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Phylogenomics

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IDTitleSection/TopicAuthorsKeywords
796A fruitful endeavor: Using RAD-seq to reveal the evolutionary relationships of the mango genus
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PhylogenomicsWarschefsky, Emily; von Wettberg, Eric.phylogenomics
Anacardiaceae
RAD-seq
perennial crop
crop wild relative
631A fully resolved phylogeny of the tropical Zingiberales using targeted gene enrichment
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PhylogenomicsCarlsen, Monica; Fer, Tomas; Kress, John.target enrichment
Zingiberales
rapid diversification
Musaceae
phylogenomics
Heliconiaceae
Next generation sequencing
202Analysis of whole chloroplast genomes from the genera of the Clauseneae, the Curry tribe (Rutaceae, Citrus family)
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PhylogenomicsShivakumar, Vikram; Appelhans, Marc; Carlsen, Monica; Johnson, Gabriel; Zimmer, Elizabeth.Rutaceae
Clauseneae
Bergera koenigii
Chloroplast Genome
Single nucleotide polymorphism
Next generation sequencing
408A phylogenetic analysis of CYCLOIDEA throughout the subgenera of Rhododendron
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PhylogenomicsDeal, Haley; Soza, Valerie Lynn; Ramage, Elizabeth; Hall, Benjamin.TCP genes
gene duplication
Ericaceae
floral symmetry
749A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach for 322 nuclear loci
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PhylogenomicsOverson, 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
170A phylogeographic approach to assessing plastid genome evolution in a non-photosynthetic orchid using targeted sequence capture
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PhylogenomicsBarrett, Craig; Sass, Chodon.Plastome
Next generation sequencing
phylogenomics
intraspecific variation
pseudogene
mycoheterotrophic
Orchidaceae
sequence capture
plastid
chloroplast
genome evolution
410A pilot study applying the Plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
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PhylogenomicsFragoso-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
869A progress report: clarifying the evolutionary history of Leucaena (Leguminosae: Mimosoideae) using chloroplast, mitochondrial, and nuclear transcriptome data
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PhylogenomicsBailey, C. Donovan; Kovar, Lynsey; Madhugiri, Nageswara-Rao; Dugas, Diana V.; Muhyi, Noor R.; Ortega-Rodriguez, Sealtiel; Koenen, Erik; Hughes, Colin E..
557Assessing genealogical discordance within Adansonia (Malvaceae) by targeted-sequence capture
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PhylogenomicsKarimi, Nisa; Stenz, Noah; Grover, Corrinne; Joseph, Gallagher; Jonathan, Wendel; Baum, David.
723Circumscribing a core set of conserved, orthologous genes for moss phylogenetics
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PhylogenomicsMalley, Claire; Johnson, Matthew; Goffinet, Bernard; Shaw, A Jonathan; Wickett, Norm.phylogenomics
transcriptomes
Mosses
Bryophytes
Bioinformatics
220DNA sequences identify cryptic species of quillworts (Isoetes L.)
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PhylogenomicsZimmer, Elizabeth; Taylor, W. Carl; Schafran, Peter; Johnson, Gabriel.Isoetes
tetraploids
low-copy nuclear markers
Chloroplast Genome
Next generation sequencing
411Enhanced phylogenetic resolution of the highly-diverse Neotropical genus Epidendrum (Orchidaceae) using Anchored Hybrid Enrichment
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PhylogenomicsGranados 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
75Estimating species relationships within Pueraria s.s.: combining phylogenies and networks
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PhylogenomicsMahadwar, Gouri; Hansen, Matthew S.; Egan, Ashley N..Pueraria
phylogeny
kudzu
taxonomy
hybridization
network analysis
430Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale
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PhylogenomicsFoster, Charles; Sauquet, Herve; van der Merwe, Marlien; McPherson, Hannah; Rossetto, Maurizio; Ho, Simon.Angiospermae
chloroplast
genome
Molecular dating
Triassic
phylogenomics
551Evolutionary Divergence of Disease Resistance Genes in Six Monocot Species
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PhylogenomicsAndersen, Ethan; Nepal, Madhav P.; Reese, R. Neil; Ali, Shaukat; Neupane, Surendra.Disease Resistance Genes 
NBS-LRR
Purifying Selection
Durable Resistance 
Monocot Genomes 
708Fast-Plast: Rapid de novo assembly and finishing for whole chloroplast genomes
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PhylogenomicsMcKain, Michael; Wilson, Mark; Kellogg, Elizabeth Anne.Chloroplast Genome
de novo assembly
automated
761From phylotranscriptomics to anchored phylogenomics
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PhylogenomicsLeebens-Mack, Jim; Heyduk, Karolina; Comer, Jason; Eserman, Lauren; Harkess, Alex; McKain, Michael.phylogenomics
sequence capture
632Gene family evolution in the carnivorous clade of Caryophyllales
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PhylogenomicsWalker, Joseph; Yang, Ya; Moore, Michael; Brockington, Samuel; Smith, Stephen.Transcriptome
phylogenomics
861Genome-Guided Phylo-Transcriptomics
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PhylogenomicsWashburn, Jacob; Pires, Joseph Chris.phylogenomics
Genomics
Transcriptomics
55Genotyping by sequencing in a 'spiny' species complex of Australian arid zone grasses (Triodia)
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PhylogenomicsAnderson, Benjamin; Grierson, Pauline; Krauss, Siegfried; Thiele, Kevin; Barrett, Matthew.ASTRAL
Australia
Genotyping by sequencing (GBS)
PyRAD
Species complex
Triodia
757Grappling with gamma--a new look at an old WGD event
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PhylogenomicsChanderbali, Andre; Berger, Brent; Howarth, Dianella; Soltis, Douglas; Soltis, Pamela S..angiosperms
gamma
WGD
phylogenomics
639Grow 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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PhylogenomicsMichener, Pryce; Sessa, Emily Butler; Bush, Caroline; Shepherd, Kelly A.; Jabaily, Rachel Schmidt.Australia
Asterales
Goodeniaceae
Next generation sequencing
genome skimming
Mitochondria
324Hitting the century mark in an understudied, hyper-diverse lineage: Transcriptome-based phylogenomic analyses across the diatoms (Bacillariophyta)
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PhylogenomicsParks, Matthew; Johnson, Matthew; Ruck, Elizabeth; Alverson, Andrew; Wickett, Norm.diatom
phylogenomics
Transcriptome
orthology
890Interrogating the phylogenomics of the Cleomaceae using transcriptomic data
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PhylogenomicsDismukes, Wade; Edger, Patrick; Hall, Jocelyn C; Washburn, Jacob; Pires, Joseph Chris.Transcriptomics
phylogenomics
polyploidy
paleopolyploidy
Brassicales
403Intraspecific plastid genome variation and phylogenetic structure within the nickel hyperaccumulator Streptanthus polygaloides (Brassicaceae)
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PhylogenomicsMincey, Katherine; Melton, Anthony; Hall, Nathan; Goertzen, Leslie; Boyd, Robert Steven.hyperaccumulation
Serpentine
chloroplast
phylogenetics
Streptanthus polygaloides
445Mitochondrial phylogenomics of mycoheterotrophic lineages of monocots
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PhylogenomicsLin, 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
636Molecules, morphology, and monophyly: revising the enigmatic Australian clade Goodenia s.l. (Goodeniaceae) using comprehensive sampling and big data
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PhylogenomicsJabaily, Rachel Schmidt; Gardner, Andy; Sessa, Emily Butler; Michener, Pryce; Johnson, Eden; Shepherd, Kelly A..taxonomy
revision
Australia
Asterales
Goodeniaceae
genome skimming
chloroplast
Mitochondria
332Multilocus phylogenetics of Pinus subsection Australes
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PhylogenomicsGernandt, 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
543Next-generation polyploid phylogenetics: Low-cost, high-throughput resolution of hybrid polyploid complexes using PacBio and PURC
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PhylogenomicsRothfels, 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
114Phylogenetic relationships of Burmeistera (Campanulaceae)—using high-throughput sequencing to improve resolution in a recent radiation
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PhylogenomicsUribe-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
705Phylogenetics of the sweet potato complex: A comparison of RAD-seq and targeted gene capture for resolving relationships
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PhylogenomicsEserman, Lauren; Leebens-Mack, Jim.sweet potato
anchored phylogenomics
RADseq
morning glory
Species complex
Ipomoea
866Phylogenetic study of the monocots using many single copy nuclear genes
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PhylogenomicsTimilsena, Prakash Raj; Wafula, Eric K.; Leebens-Mack, Jim; dePamphilis, Claude W..phylogenomics
monocots
Phylotranscriptomics
low-copy nuclear markers
phylogeny
Plants Tribe
572Phylogenomics and adaptive trait evolution of ecologically dominant grasses
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PhylogenomicsMcKain, Michael; McAllister, Chrissy; Biang, Kathrines; Clewel, Sarah; AuBuchon, Taylor; Saeidi, Saman; Welker, Cassiano; Art-han, Watchara; Pasquet, Remy; Traiperm, Paweena; Kellogg, Elizabeth Anne.
455Phylogenomics and transcriptomics of Galápagos daisy trees (Scalesia)
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PhylogenomicsMartin, 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
534Phylogenomics of Asarum subgenus Heterotropa section Hexastylis: serial derivations of similar floral forms spawned from two geographically-widespread species
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PhylogenomicsSinn, Brandon T.; Daragan, Christina; Freudenstein, John V..Asarum
phylogenomics
Hexastylis
821Phylogenomics of Temperate North American Milkweeds (Asclepias) based on 768 nuclear genes
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PhylogenomicsStraub, Shannon C.K.; Liston, Aaron; Weitemier, Kevin; McDonnell, Angela Jean; Fishbein, Mark.hyb-seq
targeted sequencing
Asclepias
Apocynaceae
phylogenomics
species tree
139Phylogenomics of the Phaseoloid legumes: an introduction
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PhylogenomicsVatanparast, Mohammad; Powell, Adrian; Sherman-Broyles, Sue; Doyle, Jane; Doyle, Jeff; Egan, Ashley N..phylogenomics
legumes
Transcriptome
polyploidy
RNA-seq
Beans
306Phylogenomics of the Ponderosa Pine Species Complex using High Throughput Sequencing
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PhylogenomicsWills, Peter; Gernandt, David S.; Vasquez Lobo, Alejandra; Willyard, Ann.low-copy nuclear markers
pine
species tree
Plastome
620Phylogenomic study of Blue/White-Fruited Dogwoods (Cornus, Cornaceae) using GBS data
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PhylogenomicsLindo, Julieta; Dong, Yibo; Obata, Shihori; Ji, Xiang; Xiang, Qiu-Yun (Jenny).phylogenomics
Cornus
Genotyping by sequencing (GBS)
623Phylogeny 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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PhylogenomicsHancock, Lillian Pine; Moore, Abigail; Holtum, Joseph; Edwards, Erika.phylogenetics
CAM photosynthesis
Succulence
Montiaceae
Australia
574
Canceled
Phylogeography of Nyssa sylvatica complex (Nyssaceae, Cornales) – Integrative evidence from GBS data and gene sequencing
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PhylogenomicsXiang, Qiu-Yun (Jenny); Dong, Yibo; Douglas, Norman; Ji, Xiang; Obata, Shihori; Pais, Andrew; Peet, Robert.Nyssa
Genotyping by sequencing (GBS)
Phylogeography
taxonomically complex group
687Re-evaluation of subfamily relationships of Araceae using phylogenomics
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PhylogenomicsZuluaga-Trochez, Alejandro; Moriarty Lemmon, Emily; Lemmon, Alan; Cameron, Ken.Araceae
phylogenomics
target enrichment
161Seeing the Protea for the (gene) trees: anchored phylogenomics resolves relationships in a rapid radiation
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PhylogenomicsMitchell, Nora; Lewis, Paul; Lemmon, Emily; Lemmon, Alan R.; Holsinger, Kent.anchored phylogenomics
Coalescence
phylogenetics
Proteaceae
radiation
564Shape and scale in RAD-seq phylogenomics: Approaches for inferring trees for hundreds of taxa and millions of SNPs
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PhylogenomicsRobert Eaton, Deren Alexander; Park, Brian; Spriggs, Elizabeth L.; Donoghue, Michael.Viburnum
RAD-seq
quartet
phylogenomics
827Species tree estimation in Cucurbita provides new insight into the genetic diversity of multiple crop species and their wild relatives
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PhylogenomicsKates, Heather Rose; Soltis, Pamela †S.; Soltis, Douglas.Cucurbits
crop wild relatives
species tree
crop evolution
microfluidic PCR-based target enrichment
low-copy nuclear markers
281Targeted 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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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
599
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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PhylogenomicsPokorny, Lisa; Johnson, Matthew; Gardner, Elliot; Olsson, Sanna; Riina, Ricarda; Wickett, Norm; Sanmartí≠n, Isabel.Biogeography
Africa
phylogenomics
macroevolution
population genetics
hyb-seq
Euphorbia
774The Natural History and Phylogeny of the Milkweed (Asclepias, Apocynaceae) Plastome
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PhylogenomicsFishbein, Mark; Straub, Shannon C.K.; Hansen, Kimberley; Cronn, Richard C.; Liston, Aaron.phylogenomics
data partition
model selection
signal
109Using tRNA class informative features to determine the phylogenetic placement of Gnetophyta
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PhylogenomicsLawrence, Travis Joseph; Ardell, David.tRNA
Gnetophyta
phylogeny

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