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Phylogenomics reveals patterns of ancient hybridization and differential diversification contributing to phylogenetic conflict in Populus L. and Salix L

https://doi.org/10.1101/2023.01.04.522772

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

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Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows

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Correlates of hybridization in plants

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POLLINATION OF THE ARROYO WILLOW, SALIX LASIOLEPIS: ROLE OF INSECTS AND WIND

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EVOLUTION OF POPULUS NIGRA (SECT. AIGEIROS):INTROGRESSIVE HYBRIDIZATION AND THE CHLOROPLAST CONTRIBUTION OF POPULUS ALBA (SECT. POPULUS)

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Molecular phylogeny ofSalicaceae and closely relatedFlacourtiaceae: Evidence from 5.8 S, ITS 1 and ITS 2 of the rDNA

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Salix martiana, a regularly hermaphrodite willow

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Species or linneon

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Phylogeny of Populus-Salix (Salicaceae) and their relative genera using molecular datasets

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Foliar pathogens of Populus angustifolia are consistent with a hypothesis of Beringian migration into North America

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Phenolic glycosides of the Salicaceae and their role as anti-herbivore defenses

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Patterns of hybridization in plants

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Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

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Gene tree discordance, phylogenetic inference and the multispecies coalescent

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Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture

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The early fossil history of Salicaceae: a brief review

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Wind pollination and insect pollination of two temperate willow species, Salix miyabeana and Salix sachalinensis

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Sex determination through X–Y heterogamety in Salix nigra

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Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

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Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants

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Morphological and molecular evidence for hybridization and introgression in a willow (Salix) hybrid zone

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Phylogenomic conflict coincides with rapid morphological innovation

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The phylogeny of Salix revealed by whole genome re-sequencing suggests different sex-determination systems in major groups of the genus

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Wind of change: new insights on the ecology and evolution of pollination and mating in wind-pollinated plants

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ASTRAL: genome-scale coalescent-based species tree estimation

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Genetic mapping of sexually dimorphic volatile and non-volatile floral secondary chemistry of a dioecious willow

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Bayesian Inference of Species Trees from Multilocus Data

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Testing for Ancient Admixture between Closely Related Populations

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

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Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation

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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

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A Robust Semi-Parametric Test for Detecting Trait-Dependent Diversification

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A genetic legacy of introgression confounds phylogeny and biogeography in oaks

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

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Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

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The aspirin story – from willow to wonder drug

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MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING

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A MODEL FOR CHLOROPLAST CAPTURE

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TAXONOMIC RELATIONSHIPS OF SALICACEAE AND FLACOURTIACEAE: THEIR BEARING ON INTERPRETATIVE FLORAL MORPHOLOGY AND DILLENIID PHYLOGENY

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Genetically based trait in a dominant tree affects ecosystem processes

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Genome‐wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus

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TREE HYBRIDIZATION AND GENOTYPIC VARIATION DRIVE CRYPTIC SPECIATION OF A SPECIALIST MITE HERBIVORE

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IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

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Understanding the spectacular failure of DNA barcoding in willows ( Salix ): Does this result from a trans‐specific selective sweep?

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Adaptive introgression and maintenance of a trispecies hybrid complex in range‐edge populations of Populus

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The role of interspecific hybridization in adaptive potential at range margins

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Adaptive introgression as a driver of local adaptation to climate in European white oaks

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Phylogenomics of the genusPopulusreveals extensive interspecific gene flow and balancing selection

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From pollen dispersal to plant diversification: genetic consequences of pollination mode

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Sequential hybridization may have facilitated ecological transitions in the Southwestern pinyon pine syngameon

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A Draft Sequence of the Neandertal Genome

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Phylogenetic relationships of Salix L. subg. Salix species (Salicaceae) according to sequencing data of intergenic spacers of the chloroplast genome and ITS rDNA

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Poplar defense against insect herbivoresThis review is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

inferredcites →https://doi.org/10.1139/b76-297openalex-snapshot

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inferredcites →https://doi.org/10.1186/s12862-015-0311-7openalex-snapshot

Phylogeny of Salix subgenus Salix s.l. (Salicaceae): delimitation, biogeography, and reticulate evolution

inferredcites →https://doi.org/10.1371/journal.pone.0089543openalex-snapshot

Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

inferredcites →https://doi.org/10.1371/journal.pone.0138963openalex-snapshot

Correction: Phylogenetic Relationships of American Willows (Salix L., Salicaceae)

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So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

inferredcites →https://doi.org/10.1534/genetics.110.118828openalex-snapshot

Genomic Admixture Analysis in European Populus spp. Reveals Unexpected Patterns of Reproductive Isolation and Mating

inferredcites →https://doi.org/10.1534/genetics.112.145037openalex-snapshot

Ancient Admixture in Human History

inferredcites →https://doi.org/10.21203/rs.3.rs-2129351/v1openalex-snapshot

An unusual origin of a ZW sex chromosome system

inferredcites →https://doi.org/10.2307/2419520openalex-snapshot

Evolutionary Patterns and Processes in Salix Sect. Longifoliae: Evidence from Chloroplast DNA

inferredcites →https://doi.org/10.2307/25096638openalex-snapshot

Infrageneric Classification of Salix (Salicaceae) in the New World

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Taxonomic revision of the Spermatopsida of the Oligocene Creede flora, southern Colorado

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Evolution of Catkins: Inflorescence Morphology of Selected Salicaceae in an Evolutionary and Developmental Context

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Phylogenetic and Taxonomic Status Analyses of the Abaso Section from Multiple Nuclear Genes and Plastid Fragments Reveal New Insights into the North America Origin of Populus (Salicaceae)

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Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data

inferredcites →https://doi.org/10.3389/fpls.2021.662715openalex-snapshot

Highly Diverse Shrub Willows (Salix L.) Share Highly Similar Plastomes

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Phylogenomics and Biogeography of Populus Based on Comprehensive Sampling Reveal Deep-Level Relationships and Multiple Intercontinental Dispersals

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The Evolutionary History, Diversity, and Ecology of Willows (Salix L.) in the European Alps

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An extinct genus of Salicaceae based on twigs with attached flowers, fruits, and foliage from the Eocene Green River Formation of Utah and Colorado, USA

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HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment

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Plant Speciation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-3-031-50787-8_1openalex-snapshot

Poplar Genomics: An Introduction

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107869openalex-snapshot

Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

inferred← citeshttps://doi.org/10.33915/etd.12125openalex-snapshot

The Birds and The Bees and The Willows: Understanding the reproductive biology of Salix nigra Marsh.

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Building better biofuel crops: A field evaluation of transgenic Populus modified to improve feedstock performance for bioenergy use

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