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Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

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What this work says

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

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From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
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A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories
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Lost Sex in the Reptiles: Constraints and Correlations
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Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status
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Phylogenomics: the beginning of incongruence?
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BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions
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Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
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Phylogenomic analyses reveal novel relationships among snake families
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How Low Can You Go?
inferredcites →https://doi.org/10.1038/nature04328openalex-snapshot
Early evolution of the venom system in lizards and snakes
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Inferring ancient divergences requires genes with strong phylogenetic signals
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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Model selection may not be a mandatory step for phylogeny reconstruction
inferredcites →https://doi.org/10.1038/s41559-016-0020openalex-snapshot
Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
inferredcites →https://doi.org/10.1038/s41559-017-0126openalex-snapshot
Contentious relationships in phylogenomic studies can be driven by a handful of genes
inferredcites →https://doi.org/10.1038/s41559-017-0240-5openalex-snapshot
Phylotranscriptomic consolidation of the jawed vertebrate timetree
inferredcites →https://doi.org/10.1038/s41559-017-0331-3openalex-snapshot
Ctenophore relationships and their placement as the sister group to all other animals
inferredcites →https://doi.org/10.1073/pnas.1503453112openalex-snapshot
Error, signal, and the placement of Ctenophora sister to all other animals
inferredcites →https://doi.org/10.1073/pnas.1518127112openalex-snapshot
Genomic data do not support comb jellies as the sister group to all other animals
inferredcites →https://doi.org/10.1080/10635150390218213openalex-snapshot
Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case
inferredcites →https://doi.org/10.1080/10635150490522340openalex-snapshot
Molecular Phylogenetics of Squamata: The Position of Snakes, Amphisbaenians, and Dibamids, and the Root of the Squamate Tree
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Profiling Phylogenetic Informativeness
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APE: Analyses of Phylogenetics and Evolution in R language
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The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq706openalex-snapshot
phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/bioinformatics/bts492openalex-snapshot
treePL: divergence time estimation using penalized likelihood for large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btt593openalex-snapshot
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
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/btv184openalex-snapshot
ExaML version 3: a tool for phylogenomic analyses on supercomputers
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/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msv023openalex-snapshot
Restriction Site-Associated DNA Sequencing (RAD-seq) Reveals an Extraordinary Number of Transitions among Gecko Sex-Determining Systems
inferredcites →https://doi.org/10.1093/molbev/msv258openalex-snapshot
Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/25.22.4692openalex-snapshot
Universal and rapid salt-extraction of high quality genomic DNA for PCR- based techniques
inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot
Gene Trees in Species 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/sys049openalex-snapshot
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syv041openalex-snapshot
Can We Identify Genes with Increased Phylogenetic Reliability?
inferredcites →https://doi.org/10.1093/sysbio/syv059openalex-snapshot
Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny
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/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/syx076openalex-snapshot
Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families
inferredcites →https://doi.org/10.1093/sysbio/syy015openalex-snapshot
Inferring Phylogenetic Networks Using PhyloNet
inferredcites →https://doi.org/10.1093/sysbio/syy043openalex-snapshot
Analyzing Contentious Relationships and Outlier Genes in Phylogenomics
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/10.1093/sysbio/syz019openalex-snapshot
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone
inferredcites →https://doi.org/10.1093/sysbio/syz062openalex-snapshot
Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships
inferredcites →https://doi.org/10.1093/sysbio/syz078openalex-snapshot
Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants
inferredcites →https://doi.org/10.1098/rsbl.2012.0703openalex-snapshot
Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species
inferredcites →https://doi.org/10.1098/rsbl.2017.0393openalex-snapshot
Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1111/1755-0998.12681openalex-snapshot
Squamate Conserved Loci (Sq CL ): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
inferredcites →https://doi.org/10.1111/ele.12168openalex-snapshot
Early origin of viviparity and multiple reversions to oviparity in squamate reptiles
inferredcites →https://doi.org/10.1111/evo.12832openalex-snapshot
Irrational exuberance for resolved species trees
inferredcites →https://doi.org/10.1111/j.1469-185x.1951.tb00646.xopenalex-snapshot
THE ORIGIN OF SNAKES
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00430.xopenalex-snapshot
RATES AND PATTERNS IN THE EVOLUTION OF SNAKE-LIKE BODY FORM IN SQUAMATE REPTILES: EVIDENCE FOR REPEATED RE-EVOLUTION OF LOST DIGITS AND LONG-TERM PERSISTENCE OF INTERMEDIATE BODY FORMS
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00169.xopenalex-snapshot
phytools: an R package for phylogenetic comparative biology (and other things)
inferredcites →https://doi.org/10.1126/science.1142430openalex-snapshot
Human Genome Ultraconserved Elements Are Ultraselected
inferredcites →https://doi.org/10.1126/science.1151532openalex-snapshot
Alignment Uncertainty and Genomic Analysis
inferredcites →https://doi.org/10.1126/science.1232455openalex-snapshot
Who Speaks with a Forked Tongue?
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/10.11646/zootaxa.4375.2.5openalex-snapshot
The original descriptions of reptiles and their subspecies
inferredcites →https://doi.org/10.1186/1471-2148-13-93openalex-snapshot
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
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/s12862-015-0358-5openalex-snapshot
The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record
inferredcites →https://doi.org/10.1186/s12862-015-0423-0openalex-snapshot
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
inferredcites →https://doi.org/10.1186/s12864-018-4619-8openalex-snapshot
The performance of coalescent-based species tree estimation methods under models of missing data
inferredcites →https://doi.org/10.1186/s12864-018-4620-2openalex-snapshot
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
inferredcites →https://doi.org/10.1371/journal.pbio.0040352openalex-snapshot
Bushes in the Tree of Life
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.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.1371/journal.pone.0118199openalex-snapshot
Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa
inferredcites →https://doi.org/10.1371/journal.pone.0202729openalex-snapshot
Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata
inferredcites →https://doi.org/10.21105/joss.01635openalex-snapshot
Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments
inferredcites →https://doi.org/10.32614/cran.package.cowplotopenalex-snapshot
cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
inferredcites →https://doi.org/10.3374/014.053.0101openalex-snapshot
Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record
inferredcites →https://doi.org/10.48550/arxiv.1202.1215openalex-snapshot
TAPIR enables high-throughput estimation and comparison of phylogenetic informativeness using locus-specific substitution models
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Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

What points at this work

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

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The world’s largest worm lizard: a new giant trogonophid (Squamata: Amphisbaenia) with extreme dental adaptations from the Eocene of Chambi, Tunisia
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Trends in diagnostic characters of Snakes species (Squamata) in the first two decades of the 21st century
inferred← citeshttps://doi.org/10.11646/zootaxa.5760.5.1zenodo-depositor-declared
A new species of blind skink (Squamata: Dibamidae: Dibamus) from Chu Yang Sin National Park, southern Vietnam, with the first description of a Dibamus clutch
inferred← citeshttps://doi.org/10.1002/ar.25142openalex-snapshot
Endocast, brain, and bones: Correspondences and spatial relationships in squamates
inferred← citeshttps://doi.org/10.1002/ar.25162openalex-snapshot
A landmarking protocol for geometric morphometric analysis of squamate endocasts
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A review of the venom microbiome and its utility in ecology and evolution including future directions for emerging research
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Cretaceous Blind Snake from Brazil Fills Major Gap in Snake Evolution
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More than meets no eyes: Taxonomic status of a Liotyphlops (Serpentes: Anomalepididae) blindsnake from the Atlantic Rainforest
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A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae
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Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes
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Convergent evolution in nuclear and mitochondrial OXPHOS subunits underlies the phylogenetic discordance in deep lineages of Squamata
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Testing a mitochondrial species radiation with exon capture data – The Antarctic sea slug Doris ‘kerguelenensis’
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Genomic Perspectives
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Using Comparative Genomics to Resolve the Origin and Early Evolution of Snakes
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The oldest known lepidosaur and origins of lepidosaur feeding adaptations
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No link between population isolation and speciation rate in squamate reptiles
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Tetrapodophis amplectusis not a snake: re-assessment of the osteology, phylogeny and functional morphology of an Early Cretaceous dolichosaurid lizard
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A new polyglyphanodontian lizard with a complete lower temporal bar from the Upper Cretaceous of southern China
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It’s a trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex-determining gene in a lizard (Anguimorpha; Shinisauridae)
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Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles
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The Squamate Clitoris: A Review and Directions for Future Research
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Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics
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Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus
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Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets
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Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs
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Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi
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Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support
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A Genomic Perspective on the Evolutionary Diversification of Turtles
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Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance
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A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data
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Evolutionary Rate Incongruences in Squamates Reveal Contrasting Patterns of Evolutionary Novelties and Innovation
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A Palaeogene stem crotaphytid ( Aciprion formosum ) and the phylogenetic affinities of early fossil pleurodontan iguanians
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The affinities of the Late Triassic Cryptovaranoides and the age of crown squamates
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It’s a Trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex determining gene in a lizard (Anguimorpha; Shinisauridae)
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Dissecting Factors Underlying Phylogenetic Uncertainty Using Machine Learning Models
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A network-based comparative method to study reptile scalation and other homologous two-dimensional patterns
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XX / XY sex chromosomes in a blind lizard (Dibamidae): Towards understanding the evolution of sex determination in squamates
inferred← citeshttps://doi.org/10.1111/joa.13871openalex-snapshot
Embryonic development of the skull in a parthenogenetic lizard, the mourning gecko (Lepidodactylus lugubris)
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/10.1126/science.adh2449openalex-snapshot
The macroevolutionary singularity of snakes
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-102723-050400openalex-snapshot
Origin and Early Evolution of Squamates and Their Kin: From Fossils to Genomes
inferred← citeshttps://doi.org/10.1186/s12915-026-02552-4openalex-snapshot
The genome of the relict earless monitor lizard, Lanthanotus borneensis, and the Toxicofera hypothesis
inferred← citeshttps://doi.org/10.1643/h2020073openalex-snapshot
Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species
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Phylogenomics of Fresh and Formalin Specimens Resolves the Systematics of Old World Mud Snakes (Serpentes: Homalopsidae) and Expands Biogeographic Inference
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2326825/v1openalex-snapshot
Mitogenome of the Brazilian critically endangered pitviper Bothrops insularis – structural genomic characterization and evolutionary aspects
inferred← citeshttps://doi.org/10.2139/ssrn.5073450openalex-snapshot
Convergent Evolution in Nuclear and Mitochondrial Oxphos Subunits Across Deep Lineages of Squamata
inferred← citeshttps://doi.org/10.2139/ssrn.6170240openalex-snapshot
Disagreement among Genomic Markers Profoundly Influences Phylogenetic Inference in Squamates
inferred← citeshttps://doi.org/10.3099/0027-4100-163.2.47openalex-snapshot
THE SQUAMATE TREE OF LIFE
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.5415openalex-snapshot
Quantifying Structure and Variation in Complex Phylogenetic Data
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles
inferred← citeshttps://doi.org/10.3390/d16090548openalex-snapshot
First Virtual Reconstruction of a Mosasaurid Brain Endocast: Description and Comparison of the Endocast of Tethysaurus nopcsai with Those of Extant Squamates
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Cytogenetic Analysis of Seven Species of Gekkonid and Phyllodactylid Geckos
inferred← citeshttps://doi.org/10.3390/genes14071387openalex-snapshot
The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order
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Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos
inferred← citeshttps://doi.org/10.3390/life10120342openalex-snapshot
Independent Evolution of Sex Chromosomes in Eublepharid Geckos, A Lineage with Environmental and Genotypic Sex Determination
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Venom Before Specialisation? A Layered Assessment of Early Venom Evolution in Lizards and Snakes
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Combinatorial topological models for phylogenetic networks and the mergegram invariant
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European origins of Squamata supported by biogeographic analysis of fossil-tip-dated phylogenies using paleocontinental plate-tectonic models
inferred← citeshttps://doi.org/10.64898/2026.03.30.714540openalex-snapshot
Signal, noise, and bias in phylogenetic inference: potential and limits to the resolution of phylogenetic trees in the phylogenomic era
inferred← citeshttps://doi.org/10.64898/2026.06.28.735080openalex-snapshot
Genomic Distortion of Jawed Vertebrate Phylogeny
inferred← citeshttps://doi.org/10.7554/elife.107021openalex-snapshot
Cryptovaranoides is not a squamate
inferred← citeshttps://doi.org/10.7554/elife.107021.1openalex-snapshot
Cryptovaranoides is not a squamate
inferred← citeshttps://doi.org/10.7554/elife.107021.2openalex-snapshot
Cryptovaranoides is not a squamate
inferred← citeshttps://doi.org/10.7554/elife.107021.3openalex-snapshot
Cryptovaranoides is not a squamate
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