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2025
A phylogenomic approach to disentangling the evolution of the large and diverse daisy tribe Anthemideae (Asteraceae)
Journal of Systematics and Evolution
2025
Genetic traceability, conservation effectiveness, and selection signatures analysis based on ancestral information: a case study of Beijing-You chicken
BMC Genomics
2025
Phylogenomic resolution of lampreys reveals the recent evolution of an ancient vertebrate lineage
Proceedings of the Royal Society B: Biological Sciences
2025
Phylotranscriptomics provides insights into the Mesoproterozoic-Neoproterozoic origin and diversification of green algae Trebouxiophyceae
Cell Reports
2025
Comparative analysis of the mitochondrial genomes of the soft-shelled turtles Palea steindachneri and Pelodiscus axenaria and phylogenetic implications for Trionychia
Scientific Reports
2025
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants
Systematic Biology
2025
Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae)
Systematic Biology
2025
Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds
Biology Letters
2025
Introgression across Narrow Contact Zones Shapes the Genomic Landscape of Phylogenetic Variation in an African Bird Clade
Systematic Biology
2025
Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River
Systematic Biology
2025
Phylogenomics reveals the slow-burning fuse of diatom evolution
Proceedings of the National Academy of Sciences
2025
Thrushes in Love: Extensive Gene Flow, With Differential Resistance and Selection, Obscures and Reveals the Evolutionary History of a Songbird Clade
Molecular Ecology
2025
CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes
BMC Bioinformatics
2025
PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets
Systematic Biology
2025
Recombination-aware phylogenomics
Trends in Ecology & Evolution
2025
Comparative Analysis of Mitogenomic and Nuclear Gene Data Reveals Phylogenetic Implications, Divergence Times, and Historical Biogeography in the Subfamily Pyrginae (Lepidoptera: Hesperiidae)
Ecology and Evolution
2024
Phylogenomic species delimitation of the twisted‐winged parasite genus Stylops (Strepsiptera)
Systematic Entomology
2024
Large‐scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea)
Cladistics
2024
Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola)
Molecular Phylogenetics and Evolution
2024
The Meaning and Measure of Concordance Factors in Phylogenomics
Molecular Biology and Evolution
2024
Complexity of avian evolution revealed by family-level genomes
Nature
2024
Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc
Integrative And Comparative Biology
2024
Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements
Molecular Phylogenetics and Evolution
2024
Seeking the identity of an enigmatic moss by embracing phylogenomics
Journal of Systematics and Evolution
2024
Leveraging museum specimens, genomics and legacy datasets to unravel the phylogeny and biogeography of cryptin wasps (Hymenoptera, Ichneumonidae, Cryptini)
Zoologica Scripta
2023
Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex
BMC Ecology and Evolution
2023
Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation
American Journal of Botany
2023
Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius)
Systematic Entomology
2023
Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters
Nucleic Acids Research
2023
ExRec: a python pipeline for generating recombination-filtered multi-locus datasets
Bioinformatics Advances
2023
Estimating transcriptome complexities across eukaryotes
BMC Genomics
2023
Ancistroceruswasps (Hymenoptera, Vespidae) from the Centre of Europe: Phylogeny, cryptic species, neutral and non‐neutral markers
Zoologica Scripta
2023
Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles
Animals
2023
Phylogenetic challenges in a recently diversified and polyploid-rich Alyssum (Brassicaceae) lineage: low divergence, reticulation, and parallel polyploid speciation
Evolution
2023
Systematics and evolution of predatory flower flies (Diptera: Syrphidae) based on exon‐capture sequencing
Systematic Entomology
2023
Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
2023
Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus
Molecular Biology and Evolution
2023
The genomes of Scedosporium between environmental challenges and opportunism
IMA Fungus
2023
Multiple origins of mountain biodiversity in New Zealand's largest plant radiation
Journal of Biogeography
2023
PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance
Molecular Biology and Evolution
2022
Plant migration under long‐lasting hyperaridity – phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth
New Phytologist
2022
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics
Systematic Biology
2022
Cell types as species: Exploring a metaphor
Frontiers in Plant Science
2022
Phylogenomics reveals extensive introgression and a case of mito-nuclear discordance in the killifish genus Kryptolebias
Molecular Phylogenetics and Evolution
2022
Omics in Horticultural Crops
2022
The Frequency and Topology of Pseudoorthologs
Systematic Biology
2022
A Practical Guide to Design and Assess a Phylogenomic Study
Genome Biology and Evolution
2022
Systematics of Thraupis (Aves, Passeriformes) reveals an extensive hybrid zone between T. episcopus (Blue-gray Tanager) and T. sayaca (Sayaca Tanager)
PLOS ONE
2022
Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication
Systematic Biology
2022
Incomplete lineage sorting and phenotypic evolution in marsupials
Cell
2022
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi
Systematic Biology
2022
Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation
Annals of Botany
2022
Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects
Genes
2022
Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship among Pinus species
Saudi Journal of Biological Sciences
2022
The evolution of insular woodiness
Proceedings of the National Academy of Sciences
2022
Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses
Molecular Phylogenetics and Evolution
2021
Brown trout phylogenetics: A persistent mirage towards (too) many species
Journal of Fish Biology
2021
Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree
Genome Biology and Evolution
2021
Genes with evidence of positive selection as potentially related to coloniality and the evolution of morphological features among the lophophorates and entoprocts
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
2021
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere
Systematic Biology
2021
PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments
Bioinformatics
2021
Phylogenomics and evolutionary history of Oreobates (Anura: Craugastoridae) Neotropical frogs along elevational gradients
Molecular Phylogenetics and Evolution
2021
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data
Systematic Biology
2021
Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species ofMauritiella
Systematic Botany
2021
What Have We Learned from the First 500 Avian Genomes?
Annual Review of Ecology, Evolution, and Systematics
2021
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study onPseudapisBees
Systematic Biology
2021
Assessing support for Blaberoidea phylogeny suggests optimal locus quality
Systematic Entomology
2021
Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of neotropical true fruit flies (Anastrepha: Tephritidae)
Molecular Phylogenetics and Evolution
2021
Next-generation cophylogeny: unravelling eco-evolutionary processes
Trends in Ecology & Evolution
2021
Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny
Molecular Phylogenetics and Evolution
2021
New Approaches for Inferring Phylogenies in the Presence of Paralogs
Trends in Genetics
2021
Ancient hybridization patterns between bighorn and thinhorn sheep
Molecular Ecology
2021
Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest
Molecular Phylogenetics and Evolution
2021
Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation
Annual Review of Animal Biosciences
2021
Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control
G3 Genes|Genomes|Genetics
2020
Emerging Frontiers in the Study of Molecular Evolution
Journal of Molecular Evolution
2020
Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents
Systematic Biology
2020
The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
Systematic Biology
2020
A multilocus phylogeny of the non-photosynthetic parasitic plant Cistanche (Orobanchaceae) refutes current taxonomy and identifies four major morphologically distinct clades
Molecular Phylogenetics and Evolution
2020
What is truth: Consensus and discordance in next‐generation phylogenetic analyses of Daucus
Journal of Systematics and Evolution
2020
Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data
Systematic Biology
2020
Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace
Brazilian Journal of Botany
2020
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds
Proceedings of the National Academy of Sciences
2020
Species Diversity in the Braconid Wasp Genus Allorhogas (Doryctinae) Associated With Cynipid Galls on Live Oaks (Quercus: Fagaceae) Using Natural History, Phylogenetics, and Morphology
Insect Systematics and Diversity
2020
Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae
Scientific Reports
2020
Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish
Systematic Biology
2020
A review of the systematics, species identification and diagnostics of the Trypanosomatidae using the maxicircle kinetoplast DNA: from past to present
International Journal for Parasitology
2020
A new taxonomic backbone for the infrageneric classification of the species‐rich genus Silene (Caryophyllaceae)
TAXON
2020
Challenges facing systematic biology
TAXON
2020
How well do multispecies coalescent methods perform with mitochondrial genomic data? A case study of butterflies and moths (Insecta: Lepidoptera)
Systematic Entomology
2020
Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq
Applications in Plant Sciences
2020
Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with genotyping‐by‐sequencing data and niche modelling
Journal of Biogeography
2020
TREEasy: An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data
Molecular Ecology Resources
2020
Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers
AoB PLANTS
2019
Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies
Diversity
2019
Species limits in butterflies (Lepidoptera: Nymphalidae): reconciling classical taxonomy with the multispecies coalescent
Systematic Entomology
2019
Phylogenetic relationships and historical biogeography of Oligosarcus (Teleostei: Characidae): Examining riverine landscape evolution in southeastern South America
Molecular Phylogenetics and Evolution
2019
Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics
Insect Systematics and Diversity
2019
Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary
Frontiers in Genetics
2019
Phylogenetic Relationships in Orobanchaceae Inferred From Low-Copy Nuclear Genes: Consolidation of Major Clades and Identification of a Novel Position of the Non-photosynthetic Orobanche Clade Sister to All Other Parasitic Orobanchaceae
Frontiers in Plant Science
2019
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone
Systematic Biology
2019
Methods in Molecular Biology
2019
A New Species of Ancylostoma (Nemata: Strongylida: Ancylostomatidae) from Two Species of Ctenomys in Lowland Bolivia
Journal of Parasitology
2019
Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species
Molecular Biology and Evolution
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