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Presentations for Program:: Phylogenomics

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SessionDate/TimeLocationTitleTypeAuthorsKeywords

Monday, July 29th

Monday, July 29th, 8:00 am to 11:45 am · San Ignacio/Starr Pass
Session PHYL1: Contributed Papers: Phylogenomics I
Presiding: Lars Chatrou, Ghent University; Lauren Eserman (PhD), Atlanta Botanical Garden
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PHYL1001July 29th 8:00 amSan Ignacio/Starr PassDeep phylogenetic incongruence in Neotropical rain forest trees (Oxandra, Annonaceae)
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Oral PaperChatrou, Lars.Genome skimming
chloroplast genome
Mitochondrial genome
nuclear ribosomal DNA
Annonaceae
Deep incongruence
PHYL1002July 29th 8:15 amSan Ignacio/Starr PassPhylogenomic analysis of Cycas section Indosinenses using RADseq
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Oral PaperLiu, Jian; Nagalingum, Nathalie; Lujan, Manuel A; Lindstrom, Anders J..Cycas
Indochina
RADseq
phylogenomics
PHYL1003July 29th 8:30 amSan Ignacio/Starr PassA phylogenetic analysis of the eucalypts using targeted genes
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Oral PaperCrisp, Michael; Kulheim, Carsten; Toon, Alicia; Edwards, Robert; Lin, Yen-Po; Meuesemann, Karen; Bui, Minh; Cook, Lyn.illumina
genome
paralogy
Myrtaceae
Eucalyptus
classification
perianth evolution
PHYL1004July 29th 8:45 amSan Ignacio/Starr PassTarget sequence capture in orchids: Developing a kit to sequence hundreds of single copy loci across all orchids
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Oral PaperEserman, Lauren; Thomas, Shawn; Coffey, Emily; Leebens-Mack, Jim.phylogenomics
target enrichment
Next Generation Sequencing
PHYL1005July 29th 9:00 amSan Ignacio/Starr PassA phylogenomic approach to decode contentious relationships across all angiosperm families
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Oral PaperPokorny, 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
PHYL1006July 29th 9:15 amSan Ignacio/Starr PassThe Plant and Fungal Trees of Life (PAFTOL) project: a case study from the carrot family (Apiaceae)
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Oral PaperClarkson, 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
PHYL1007July 29th 9:30 amSan Ignacio/Starr PassDisentangling the evolutionary relationships of Aizoaceae using transcriptome data
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Oral PaperZhao, Lijun; Walker, Joseph; Yang, Ya; Wang, Ning; Marx, Hannah; Brockington, Samuel; Moore, Michael; Smith, Stephen.phylogenomics
Transcriptome
Aizoaceae
July 29th 9:45 amSan Ignacio/Starr PassBreak
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PHYL1009July 29th 10:15 amSan Ignacio/Starr PassLewis’s lost Lomatium found: Investigating species boundaries in the rare plant species subcomplex, Lomatium packardiae/anomalum
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Oral PaperOttenlips, Michael; Buerki, Sven; Mansfield, Don; Dodsworth, Steven; Forest, Felix; Smith, James.incomplete lineage sorting
Angiosperm 353
target-enrichment
PHYL1010July 29th 10:30 amSan Ignacio/Starr PassPlastid Genome-based Phylogeny of Cornales – Insights Into Biogeographic History and Diversification
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Oral PaperXiang, Jenny; Fu, Chaonan; Gao, Lianming.The complete cp genome phylogeny 
Cornales
biogeography
Micaroevolution
PHYL1011July 29th 10:45 amSan Ignacio/Starr PassUsing a phylogenomic approach to resolve the systematics and taxonomy of Tibouchina s.s.
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Oral PaperJantzen, Johanna; Oliveira, Ana Luiza Freitas; Soltis, Douglas; Soltis, Pamela.phylogenomics
target enrichment
Melastomataceae
Tibouchina
Cerrado
Campos rupestres
PHYL1012July 29th 11:00 amSan Ignacio/Starr PassThe 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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Oral PaperCooper, Benjamin; Moore, Michael; Wickett, Norman; Wagner, Warren; Johnson, Matthew; Overson, Rick; Skogen, Krissa.target enrichment
HybPiper
multispecies coalescent
Onagraceae
Oenothera
Calylophus
Pollinator Shifts
gypsum
PHYL1013July 29th 11:15 amSan Ignacio/Starr PassRevisiting the origin of the octoploid strawberry
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Oral PaperListon, A.; Wei, Na; Tennessen, Jacob; Li, Junmin; Dong, Ming; Ashman, Tia-Lynn.Fragaria
polyploidy
Whole Genome Sequencing
PHYL1014July 29th 11:30 amSan Ignacio/Starr PassPlastome structure and phylogenomics of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii (Orchidaceae)
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Oral PaperKlimpert, Nathaniel; Mayer, Juliana; Pinheiro, Fabio; Proscdocimi, Francisco; Sarzi, Diese; Furtado, Carolina; Graham, Sean.Mycoheterotrophy
gene loss
Genome Evolution
plastid
Orchidaceae
Monday, July 29th, 5:30 pm to 7:00 pm · Arizona Ballroom/Starr Pass
Session P: Contributed Posters: Phylogenomics Posters
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PPL001July 29th 5:30 pmArizona Ballroom/Starr PassSystematics of Sanvitalia and Future Phylogenetics of Subtribe Zinniinae
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Poster: PhylogenomicsSkibicki, Sam.Phylogenetics
Sanvitalia
Zinniinae
Heliantheae
Asteraceae
biogeography
PPL002July 29th 5:30 pmArizona Ballroom/Starr PassBiogeography of the whorled wattles (Acacia section Lycopodiifoliae) in the Australian Monsoon Tropics
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Poster: PhylogenomicsConejo, Nancy; Martine, Christopher; Jobson, Peter; Cantley, Jason; Cantley, Jason; J. McDonnell, Angela.biogeography
Barriers
phylogeny
Australian Monsoon Tropics
population genetics
PPL003July 29th 5:30 pmArizona Ballroom/Starr PassGenomic phylogeography and species delimitation in Phycella s.l. (Amaryllidaceae tribe Hippeastreae)
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Poster: PhylogenomicsGarcia, Nicolas; Folk, Ryan.speciation
target enrichment
monocots
Chile
PPL004July 29th 5:30 pmArizona Ballroom/Starr PassInitial analyses of Magnolia genome data
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Poster: PhylogenomicsWeinheimer, Ellen; Pease, James; Whitener, Makenzie.phylogenomics
genome
magnolia
PPL005July 29th 5:30 pmArizona Ballroom/Starr PassThe Evolutionary Relationships in Pertyeae (Asteraceae) inferred from Hyb-Seq Data
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Poster: PhylogenomicsGomez, Jorge; Siniscalchi, Carolina; Mandel, Jennifer.Compositae
systematics
phylogenomics
PPL006July 29th 5:30 pmArizona Ballroom/Starr PassEvolutionary Relationships in the Euglossine Bee Pollinated Orchid Genus, Stanhopea
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Poster: PhylogenomicsJordan, Chazz; Brinkman, Becky; Coffey (PhD), Emily; Eserman (PhD), Lauren.0rchid
PPL007July 29th 5:30 pmArizona Ballroom/Starr PassPhylogenetic patterns of ecological niche evolution in Diapensiaceae
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Poster: PhylogenomicsGaynor, Michelle; Soltis, Douglas; Soltis, Pamela.phylogenomics
biogeography
ecological niche modelling
Diapensiaceae
PPL008July 29th 5:30 pmArizona Ballroom/Starr PassDeveloping a new bioinformatics pipeline to capture low-copy nuclear loci for two distant clades of Melastomataceae
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Poster: PhylogenomicsAmarasinghe, Prabha; Jantzen, Johanna; Folk, Ryan; Soltis, Douglas; Soltis, Pamela; Cellinese, Nico.Memecylon
Tibouchina
Melastomataceae
phylogenomics
target enrichment
MarkerMiner
HybPiper
PPL009July 29th 5:30 pmArizona Ballroom/Starr PassGenome sequencing based phylogenetic analyses of Streptanthus, Caulanthus, and related genera (Brassicacae)
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Poster: PhylogenomicsDaundasekara, Kasuni; Garza, Elyssa; Pepper, Alan.Brassicaceae
serpentine
low-coverage genome sequencing
phylogeny
PPL010July 29th 5:30 pmArizona Ballroom/Starr PassPhylogenomics of Adesmia (Fabaceae) and the discordance between nuclear and plastome phylogenies
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Poster: 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

Wednesday, July 31st

Wednesday, July 31st, 1:30 pm to 5:15 pm · Tucson F/Starr Pass
Session PHYL2: Contributed Papers: Phylogenomics II
Presiding: Amanda Fisher, California State University Long Beach; Wenbin Zhou, North Carolina State University
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PHYL2001July 31st 1:30 pmTucson F/Starr PassPhylogeny and Biogeography of the Cladrastis clade (Leguminosae: Papilonoideae)
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Oral PaperDuan, Lei; Wen, Jun; Harris, Aj; Chen, Hong-Feng.biome shift
Cladrastideae
Cladrastis
Leguminosae
Styphnolobium
the Cladrastis clade
PHYL2002July 31st 1:45 pmTucson F/Starr PassSpecies level phylogeny for the order Cornales based on molecular data from nuclear gene target enrichment
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Oral PaperThomas, Shawn; Liu, Xiang; Cummings, Amanda; Xiang, Jenny; Leebens-Mack, Jim.phylogenomics
target-enrichment
Sequence Capture
Next Generation Sequencing
PHYL2003July 31st 2:00 pmTucson F/Starr PassPhylogenomic discordance in the New World grapes suggests widespread introgressions as a driver for species diversifications
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Oral PaperNie, Zelong; Ma, Zhiyao; Johnson, Gabriel; Ren, Chen; Ickert-Bond, Stefanie; Zimmer, Elizabeth; Wen, Jun.phylogenomics
grapes
Vitis
Vitaceae
introgressionj
discordance
PHYL2004July 31st 2:15 pmTucson F/Starr PassA fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae
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Oral PaperMandel, Jennifer; Dikow, Rebecca; Siniscalchi, Carolina; Thapa, Ramhari; Watson, Linda; Funk, Vicki.Compositae
systematics
Sunflower
PHYL2005July 31st 2:30 pmTucson F/Starr PassCombining Genome Skims and Transcriptomes for a Phylogenomic framework of Acanthaceae
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Oral PaperArias, Joshua; McDade, Lucinda; Kiel, Carrie; Tripp, Erin; Fisher, Amanda.Lamiales
phylogenomics
PHYL2006July 31st 2:45 pmTucson F/Starr PassPhylogenomics 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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Oral PaperZhou, Wenbin; Xiang, Jenny.phylogenomics
EA-NAM disjunction
morphostasis
biogeographic history
morphological evolution
niche evolution
PHYL2007July 31st 3:00 pmTucson F/Starr PassPhylogenomics of the Neotropical spiral gingers (Costaceae)
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Oral PaperValderrama, 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
July 31st 3:15 pmTucson F/Starr PassBreak
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PHYL2009July 31st 3:45 pmTucson F/Starr PassDeveloping Phylyogenetic Hypotheses for Leucaena through Reference Guided and de novo Transcriptomics
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Oral PaperAbair, Alexander; Dugas, Diana; Madhugiri, Nageswara-Rao; Hughes, Colin; Bailey, C. Donovan.Leucaena
Leguminosae
Polyploid
phylogeny
genomics
Transcriptomics
hybridization
orthology
paralogy
PHYL2010July 31st 4:00 pmTucson F/Starr PassAn 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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Oral PaperOrtiz, Edgardo M.; Vargas, Oscar M; Schaefer, Hanno.Cucumis
Cucurbitaceae
targeted capture
target enrichment
nuclear genes
orthologs
plastome
marker selection
bait design
bioinformatics
pipeline
PHYL2011July 31st 4:15 pmTucson F/Starr PassIris of the Mediterranean: using phylogenomics to investigate putative color forms, phenological variants, and hybrids in subgenus Xiphium
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Oral PaperWilson, Carol; Boosalis, Zoe A.; Sandor, Michael; Crespo, Manuel B; Azorin, Mario M.Genome skimming
Iridaceae
targeted capture
PHYL2012July 31st 4:30 pmTucson F/Starr PassTowards a reclassification of Dioscoreales using organellar phylogenomics and morphology
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Oral PaperSoto 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
PHYL2013July 31st 4:45 pmTucson F/Starr PassChloroplast phylogenomics in the New World clade of Astragalus L. (Fabaceae)
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Oral PaperCharboneau, Joseph; Cronn, Richard; Liston, A.; Wojciechowski, Martin; Sanderson, Michael.chloroplast genome

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