rocío; Dunbar-Wallis, Amy; Backes, Alice; Pezzi, Pedro H.; Brandão de Freitas, Loreta; Barboza, Gloria E.; Moyroud, Edwige; Smith, Stacey. | transcriptomics
Phylogenetics
Solanaceae
Petunieae |
| 605 | Reconstructing the rapid radiation of pleurocarpous mosses using 802 nuclear genes | Phylogenomics | Angulo, Juan; Wickett, Norman; Pokorny, Lisa; Johnson, Matt; Medina, Rafael; Goffinet, Bernard; Shaw, Jonathan; Liu, Yang. | moss
Hypnanae
phylogenomics |
| 228 | Sex determination, speciation, and reproductive incompatibility in Amaranthus | Phylogenomics | Dzurlic, Jasmina. | phylogenomics |
| 410 | Untangling big genera using big data: Phylogenomics of Piper and Peperomia (Piperacae) | Phylogenomics | Simmonds, Sara; Smith, James; Davidson, Christopher; Buerki, Sven. | chloroplast
genome skimming
nuclear ribosomal DNA
phylogenomics
comparative genomics
Pipera |
| 795 | Using ipcoal to simulate and visualize genealogies and sequences on species trees or networks | Phylogenomics | McKenzie, Patrick; Eaton, Deren. | methods
Multispecies Coalescent
simulation
phylogeny |
