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2024
Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)
Plant Diversity
2024
Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae
Ecology and Evolution
2024
Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae)
Ecology and Evolution
2024
Demographic dynamics and molecular evolution of the rare and endangered subsect. Gerardianae of Pinus: insights from chloroplast genomes and mitochondrial DNA markers
Planta
2024
Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae)
Molecular Phylogenetics and Evolution
2023
Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)
Plants
2023
Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto‐nuclear discordance and provides new insights into generic relationships
Journal of Systematics and Evolution
2023
Phylogenomics and plastome evolution of Indigofera (Fabaceae)
Frontiers in Plant Science
2023
Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants
Frontiers in Plant Science
2023
Systematics and biogeography of Oleaceae subtribe Schreberinae, with recircumscription and revision of the Malagasy members
Botanical Journal of the Linnean Society
2023
Plastome evolution and phylogenomic insights into the evolution of Lysimachia (Primulaceae: Myrsinoideae)
BMC Plant Biology
2023
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses
Cladistics
2023
More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae)
Annals of Botany
2023
Comparative Analysis Revealed Intrageneric and Intraspecific Genomic Variation in Chloroplast Genomes of Actinidia spp. (Actinidiaceae, Viridiplantae)
Horticulturae
2023
Phylogenomics sheds new light on the drivers behind a long‐lasting systematic riddle: the figwort family Scrophulariaceae
New Phytologist
2023
Chloroplast phylogenomics of unicellular and colonial Volvocales provides perspectives on the evolution of morphological characters
Journal of Systematics and Evolution
2023
Phylogenomics and the flowering plant tree of life
Journal of Integrative Plant Biology
2023
Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae
Biology
2023
HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources
Molecular Ecology Resources
2022
Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns
Frontiers in Plant Science
2022
New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq)
Frontiers in Plant Science
2022
Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics
Frontiers in Plant Science
2022
Phylogenomic and comparative analyses of Rheum (Polygonaceae, Polygonoideae)
Journal of Systematics and Evolution
2022
A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use
PeerJ
2022
Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants
PeerJ
2022
Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)
Frontiers in Plant Science
2022
Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
Journal of Integrative Plant Biology
2022
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics
Systematic Biology
2022
Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales)
BMC Plant Biology
2022
Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis
BMC Plant Biology
2022
Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies
Genetics and Molecular Biology
2022
ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications
Molecular Ecology Resources
2022
From the Mediterranean to the Pacific: re-circumscription towardsNotelaea s.l.and historical biogeography of a generic complex in Oleinae (Oleaceae)
Botanical Journal of the Linnean Society
2022
Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
BMC Genomics
2021
Calophyllaceae plastomes, their structure and insights in relationships within the clusioids
Scientific Reports
2021
Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic
Cladistics
2021
Whole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae)
Botany Letters
2021
Comparative analyses of Mikania (Asteraceae: Eupatorieae) plastomes and impact of data partitioning and inference methods on phylogenetic relationships
Scientific Reports
2021
Resolving robust phylogenetic relationships of core Brassicaceae using genome skimming data
Journal of Systematics and Evolution
2021
Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides
Frontiers in Plant Science
2021
Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture
Molecular Phylogenetics and Evolution
2021
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l
Systematic Biology
2021
Green giant—a tiny chloroplast genome with mighty power to produce high‐value proteins: history and phylogeny
Plant Biotechnology Journal
2021
Plastome evolution in the Caesalpinia group (Leguminosae) and its application in phylogenomics and populations genetics
Planta
2021
Whole plastomes are not enough: phylogenomic and morphometric exploration at multiple demographic levels of the bee orchid clade Ophrys sect. Sphegodes
Journal of Experimental Botany
2021
Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data fromParastyrax
Systematic Botany
2021
Hundreds of nuclear and plastid loci yield novel insights into orchid relationships
American Journal of Botany
2021
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)
Systematic Biology
2021
Plastid phylogenomics provides novel insights into the infrafamilial relationship of Polypodiaceae
Cladistics
2021
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
Bioinformatics
2021
Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms
Nature Plants
2021
Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing
Frontiers in Plant Science
2021
Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif‐based sequence alignment amid low genetic distances
American Journal of Botany
2021
Phenotypic versus genotypic disparity in the Eurasian orchid genus Gymnadenia: exploring the limits of phylogeny reconstruction
Systematics and Biodiversity
2021
Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region
Frontiers in Plant Science
2021
The importance of the Mexican taxa of Asteraceae in the family phylogeny
Journal of Systematics and Evolution
2021
Comparative chloroplast genomes and phylogenetic analysis of Aquilegia
Applications in Plant Sciences
2020
Historical biogeography of Vochysiaceae reveals an unexpected perspective of plant evolution in the Neotropics
American Journal of Botany
2020
Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies
Frontiers in Plant Science
2020
Phylogenomics of the hyperdiverse daisy tribes: Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae
Journal of Systematics and Evolution
2020
A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales
American Journal of Botany
2020
Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis
Journal of Systematics and Evolution
2020
ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines
PeerJ
2020
The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants
Nature Ecology & Evolution
2020
Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes
BMC Plant Biology
2020
Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)
PeerJ
2020
Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae
Systematic Biology
2020
Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution
Molecular Phylogenetics and Evolution
2020
Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)
Journal of Systematics and Evolution
2020
Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages
American Journal of Botany
2020
Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses
Nordic Journal of Botany
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