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American Bryological and Lichenological Society (ABLS)
American Fern Society (AFS)
American Society of Plant Taxonomists (ASPT)
Botanical Society of America (BSA)
Canadian Botanical Association (CBA/ABC)
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International Association for Plant Taxonomy (IAPT)
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Presentations for Program:: Phylogenomics

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SessionDate/TimeLocationTitleTypeAuthorsKeywords

Monday, July 23rd

Monday, July 23rd, 8:00 am to 11:30 am · 114/Mayo Civic Center
Session 1: Contributed Papers: Phylogenomics I
Presiding: Liming Cai, Harvard University
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1001July 23rd 8:00 am114/Mayo Civic CenterComparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics
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Oral PaperChau, John; Olmstead, Richard.hybrid enrichment
single-copy nuclear genes
PPR genes
Buddleja
Scrophulariaceae
Lamiales
1002July 23rd 8:15 am114/Mayo Civic CenterElucidating the Multiple Independent Whole Genomes Duplication Events in the Brassicales
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Oral PaperBrose, Julia; Mabry, Makenzie; Dismukes, Wade; Beric, Aleksandra; Washburn, Jacob; Edger, Patrick; Hall, Jocelyn; McKain, Michael; Al-Shehbaz, Ihsan; Harkess, Alex; Schranz, M. Eric; Conant, Gavin; Pires, Joseph Chris.Brassicales
whole chloroplast
Phylogenomics
1003July 23rd 8:30 am114/Mayo Civic CenterNested phylogenetic conflicts and deep phylogenomics in plants
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Oral PaperSmith, Stephen; Brown, Joseph; Walker, Joseph.Phylogenomics
land plants
Phylogenetics
heterogeneity
conflict
1004July 23rd 8:45 am114/Mayo Civic CenterExtensive gene tree discordance in Malpighiales not explained by incomplete lineage sorting and gene tree estimation error
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Oral PaperCai, Liming; Xi, Zhenxiang; Lemmon, Emily; Lemmon, Alan; Mast, Austin; Buddenhagen, Christopher; Liu, Liang; Davis, Charles.Anchored hybrid enrichment
Subsampling
Gene tree-species tree conflict
Hybridization
Rapid radiation
Coalescent method
1005July 23rd 9:00 am114/Mayo Civic CenterEvolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments
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Oral PaperWang, Ning; Yang, Ya; Moore, Michael J.; Brockington, Samuel; Walker, Joseph; Brown, Joseph; Eggli, Urs; Majure, Lucas; Smith, Stephen.gene tree conflict
gene duplication
molecular evolution
paleopolyploidy
Portulacineae
stress adaptation
1006July 23rd 9:15 am114/Mayo Civic CenterMassive polyploidization but no obvious role for polyploids in the radiation of southern African Oxalis L.: insights from phylogenomics and cytogenetics
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Oral PaperSchmickl, Roswitha; Oberlander, Kenneth; Zeisek, Vojtěch; Liston, Aaron; Schneeweiss, Hanna; Záveská, Eliška; Emshwiller, Eve; Dreyer, Leanne; Suda, Jan.radiation
whole genome duplication
Hyb-Seq
Greater Cape Floristic Region
July 23rd 9:30 am114/Mayo Civic CenterBreak
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1008July 23rd 10:15 am114/Mayo Civic CenterEvolution of function and structure in the leucine-rich repeat gene family in flowering plants
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Oral PaperGallagher, Joseph; Man, Jarrett; Bartlett, Madelaine.leucine-rich repeat
molecular evolution
Phylogenomics
1009July 23rd 10:30 am114/Mayo Civic CenterPhylogenomics of Aesculus L. (Sapindaceae) inferred from RAD-seq data – insights into biogeography and evolution of the genus
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Oral PaperDu, Zhiyuan; Xiang, Jenny; Harris, AJ.Aesculus
RAD-seq
intercontinental disjunction
Niche Evolution
Biogeography
1010July 23rd 10:45 am114/Mayo Civic CenterOrigin(s) of a hybrid: History of allopolyploid Brassica napus using genome-wide data
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Oral PaperAn, Hong; Gaynor, Michelle; Gebken, Sarah; Qi, Xinshuai; Barker, Michael; Pires, Joseph Chris.Brassica
Phylogenomics
1011July 23rd 11:00 am114/Mayo Civic CenterCharacterizing gene-tree conflict and systematic error in plastome-inferred phylogenies
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Oral PaperWalker, Joseph; Stull, Gregory; Walker-Hale, Nathanael; Vargas, Oscar M; Larson, Drew.Chloroplast genome
plastome
angiosperms
Genomic conflict
gene tree conflict
Systematic error
Phylogenomics
rpoC2
1012July 23rd 11:15 am114/Mayo Civic CenterREPHINE: REcursive PHylogenetic INferencE
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Oral PaperMiller, Joe.Phylogenetics
DNA alignments
Monday, July 23rd, 1:30 pm to 5:15 pm · 114/Mayo Civic Center
Session 11: Contributed Papers: Phylogenomics II
Presiding: Sarah Mathews, CSIRO National Research Collections Australia; Mark Fishbein, Oklahoma State University
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11001July 23rd 1:30 pm114/Mayo Civic CenterAssessing the reticulate history of white oaks (Quercus) using hundreds of nuclear loci
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Oral PaperCrowl, Andrew; McVay, John; Hipp, Andrew; Manos, Paul.Quercus
Hybridization
Oaks
SNAQ
Introgression
gene flow
HybSeq
11002July 23rd 1:45 pm114/Mayo Civic CenterEmbracing gene tree conflict to inform species relationships: An example in the clade Caryophyllales
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Oral PaperWalker, Joseph; Brown, Joseph; Smith, Stephen.Phylogenomics
gene tree conflict
Caryophyllales
supermatrix
Coalescent
11003July 23rd 2:00 pm114/Mayo Civic CenterDifferential Decay of an Ancient Mitochondrial Insertion in the Plastid Genomes of Paspalum (Poaceae)
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Oral PaperBurke, Sean; Ungerer, Mark; Duvall, M.Poaceae
Paspalum
mtDNA
ptDNA
molecular evolution
inserts
Next generation sequencing
Grasses
11004July 23rd 2:15 pm114/Mayo Civic CenterPlastome phylogenomics and characterization of rare genomic changes in plastome groups 1 and 2 Poeae (Pooideae; Poaceae)
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Oral PaperOrton, Lauren; Burke, Sean; Duvall, M.chloroplast
plastome
Plastid
Poeae
Pooideae
Poaceae
Phylogenomics
11005July 23rd 2:30 pm114/Mayo Civic CenterDetecting Hybridization in Hawaiian Cyrtandra (Gesneriaceae) Using Genome-wide Data
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Oral PaperKleinkopf, Jospeh; Wagner, Warren; Roalson, Eric.Cyrtandra
Gesneriaceae
Hawaii
Hyb-Seq
Hybridization
July 23rd 2:45 pm114/Mayo Civic CenterBreak
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11007July 23rd 3:45 pm114/Mayo Civic CenterSeed plant phylogeny inferred from integrated analyses of morphological and molecular data
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Oral PaperMathews, Sarah; Campbell, Christopher; Cronn, Richard; Gernandt, David; Graham, Sean; Hansen, Kimberly; Holman, Garth; G.Kelch, Dean; Lam, Vivienne; Li, Jianhua; Liston, Aaron; Little, Damon; Mapes, Gene; Mei, Wenbin; Moore, Abigail; Nagalingum, Nathalie; Parks, Matthew; Peery, Rhiannon; Rai, Hardeep; Raubeson, Linda; Ross, Gregory; Rothwell, Gar; Ruhsam, Markus; Ryberg, Patricia E.; Schwarzbach, Andrea; Stevenson, Dennis; Stockey, Ruth; Yang, Yong.seed plant
phylogeny
fossils
molecules
morphology
11008July 23rd 4:00 pm114/Mayo Civic CenterPhylogenomics of Nyssa from single copy genes and Fluidgim sequencing – insights into biogeography and character evolution
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Oral PaperZhou, Wenbin; Xiang, Jenny; Wen, Jun.eastern Asia-eastern North American disjunction
Nyssa
Fluidigm sequencing
Ancestral character estimation
Biogeography
11009July 23rd 4:15 pm114/Mayo Civic CenterMilkweed Phylogenomics: Assessing Incomplete Lineage Sorting and Intergenomic Discordance
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Oral PaperFishbein, Mark; Straub, Shannon; Boutte, Julien; Weitemeier, Kevin A.; Cronn, Richard; Liston, Aaron.Phylogenomics
Phylogenetics
nuclear genes
target enrichment
HybSeq
Incomplete Lineage Sorting
milkweed
Asclepias
Apocynaceae
11010July 23rd 4:30 pm114/Mayo Civic CenterAllele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
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Oral PaperKates, Heather; Johnson, Matthew; Gardner, Elliot; Zerega, Nyree; Wickett, Norman.Targeted Sequence Capture
Hyb-Seq
heterozygosity
allelic sequence data
Phylogenomics methods
11011July 23rd 4:45 pm114/Mayo Civic CenterEvolution and Historical Biogeography of Asteraceae using Hyb-Seq Data
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Oral PaperMandel, Jennifer; Siniscalchi, Carolina; Thapa, Ramhari; Dikow, Rebecca; Watson, Linda E; Funk, Vicki.Compositae
Phylogenomics
Biogeography
Hyb-Seq
Sunflower
Monday, July 23rd, 5:30 pm to 7:00 pm · Grand Ballroom - Exhibit Hall/Mayo Civic Center
Session P: Contributed Posters: Phylogenomics
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PPH001July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterDifficulties in the Inference of Ancient Whole-Genome Duplications
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Poster: PhylogenomicsSong, Michael; Rothfels, Carl; Igic, Boris.Polyploidy
whole genome duplication
ks plot
PPH002July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterPhyscraper: automatic updating of phylogenies
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Poster: PhylogenomicsKandziora, Martha; McTavish, Emily Jane.Phylogenetics
workflow
automatic updating
python
Senecioneae
Asteraceae
PPH003July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterDeveloping tools to capture loci of two distant clades of Melastomataceae
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Poster: PhylogenomicsAmarasinghe, Prabha; Jantzen, Johanna; Soltis, Douglas; Soltis, Pamela S.; Cellinese, Nico.Memecylon
Tibouchina
Melastomataceae
target enrichment
HybPiper
PPH004July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterHunting the treasure of Cape Oxalis diversity
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Poster: PhylogenomicsZeisek, Vojtěch; Oberlander, Kenneth; Dreyer, Leanne; Schmickl, Roswitha.Phylogenomics
Phylogenetics
biodiversity
Taxonomy
Evolution
Oxalis
HTS
South Africa
Greater Cape Floristic Region
PPH005July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterPhylogenomic analyses reveal extensive gene flow within the magic flowers (Achimenes)
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Poster: PhylogenomicsRoberts, Wade; Roalson, Eric.Achimenes
Gesneriaceae
Hybridization
Introgression
Phylogenomics
transcriptomics
PPH006July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterThe Evolutionary and Ecological Roles of Illinois Listed Endangered and Threatened Grasses
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Poster: PhylogenomicsPischl, Phyllis; Duvall, M.Poaceae
Endangered Species
Phylogenomics
PPH007July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterCapsi-conundrum: Resolving Relationships within Capsiceae (Solanaceae)
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Poster: PhylogenomicsSanbonmatsu , Katie K; Mukai, Maya; Spalink, Daniel; Bohs, Lynn Allison.Capsicum
Solanaceae
Lycianthes
Capsiceae
Phylogenomics
Phylogenetics
genealogical discordance
Incomplete Lineage Sorting
concordance
Evolution
MrBayes
BUCKy
PPH008July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterResolving the Phylogeny and Understanding the Molecular Evolution of Rapidly Diversifying South American Pitcher Plants Heliamphora(Sarraceniaceae)
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Poster: PhylogenomicsLiu, Sukuan; Smith, Stacey D..Carnivorous Plants
Evolution
RNA-Seq
Phylogenetics
PPH009July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterResolving Relationships in Leucaena through Reference Guided and de novo Transcriptomics
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Poster: PhylogenomicsAbair, Alexander; Nageswara-Rao, Madhugiri; Dugas, Diana; Hughes, Colin; Bailey, Donovan.Leucaena
Leguminosae
Polyploid
phylogeny
Genomics
transcriptomics
Hybridization
orthology
paralogy

Wednesday, July 25th

Wednesday, July 25th, 8:00 am to 11:30 am · 107/Mayo Civic Center
Session 36: Contributed Papers: Phylogenomics III
Presiding: Carol Wilson, ; John Schenk, Georgia Southern University
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36001July 25th 8:00 am107/Mayo Civic CenterEvolutionary origins of cultivated sweetpotato and relationships in the Batatas complex
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Oral PaperEserman, Lauren; Leebens-Mack, Jim.sweetpotato
Ipomoea
Phylogenomics
Crop wild relatives
36002July 25th 8:15 am107/Mayo Civic CenterMonocot plastid phylogenomics, timeline, and the power of multi-gene analyses
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Oral PaperGivnish, Thomas J; Zuluaga-Trochez, Alejandro; Spalink, Daniel; Graham, Sean; Barrett, Craig; Soto Gomez, Marybel; Lam, Vivienne; Saarela, Jeffery; Sass, Chodon; LIma, Danilo; Leebens-Mack, Jim; Pires, Joseph Chris; Zomlefer, Wendy; Gandolfo, Maria A; Davis, Jerrold; Stevenson, Dennis; Specht, Chelsea.Commelinids
partitioned maximum likelihood
net rates of species diversification
mycoheterotrophy
36003July 25th 8:30 am107/Mayo Civic CenterA phylogenomics pipeline for identifying crop wild relatives: an example from the Dioscorea yams, a major pantropical crop
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Oral PaperSoto Gomez, Marybel; Viruel, Juan ; Kantar , Michael; Wilkin, Paul; Graham, Sean.Phylogenomics methods
Nuclear monocot phylogenomics
Hyb-Seq
Dioscoreaceae
Dioscoreales
low-copy nuclear loci
36004July 25th 8:45 am107/Mayo Civic CenterTesting for the Monophyly of the Mentzelia Section Bartonia (Loasaceae) Pinnatisect-Leaved Species with Genome Skimming
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Oral PaperSchenk, John; Kelly, Khadijah.phylogeny
Phylogenomics
genome skimming
Cytonuclear discordance
Mentzelia
Loasaceae
Incomplete Lineage Sorting
Next generation sequencing
convergent evolution
36005July 25th 9:00 am107/Mayo Civic CenterDesigning and testing a kit to enrich phylogenetically informative exons for all angiosperms
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Oral PaperWickett, Norman; Johnson, Matthew; Botigue, Laura; Devault, Alison; Dodsworth, Stephen; Forest, Felix; Kim, Jan; Leebens-Mack, Jim; Soltis, Douglas; Soltis, Pamela S.; Baker, William J.; Pokorny, Lisa.HybSeq
HybPiper
Sequence capture
Machine Learning
single-copy nuclear genes
36006July 25th 9:15 am107/Mayo Civic CenterGenomic patterns of gene flow and divergence in the genus Antirrhinum
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Oral PaperDuran Castillo , Mario Saturnino; Hudson, Andrew; Twyford, Alex.Speciation
Phylogenetics
Hybridization
Antirrhinum
July 25th 9:30 am107/Mayo Civic CenterBreak
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36008July 25th 10:15 am107/Mayo Civic CenterPhylogenomic Analysis of Polyploidy in “Reedy” Arundinoids (Poaceae)
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Oral PaperTeisher, Jordan; McKain, Michael; Kellogg, Elizabeth.Phragmites australis
Arundo donax
Grass
Evolution
36009July 25th 10:30 am107/Mayo Civic CenterTesting the monophyly of bryophytes using expanded genome and transcriptome sampling
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Oral PaperWickett, Norman; Parks, Matthew; Johnson, Matthew; Mirarab, Siavash; Mai, Uyen; Peter, Szovenyi; Kirbis, Alexander; Waller, Manuel; Neubauer, Anna.Bryophytes
land plants
gene tree conflict
gene genealogy interrogation
single-copy nuclear genes
36010July 25th 10:45 am107/Mayo Civic CenterTarget-enrichment phylogenomics improves the resolution of legume lineages at generic, tribal, and subfamily levels
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Oral PaperVatanparast, Mohammad; Egan, Ashley.Sequence capture
Hyb-Seq
Fabaceae
Systematics
36011July 25th 11:00 am107/Mayo Civic CenterPhylogenomic analysis of the wheat tribe Triticeae (Poaceae) based on chloroplast and nuclear data acquired using a Hyb-Seq approach
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Oral PaperMason-Gamer, Roberta; White, Dawson.Poaceae
Gramineae
target enrichment
36012July 25th 11:15 am107/Mayo Civic CenterPhylogenomics subgenus Hermodactyloides, a small lineage of bulbous Iris that are mostly narrow endemics
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Oral PaperWilson, Carol; Freyman, Will.Biogeography
Endemism
genome skimming
Iris
Iridaceae
Targeted Sequence Capture
Next generation sequencing

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