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Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)

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

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Holarctic Evolution and Dispersal of Squirrels (Rodentia: Sciuridae)
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Missing data and the design of phylogenetic analyses
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Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
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Computational approaches to species phylogeny inference and gene tree reconciliation
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Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi)
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Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
inferredcites →https://doi.org/10.1016/j.ympev.2015.05.027openalex-snapshot
Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes
inferredcites →https://doi.org/10.1016/j.ympev.2015.07.018openalex-snapshot
The gene tree delusion
inferredcites →https://doi.org/10.1016/j.ympev.2016.04.015openalex-snapshot
Phylogenomic analyses reveal novel relationships among snake families
inferredcites →https://doi.org/10.1016/j.ympev.2016.05.040openalex-snapshot
Rapid divergence and gene flow at high latitudes shape the history of Holarctic ground squirrels (Urocitellus)
inferredcites →https://doi.org/10.1016/s1055-7903(03)00204-5openalex-snapshot
Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1
inferredcites →https://doi.org/10.1017/cbo9780511541438.022openalex-snapshot
Sciuridae
inferredcites →https://doi.org/10.1017/cbo9781107360150.010openalex-snapshot
Marmot evolution and global change in the past 10 million years
inferredcites →https://doi.org/10.1023/b:jomm.0000015105.96065.f0openalex-snapshot
Phylogeny and Evolutionary History of the Ground Squirrels (Rodentia: Marmotinae)
inferredcites →https://doi.org/10.1027/1614-2241/a000062openalex-snapshot
How Low Can You Go?
inferredcites →https://doi.org/10.1038/hdy.2014.27openalex-snapshot
Divergence with gene flow within the recent chipmunk radiation (Tamias)
inferredcites →https://doi.org/10.1038/nature12130openalex-snapshot
Inferring ancient divergences requires genes with strong phylogenetic signals
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/s41598-017-16810-7openalex-snapshot
Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering
inferredcites →https://doi.org/10.1073/pnas.0505700102openalex-snapshot
Decoupled taxonomic radiation and ecological expansion of open-habitat grasses in the Cenozoic of North America
inferredcites →https://doi.org/10.1073/pnas.1211733109openalex-snapshot
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
inferredcites →https://doi.org/10.1080/10635150500354928openalex-snapshot
Inferring Phylogeny Despite Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
inferredcites →https://doi.org/10.1080/10635150701311362openalex-snapshot
Profiling Phylogenetic Informativeness
inferredcites →https://doi.org/10.1080/10635150802570791openalex-snapshot
Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence
inferredcites →https://doi.org/10.1080/106351598261067openalex-snapshot
On the Best Evolutionary Rate for Phylogenetic Analysis
inferredcites →https://doi.org/10.1080/106351599259988openalex-snapshot
Molecular Phylogeny of the Marmots (Rodentia: Sciuridae): Tests of Evolutionary and Biogeographic Hypotheses
inferredcites →https://doi.org/10.1093/beheco/9.1.8openalex-snapshot
Life history consequences of social complexity a comparative study of ground-dwelling sciurids
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot
ASTRAL: genome-scale coalescent-based species tree estimation
inferredcites →https://doi.org/10.1093/bioinformatics/btu530openalex-snapshot
Quartet Inference from SNP Data Under the Coalescent Model
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
inferredcites →https://doi.org/10.1093/bioinformatics/btv646openalex-snapshot
PHYLUCE is a software package for the analysis of conserved genomic loci
inferredcites →https://doi.org/10.1093/gbe/evv026openalex-snapshot
Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
inferredcites →https://doi.org/10.1093/gbe/evx168openalex-snapshot
Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements
inferredcites →https://doi.org/10.1093/molbev/msh137openalex-snapshot
Genome-Scale Phylogeny and the Detection of Systematic Biases
inferredcites →https://doi.org/10.1093/molbev/msh182openalex-snapshot
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
inferredcites →https://doi.org/10.1093/molbev/msm091openalex-snapshot
Phylogeny of Primary Photosynthetic Eukaryotes as Deduced from Slowly Evolving Nuclear Genes
inferredcites →https://doi.org/10.1093/molbev/mss208openalex-snapshot
Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msv347openalex-snapshot
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
inferredcites →https://doi.org/10.1093/sysbio/40.4.458openalex-snapshot
When are Fossils Better than Extant Taxa in Phylogenetic Analysis?
inferredcites →https://doi.org/10.1093/sysbio/44.1.17openalex-snapshot
Performance of Phylogenetic Methods in Simulation
inferredcites →https://doi.org/10.1093/sysbio/syp031openalex-snapshot
Estimating Species Phylogenies Using Coalescence Times among Sequences
inferredcites →https://doi.org/10.1093/sysbio/syp047openalex-snapshot
What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?
inferredcites →https://doi.org/10.1093/sysbio/syr025openalex-snapshot
Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data
inferredcites →https://doi.org/10.1093/sysbio/syr027openalex-snapshot
Estimating Species Trees from Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/sys004openalex-snapshot
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
inferredcites →https://doi.org/10.1093/sysbio/syt050openalex-snapshot
Ecological Opportunity and Incumbency in the Diversification of Repeated Continental Colonizations by Muroid Rodents
inferredcites →https://doi.org/10.1093/sysbio/syt059openalex-snapshot
Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syt073openalex-snapshot
Conserved Genes, Sampling Error, and Phylogenomic Inference
inferredcites →https://doi.org/10.1093/sysbio/syu046openalex-snapshot
Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences
inferredcites →https://doi.org/10.1093/sysbio/syu063openalex-snapshot
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/sysbio/syv016openalex-snapshot
On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
inferredcites →https://doi.org/10.1093/sysbio/syv029openalex-snapshot
The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews
inferredcites →https://doi.org/10.1093/sysbio/syv041openalex-snapshot
Can We Identify Genes with Increased Phylogenetic Reliability?
inferredcites →https://doi.org/10.1093/sysbio/syw001openalex-snapshot
Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).
inferredcites →https://doi.org/10.1093/sysbio/syw005openalex-snapshot
Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus:Piranga)
inferredcites →https://doi.org/10.1093/sysbio/syw014openalex-snapshot
Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods
inferredcites →https://doi.org/10.1093/sysbio/syw027openalex-snapshot
Phylogenomics for Systematic Biology
inferredcites →https://doi.org/10.1093/sysbio/syw082openalex-snapshot
Incomplete Lineage Sorting in Mammalian Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syw089openalex-snapshot
Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards
inferredcites →https://doi.org/10.1093/sysbio/syw101openalex-snapshot
Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses
inferredcites →https://doi.org/10.1093/sysbio/syx051openalex-snapshot
More on the Best Evolutionary Rate for Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/syx070openalex-snapshot
Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats
inferredcites →https://doi.org/10.1093/sysbio/syx077openalex-snapshot
To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
inferredcites →https://doi.org/10.1093/sysbio/syy047openalex-snapshot
Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets
inferredcites →https://doi.org/10.1098/rsbl.2012.0331openalex-snapshot
More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
inferredcites →https://doi.org/10.1098/rstb.2007.2236openalex-snapshot
Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
inferredcites →https://doi.org/10.1101/gr.125864.111openalex-snapshot
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
inferredcites →https://doi.org/10.1109/gce.2010.5676129openalex-snapshot
Creating the CIPRES Science Gateway for inference of large phylogenetic trees
inferredcites →https://doi.org/10.1109/tcbb.2016.2604812openalex-snapshot
Species Tree Inference from Gene Splits by Unrooted STAR Methods
inferredcites →https://doi.org/10.1111/evo.12280openalex-snapshot
THE INFLUENCE OF SAMPLING DESIGN ON SPECIES TREE INFERENCE: A NEW RELATIONSHIP FOR THE NEW WORLD CHICKADEES (AVES:POECILE)
inferredcites →https://doi.org/10.1111/evo.12642openalex-snapshot
Relationships of diversity, disparity, and their evolutionary rates in squirrels (Sciuridae)
inferredcites →https://doi.org/10.1111/evo.12712openalex-snapshot
Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks
inferredcites →https://doi.org/10.1111/evo.12832openalex-snapshot
Irrational exuberance for resolved species trees
inferredcites →https://doi.org/10.1111/evo.12871openalex-snapshot
Repeated evolution of carnivory among Indo-Australian rodents
inferredcites →https://doi.org/10.1111/evo.13422openalex-snapshot
Trait‐specific processes of convergence and conservatism shape ecomorphological evolution in ground‐dwelling squirrels
inferredcites →https://doi.org/10.1111/mec.12023openalex-snapshot
Genome‐wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the L ake V ictoria cichlid adaptive radiation
inferredcites →https://doi.org/10.1126/science.1079705openalex-snapshot
The Effects of Cenozoic Global Change on Squirrel Phylogeny
inferredcites →https://doi.org/10.1126/science.1098119openalex-snapshot
Ultraconserved Elements in the Human Genome
inferredcites →https://doi.org/10.1126/science.1116759openalex-snapshot
Animal Evolution and the Molecular Signature of Radiations Compressed in Time
inferredcites →https://doi.org/10.1126/science.1147555openalex-snapshot
Molecular and Genomic Data Identify the Closest Living Relative of Primates
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1186/1471-2148-12-88openalex-snapshot
A glimpse on the pattern of rodent diversification: a phylogenetic approach
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s2openalex-snapshot
A comparative study of SVDquartets and other coalescent-based species tree estimation methods
inferredcites →https://doi.org/10.1186/s12859-018-2021-9openalex-snapshot
LocText: relation extraction of protein localizations to assist database curation
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1186/s12862-016-0650-zopenalex-snapshot
Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pbio.1002379openalex-snapshot
Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation
inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.1371/journal.pone.0054848openalex-snapshot
A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0122239openalex-snapshot
Measuring the Outcome of Biomedical Research: A Systematic Literature Review
inferredcites →https://doi.org/10.1371/journal.pone.0129183openalex-snapshot
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
inferredcites →https://doi.org/10.1515/mammalia-2015-0004openalex-snapshot
Towards a uniform nomenclature for ground squirrels: the status of the Holarctic chipmunks
inferredcites →https://doi.org/10.1534/genetics.116.190173openalex-snapshot
Challenges in Species Tree Estimation Under the Multispecies Coalescent Model
inferredcites →https://doi.org/10.1644/07-mamm-a-309.1openalex-snapshot
Generic Revision in the Holarctic Ground Squirrel GenusSpermophilus
inferredcites →https://doi.org/10.1644/10-mamm-a-272.1openalex-snapshot
Molecular data resolve placement of the Olympic marmot and estimate dates of trans-Beringian interchange
inferredcites →https://doi.org/10.2307/1380669openalex-snapshot
Reproductive Tract and Evolutionary Relationships of the Chinese Rock Squirrel, Sciurotamias davidianus
inferredcites →https://doi.org/10.2307/1382319openalex-snapshot
Pliocene-Pleistocene Biogeographic History of Prairie Dogs, Genus Cynomys (Sciuridae)
inferredcites →https://doi.org/10.2307/2421337openalex-snapshot
Phylogeny of Nearctic Sciuridae
inferredcites →https://doi.org/10.2307/2666186openalex-snapshot
The Origin of Grass-Dominated Ecosystems
inferredcites →https://doi.org/10.2307/2992240openalex-snapshot
When are Fossils better than Extant Taxa in Phylogenetic Analysis?
inferredcites →https://doi.org/10.3996/nafa.56.0001openalex-snapshot
Revision of the North American Ground Squirrels, with a Classification of the North American Sciuridae
inferredcites →https://doi.org/10.56021/9780801882210openalex-snapshot
Mammal Species of the World
inferredcites →https://doi.org/10.6079/j9illopenalex-snapshot
Illumiprocessor - software for Illumina read quality filtering
inferredcites →https://doi.org/10.7717/peerj.1660openalex-snapshot
AMAS: a fast tool for alignment manipulation and computing of summary statistics

What points at this work

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

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Integrative species delimitation reveals an Idaho-endemic ground squirrel, Urocitellus idahoensis (Merriam 1913)
inferred← citeshttps://doi.org/10.1002/ajb2.1678openalex-snapshot
Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica
inferred← citeshttps://doi.org/10.1002/ece3.71737openalex-snapshot
Altered Mitochondrial Respiration Is Associated With Loss of Nuclear‐Encoded OXPHOS Genes in Parasitic Broomrapes
inferred← citeshttps://doi.org/10.1002/ece3.73863openalex-snapshot
Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms ( Ephedra , Gnetales)
inferred← citeshttps://doi.org/10.1007/s12686-021-01192-wopenalex-snapshot
Genomic resources for an ecologically important rodent, Gunnison’s prairie dogs (Cynomys gunnisoni)
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106899openalex-snapshot
Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107092openalex-snapshot
Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107396openalex-snapshot
SNP-based phylogenomic inference in Holarctic ground squirrels (Urocitellus)
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107576openalex-snapshot
Old specimens for old branches: Assessing effects of sample age in resolving a rapid Neotropical radiation of squirrels
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107581openalex-snapshot
Out of chaos: Phylogenomics of Asian Sonerileae
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107785openalex-snapshot
Ultraconserved elements improve resolution of marmot phylogeny and offer insights into biogeographic history
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107863openalex-snapshot
Genomic data provide a robust phylogeny backbone for Rhodiola L. (Crassulaceae) and reveal extensive reticulate evolution during its rapid radiation
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108193openalex-snapshot
Historical biogeography and the evolution of habitat preference in the North American camel spider family, Eremobatidae (Arachnida:Solifugae)
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/10.1017/jpa.2026.10266openalex-snapshot
Diverse Early Pleistocene ground squirrels from northeastern Nebraska including a new genus and species
inferred← citeshttps://doi.org/10.1080/14772000.2019.1646834openalex-snapshot
Does nomenclatural stability justify para/polyphyletic taxa? A phylogenetic classification in the xeric clade Pitcairnioideae (Bromeliaceae)
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab875openalex-snapshot
Completing gene trees without species trees in sub-quadratic time
inferred← citeshttps://doi.org/10.1093/botlinnean/boae074openalex-snapshot
New insights into the classification, diversification, and evolutionary dynamics of bromeliads
inferred← citeshttps://doi.org/10.1093/gbe/evaa113openalex-snapshot
Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets
inferred← citeshttps://doi.org/10.1093/gbe/evad070openalex-snapshot
Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae)
inferred← citeshttps://doi.org/10.1093/isd/ixz016openalex-snapshot
Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics
inferred← citeshttps://doi.org/10.1093/jhered/esaf045openalex-snapshot
A genome assembly for a textbook mammalian study species, the California ground squirrel ( Otospermophilus beecheyi )
inferred← citeshttps://doi.org/10.1093/jmammal/gyae054openalex-snapshot
A review of molt in mammals, with an emphasis on marmots (Rodentia: Sciuridae: Marmota)
inferred← citeshttps://doi.org/10.1093/molbev/msab151openalex-snapshot
Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci
inferred← citeshttps://doi.org/10.1093/sysbio/syaa008openalex-snapshot
The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
inferred← citeshttps://doi.org/10.1093/sysbio/syaa066openalex-snapshot
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l
inferred← citeshttps://doi.org/10.1093/sysbio/syab023openalex-snapshot
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)
inferred← citeshttps://doi.org/10.1093/sysbio/syab068openalex-snapshot
Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene
inferred← citeshttps://doi.org/10.1093/sysbio/syaf077openalex-snapshot
Whole Genomes Illuminate the Drivers of Gene Tree Discordance and the Tempo of Tinamou Diversification (Aves: Tinamidae)
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlag151openalex-snapshot
Phylogenetic reconstruction and taxonomy of Retinella land snails: congruence and conflicts across morphological, mitochondrial, and nuclear datasets
inferred← citeshttps://doi.org/10.1101/2021.11.19.469195openalex-snapshot
A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation
inferred← citeshttps://doi.org/10.1101/2022.03.08.483551openalex-snapshot
Iterative deletion of gene trees detects extreme biases in distance-based phylogenomic coalescent analyses
inferred← citeshttps://doi.org/10.1101/765610openalex-snapshot
Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana )
inferred← citeshttps://doi.org/10.1101/794370openalex-snapshot
Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l
inferred← citeshttps://doi.org/10.1101/832683openalex-snapshot
Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata )
inferred← citeshttps://doi.org/10.1101/860809openalex-snapshot
The Multispecies Coalescent Model Outperforms Concatenation across Diverse Phylogenomic Data Sets
inferred← citeshttps://doi.org/10.1111/cla.12404openalex-snapshot
Divergence and support among slightly suboptimal likelihood gene trees
inferred← citeshttps://doi.org/10.1111/cla.12540openalex-snapshot
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses
inferred← citeshttps://doi.org/10.1111/mam.12215openalex-snapshot
A multi‐layered approach to the diversification of squirrels
inferred← citeshttps://doi.org/10.1111/mec.15603openalex-snapshot
Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
inferred← citeshttps://doi.org/10.1111/zsc.70081openalex-snapshot
Integrating Phylogenomics and Biogeography of Spectracanthicus (Siluriformes: Loricariidae) Reveals Complex Evolutionary History in a Brazilian Shield Endemic Genus
inferred← citeshttps://doi.org/10.11606/t.91.2020.tde-07012021-171352openalex-snapshot
Phylogenomics, diversification, and biogeography of Neotropical squirrels (Sciurillinae and Sciurinae: Sciurini)
inferred← citeshttps://doi.org/10.1186/s12862-018-1300-4openalex-snapshot
A phylogenomic resolution of the sea urchin tree of life
inferred← citeshttps://doi.org/10.1645/24-135openalex-snapshot
Genomics and Morphology Resolve Chipmunk Sucking Louse Systematics (Genus Hoplopleura)
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.5415openalex-snapshot
Quantifying Structure and Variation in Complex Phylogenetic Data
inferred← citeshttps://doi.org/10.3389/fevo.2022.969581openalex-snapshot
Simultaneously collecting coding and non-coding phylogenomic data using homemade full-length cDNA probes, tested by resolving the high-level relationships of Colubridae
inferred← citeshttps://doi.org/10.3389/fpls.2021.745988openalex-snapshot
Natural Hybrid Origin of the Controversial “Species” Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence
inferred← citeshttps://doi.org/10.3390/ijms26041581openalex-snapshot
Unraveling the Ancient Introgression History of Xanthoceras (Sapindaceae): Insights from Phylogenomic Analysis
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