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Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora.

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What this work says

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

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Inferring Evolutionary Trees with PAUP *

inferredcites →https://doi.org/10.1002/ajb2.1468openalex-snapshot

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

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Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree

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Non-invasive genetic sampling and individual identification

inferredcites →https://doi.org/10.1007/s10592-005-9073-xopenalex-snapshot

Development and characterization of polymorphic microsatellite loci in endangered fern Adiantum reniforme var. sinense

inferredcites →https://doi.org/10.1007/s12686-017-0948-1openalex-snapshot

Characterization of the complete plastome of western red cedar, Thuja plicata (Cupressaceae)

inferredcites →https://doi.org/10.1016/j.cub.2018.08.041openalex-snapshot

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

inferredcites →https://doi.org/10.1016/j.molp.2020.11.008openalex-snapshot

Hybrid speciation via inheritance of alternate alleles of parental isolating genes

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A new discovery of Chamaecyparis from the Lower Cretaceous of Inner Mongolia, North China and its significance

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Taxon sampling effects in molecular clock dating: An example from the African Restionaceae

inferredcites →https://doi.org/10.1016/j.ympev.2008.02.001openalex-snapshot

Reticulate evolution in Thuja inferred from multiple gene sequences: Implications for the study of biogeographical disjunction between eastern Asia and North America

inferredcites →https://doi.org/10.1016/j.ympev.2014.02.005openalex-snapshot

Evolution and biogeography of gymnosperms

inferredcites →https://doi.org/10.1016/j.ympev.2018.10.033openalex-snapshot

Multi-allele species reconstruction using ASTRAL

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Miocene climate change as a driving force for multiple origins of annual species in Astragalus (Fabaceae, Papilionoideae)

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Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae)

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Multilocus data reveal deep phylogenetic relationships and intercontinental biogeography of the Eurasian-North American genus Corylus (Betulaceae)

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Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution

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The origin and evolution of tertiary relict floras

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An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics

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The complete genome sequence of a Neanderthal from the Altai Mountains

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

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Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot

ModelFinder: fast model selection for accurate phylogenetic estimates

inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

inferredcites →https://doi.org/10.1038/s41559-018-0777-yopenalex-snapshot

Insights from genomes into the evolutionary importance and prevalence of hybridization in nature

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Ancient admixture from an extinct ape lineage into bonobos

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Phylogenetic tree building in the genomic age

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Million-year-old DNA sheds light on the genomic history of mammoths

inferredcites →https://doi.org/10.1038/s42003-018-0176-6openalex-snapshot

Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent

inferredcites →https://doi.org/10.1046/j.1095-8339.2002.00087.xopenalex-snapshot

Thuja sutchuenensis: a rediscovered species of the Cupressaceae

inferredcites →https://doi.org/10.1073/pnas.1114319109openalex-snapshot

Distribution of living Cupressaceae reflects the breakup of Pangea

inferredcites →https://doi.org/10.1080/10635150500354928openalex-snapshot

Inferring Phylogeny Despite Incomplete Lineage Sorting

inferredcites →https://doi.org/10.1086/323278openalex-snapshot

Phylogenetic Patterns in Northern Hemisphere Plant Geography

inferredcites →https://doi.org/10.1086/323880openalex-snapshot

The Use of Geological and Paleontological Evidence in Evaluating Plant Phylogeographic Hypotheses in the Northern Hemisphere Tertiary

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

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Northern Hemisphere Plant Disjunctions: A Window on Tertiary Land Bridges and Climate Change?

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APE: Analyses of Phylogenetics and Evolution in R language

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

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Fast and accurate short read alignment with Burrows–Wheeler transform

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DensiTree: making sense of sets of phylogenetic trees

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DendroPy: a Python library for phylogenetic computing

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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

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Trimmomatic: a flexible trimmer for Illumina sequence data

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Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids

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PAML 4: Phylogenetic Analysis by Maximum Likelihood

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Testing for Ancient Admixture between Closely Related Populations

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

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Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot

UFBoot2: Improving the Ultrafast Bootstrap Approximation

inferredcites →https://doi.org/10.1093/molbev/msy147openalex-snapshot

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

inferredcites →https://doi.org/10.1093/molbev/msz142openalex-snapshot

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

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“Ghost Introgression” As a Cause of Deep Mitochondrial Divergence in a Bird Species Complex

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RASP 4: Ancestral State Reconstruction Tool for Multiple Genes and Characters

inferredcites →https://doi.org/10.1093/molbev/msz296openalex-snapshot

A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

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PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

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Sequence-Repeat Polymorphisms Exhibit the Signature of Recombination in Lodgepole Pine Chloroplast DNA

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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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Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)

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The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

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Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

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Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades

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Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

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Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species

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Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms

inferredcites →https://doi.org/10.1093/sysbio/syy015openalex-snapshot

Inferring Phylogenetic Networks Using PhyloNet

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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

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Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)

inferredcites →https://doi.org/10.1098/rstbopenalex-snapshot

Philosophical Transactions of the Royal Society B: biological sciences

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Patterns in the assembly of temperate forests around the Northern Hemisphere

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Practical Aspects of Phylogenetic Network Analysis Using PhyloNet

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Biological Journal of the Linnean Society

inferredcites →https://doi.org/10.1111/2041-210x.12846openalex-snapshot

Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models

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Phylogeny and Biogeography of Thuja L. (Cupressaceae), an Eastern Asian and North American Disjunct Genus

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Proceedings of the National Academy of Sciences of the United States of America

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Conceptual and statistical problems with the DEC +J model of founder‐event speciation and its comparison with DEC via model selection

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Maple phylogeny and biogeography inferred from phylogenomic data

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The on‐again, off‐again relationship between mitochondrial genomes and species boundaries

inferredcites →https://doi.org/10.1111/mec.14097openalex-snapshot

Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor

inferredcites →https://doi.org/10.1111/mec.14909openalex-snapshot

Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

inferredcites →https://doi.org/10.1111/mec.15407openalex-snapshot

Allopatric divergence and hybridization withinCupressus chengiana(Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China

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Puzzling rocks and complicated clocks: how to optimize molecular dating approaches in historical phytogeography

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Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

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Trends, Rhythms, and Aberrations in Global Climate 65 Ma to Present

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A Draft Sequence of the Neandertal Genome

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

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Evolution of Eastern Asian and Eastern North American Disjunct Distributions in Flowering Plants

inferredcites →https://doi.org/10.1155/2020/8426287openalex-snapshot

Plastome Phylogenomic and Biogeographical Study on Thuja (Cupressaceae)

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A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

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Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy

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OrthoFinder: phylogenetic orthology inference for comparative genomics

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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

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inferredcites →https://doi.org/10.3389/fpls.2015.00586openalex-snapshot

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A major reorganization of Asian climate by the early Miocene

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EvobiR: Tools for comparative analyses and teaching evolutionary biology.

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Conifers of the world: the complete reference

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What points at this work

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

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inferred← citeshttps://doi.org/10.1111/jse.13179openalex-snapshot

Genomic vulnerability and local adaptation of an arid tolerant tree species on the Qinghai–Tibet Plateau

inferred← citeshttps://doi.org/10.1111/jse.70005openalex-snapshot

Advancing plant phylogenetics and evolution through genomic data bursts and methodological innovations

inferred← citeshttps://doi.org/10.1111/jse.70013openalex-snapshot

A cautionary note on using STRUCTURE to detect hybridization in a phylogenetic context

inferred← citeshttps://doi.org/10.1111/mec.16325openalex-snapshot

When tropical and subtropical congeners met: Multiple ancient hybridization events within Eriobotrya in the Yunnan‐Guizhou Plateau, a tropical‐subtropical transition area in China

inferred← citeshttps://doi.org/10.1111/mec.70072openalex-snapshot

Ecological Selection as Drivers During Early Speciation: Insights From Two Allopatric Cypress Species in the Himalaya

inferred← citeshttps://doi.org/10.1111/tpj.16859openalex-snapshot

Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species

inferred← citeshttps://doi.org/10.1186/s12870-024-05073-wopenalex-snapshot

Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer

inferred← citeshttps://doi.org/10.18061/bssb.v2i2.9255openalex-snapshot

Perspectives on the Grey Zone of Species Delimitation With Notes on Invertebrates in the Marine Environment

inferred← citeshttps://doi.org/10.22621/cfn.v137i1.3193openalex-snapshot

The lichen genus Rinodina (Physciaceae) in New Brunswick, Canada

inferred← citeshttps://doi.org/10.2737/sna.thuja.occidentalisopenalex-snapshot

Northern white-cedar (Thuja occidentalis)

inferred← citeshttps://doi.org/10.3390/plants12122237openalex-snapshot

Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)

inferred← citeshttps://doi.org/10.3390/su151411035openalex-snapshot

Estimation of Potential Suitable Habitats for the Relict Plant Euptelea pleiosperma in China via Comparison of Three Niche Models

inferred← citeshttps://doi.org/10.64898/2026.02.14.705539openalex-snapshot

TriMouNet: An Algorithm for Inferring Level-1 Phylogenetic Networks from Multi-Locus Gene Tree Distributions

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