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American Bryological and Lichenological Society (ABLS)
American Fern Society (AFS)
American Society of Plant Taxonomists (ASPT)
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Mycological Section (MSA)

Presentations for Program:: Phylogenomics

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SessionDate/TimeLocationTitleTypeAuthorsKeywords

Monday, August 1st

Monday, August 1st, 8:00 am to 11:45 am · 101/Savannah International Trade and Convention Center
Session 1: Contributed Papers: Phylogenomics I
Presiding: Elizabeth Zimmer, Smithsonian Institution, National Museum of Natural History; Michael D. Martin, University Museum
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1001August 1st 8:00 am101/Savannah International Trade and Convention CenterGenotyping by sequencing in a 'spiny' species complex of Australian arid zone grasses (Triodia)
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Oral PaperAnderson, Benjamin; Grierson, Pauline; Krauss, Siegfried; Thiele, Kevin; Barrett, Matthew.ASTRAL
Australia
Genotyping by sequencing (GBS)
PyRAD
Species complex
Triodia
1002August 1st 8:15 am101/Savannah International Trade and Convention CenterPhylogenetic relationships of Burmeistera (Campanulaceae)—using high-throughput sequencing to improve resolution in a recent radiation
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Oral PaperUribe-Convers, Simon; Carlsen, Monica; Lagomarsino, Laura; Knox, Eric; Muchhala, Nathan C..phylogenomics
Plastome
Capture Probes
Chloroplast Genome
genome skimming
species tree
Coalescence
High-Throughput Sequencing 
phylogenetics
Next generation sequencing
Campanulaceae
Burmeistera
1003August 1st 8:30 am101/Savannah International Trade and Convention CenterPhylogenomics of the Phaseoloid legumes: an introduction
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Oral PaperVatanparast, Mohammad; Powell, Adrian; Sherman-Broyles, Sue; Doyle, Jane; Doyle, Jeff; Egan, Ashley N..phylogenomics
legumes
Transcriptome
polyploidy
RNA-seq
Beans
1004August 1st 8:45 am101/Savannah International Trade and Convention CenterSeeing the Protea for the (gene) trees: anchored phylogenomics resolves relationships in a rapid radiation
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Oral PaperMitchell, Nora; Lewis, Paul; Lemmon, Emily; Lemmon, Alan R.; Holsinger, Kent.anchored phylogenomics
Coalescence
phylogenetics
Proteaceae
radiation
1005August 1st 9:00 am101/Savannah International Trade and Convention CenterA phylogeographic approach to assessing plastid genome evolution in a non-photosynthetic orchid using targeted sequence capture
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Oral PaperBarrett, Craig; Sass, Chodon.Plastome
Next generation sequencing
phylogenomics
intraspecific variation
pseudogene
mycoheterotrophic
Orchidaceae
sequence capture
plastid
chloroplast
genome evolution
1006August 1st 9:15 am101/Savannah International Trade and Convention CenterDNA sequences identify cryptic species of quillworts (Isoetes L.)
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Oral PaperZimmer, Elizabeth; Taylor, W. Carl; Schafran, Peter; Johnson, Gabriel.Isoetes
tetraploids
low-copy nuclear markers
Chloroplast Genome
Next generation sequencing
1007August 1st 9:30 am101/Savannah International Trade and Convention CenterHitting the century mark in an understudied, hyper-diverse lineage: Transcriptome-based phylogenomic analyses across the diatoms (Bacillariophyta)
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Oral PaperParks, Matthew; Johnson, Matthew; Ruck, Elizabeth; Alverson, Andrew; Wickett, Norm.diatom
phylogenomics
Transcriptome
orthology
August 1st 9:45 am101/Savannah International Trade and Convention CenterBreak
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1009August 1st 10:15 am101/Savannah International Trade and Convention CenterMultilocus phylogenetics of Pinus subsection Australes
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Oral PaperGernandt, David S.; Aguirre, Xitlali; Vázquez Lobo, Alejandra; Willyard, Ann; Moreno, Alejandra; Jaramillo Correa, Juan Pablo; Piñero, Daniel; Liston, Aaron.Coalescence
mtDNA
low-copy nuclear markers
pine
Plastome
1010August 1st 10:30 am101/Savannah International Trade and Convention CenterA pilot study applying the Plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
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Oral PaperFragoso-Martínez, Itzi; Salazar, Gerardo A.; Martí≠nez-Gordillo, Martha; Magallón, Susana; Lemmon, Alan R.; Moriarty Lemmon, Emily; Moreno-Letelier, Alejandra; Granados Mendoza, Carolina.anchored phylogenomics
Lamiales
Lamiaceae
Salvia
Calosphace
1011August 1st 10:45 am101/Savannah International Trade and Convention CenterEnhanced phylogenetic resolution of the highly-diverse Neotropical genus Epidendrum (Orchidaceae) using Anchored Hybrid Enrichment
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Oral PaperGranados Mendoza, Carolina; Salazar, Gerardo A.; Hagsater, Eric; van der Berg, Cassio; Magallón, Susana; Moriarty Lemmon, Emily; Lemmon, Alan R..Epidendrum
Orchidaceae
anchored phylogenomics
Genomic Partitioning Strategies
1012August 1st 11:00 am101/Savannah International Trade and Convention CenterEvaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale
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Oral PaperFoster, Charles; Sauquet, Herve; van der Merwe, Marlien; McPherson, Hannah; Rossetto, Maurizio; Ho, Simon.Angiospermae
chloroplast
genome
Molecular dating
Triassic
phylogenomics
1013August 1st 11:15 am101/Savannah International Trade and Convention CenterMitochondrial phylogenomics of mycoheterotrophic lineages of monocots
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Oral PaperLin, Qianshi; Lam, Vivienne K. Y.; Gomez, Marybel Soto; Marques, Isabel; Merckx, Vincent; Graham, Sean W..mitochondrial genome
higher-order classification
mycoheterotrophic plants
mycoheterotrophy
Pandanales
Petrosaviales
Dioscoreales
Burmanniaceae
Thismiaceae
1014August 1st 11:30 am101/Savannah International Trade and Convention CenterPhylogenomics and transcriptomics of Galápagos daisy trees (Scalesia)
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Oral PaperMartin, Michael D.; Wales, Nathan; Madrigal, Jazmí≠n R.; Hansen, Anders J.; Mundy, John; Petersen, Gitte; Seberg, Ole; Gilbert, M. Thomas P..Scalesia
phylogenetics
phylogenomics
Genomics
comparative genomics
Monday, August 1st, 5:30 pm to 7:00 pm · Exhibit Hall/Savannah International Trade and Convention Center
Session P: Contributed Posters: Phylogenomics Posters
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PPY001August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterEstimating species relationships within Pueraria s.s.: combining phylogenies and networks
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Poster: PhylogenomicsMahadwar, Gouri; Hansen, Matthew S.; Egan, Ashley N..Pueraria
phylogeny
kudzu
taxonomy
hybridization
network analysis
PPY002August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterUsing tRNA class informative features to determine the phylogenetic placement of Gnetophyta
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Poster: PhylogenomicsLawrence, Travis Joseph; Ardell, David.tRNA
Gnetophyta
phylogeny
PPY003August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterAnalysis of whole chloroplast genomes from the genera of the Clauseneae, the Curry tribe (Rutaceae, Citrus family)
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Poster: PhylogenomicsShivakumar, Vikram; Appelhans, Marc; Carlsen, Monica; Johnson, Gabriel; Zimmer, Elizabeth.Rutaceae
Clauseneae
Bergera koenigii
Chloroplast Genome
Single nucleotide polymorphism
Next generation sequencing
PPY004August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterTargeted capture of putative single copy genes using next generation sequencing yields new insights into polyploid evolution of Ludwigia section Macrocarpon (Onagraceae)
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Poster: PhylogenomicsLiu, Shih-Hui; Chiang, Tzen-Yuh; Huang, Chao-Li; Hsu, Tsai-Wen; Chang, Chia-Hao; Raven, Peter H.; Hoch, Peter C.; Barber, Janet C..Ludwigia
Homoeologous
allopolyploidization
PPY005August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterPhylogenomics of the Ponderosa Pine Species Complex using High Throughput Sequencing
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Poster: PhylogenomicsWills, Peter; Gernandt, David S.; Vasquez Lobo, Alejandra; Willyard, Ann.low-copy nuclear markers
pine
species tree
Plastome
PPY006August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterIntraspecific plastid genome variation and phylogenetic structure within the nickel hyperaccumulator Streptanthus polygaloides (Brassicaceae)
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Poster: PhylogenomicsMincey, Katherine; Melton, Anthony; Hall, Nathan; Goertzen, Leslie; Boyd, Robert Steven.hyperaccumulation
Serpentine
chloroplast
phylogenetics
Streptanthus polygaloides
PPY007August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterA phylogenetic analysis of CYCLOIDEA throughout the subgenera of Rhododendron
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Poster: PhylogenomicsDeal, Haley; Soza, Valerie Lynn; Ramage, Elizabeth; Hall, Benjamin.TCP genes
gene duplication
Ericaceae
floral symmetry
PPY008August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterEvolutionary Divergence of Disease Resistance Genes in Six Monocot Species
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Poster: PhylogenomicsAndersen, Ethan; Nepal, Madhav P.; Reese, R. Neil; Ali, Shaukat; Neupane, Surendra.Disease Resistance Genes 
NBS-LRR
Purifying Selection
Durable Resistance 
Monocot Genomes 
PPY009August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterFast-Plast: Rapid de novo assembly and finishing for whole chloroplast genomes
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Poster: PhylogenomicsMcKain, Michael; Wilson, Mark; Kellogg, Elizabeth Anne.Chloroplast Genome
de novo assembly
automated
PPY010August 1st 5:30 pmExhibit Hall/Savannah International Trade and Convention CenterInterrogating the phylogenomics of the Cleomaceae using transcriptomic data
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Poster: PhylogenomicsDismukes, Wade; Edger, Patrick; Hall, Jocelyn C; Washburn, Jacob; Pires, Joseph Chris.Transcriptomics
phylogenomics
polyploidy
paleopolyploidy
Brassicales

Tuesday, August 2nd

Tuesday, August 2nd, 8:00 am to 11:45 am · 202/Savannah International Trade and Convention Center
Session 16: Contributed Papers: Phylogenomics II
Presiding: Deren Alexander Robert Eaton, Yale University; Michael McKain, Donald Danforth Plant Science Center
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16001August 2nd 8:00 am202/Savannah International Trade and Convention CenterPhylogenomics of Asarum subgenus Heterotropa section Hexastylis: serial derivations of similar floral forms spawned from two geographically-widespread species
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Oral PaperSinn, Brandon T.; Daragan, Christina; Freudenstein, John V..Asarum
phylogenomics
Hexastylis
16002August 2nd 8:15 am202/Savannah International Trade and Convention CenterNext-generation polyploid phylogenetics: Low-cost, high-throughput resolution of hybrid polyploid complexes using PacBio and PURC
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Oral PaperRothfels, Carl; Pryer, Kathleen; Li, Fay-Wei.Allopolyploidy
High-Throughput Sequencing
Next generation sequencing
reticulate evolution
Cystopteris
Gymnocarpium
Cystopteridaceae
ferns
low-copy nuclear markers
PacBio
species tree
chimeric sequences
phylogenetic networks
16003August 2nd 8:30 am202/Savannah International Trade and Convention CenterAssessing genealogical discordance within Adansonia (Malvaceae) by targeted-sequence capture
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Oral PaperKarimi, Nisa; Stenz, Noah; Grover, Corrinne; Joseph, Gallagher; Jonathan, Wendel; Baum, David.
16004August 2nd 8:45 am202/Savannah International Trade and Convention CenterPhylogenomics and adaptive trait evolution of ecologically dominant grasses
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Oral PaperMcKain, Michael; McAllister, Chrissy; Biang, Kathrines; Clewel, Sarah; AuBuchon, Taylor; Saeidi, Saman; Welker, Cassiano; Art-han, Watchara; Pasquet, Remy; Traiperm, Paweena; Kellogg, Elizabeth Anne.
16005August 2nd 9:00 am202/Savannah International Trade and Convention CenterShape and scale in RAD-seq phylogenomics: Approaches for inferring trees for hundreds of taxa and millions of SNPs
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Oral PaperRobert Eaton, Deren Alexander; Park, Brian; Spriggs, Elizabeth L.; Donoghue, Michael.Viburnum
RAD-seq
quartet
phylogenomics
16006August 2nd 9:15 am202/Savannah International Trade and Convention Center
Canceled
Phylogeography of Nyssa sylvatica complex (Nyssaceae, Cornales) – Integrative evidence from GBS data and gene sequencing
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Oral PaperXiang, Qiu-Yun (Jenny); Dong, Yibo; Douglas, Norman; Ji, Xiang; Obata, Shihori; Pais, Andrew; Peet, Robert.Nyssa
Genotyping by sequencing (GBS)
Phylogeography
taxonomically complex group
August 2nd 9:30 am202/Savannah International Trade and Convention CenterBreak
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16008August 2nd 10:00 am202/Savannah International Trade and Convention Center
Canceled
The evolutionary origins of the Rand Flora pattern in the Sweet Tabaiba (Euphorbia balsamifera): Hyb-Seq helps bridge the micro-macroevolutionary gap
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Oral PaperPokorny, Lisa; Johnson, Matthew; Gardner, Elliot; Olsson, Sanna; Riina, Ricarda; Wickett, Norm; Sanmartí≠n, Isabel.Biogeography
Africa
phylogenomics
macroevolution
population genetics
hyb-seq
Euphorbia
16009August 2nd 10:15 am202/Savannah International Trade and Convention CenterPhylogenomic study of Blue/White-Fruited Dogwoods (Cornus, Cornaceae) using GBS data
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Oral PaperLindo, Julieta; Dong, Yibo; Obata, Shihori; Ji, Xiang; Xiang, Qiu-Yun (Jenny).phylogenomics
Cornus
Genotyping by sequencing (GBS)
16010August 2nd 10:30 am202/Savannah International Trade and Convention CenterPhylogeny and evolution of Australian Calandrinia (Montiaceae): a CAM-evolving, succulent plant lineage from Australia, and the coolest plant radiation you’ve never heard of
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Oral PaperHancock, Lillian Pine; Moore, Abigail; Holtum, Joseph; Edwards, Erika.phylogenetics
CAM photosynthesis
Succulence
Montiaceae
Australia
16011August 2nd 10:45 am202/Savannah International Trade and Convention CenterA fully resolved phylogeny of the tropical Zingiberales using targeted gene enrichment
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Oral PaperCarlsen, Monica; Fer, Tomas; Kress, John.target enrichment
Zingiberales
rapid diversification
Musaceae
phylogenomics
Heliconiaceae
Next generation sequencing
16012August 2nd 11:00 am202/Savannah International Trade and Convention CenterGene family evolution in the carnivorous clade of Caryophyllales
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Oral PaperWalker, Joseph; Yang, Ya; Moore, Michael; Brockington, Samuel; Smith, Stephen.Transcriptome
phylogenomics
16013August 2nd 11:15 am202/Savannah International Trade and Convention CenterMolecules, morphology, and monophyly: revising the enigmatic Australian clade Goodenia s.l. (Goodeniaceae) using comprehensive sampling and big data
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Oral PaperJabaily, Rachel Schmidt; Gardner, Andy; Sessa, Emily Butler; Michener, Pryce; Johnson, Eden; Shepherd, Kelly A..taxonomy
revision
Australia
Asterales
Goodeniaceae
genome skimming
chloroplast
Mitochondria

Wednesday, August 3rd

Wednesday, August 3rd, 8:00 am to 12:00 pm · 204/Savannah International Trade and Convention Center
Session 38: Contributed Papers: Phylogenomics III
Presiding: Mark Fishbein, Oklahoma State University; Lauren Eserman, University Of Georgia
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38001August 3rd 8:00 am204/Savannah International Trade and Convention CenterGrow a backbone: mitochondrial exome sequencing provides a surprisingly rich source of phylogenetically informative characters in the enigmatic Australian clade Goodenia s.l
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Oral PaperMichener, Pryce; Sessa, Emily Butler; Bush, Caroline; Shepherd, Kelly A.; Jabaily, Rachel Schmidt.Australia
Asterales
Goodeniaceae
Next generation sequencing
genome skimming
Mitochondria
38002August 3rd 8:15 am204/Savannah International Trade and Convention CenterRe-evaluation of subfamily relationships of Araceae using phylogenomics
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Oral PaperZuluaga-Trochez, Alejandro; Moriarty Lemmon, Emily; Lemmon, Alan; Cameron, Ken.Araceae
phylogenomics
target enrichment
38003August 3rd 8:30 am204/Savannah International Trade and Convention CenterPhylogenetics of the sweet potato complex: A comparison of RAD-seq and targeted gene capture for resolving relationships
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Oral PaperEserman, Lauren; Leebens-Mack, Jim.sweet potato
anchored phylogenomics
RADseq
morning glory
Species complex
Ipomoea
38004August 3rd 8:45 am204/Savannah International Trade and Convention CenterCircumscribing a core set of conserved, orthologous genes for moss phylogenetics
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Oral PaperMalley, Claire; Johnson, Matthew; Goffinet, Bernard; Shaw, A Jonathan; Wickett, Norm.phylogenomics
transcriptomes
Mosses
Bryophytes
Bioinformatics
38005August 3rd 9:00 am204/Savannah International Trade and Convention CenterA phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach for 322 nuclear loci
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Oral PaperOverson, Rick; Johnson, Matthew; Fant, Jeremie; Levin, Rachel; Moore, Michael; Wagner, Warren L.; Raguso, Robert A.; Skogen, Krissa; Wickett, Norm.phylogenomics
evening primrose
RADseq
onagraceae
hyb-seq
HybPiper
38006August 3rd 9:15 am204/Savannah International Trade and Convention CenterGrappling with gamma--a new look at an old WGD event
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Oral PaperChanderbali, Andre; Berger, Brent; Howarth, Dianella; Soltis, Douglas; Soltis, Pamela S..angiosperms
gamma
WGD
phylogenomics
38007August 3rd 9:30 am204/Savannah International Trade and Convention CenterThe Natural History and Phylogeny of the Milkweed (Asclepias, Apocynaceae) Plastome
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Oral PaperFishbein, Mark; Straub, Shannon C.K.; Hansen, Kimberley; Cronn, Richard C.; Liston, Aaron.phylogenomics
data partition
model selection
signal
August 3rd 9:45 am204/Savannah International Trade and Convention CenterBreak
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38009August 3rd 10:15 am204/Savannah International Trade and Convention CenterA fruitful endeavor: Using RAD-seq to reveal the evolutionary relationships of the mango genus
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Oral PaperWarschefsky, Emily; von Wettberg, Eric.phylogenomics
Anacardiaceae
RAD-seq
perennial crop
crop wild relative
38010August 3rd 10:30 am204/Savannah International Trade and Convention CenterPhylogenomics of Temperate North American Milkweeds (Asclepias) based on 768 nuclear genes
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Oral PaperStraub, Shannon C.K.; Liston, Aaron; Weitemier, Kevin; McDonnell, Angela Jean; Fishbein, Mark.hyb-seq
targeted sequencing
Asclepias
Apocynaceae
phylogenomics
species tree
38011August 3rd 10:45 am204/Savannah International Trade and Convention CenterSpecies tree estimation in Cucurbita provides new insight into the genetic diversity of multiple crop species and their wild relatives
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Oral PaperKates, Heather Rose; Soltis, Pamela †S.; Soltis, Douglas.Cucurbits
crop wild relatives
species tree
crop evolution
microfluidic PCR-based target enrichment
low-copy nuclear markers
38012August 3rd 11:00 am204/Savannah International Trade and Convention CenterGenome-Guided Phylo-Transcriptomics
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Oral PaperWashburn, Jacob; Pires, Joseph Chris.phylogenomics
Genomics
Transcriptomics
38013August 3rd 11:15 am204/Savannah International Trade and Convention CenterPhylogenetic study of the monocots using many single copy nuclear genes
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Oral PaperTimilsena, Prakash Raj; Wafula, Eric K.; Leebens-Mack, Jim; dePamphilis, Claude W..phylogenomics
monocots
Phylotranscriptomics
low-copy nuclear markers
phylogeny
Plants Tribe
38014August 3rd 11:30 am204/Savannah International Trade and Convention CenterA progress report: clarifying the evolutionary history of Leucaena (Leguminosae: Mimosoideae) using chloroplast, mitochondrial, and nuclear transcriptome data
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Oral PaperBailey, C. Donovan; Kovar, Lynsey; Madhugiri, Nageswara-Rao; Dugas, Diana V.; Muhyi, Noor R.; Ortega-Rodriguez, Sealtiel; Koenen, Erik; Hughes, Colin E..
38015August 3rd 11:45 am204/Savannah International Trade and Convention CenterFrom phylotranscriptomics to anchored phylogenomics
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Oral PaperLeebens-Mack, Jim; Heyduk, Karolina; Comer, Jason; Eserman, Lauren; Harkess, Alex; McKain, Michael.phylogenomics
sequence capture

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