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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 AsteraceaePhylogenomicsMandel, 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 CucurbitaceaePhylogenomicsOrtiz, 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 genesPhylogenomicsCrisp, Michael; Kulheim, Carsten; Toon, Alicia; Edwards, Robert; Lin, Yen-Po; Meuesemann, Karen; Bui, Minh; Cook, Lyn.illumina
genome
paralogy
Myrtaceae
Eucalyptus
classification
393A phylogenomic approach to decode contentious relationships across all angiosperm familiesPhylogenomicsPokorny, 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 TropicsPhylogenomicsConejo, 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)PhylogenomicsCharboneau, Joseph; Cronn, Richard; Liston, A.; Wojciechowski, Martin; Sanderson, Michael.chloroplast genome
887Combining Genome Skims and Transcriptomes for a Phylogenomic framework of AcanthaceaePhylogenomicsArias, Joshua; McDade, Lucinda; Kiel, Carrie; Tripp, Erin; Fisher, Amanda.Lamiales
phylogenomics
225Deep phylogenetic incongruence in Neotropical rain forest trees (Oxandra, Annonaceae)PhylogenomicsChatrou, Lars.Genome skimming
chloroplast genome
Mitochondrial genome
nuclear ribosomal DNA
Annonaceae
Deep incongruence
923Developing Phylyogenetic Hypotheses for Leucaena through Reference Guided and de novo Transcriptomics PhylogenomicsAbair, Alexander; Dugas, Diana; Madhugiri, Nageswara-Rao; Hughes, Colin; Bailey, C. Donovan.Leucaena
Leguminosae
Polyploid
phylogeny
genomics
Transcriptomics
hybridization
orthology
paralogy
595Developing a new bioinformatics pipeline to capture low-copy nuclear loci for two distant clades of MelastomataceaePhylogenomicsAmarasinghe, Prabha; Jantzen, Johanna; Folk, Ryan; Soltis, Douglas; Soltis, Pamela; Cellinese, Nico.Memecylon
Tibouchina
Melastomataceae
phylogenomics
target enrichment
MarkerMiner
HybPiper
510Disentangling the evolutionary relationships of Aizoaceae using transcriptome dataPhylogenomicsZhao, 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, StanhopeaPhylogenomicsJordan, Chazz; Brinkman, Becky; Coffey (PhD), Emily ; Eserman (PhD), Lauren.0rchid
753Genome sequencing based phylogenetic analyses of Streptanthus, Caulanthus, and related genera (Brassicacae) 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)PhylogenomicsGarcia, Nicolas; Folk, Ryan.speciation
target enrichment
monocots
Chile
954Herbariomics of the Barbardos cherries: 1200 plastid genomes elucidate the tempo and mode of Malpighiaceae diversificationPhylogenomicsDavis, Charles; Cai, Liming; Lyra, Goia; Marinho, Lucas; Peterson, Kylee; Anderson, Christiane; Amorim, André; Yin, Xiaofeng; Yan, Yujing; Zhang, Wenheng.systematics
Tropical Biology
phylogenomics
Malpighiales
rosids
398Initial analyses of Magnolia genome dataPhylogenomicsWeinheimer, Ellen; Pease, James.phylogenomics
genome
magnolia
976Iris of the Mediterranean: using phylogenomics to investigate putative color forms, phenological variants, and hybrids in subgenus XiphiumPhylogenomicsWilson, 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/anomalumPhylogenomicsOttenlips, 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 DiapensiaceaePhylogenomicsGaynor, Michelle; Soltis, Douglas; Soltis, Pamela.phylogenomics
biogeography
ecological niche modelling
Diapensiaceae
246Phylogenomic analysis of Cycas section Indosinenses using RADseqPhylogenomicsLiu, 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 diversificationsPhylogenomicsNie, 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 phylogeniesPhylogenomicsOrtiz, 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 patternPhylogenomicsZhou, Wenbin; Xiang, Jenny.phylogenomics
EA-NAM disjunction
morphostasis
biogeographic history
morphological evolution
niche evolution
900Phylogenomics of the Neotropical spiral gingers (Costaceae) 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)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 DiversificationPhylogenomicsXiang, 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)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 strawberryPhylogenomicsListon, 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 enrichmentPhylogenomicsThomas, 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 ZinniinaePhylogenomicsSkibicki, Sam.Phylogenetics
Sanvitalia
Zinniinae
Heliantheae
Asteraceae
biogeography
391Target sequence capture in orchids: Developing a kit to sequence hundreds of single copy loci across all orchidsPhylogenomicsEserman, Lauren; Thomas, Shawn; Coffey, Emily; Leebens-Mack, Jim.phylogenomics
target enrichment
Next Generation Sequencing
430The Evolutionary Relationships in Pertyeae (Asteraceae) inferred from Hyb-Seq DataPhylogenomicsGomez, 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)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. CalyPhylogenomicsCooper, 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   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.PhylogenomicsJantzen, Johanna; Oliveira, Ana Luiza Freitas; Soltis, Douglas; Soltis, Pamela.phylogenomics
target enrichment
Melastomataceae
Tibouchina
Cerrado
Campos rupestres

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