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Phylogenomics

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IDTitleSection/TopicAuthorsKeywords
507A bird’s eye view of the systematics of Convolvulaceae: novel insights from nuclear genomic dataPhylogenomicsSimões, 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
237A comprehensive phylogenomic tree of life sheds new light on angiosperm diversificationPhylogenomicsCarruthers, 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
204A First Plastome Phylogeny for Rumex L. (Polygonaceae), with Fossil-Aided Date CalibrationPhylogenomicsKoenemann, Daniel Mark; Kistler, Logan; Burke, Janelle.RAxML
BEAST
Fossil Calibration
Cenozoic
Plastomics
347A genome-wide approach for resolving phylogenetic relationships of subfamily Arbutoideae (Ericaceae)PhylogenomicsRamadoss, Niveditha; McElwee-Adame, Alexandra; Parker, V. T.; Gonzalez-Elizondo, Socorro; Litt, Amy; Flores-Renteria, Lluvia.Arbutoideae 
phylogenetics
Arbutus paraphyly
840A Hyb-Seq phylogeny of Boechera (Brassicaceae) and related generaPhylogenomicsHay, Nikolai; Bailey, C. Donovan; Mandakova, Terezie; Hendriks, Kasper; Pryer, Kathleen; Windham, Michael.Boechera
Hyb-Seq
phylogenetics
Brassicaceae
102Ancient allopolyploidy, early radiation and extensive hybridization have shaped the evolutionary history of the Asian Palmate Group (Araliaceae)PhylogenomicsGallego-Narbón, Angélica; Wen, Jun; Valcarcel, Virginia.Araliaceae
phylogenomics
hybridization
Radiation
ILS
810A nuclear phylogenomic overview of RosaceaePhylogenomicsStull, 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
85An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic dataPhylogenomicsXiang, 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
904A phylogenomic baseline to study the evolution of extreme floral curvature in Centropogon subgenus Centropogon (Campanulaceae)PhylogenomicsMansaray, Janet; Frost, Laura; Bedoya, Ana Maria; Lagomarsino, Laura.
302A phylogenomic study of Scutellaria (Lamiaceae) based on chloroplast genomes and 272 nuclear single-copy genesPhylogenomicsLee, Yoonkyung; Paton, Alan; Olmstead, Richard; Kim, Sangtae.Scutellaria
Lamiaceae
Chlroplast genome
Nuclear genome
phylogenomics
Hyb-Seq
1036A phylogeny of the evening primrose family (Onagraceae) with a focus on tribe Onagreae using a target enrichment approachPhylogenomicsOverson, 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
828A tale of two Hyb-Seq probe sets: Comparing the Compositae-1061 probe set with a new probe set targeting 2424 functional genesPhylogenomicsGomez, Jorge; Moore, Erika; Burke, John; Mandel, Jennifer.Asteraceae
Compositae
Hyb-Seq
phylogeny
candidate genes
probe sets
713Boreotropical refugia and extensive introgressions explain the revival of north temperate diversity in the New World grapesPhylogenomicsNie, 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
166Characterization of the entire USDA germplasm collection of AmaranthusPhylogenomicsHoffberg, Sandra; Eaton, Deren.RADseq
crop
collection
676Comparative Genomics and Phylogenetic Utility of the Mitochondrial Genome in ApialesPhylogenomicsNicolas, Antoine; Earl, Victoria; Hughes, Emily; Molina, Giselle; Scollan, Brianna; Zandel, Stephanie; Plunkett, Gregory.mitogenome
Apiales
Hydrocotyle
Shotgun Sequencing
303Complete chloroplast genomes of seven species of Elsholtzia (Lamiaceae): Comparative and phylogenetic analysesPhylogenomicsLee, Yoonkyung; Yun, Narae; Jeon, Yun-Chang; Choi, Sangho; Paik, Jin-Hyub.Elsholtzia
Lamiaceae
Endemic Species
Chloroplast genome
phylogeny
409Completing the angiosperm tree of life - over half-way therePhylogenomicsBaker, William; PAFTOL, Team.phylogenomics
Angiosperms353
Open Access
herbariomics
target-capture
Hyb-Seq
Angiosperms
tree of life
603Cyto-nuclear Discordance in AdeniaPhylogenomicsNetherland, Michael; Hearn, David.phylogenomics
Species tree
cytonuclear discordance
introgression
100Differential role of climatic niche in colonization and in-situ evolutionary processes of Macaronesian ivies (Hedera L., Araliaceae)PhylogenomicsGallego-Narbón, Angélica; Alonso Hernandez, Alejandro; Valcarcel, Virginia; Fernandez-Mazuecos Santa Teresa, Mario.Hedera
Macaronesia
Climatic niche
phylogenomics
GBS
914Dissecting pollinator-driven floral-trait evolution in Agave subg. ManfredaPhylogenomicsMacNeill, Bryan; McKain, Michael; Ruiz-Sanchez, Eduardo; Rodriguez Contreras, Aaron.
706Dissecting the role of reticulate evolution in the diversification of Prunus (Rosaceae)PhylogenomicsHodel, Richard; Zimmer, Elizabeth; Liu, Bin-Bin; Johnson, Gabriel; Potter, Daniel; Wen, Jun.allopolyploidy
hybridization
phylogenetic network
cytonuclear discord
Hyb-Seq
biogeography
703Effects of taxon sampling and shifts in mode of organellar inheritance on Gymnosperm phylogenyPhylogenomicsParadiso, Lydia.gymnosperm
organelle inheritance
taxon sampling
Pinaceae
671Environment and geography drive diversification within the Amazon tree, Protium subserratumPhylogenomicsMisiewicz, Tracy.Amazon
speciation
Ecological divergence
soils
Tropical biodiversity
553Evidence of admixture among hyperdominant rainforest tree species in the Parvifolia clade of EschweileraPhylogenomicsLarson, Drew; Vargas, Oscar; Dick, Christopher.phylogenomics
Lecythidaceae
Ericales
admixture
Neotropics
hybridization
introgression
Tropical biodiversity
targeted sequencing
388Evolutionary History of Caryophyllaceae Using DNA sequencesPhylogenomicsRees, Riley J.; Schenk, John.phylogeny
Caryophyllaceae
targeted sequencing
Floral Development
212Evolution of Asparagus: multiple origins of dioecy and sex chromosomesPhylogenomicsBentz, Philip; Carey, Sarah; Harkess, Alex; Leebens-Mack, Jim.comparative genomics
asparagus
asparagaceae
Monocots
Evolution
Dioecy
sex chromosomes
sex-determination
950Evolution of nuclear ribosomal DNA in Asclepias (milkweeds): Patterns of intragenomic polymorphisms and copy number variationPhylogenomicsBirkenholz, Jude; Fishbein, Mark; Straub, Shannon.ribosomal DNA
convergent evolution
phylogenomics
gene family
754Generation time differences amplify concatenation bias in phylogenetic inferencePhylogenomicsAu, Scarlet; McKenzie, Patrick; Eaton, Deren.multispecies coalescent (MSC)
concatenation
generation times
phylogenetic inference
294Goldenrod herbariomics: Hybrid-sequence capture reveals the phylogeny of Solidago (Asteraceae)PhylogenomicsBeck, James; McMinn-Sauder, Harper; Stover, Melissa; Lemmon, Alan; Lemmon, Emily; Semple, John.Anchored Hybrid Enrichment
Chrysoma
herbarium specimens
North America
Solidago
phylogenomics
Oligoneuron
polyploidy
305High-molecular-weight DNA extraction for sequencing plant genomes – an optimization of standard methodsPhylogenomicsKang, Myeongbo; Chanderbali, Andre; Lee, Seungyeon; Soltis, Pamela; Soltis, Douglas; Kim, Sangtae.DNA extraction
genomic DNA
high molecular weight DNA
plant DNA
79Hybridization in Octoploid FragariaPhylogenomicsMortimer, Sebastian; Ashman, Tia-Lynn; Liston, Aaron.WGS
Fragaria
hybridization
498Identifying serpentine adaptation genes by tracing evolutionary-genomic history of Streptanthus, Caulanthus, and their allied genera (Brassicaceae) PhylogenomicsDaundasekara, Kasuni; Garza, Elyssa; Pepper, Alan.Brassicaceae
Serpentine
hybridization
phylogenomics
candidate genes
279Incorporating Phased Alleles to Reconstruct a Recent and Rapid Radiation in Schiedea (Caryophyllaceae)PhylogenomicsLoke, 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
432Integrating phylogenomic and cytological evidence for the allopolyploid origin of Drosera anglica (Droseraceae)PhylogenomicsMohn, Rebekah; Yang, Ya.polyploid
transcriptome
WGD
carnivorous plant
Caryophyllales
379New Plastome Structural Rearrangements Discovered in Core Tillandsioideae (Bromeliaceae) Support recently adopted taxonomyPhylogenomicsDíaz 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
284Nuclear gene-based phylogenomic study resolves Poaceae phylogeny and provides insight to the evolution of C4 photosynthesisPhylogenomicsHuang, 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
737Patterns of Species Diversification in Geissorhiza (Iridaceae): Morphological and Habitat Traits Through TimePhylogenomicsEifler, Evan; Karimi, Nisa; Lemmon, Alan; Lemmon, Emily; Givnish, Thomas.phylogenomics
Iridaceae
Diversification
molecular dating
Psammophory
824Phylogenetic analysis of Perennial Endemic North American (PENA) Clade of ApiaceaePhylogenomicsOdufuwa, Phebian; Smith, James (Jim); Mansfield, Don; Feist, Mary Ann; Darrach, Mark.phylogenetics
species delimitation
Generic boundaries delineation
Angiosperms353
Geophyte
Lomatium
endemic flora
811Phylogenomic analyses based on nuclear and plasmid data yield novel insights into the reticulate evolution of Asarum (Aristolochiaceae)PhylogenomicsZuo, Lei; Freudenstein, John.Asarum
reticulate evolution
473Phylogenomics and Evolution of Leaf Volatiles in the California SagesPhylogenomicsRose, 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
773Phylogenomics of Spanish irises, Iris subgenus XiphiumPhylogenomicsWilson, Carol.biodiversity hotspot
Constraint trees
Iris
Iridaceae
mediterranean basin
missing data
nuclear genes
phylogenomics
plastomes
Strait of Gibraltar
targeted enrichment
510Phylogenomics of willow (Salix L.) species in AlaskaPhylogenomicsWebb, Campbell O; Burleigh, J Gordon; Ickert-Bond, Steffi.Salix L.
willow
molecular phylogenetics
Classification 
GoFlag 408
59Plastid phylogenomics of the Sansevieria Clade of Dracaena (Asparagaceae) resolves a recent radiationPhylogenomicsLarridon, 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
229Rampant nuclear-mitochondrial-plastid phylogenomic discordance in globally distributed calcifying microalgaePhylogenomicsKao, Tzu-Tong; Wang, Tzu-Haw; Ku, Chuan.coccolithophore
cytonuclear discordance
heteroplasmy
hybridization
inter-organellar discordance
organelle inheritance
marine phytoplankton
protist
138Reconstructing evolutionary relationships in the genus Packera (Asteraceae: Senecioneae)PhylogenomicsMoore, Erika; Mandel, Jennifer.chloroplast
nuclear genes
paralogs
phylogenomics
polyploidy
143Red gold or corn silk? Detecting economic adulteration in the world’s most expensive spice: saffronPhylogenomicsHunter, Elizabeth; Literman, Robert; Handy, Sara.saffron
genome skimming
adulteration
economic adulteration
genomics
77Reference-free and bait-guided phylogenetic inference and species identification in the ginseng genus Panax (Araliaceae) using genome skim dataPhylogenomicsLiterman, 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
866Resolving taxonomic uncertainty and clarifying species boundaries in the Cymopterus terebinthinus species complexPhylogenomicsTaylor, Annie; Smith, James (Jim); Mansfield, Don; Feist, Mary Ann; Buerki, Sven; Darrach, Mark.phylogenetics
species delimitation
Apiaceae
Angiosperms353
species complex
next generation sequencing
198Resolving the reticulate evolutionary history of the New Zealand polyploid-rich genus Azorella (Apiaceae)PhylogenomicsNing, Weixuan; Meudt, Heidi; Nicolas, Antoine; Plunkett, Gregory; Lee, William; Tate, Jennifer.Azorella
Apiaceae
hybridization
Hyb-Seq
whole-genome duplication
phylogenomics
Reticulation
genome skimming
357Reticulate evolution as a potential driver of ecological niche adaptation in Quercus.PhylogenomicsLandis, Henry; Roalson, Eric; Busch, Jeremiah.quercus
phylogenomics
phylogenetics
Reticulation
adaptation
niche evolution
Evolution
405The Australian Angiosperm Tree of Life projectPhylogenomicsAllnutt, 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
496The true blueberries (Vaccinium sect. Cyanococcus) - A first complete phylogenomic hypothesis of diploid taxa and preliminary investigation into polyploidsPhylogenomicsCrowl, Andrew; Fritsch, Peter; Ashrafi, Hamid; Manos, Paul.Alleles
ericaceae
HybSeq
phylogenomics
polyploidy
Target Enrichment
Vaccinium
hybridization
50Trait diversity – a novel phylodiversity measure to investigate eco-evolutionary mechanisms of community assemblyPhylogenomicsBorokini, Israel; Allen, Julie; Smith, Stephen; Guralnick, Robert; Soltis, Pamela; Soltis, Douglas; Laffan, Shawn; Mishler, Brent.trait diversity
55Untying Gordian knots: Unraveling reticulate polyploid plant evolution by RRS genomic data using a large non-model species complexPhylogenomicsKarbstein, 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
37Whom to trust wehn a microsynteny- and gene-content-based topology differs drastically from sequenced-based trees: Juglandaceae as a test casePhylogenomicsRenner, Susanne S.; Bai, Wei-Ning; Zhang, Da-Yong.allopolyploidy
DNA repair
gene-content-based tree
whole-genome duplication
introgression
36Whom to trust when a microsynteny-based topology differs drastically from sequence-based phylogenies: the Juglandaceae as a test casePhylogenomicsRenner, Susanne S.; Bai, Wei-Ning; Zhang, Da-Yong.Microsynteny
Gene content
allopolyploidy
gene-content-based tree
whole-genome duplication
introgression

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