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Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

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What this work says

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

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Molecular Phylogeny for Marine Turtles Based on Sequences of the ND4-Leucine tRNA and Control Regions of Mitochondrial DNA
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Phylogenetic Supertrees
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Structural and Sequence Evolution of U17 Small Nucleolar RNA (snoRNA) and Its Phylogenetic Congruence in Chelonians
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Recent hybrid origin of three rare Chinese turtles
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Phylogenetic inference based on matrix representation of trees
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Missing data and the design of phylogenetic analyses
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The supermatrix approach to systematics
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Turtle phylogeny: insights from a novel nuclear intron
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Phylogenetic hypotheses for the turtle family Geoemydidae
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Identifying optimal incomplete phylogenetic data sets from sequence databases
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Molecular phylogenetics and evolution of turtles
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Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles
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Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood
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New Chinese turtles: endangered or invalid? A reassessment of two species using mitochondrial DNA, allozyme electrophoresis and known-locality specimens
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Genome-scale approaches to resolving incongruence in molecular phylogenies
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Ecological diversification and phylogeny of emydid turtles
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Resolution of a Supertree/Supermatrix Paradox
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Performance-Based Selection of Likelihood Models for Phylogeny Estimation
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Supertrees Are a Necessary Not-So-Evil: A Comment on Gatesy et al.
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Inconsistencies in Arguments for the Supertree Approach: Supermatrices versus Supertrees of Crocodylia
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Phylogenetic Supermatrix Analysis of GenBank Sequences from 2228 Papilionoid Legumes
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The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research
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DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
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MrBayes 3: Bayesian phylogenetic inference under mixed models
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
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Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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DIALIGN: multiple DNA and protein sequence alignment at BiBiServ
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Automatic assessment of alignment quality
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Assembling the Tree of Life
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Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
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Congruence Between Morphometric and Allozyme Data for Menidia Species: A Reappraisal
inferredcites →https://doi.org/10.1093/sysbio/43.4.543openalex-snapshot
Molecular Systematics of Map Turtles (Graptemys): A Comparison of Mitochondrial Restriction Site Versus Sequence Data
inferredcites →https://doi.org/10.1093/sysbio/46.2.235openalex-snapshot
Tests of Turtle Phylogeny: Molecular, Morphological, and Paleontological Approaches
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The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference
inferredcites →https://doi.org/10.1109/csb.2004.1332422openalex-snapshot
Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees
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The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
inferredcites →https://doi.org/10.1111/j.1463-6409.2007.00293.xopenalex-snapshot
Phylogeny and taxonomy of endangered South and South‐east Asian freshwater turtles elucidated by mtDNA sequence variation (Testudines: Geoemydidae: Batagur, Callagur, Hardella, Kachuga, Pangshura)
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/10.1126/science.1102036openalex-snapshot
Prospects for Building the Tree of Life from Large Sequence Databases
inferredcites →https://doi.org/10.1126/science.1163197openalex-snapshot
Rates of Molecular Evolution Are Linked to Life History in Flowering Plants
inferredcites →https://doi.org/10.1146/annurev.ecolsys.33.010802.150509openalex-snapshot
Troubleshooting Molecular Phylogenetic Analyses
inferredcites →https://doi.org/10.1146/annurev.ecolsys.34.011802.132421openalex-snapshot
Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA
inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.091704.175513openalex-snapshot
The Population Biology of Mitochondrial DNA and Its Phylogenetic Implications
inferredcites →https://doi.org/10.1186/1471-2148-6-11openalex-snapshot
The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA
inferredcites →https://doi.org/10.1186/1471-2148-9-56openalex-snapshot
Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles
inferredcites →https://doi.org/10.1201/9781420009538openalex-snapshot
Reconstructing the Tree of Life
inferredcites →https://doi.org/10.1201/9781420009538.ch14openalex-snapshot
Cichlid Fish Diversity and Speciation
inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.2307/1222480openalex-snapshot
Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
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Congruence Between Morphometric and Allozyme Data for Menidia Species: A Reappraisal
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Assembling the tree of life
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IUCN Red List of Threatened Species

What points at this work

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

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Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
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Do turtles get cancer?
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Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human
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Performance Surface Analysis Identifies Consistent Functional Patterns across 10 Morphologically Divergent Terrestrial Turtle Lineages
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Phylogenetics Identifies Two Eumetazoan TRPM Clades and an Eighth TRP Family, TRP Soromelastatin (TRPS)
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Phylogeny and Biogeography of the Core Babblers (Aves: Timaliidae)
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Using Supermatrices for Phylogenetic Inquiry: An Example Using the Sedges
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Resolving Ambiguity of Species Limits and Concatenation in Multilocus Sequence Data for the Construction of Phylogenetic Supermatrices
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Evolution of Neck Vertebral Shape and Neck Retraction at the Transition to Modern Turtles: an Integrated Geometric Morphometric Approach
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
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Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles
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Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes
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Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?
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The evolution of island gigantism and body size variation in tortoises and turtles
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Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites
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A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation
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Unraveling the relationship between cancer and life history traits in vertebrates
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A Simple and Accurate Method for Rogue Taxon Identification
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A Genetic Algorithm Formulation for Rogue Taxa Problem
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The shell bone histology of fossil and extant marine turtles revisited
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Does the timing of attainment of maturity influence sexual size dimorphism and adult sex ratio in turtles?
inferred← citeshttps://doi.org/10.1111/boj.12184openalex-snapshot
Phylogenetic perspectives on diversification and character evolution in the species-rich genusErysimum(Erysimeae; Brassicaceae) based on a densely sampled ITS approach
inferred← citeshttps://doi.org/10.1111/cla.12064openalex-snapshot
Morphology reinforces proposed molecular phylogenetic affinities: a revised classification for Gelechioidea (Lepidoptera)
inferred← citeshttps://doi.org/10.1111/cla.12127openalex-snapshot
A morphological supermatrix‐based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny, missing data and homoplasy
inferred← citeshttps://doi.org/10.1111/cla.12191openalex-snapshot
Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)
inferred← citeshttps://doi.org/10.1111/ecog.02589openalex-snapshot
Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo‐Pacific
inferred← citeshttps://doi.org/10.1111/evo.13561openalex-snapshot
The influence of multiple functional demands on morphological diversification: A test on turtle shells
inferred← citeshttps://doi.org/10.1111/geb.12149openalex-snapshot
Is the island rule general? Turtles disagree
inferred← citeshttps://doi.org/10.1111/ibi.12464openalex-snapshot
The phylogeny of the world's bulbuls (Pycnonotidae) inferred using a supermatrix approach
inferred← citeshttps://doi.org/10.1111/j.1095-8312.2012.01946.xopenalex-snapshot
Are the liverworts really that old? Cretaceous origins and Cenozoic diversifications in Lepidoziaceae reflect a recurrent theme in liverwort evolution
inferred← citeshttps://doi.org/10.1111/j.1095-8312.2012.02015.xopenalex-snapshot
Patterns of sexual size dimorphism in Chelonia
inferred← citeshttps://doi.org/10.1111/j.1365-2435.2012.02057.xopenalex-snapshot
Macrostress: do large‐scale ecological patterns exist in the glucocorticoid stress response of vertebrates?
inferred← citeshttps://doi.org/10.1111/j.1420-9101.2011.02391.xopenalex-snapshot
Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots
inferred← citeshttps://doi.org/10.1111/j.1439-0469.2010.00565.xopenalex-snapshot
Mitochondrial phylogeography and subspecies of the wide-ranging sub-Saharan leopard tortoise Stigmochelys pardalis (Testudines: Testudinidae) - a case study for the pitfalls of pseudogenes and GenBank sequences
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2011.01294.xopenalex-snapshot
TROPHIC NOVELTY IS LINKED TO EXCEPTIONAL RATES OF MORPHOLOGICAL DIVERSIFICATION IN TWO ADAPTIVE RADIATIONS OF CYPRINODON PUPFISH
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2012.01619.xopenalex-snapshot
MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN-UHLENBECK MODEL OF ADAPTIVE EVOLUTION
inferred← citeshttps://doi.org/10.1111/j.1600-0587.2012.07773.xopenalex-snapshot
Building megaphylogenies for macroecology: taking up the challenge
inferred← citeshttps://doi.org/10.1111/jeb.12031openalex-snapshot
The determinants of the molecular substitution process in turtles
inferred← citeshttps://doi.org/10.1111/jpy.12404openalex-snapshot
Phylogenetic relationships of corallinaceae (Corallinales, Rhodophyta): taxonomic implications for reef‐building corallines
inferred← citeshttps://doi.org/10.1111/jzo.13109openalex-snapshot
Ecoimmunological differences among congeneric tortoises in the United States
inferred← citeshttps://doi.org/10.1111/mec.12269openalex-snapshot
The evolutionary history of X iphophorus fish and their sexually selected sword: a genome‐wide approach using restriction site‐associated DNA sequencing
inferred← citeshttps://doi.org/10.1111/syen.12275openalex-snapshot
Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)
inferred← citeshttps://doi.org/10.1111/syen.12324openalex-snapshot
A comprehensive molecular phylogeny of tiger beetles (Coleoptera, Carabidae, Cicindelinae)
inferred← citeshttps://doi.org/10.1111/syen.12414openalex-snapshot
The phylogeny of insects in the data‐driven era
inferred← citeshttps://doi.org/10.1111/zsc.12007openalex-snapshot
Multilocus phylogeny reveals unexpected diversification patterns in A sian wolf snakes (genus L ycodon)
inferred← citeshttps://doi.org/10.1126/science.1254449openalex-snapshot
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
inferred← citeshttps://doi.org/10.11606/d.38.2019.tde-01042019-162449openalex-snapshot
Análise cladística de Incini Burmeister, 1842 (Coleoptera, Scarabaeidae, Cetoniinae)
inferred← citeshttps://doi.org/10.1163/18759866-07903002openalex-snapshot
Phylogenetic relationships among extinct and extant turtles: the position of Pleurodira and the effects of the fossils on rooting crown-group turtles
inferred← citeshttps://doi.org/10.1163/18759866-08103002openalex-snapshot
A large phylogeny of turtles (Testudines) using molecular data
inferred← citeshttps://doi.org/10.1186/1471-2148-12-129openalex-snapshot
A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment
inferred← citeshttps://doi.org/10.1186/1471-2148-12-30openalex-snapshot
Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae
inferred← citeshttps://doi.org/10.1186/1471-2148-13-93openalex-snapshot
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
inferred← citeshttps://doi.org/10.1186/1741-7007-8-19openalex-snapshot
Rapid progress on the vertebrate tree of life
inferred← citeshttps://doi.org/10.1186/1741-7007-9-55openalex-snapshot
The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences
inferred← citeshttps://doi.org/10.1186/s12862-015-0520-0openalex-snapshot
Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera)
inferred← citeshttps://doi.org/10.1186/s12862-016-0628-xopenalex-snapshot
Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?
inferred← citeshttps://doi.org/10.1186/s12862-018-1162-9openalex-snapshot
The prevalence of terraced treescapes in analyses of phylogenetic data sets
inferred← citeshttps://doi.org/10.1186/s12862-020-01642-3openalex-snapshot
Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs)
inferred← citeshttps://doi.org/10.1186/s12862-022-01994-yopenalex-snapshot
Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians
inferred← citeshttps://doi.org/10.1242/jeb.249959openalex-snapshot
Using the axial skeleton as armor: mechanical behavior of sea turtle carapaces throughout ontogeny
inferred← citeshttps://doi.org/10.1371/journal.pone.0024851openalex-snapshot
Towards Resolving the Complete Fern Tree of Life
inferred← citeshttps://doi.org/10.1371/journal.pone.0047852openalex-snapshot
The Head and Neck Anatomy of Sea Turtles (Cryptodira: Chelonioidea) and Skull Shape in Testudines
inferred← citeshttps://doi.org/10.1371/journal.pone.0059741openalex-snapshot
Global Taxonomic Diversity of Living Reptiles
inferred← citeshttps://doi.org/10.1371/journal.pone.0093975openalex-snapshot
A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data
inferred← citeshttps://doi.org/10.1371/journal.pone.0098986openalex-snapshot
Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants)
inferred← citeshttps://doi.org/10.1371/journal.pone.0109704openalex-snapshot
Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing
inferred← citeshttps://doi.org/10.1371/journal.pone.0118247openalex-snapshot
Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case
inferred← citeshttps://doi.org/10.1371/journal.pone.0161070openalex-snapshot
A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus
inferred← citeshttps://doi.org/10.1371/journal.pone.0174902openalex-snapshot
Comprehensive species set revealing the phylogeny and biogeography of Feliformia (Mammalia, Carnivora) based on mitochondrial DNA
inferred← citeshttps://doi.org/10.1534/genetics.114.164269openalex-snapshot
Estimating Tempo and Mode of Y Chromosome Turnover: Explaining Y Chromosome Loss With the Fragile Y Hypothesis
inferred← citeshttps://doi.org/10.1590/s1984-46702011000400011openalex-snapshot
Organization and variation of mitochondrial DNA control region in pleurodiran turtles
inferred← citeshttps://doi.org/10.1655/d-17-00066openalex-snapshot
Effects of Sutured Pelvic Elements on Turtle Shell Strength: A Comparison of Pleurodire and Cryptodire Shell Mechanics
inferred← citeshttps://doi.org/10.1655/d-18-00054openalex-snapshot
Where Has Turtle Ecology Been, and Where Is It Going?
inferred← citeshttps://doi.org/10.1655/herpetologica-d-15-00037openalex-snapshot
Convergent Evolution Provides Evidence of Similar Radiations in Shell Shape in the Turtle Families Emydidae and Geoemydidae
inferred← citeshttps://doi.org/10.1655/herpetologica-d-15-00038openalex-snapshot
Side-necked Versus Hidden-necked: A Comparison of Shell Morphology Between Pleurodiran and Cryptodiran Turtles
inferred← citeshttps://doi.org/10.1890/11-0638.1openalex-snapshot
Synthesizing phylogenetic knowledge for ecological research
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2206377/v1openalex-snapshot
Marine introgressions and Andean uplift drives diversification in neotropical Monkey tree frogs (Anura,Phyllomedusinae)
inferred← citeshttps://doi.org/10.31237/osf.io/7sa6dopenalex-snapshot
Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life
inferred← citeshttps://doi.org/10.31274/etd-180810-115openalex-snapshot
Constructing liberal and conservative supertrees and exact solutions for reduced consensus problems
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.5187openalex-snapshot
Genomics and Population History of Black-headed Bulbul (Brachypodius atriceps) Color Morphs
inferred← citeshttps://doi.org/10.32614/cran.package.rogueopenalex-snapshot
Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees
inferred← citeshttps://doi.org/10.3389/fgene.2014.00394openalex-snapshot
Historical factors that have shaped the evolution of tropical reef fishes: a review of phylogenies, biogeography, and remaining questions
inferred← citeshttps://doi.org/10.3389/fpls.2019.01005openalex-snapshot
Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm
inferred← citeshttps://doi.org/10.3390/genes11080945openalex-snapshot
Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution
inferred← citeshttps://doi.org/10.3390/insects10030072openalex-snapshot
Morphological and Molecular Analysis of Australian Earwigs (Dermaptera) Points to Unique Species and Regional Endemism in the Anisolabididae Family
inferred← citeshttps://doi.org/10.3854/crm.5.115.spekii.v1.2021openalex-snapshot
Kinixys spekii Gray 1863 – Speke’s Hinge-back Tortoise, Speke’s Hinged Tortoise
inferred← citeshttps://doi.org/10.3897/rio.3.e13589openalex-snapshot
A machine-compiled microbial supertree from figure-mining thousands of papers
inferred← citeshttps://doi.org/10.3897/vz.67.e31535openalex-snapshot
A systematic review of the turtle family Emydidae
inferred← citeshttps://doi.org/10.5860/choice.187286openalex-snapshot
Biology and conservation of North American tortoises
inferred← citeshttps://doi.org/10.70675/28835658ze3c8z4a59z94bcz6db7a7e22084openalex-snapshot
Les causes des variations du taux d’évolution moléculaire entre lignées
inferred← citeshttps://doi.org/10.70675/98c36434za02ez46b7zb628z3b08e3325812openalex-snapshot
Diversité globale des poissons coralliens : histoire évolutive et influence de l'environnement passé
inferred← citeshttps://doi.org/10.7287/peerj.1172v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.1172v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.1172v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.1172v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution (v0.2)"
inferred← citeshttps://doi.org/10.7550/rmb.43236openalex-snapshot
Biodiversidad de reptiles en México
inferred← citeshttps://doi.org/10.7717/peerj.1172openalex-snapshot
Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution
inferred← citeshttps://doi.org/10.7717/peerj.17232openalex-snapshot
Marine introgressions and Andean uplift have driven diversification in neotropical Monkey tree frogs (Anura, Phyllomedusinae)
inferred← citeshttps://doi.org/10.7717/peerj.4338openalex-snapshot
A new slider turtle (Testudines: Emydidae: Deirochelyinae: Trachemys ) from the late Hemphillian (late Miocene/early Pliocene) of eastern Tennessee and the evolution of the deirochelyines
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.