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Phylogenomics

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IDTitleSection/TopicAuthorsKeywords
850A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae
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PhylogenomicsMandel, Jennifer; Dikow, Rebecca; Siniscalchi, Carolina; Thapa, Ramhari; Watson, Linda; Funk, Vicki.Compositae
systematics
Sunflower
943An integrated pipeline for ortholog discovery, bait design, and targeted capture data assembly and the development of a bait set for the Cucurbitaceae
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PhylogenomicsOrtiz, Edgardo M.; Vargas, Oscar M; Schaefer, Hanno.Cucumis
Cucurbitaceae
targeted capture
target enrichment
nuclear genes
orthologs
plastome
marker selection
bait design
bioinformatics
pipeline
282A phylogenetic analysis of the eucalypts using targeted genes
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PhylogenomicsCrisp, Michael; Kulheim, Carsten; Toon, Alicia; Edwards, Robert; Lin, Yen-Po; Meuesemann, Karen; Bui, Minh; Cook, Lyn.illumina
genome
paralogy
Myrtaceae
Eucalyptus
classification
perianth evolution
393A phylogenomic approach to decode contentious relationships across all angiosperm families
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PhylogenomicsPokorny, Lisa; Steven, Dodsworth; Johnson, Matthew; Maurin, Olivier; Epitawalage, Niroshini; Bellot, Sidonie; Botigué, Laura R.; Brewer, Grace; Chase, Mark; Cowan, Robyn; Eiserhardt, Wolf; de la Estrella, Manuel; Hidalgo, Oriane; Kersey, Paul; Kim, Jan; Larridon, Isabel; Murphy, Bruce; Pellicer, Jaume; de Vos, Jurriaan; Wickett, Norman; Leitch, Ilia; Forest, Felix; Baker, William.Angiosperms
phylogenomics
Hyb-Seq
target enrichment
Sequence Capture
Systematic Botany
Phylogenetic Conflict
188Biogeography of the whorled wattles (Acacia section Lycopodiifoliae) in the Australian Monsoon Tropics
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PhylogenomicsConejo, Nancy; Martine, Christopher; Jobson, Peter; Cantley, Jason; Cantley, Jason; J. McDonnell, Angela.biogeography
Barriers
phylogeny
Australian Monsoon Tropics
population genetics
1055Chloroplast phylogenomics in the New World clade of Astragalus L. (Fabaceae)
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PhylogenomicsCharboneau, Joseph; Cronn, Richard; Liston, A.; Wojciechowski, Martin; Sanderson, Michael.chloroplast genome
887Combining Genome Skims and Transcriptomes for a Phylogenomic framework of Acanthaceae
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PhylogenomicsArias, Joshua; McDade, Lucinda; Kiel, Carrie; Tripp, Erin; Fisher, Amanda.Lamiales
phylogenomics
225Deep phylogenetic incongruence in Neotropical rain forest trees (Oxandra, Annonaceae)
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PhylogenomicsChatrou, Lars.Genome skimming
chloroplast genome
Mitochondrial genome
nuclear ribosomal DNA
Annonaceae
Deep incongruence
595Developing a new bioinformatics pipeline to capture low-copy nuclear loci for two distant clades of Melastomataceae
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PhylogenomicsAmarasinghe, Prabha; Jantzen, Johanna; Folk, Ryan; Soltis, Douglas; Soltis, Pamela; Cellinese, Nico.Memecylon
Tibouchina
Melastomataceae
phylogenomics
target enrichment
MarkerMiner
HybPiper
923Developing Phylyogenetic Hypotheses for Leucaena through Reference Guided and de novo Transcriptomics
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PhylogenomicsAbair, Alexander; Dugas, Diana; Madhugiri, Nageswara-Rao; Hughes, Colin; Bailey, C. Donovan.Leucaena
Leguminosae
Polyploid
phylogeny
genomics
Transcriptomics
hybridization
orthology
paralogy
510Disentangling the evolutionary relationships of Aizoaceae using transcriptome data
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PhylogenomicsZhao, Lijun; Walker, Joseph; Yang, Ya; Wang, Ning; Marx, Hannah; Brockington, Samuel; Moore, Michael; Smith, Stephen.phylogenomics
Transcriptome
Aizoaceae
546Evolutionary Relationships in the Euglossine Bee Pollinated Orchid Genus, Stanhopea
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PhylogenomicsJordan, Chazz; Brinkman, Becky; Coffey (PhD), Emily; Eserman (PhD), Lauren.0rchid
753Genome sequencing based phylogenetic analyses of Streptanthus, Caulanthus, and related genera (Brassicacae)
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PhylogenomicsDaundasekara, Kasuni; Garza, Elyssa; Pepper, Alan.Brassicaceae
serpentine
low-coverage genome sequencing
phylogeny
356Genomic phylogeography and species delimitation in Phycella s.l. (Amaryllidaceae tribe Hippeastreae)
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PhylogenomicsGarcia, Nicolas; Folk, Ryan.speciation
target enrichment
monocots
Chile
398Initial analyses of Magnolia genome data
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PhylogenomicsWeinheimer, Ellen; Pease, James; Whitener, Makenzie.phylogenomics
genome
magnolia
976Iris of the Mediterranean: using phylogenomics to investigate putative color forms, phenological variants, and hybrids in subgenus Xiphium
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PhylogenomicsWilson, Carol; Boosalis, Zoe A.; Sandor, Michael; Crespo, Manuel B; Azorin, Mario M.Genome skimming
Iridaceae
targeted capture
512Lewis’s lost Lomatium found: Investigating species boundaries in the rare plant species subcomplex, Lomatium packardiae/anomalum
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PhylogenomicsOttenlips, Michael; Buerki, Sven; Mansfield, Don; Dodsworth, Steven; Forest, Felix; Smith, James.incomplete lineage sorting
Angiosperm 353
target-enrichment
571Phylogenetic patterns of ecological niche evolution in Diapensiaceae
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PhylogenomicsGaynor, Michelle; Soltis, Douglas; Soltis, Pamela.phylogenomics
biogeography
ecological niche modelling
Diapensiaceae
246Phylogenomic analysis of Cycas section Indosinenses using RADseq
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PhylogenomicsLiu, Jian; Nagalingum, Nathalie; Lujan, Manuel A; Lindstrom, Anders J..Cycas
Indochina
RADseq
phylogenomics
840Phylogenomic discordance in the New World grapes suggests widespread introgressions as a driver for species diversifications
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PhylogenomicsNie, Zelong; Ma, Zhiyao; Johnson, Gabriel; Ren, Chen; Ickert-Bond, Stefanie; Zimmer, Elizabeth; Wen, Jun.phylogenomics
grapes
Vitis
Vitaceae
introgressionj
discordance
932Phylogenomics of Adesmia (Fabaceae) and the discordance between nuclear and plastome phylogenies
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PhylogenomicsOrtiz, Edgardo M.; Vargas, Oscar M; Goncalves, Deise; Simpson, Beryl.low copy nuclear genes
plastome
nuclear ribosomal DNA
de novo
Genome skimming
discordance
Fabaceae
Dalbergieae
Adesmia
889Phylogenomics of Castenea, Hamamelis, and Torreya inferred from RAD-Seq data – Insights into origin and evolution of eastern Asia-North American disjunct biogeography pattern
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PhylogenomicsZhou, Wenbin; Xiang, Jenny.phylogenomics
EA-NAM disjunction
morphostasis
biogeographic history
morphological evolution
niche evolution
900Phylogenomics of the Neotropical spiral gingers (Costaceae)
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PhylogenomicsValderrama, Eugenio; Sass, Chodon; Guan, Clarice; André, Thiago; Maas, Paul J. M.; Maas-van de Kamer, Hiltje; Skinner, David L.; Specht, Chelsea.Costaceae
Costus
Chamaecostus
Neotropical
phylogenomics
taxonomy
786Phylogeny and Biogeography of the Cladrastis clade (Leguminosae: Papilonoideae)
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PhylogenomicsDuan, Lei; Wen, Jun; Harris, Aj; Chen, Hong-Feng.biome shift
Cladrastideae
Cladrastis
Leguminosae
Styphnolobium
the Cladrastis clade
523Plastid Genome-based Phylogeny of Cornales – Insights Into Biogeographic History and Diversification
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PhylogenomicsXiang, Jenny; Fu, Chaonan; Gao, Lianming.The complete cp genome phylogeny 
Cornales
biogeography
Micaroevolution
783Plastome structure and phylogenomics of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii (Orchidaceae)
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PhylogenomicsKlimpert, Nathaniel; Mayer, Juliana; Pinheiro, Fabio; Proscdocimi, Francisco; Sarzi, Diese; Furtado, Carolina; Graham, Sean.Mycoheterotrophy
gene loss
Genome Evolution
plastid
Orchidaceae
720Revisiting the origin of the octoploid strawberry
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PhylogenomicsListon, A.; Wei, Na; Tennessen, Jacob; Li, Junmin; Dong, Ming; Ashman, Tia-Lynn.Fragaria
polyploidy
Whole Genome Sequencing
796Species level phylogeny for the order Cornales based on molecular data from nuclear gene target enrichment
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PhylogenomicsThomas, Shawn; Liu, Xiang; Cummings, Amanda; Xiang, Jenny; Leebens-Mack, Jim.phylogenomics
target-enrichment
Sequence Capture
Next Generation Sequencing
124Systematics of Sanvitalia and Future Phylogenetics of Subtribe Zinniinae
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PhylogenomicsSkibicki, Sam.Phylogenetics
Sanvitalia
Zinniinae
Heliantheae
Asteraceae
biogeography
391Target sequence capture in orchids: Developing a kit to sequence hundreds of single copy loci across all orchids
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PhylogenomicsEserman, Lauren; Thomas, Shawn; Coffey, Emily; Leebens-Mack, Jim.phylogenomics
target enrichment
Next Generation Sequencing
430The Evolutionary Relationships in Pertyeae (Asteraceae) inferred from Hyb-Seq Data
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PhylogenomicsGomez, Jorge; Siniscalchi, Carolina; Mandel, Jennifer.Compositae
systematics
phylogenomics
400The Plant and Fungal Trees of Life (PAFTOL) project: a case study from the carrot family (Apiaceae)
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PhylogenomicsClarkson, James; Maurin, Olivier; Brewer, Grace; Epitawalage, Niroshini; Zuntini, Alexandre; Kim, Jan; Bailey, Paul; Smith, James; Plunkett, Gregory; Downie, Stephen; Forest, Felix; Baker, William.Tree of Life
PAFTOL
Angiosperms 353
Sequence Capture
Apiaceae
678The power of population sampling, splash-zone introns, and summary coalescent methods in targeted enrichment: untangling species relationships in Oenothera sect. Calylophus
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PhylogenomicsCooper, Benjamin; Moore, Michael; Wickett, Norman; Wagner, Warren; Johnson, Matthew; Overson, Rick; Skogen, Krissa.target enrichment
HybPiper
multispecies coalescent
Onagraceae
Oenothera
Calylophus
Pollinator Shifts
gypsum
1005Towards a reclassification of Dioscoreales using organellar phylogenomics and morphology
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PhylogenomicsSoto Gomez, Marybel; Lin, Qianshi; Lam, Vivienne; Merckx, Vincent; Rudall, Paula J; Graham, Sean.Afrothismia
APG update
molecular and morphological data
non-photosynthetic monocots
plastid and mitochondrial phylogenomics
569Using a phylogenomic approach to resolve the systematics and taxonomy of Tibouchina s.s.
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PhylogenomicsJantzen, Johanna; Oliveira, Ana Luiza Freitas; Soltis, Douglas; Soltis, Pamela.phylogenomics
target enrichment
Melastomataceae
Tibouchina
Cerrado
Campos rupestres

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