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Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

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

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Lattice: Multivariate Data Visualization with R

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ggplot2: Elegant Graphics for Data Analysis

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Effects of missing data on species tree estimation under the coalescent

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Multi-allele species reconstruction using ASTRAL

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Global peatland dynamics since the Last Glacial Maximum

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Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss)

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adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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hierfstat , a package for r to compute and test hierarchical F ‐statistics

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NORTH AMERICAN ORIGIN AND RECENT EUROPEAN ESTABLISHMENTS OF THE AMPHI-ATLANTIC PEAT MOSS SPHAGNUM ANGERMANICUM

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Spore rain in relation to regional sources and beyond

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phytools: an R package for phylogenetic comparative biology (and other things)

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inferredcites →https://doi.org/10.25227/linbg.01107openalex-snapshot

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inferredcites →https://doi.org/10.3732/ajb.1000055openalex-snapshot

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inferredcites →https://doi.org/10.3732/ajb.1100410openalex-snapshot

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Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108361openalex-snapshot

Phylogenomics provides new insight into the phylogeny and diversification of Asian Lappula (Boraginaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108421openalex-snapshot

Integrated morphological and phylogenomic analyses revealed a novel genus Paramicrotoena (Lamiaceae − Pogostemoneae) discovered in the Pan-Himalaya

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108472openalex-snapshot

Hybridization and incomplete lineage sorting characterize the evolutionary history of two East Asian clades of Stewartia (Theaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108476openalex-snapshot

Incomplete lineage sorting, hybridization and polyploidization blurred phylogenetic relationships of gentians from the Qinghai-Tibetan Plateau

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108591openalex-snapshot

The species delimitation challenge resulting from mito-nuclear discordance: A case of Macroscytus burrower bugs from China (Hemiptera: Heteroptera: Cydnidae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108687openalex-snapshot

Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108700openalex-snapshot

Phylogenomics reveal extensive phylogenetic discordances in Diospyros (Ebenaceae) of China

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108745openalex-snapshot

Phylogenomics provides comprehensive insights into the phylogenetic and evolutionary uncertainty in Allium subgenus Alpinoprasum (Amaryllidaceae)

inferred← citeshttps://doi.org/10.1038/s41477-022-01333-5openalex-snapshot

Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics

inferred← citeshttps://doi.org/10.1038/s41576-023-00620-xopenalex-snapshot

Incongruence in the phylogenomics era

inferred← citeshttps://doi.org/10.1038/s41586-024-07447-4openalex-snapshot

The rise of baobab trees in Madagascar

inferred← citeshttps://doi.org/10.1038/s41588-025-02294-zopenalex-snapshot

Super-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity

inferred← citeshttps://doi.org/10.1038/s41598-024-83292-9openalex-snapshot

Subfamily evolution analysis using nuclear and chloroplast data from the same reads

inferred← citeshttps://doi.org/10.1038/s42003-025-08120-wopenalex-snapshot

Standing genetic variation and introgression shape the cryptic radiation of Aquilegia in the mountains of Southwest China

inferred← citeshttps://doi.org/10.1073/pnas.2121819119openalex-snapshot

Genomic insights into zokors’ phylogeny and speciation in China

inferred← citeshttps://doi.org/10.1073/pnas.2121822119openalex-snapshot

Sympatric speciation of the spiny mouse from Evolution Canyon in Israel substantiated genomically and methylomically

inferred← citeshttps://doi.org/10.1080/03736687.2023.2188389openalex-snapshot

A molecular and morphological study of Leucobryum in Britain and Europe: the presence of L. albidum (P.Beauv.) Lindb. confirmed

inferred← citeshttps://doi.org/10.1080/03736687.2024.2318161openalex-snapshot

Phylogeographical patterns in the northwestern European moss Scorpidium revolvens (Sw. ex Anonymo) Rubers (Scorpidiaceae, Bryophyta)

inferred← citeshttps://doi.org/10.1086/724310openalex-snapshot

Diversification and Biogeography of North American Thistles (Cirsium: Carduoideae: Compositae): Drivers of a Rapid Continent-Wide Radiation

inferred← citeshttps://doi.org/10.1093/aob/mcac113openalex-snapshot

Phylotranscriptomics of liverworts: revisiting the backbone phylogeny and ancestral gene duplications

inferred← citeshttps://doi.org/10.1093/aob/mcae224openalex-snapshot

Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting in the rapidly radiated East Asian genus Nekemias (Vitaceae)

inferred← citeshttps://doi.org/10.1093/aob/mcaf002openalex-snapshot

Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification

inferred← citeshttps://doi.org/10.1093/aob/mcaf329openalex-snapshot

Genomic insights into the rapid diversification of Petunia in a biodiversity hotspot in the South American grasslands

inferred← citeshttps://doi.org/10.1093/botlinnean/boab060openalex-snapshot

Adaptive divergence in the neglected alpine mossLewinskya killiasii(Orthotrichaceae), an example of vicariance on different rock types in bryophytes

inferred← citeshttps://doi.org/10.1093/botlinnean/boaf077openalex-snapshot

Molecular species delimitation of Sphagnum subgenus Subsecunda in Europe

inferred← citeshttps://doi.org/10.1093/evolut/qpag085openalex-snapshot

Diversification and divergence in Myioborus warblers: insights into evolutionary relationships and plumage genetics

inferred← citeshttps://doi.org/10.1093/hr/uhae103openalex-snapshot

Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot

inferred← citeshttps://doi.org/10.1093/jxb/erac052openalex-snapshot

An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes

inferred← citeshttps://doi.org/10.1093/plphys/kiac276openalex-snapshot

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage

inferred← citeshttps://doi.org/10.1093/sysbio/syac017openalex-snapshot

Origin and Diversification of the Saguaro Cactus (Carnegiea gigantea): A Within-Species Phylogenomic Analysis

inferred← citeshttps://doi.org/10.1093/sysbio/syac062openalex-snapshot

Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)

inferred← citeshttps://doi.org/10.1093/sysbio/syad008openalex-snapshot

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

inferred← citeshttps://doi.org/10.1093/sysbio/syad077openalex-snapshot

Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information

inferred← citeshttps://doi.org/10.1093/sysbio/syae018openalex-snapshot

Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and Sistrurus )

inferred← citeshttps://doi.org/10.1093/sysbio/syae036openalex-snapshot

Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies

inferred← citeshttps://doi.org/10.1093/sysbio/syae049openalex-snapshot

Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)

inferred← citeshttps://doi.org/10.1093/sysbio/syaf016openalex-snapshot

Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae)

inferred← citeshttps://doi.org/10.1093/sysbio/syaf052openalex-snapshot

Species Diversification in the Sky Islands of Southwestern China Revealed by Genomic, Introgression, and Demographic Analyses of Asian Shrew Moles

inferred← citeshttps://doi.org/10.1093/sysbio/syaf053openalex-snapshot

Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC

inferred← citeshttps://doi.org/10.1093/sysbio/syaf069openalex-snapshot

Nuclear Phylogenomic Insights into Relationships, Support, and Conflict Among the Early Diverging Lineages of the Megadiverse Epidendroid Orchids

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlaf199openalex-snapshot

Whole-genome sequencing uncovers genomic divergence and gene flow in closely related virus-harbouring horseshoe bats ( Rhinolophus )

inferred← citeshttps://doi.org/10.1101/2022.07.08.499304openalex-snapshot

Extensive hybridisation throughout clownfishes evolutionary history

inferred← citeshttps://doi.org/10.1101/2023.01.10.523206openalex-snapshot

Introgressive Descent and Hypersexuality Drive The Evolution Of Sexual Parasitism and Morphological Reduction In a Fungal Species Complex

inferred← citeshttps://doi.org/10.1101/2024.03.11.584438openalex-snapshot

Islands promote diversification within the silvereye clade: a phylogenomic analysis of a great speciator

inferred← citeshttps://doi.org/10.1101/2024.07.29.605463openalex-snapshot

Unraveling the Web of Life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species

inferred← citeshttps://doi.org/10.1111/1755-0998.70029openalex-snapshot

Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species

inferred← citeshttps://doi.org/10.1111/1755-0998.70161openalex-snapshot

Combining Annotation Software to Identify Orthologous Genes ( CASIO ) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies

inferred← citeshttps://doi.org/10.1111/ele.14359openalex-snapshot

A phylogenomic perspective on interspecific competition

inferred← citeshttps://doi.org/10.1111/eva.13767openalex-snapshot

Linked Selection and Gene Density Shape Genome‐Wide Patterns of Diversification in Peatmosses

inferred← citeshttps://doi.org/10.1111/jipb.13415openalex-snapshot

Phylogenomics and the flowering plant tree of life

inferred← citeshttps://doi.org/10.1111/jse.12931openalex-snapshot

Integrative taxonomy of the stalk‐eyed bug genus Chauliops (Heteroptera: Malcidae: Chauliopinae) reveals orogeny‐driven speciation

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/jse.70061openalex-snapshot

The uplift of the Qinghai–Xizang Plateau and global climate cooling triggered spatiotemporal evolution of Lonicera (Caprifoliaceae)

inferred← citeshttps://doi.org/10.1111/jse.70102openalex-snapshot

From genomes to graphs: Why macroevolution still matters in the pangenome era

inferred← citeshttps://doi.org/10.1111/mec.17082openalex-snapshot

Multiple paths toward repeated phenotypic evolution in the spiny‐leg adaptive radiation ( Tetragnatha ; Hawai'i)

inferred← citeshttps://doi.org/10.1111/mec.17569openalex-snapshot

Contrast and Genomic Characterisation of Ancient and Recent Interspecific Introgression Between Deeply Diverged Moustache Toads (Leptobrachium)

inferred← citeshttps://doi.org/10.1111/mec.17830openalex-snapshot

Islands Promote Diversification of the Silvereye Species Complex: A Phylogenomic Analysis of a Great Speciator

inferred← citeshttps://doi.org/10.1111/mec.70306openalex-snapshot

Phylogeomics Reveals Ancestral Introgression and Paleogeoclimate Co‐Facilitated Speciation and Diversification of Chinese Endemic Cavefishes

inferred← citeshttps://doi.org/10.1111/nph.18219openalex-snapshot

Rampant nuclear–mitochondrial–plastid phylogenomic discordance in globally distributed calcifying microalgae

inferred← citeshttps://doi.org/10.1111/nph.18297openalex-snapshot

Genomic consequences of artificial selection during early domestication of a wood fibre crop

inferred← citeshttps://doi.org/10.1111/nph.18525openalex-snapshot

Whole‐genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot

inferred← citeshttps://doi.org/10.1111/nph.70039openalex-snapshot

Unraveling the extensive phylogenetic discordance and evolutionary history of spurless taxa within the Aquilegia ecalcarata complex

inferred← citeshttps://doi.org/10.1111/nph.70360openalex-snapshot

Ancient hybridization drives arid adaptation and species diversification in Caragana (Fabaceae)

inferred← citeshttps://doi.org/10.1111/syen.12592openalex-snapshot

Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius )

inferred← citeshttps://doi.org/10.1111/syen.12686openalex-snapshot

Extensive hybridisation and complex evolutionary history in the leafhopper genus Agnesiella (Hemiptera: Cicadellidae: Typhlocybinae)

inferred← citeshttps://doi.org/10.1111/tpj.16480openalex-snapshot

Reticulate evolution of the tertiary relict Osmanthus

inferred← citeshttps://doi.org/10.1128/mbio.02133-24openalex-snapshot

Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi

inferred← citeshttps://doi.org/10.1134/s2079086422030045openalex-snapshot

Approaches to the Detection of Hybridization Events and Genetic Introgression upon Phylogenetic Incongruence

inferred← citeshttps://doi.org/10.1139/gen-2025-0118openalex-snapshot

Unraveling evolutionary relationships in the Sida generic alliance (Malvaceae, Malvoideae): a phylogenetic and cytotaxonomic overview

inferred← citeshttps://doi.org/10.1186/s12864-025-11763-yopenalex-snapshot

Comparative analysis of plastome structure in Sphagnum species from China

inferred← citeshttps://doi.org/10.1186/s12870-024-04917-9openalex-snapshot

Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.1186/s12870-025-06963-3openalex-snapshot

Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae)

inferred← citeshttps://doi.org/10.1186/s12870-025-06982-0openalex-snapshot

Phylogenomics of East Asian lineage within subgenus Anguinum (Allium, Amaryllidaceae): insights into its taxonomic puzzles and phylogenetic conflicts

inferred← citeshttps://doi.org/10.1186/s12870-026-08791-5openalex-snapshot

Comparative chloroplast genomics of Hibiscus (Malvaceae) and its phylogenetic implications

inferred← citeshttps://doi.org/10.1186/s12915-022-01297-0openalex-snapshot

Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

inferred← citeshttps://doi.org/10.1371/journal.pbio.3001827openalex-snapshot

OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

inferred← citeshttps://doi.org/10.15298/arctoa.31.15openalex-snapshot

On the morphological delimitation Of Sphagnum henryense

inferred← citeshttps://doi.org/10.15298/arctoa.32.15openalex-snapshot

Sphagnum Warnstorfii complex in Northern Asia

inferred← citeshttps://doi.org/10.1639/0007-2745-125.1.102openalex-snapshot

Potentially misleading phylogenetic signal and its explanation in single species studies – contrasting Loeskypnum badium, Sarmentypnum exannulatum and Warnstorfia fluitans

inferred← citeshttps://doi.org/10.2139/ssrn.4828563openalex-snapshot

Deciphering the Reticulate Evolution and Phylo-Biogeography of Ant-Ferns Lecanopteris S.S

inferred← citeshttps://doi.org/10.2139/ssrn.4884258openalex-snapshot

Phylogenomics of Paragymnopteris S.L. (Cheilanthoideae, Pteridaceae) with the Segeration of Sericopteris Gen. Nov

inferred← citeshttps://doi.org/10.2139/ssrn.6097240openalex-snapshot

Discerning incomplete lineage sorting and reticulate evolution—the case of Hoya (Apocynaceae)

inferred← citeshttps://doi.org/10.2139/ssrn.6553953openalex-snapshot

First molecular evidence for ancient hybridization in Hoya (Apocynaceae)

inferred← citeshttps://doi.org/10.24072/pcjournal.359openalex-snapshot

An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla

inferred← citeshttps://doi.org/10.25227/linbg.01161openalex-snapshot

Sphagnum magniporosum (Sphagnaceae, subgenus Subsecunda) a new peatmoss species from Venezuela

inferred← citeshttps://doi.org/10.33612/diss.985985382openalex-snapshot

The Evolutionary History of Baleen Whales in The Genome Era

inferred← citeshttps://doi.org/10.3389/fpls.2022.1045423openalex-snapshot

Phylogenomic analyses based on the plastid genome and concatenated nrDNA sequence data reveal cytonuclear discordance in genus Atractylodes (Asteraceae: Carduoideae)

inferred← citeshttps://doi.org/10.3389/fpls.2022.882960openalex-snapshot

An NGS-Based Phylogeny of Orthotricheae (Orthotrichaceae, Bryophyta) With the Proposal of the New Genus Rehubryum From Zealandia

inferred← citeshttps://doi.org/10.3389/fpls.2024.1340056openalex-snapshot

Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales)

inferred← citeshttps://doi.org/10.3389/fpls.2025.1544247openalex-snapshot

Intergeneric and interspecific relationships in tribe Ricineae revealed by phylogenomics of the plastome and transcriptome

inferred← citeshttps://doi.org/10.3390/genes17040455openalex-snapshot

Morphological and Cyto-Nuclear Conflicting Signals Across Non-Sister Lineages in Darkling Beetles (Tenebrionidae: Akis)

inferred← citeshttps://doi.org/10.3390/jof8010002openalex-snapshot

Twelve New Species Reveal Cryptic Diversification in Foliicolous Lichens of Strigula s.lat. (Strigulales, Ascomycota)

inferred← citeshttps://doi.org/10.3390/life15091446openalex-snapshot

Mouflon and Domestic Sheep Phylogeny: Ancestry, Domestication, and Evolutionary Dynamics

inferred← citeshttps://doi.org/10.3390/plants12061250openalex-snapshot

De Novo Transcriptome Assembly and Comparative Analysis of Differentially Expressed Genes Involved in Cold Acclimation and Freezing Tolerance of the Arctic Moss Aulacomnium turgidum (Wahlenb.) Schwaegr

inferred← citeshttps://doi.org/10.3390/plants14132083openalex-snapshot

Phylogenomic Analyses Reveal Species Relationships and Phylogenetic Incongruence with New Member Detected in Allium Subgenus Cyathophora

inferred← citeshttps://doi.org/10.3390/plants14152373openalex-snapshot

Phylogenetic Insights from a Novel Rehubryum Species Challenge Generic Boundaries in Orthotrichaceae

inferred← citeshttps://doi.org/10.3390/plants15081261openalex-snapshot

The Importance of the Physcomitrium patens Genome in the Evolutionary Genomics of Terrestrial Plants

inferred← citeshttps://doi.org/10.3897/phytokeys.213.82627openalex-snapshot

Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae)

inferred← citeshttps://doi.org/10.6084/m9.figshare.25591262openalex-snapshot

Additional file 1 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.25591517openalex-snapshot

Additional file 2 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.26705349openalex-snapshot

Additional file 3 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.26705352openalex-snapshot

Additional file 4 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.26705355openalex-snapshot

Additional file 5 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.26705358openalex-snapshot

Additional file 6 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.26705361openalex-snapshot

Additional file 7 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.26705364openalex-snapshot

Additional file 8 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.26705367openalex-snapshot

Additional file 9 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.6084/m9.figshare.26705370openalex-snapshot

Additional file 10 of Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

inferred← citeshttps://doi.org/10.64898/2025.12.17.694994openalex-snapshot

Bypassing the Batch Effects to Improve the Reusability of RAD-seq Data: A Case Study of Recurrent Hybridization in the Japanese Torreya Species Complex

inferred← citeshttps://doi.org/10.64898/2026.02.01.702050openalex-snapshot

An Integrative Phylogenomic Framework Quantifies the Dominant Role of Introgression in Phylogenetic Discordance among Diploid Oryza Species

inferred← citeshttps://doi.org/10.64898/2026.03.04.709403openalex-snapshot

PhyloNOW: Using Variable Window Sizes for Phylogenomic Analyses of Whole Genome Alignments

inferred← citeshttps://doi.org/10.70675/93c8ab12z165ez4242zb0a2z28dc994375e4openalex-snapshot

Analyse taxonomique intégrative des espèces cubaines de Magnolia subsect. Talauma (Magnoliaceae)

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