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Multilocus phylogeny of alligator lizards ( Elgaria , Anguidae): Testing mtDNA introgression as the source of discordant molecular phylogenetic hypotheses

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

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Influence of Sediment Input and Plate‐Motion Obliquity on Basin Development Along an Active Oblique‐Divergent Plate Boundary: Gulf of California and Salton Trough
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New finds of anguines (Squamata, Anguidae) from the Early Miocene of Northwest Bohemia (Czech Republic)
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Computational approaches to species phylogeny inference and gene tree reconciliation
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Molecular phylogeography of the asp viper Vipera aspis (Linnaeus, 1758) in Italy: Evidence for introgressive hybridization and mitochondrial DNA capture
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Vicariance and dispersal form a ring distribution in nightsnakes around the Gulf of California
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Molecular evidence for hybridization between two Australian desert skinks, Ctenotus leonhardii and Ctenotus quattuordecimlineatus (Scincidae: Squamata)
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Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification
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Free from mitochondrial DNA: Nuclear genes and the inference of species trees among closely related darter lineages (Teleostei: Percidae: Etheostomatinae)
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A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae)
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A new lizard assemblage from the earliest eocene (Zone Wa0) of the bighorn basin, wyoming, USA: Biogeography during the warmest interval of the cenozoic
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A new species ofPseudopus(Squamata, Anguidae) from the early Miocene of Northwest Bohemia (Czech Republic)
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Inferring Phylogeny Despite Incomplete Lineage Sorting
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A Rapid Bootstrap Algorithm for the RAxML Web Servers
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A New Statistical Method for Haplotype Reconstruction from Population Data
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A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
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A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting
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TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments
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TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
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STEM: species tree estimation using maximum likelihood for gene trees under coalescence
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THE SENSITIVITY OF GEL ELECTROPHORESIS AS A DETECTOR OF GENETIC VARIATION
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Bayesian Estimation of Concordance among Gene Trees
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jModelTest: Phylogenetic Model Averaging
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Bayesian Inference of Species Trees from Multilocus Data
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Testing for Ancient Admixture between Closely Related Populations
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Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
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Relationships between gene trees and species trees.
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Gene Trees in Species Trees
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Conflicting Mitochondrial and Nuclear Phylogenies for the Widely Disjunct Emys (Testudines: Emydidae) Species Complex, and What They Tell Us about Biogeography and Hybridization
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Estimating Species Phylogenies Using Coalescence Times among Sequences
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Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting
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Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection
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Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer
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Phylogenetic and Coalescent Strategies of Species Delimitation in Snubnose Darters (Percidae: Etheostoma)
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Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)
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Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting
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The Influence of Gene Flow on Species Tree Estimation: A Simulation Study
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Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data
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Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)
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Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs
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Assembly of the eastern North American herpetofauna: new evidence from lizards and frogs
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Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species
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Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution
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Introduction. Extent, processes and evolutionary impact of interspecific hybridization in animals
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hybridcheck : software for the rapid detection, visualization and dating of recombinant regions in genome sequence data
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PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES
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MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING
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TESTING MITOCHONDRIAL CAPTURE AND DEEP COALESCENCE IN AMAZONIAN CICHLID FISHES (CICHLIDAE:CICHLA)
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DISPERSAL OF VIVIPARITY ACROSS CONTACT ZONES IN IBERIAN POPULATIONS OF FIRE SALAMANDERS (SALAMANDRA) INFERRED FROM DISCORDANCE OF GENETIC AND MORPHOLOGICAL TRAITS
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A MULTILOCUS PERSPECTIVE ON REFUGIAL ISOLATION AND DIVERGENCE IN RAINFOREST SKINKS (CARLIA)
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Deep genealogies and the mid‐peninsular seaway of Baja California
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Phylogeography of the pool frog Rana (Pelophylax) lessonae in the Italian peninsula and Sicily: multiple refugia, glacial expansions and nuclear–mitochondrial discordance
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Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander,Plethodon shermani
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Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion
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Multi‐locus DNA sequence data reveal a history of deep cryptic vicariance and habitat‐driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae)
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Ancient hybridization and mitochondrial capture between two species of chipmunks
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Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish
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Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle,Emys marmoratain California
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Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa
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Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes
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INFERRING PHYLOGENIES FROM mt DNA VARIATION: MITOCHONDRIAL-GENE TREES VERSUS NUCLEAR-GENE TREES
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MITOCHONDRIAL INTROGRESSION AND INCOMPLETE LINEAGE SORTING THROUGH SPACE AND TIME: PHYLOGENETICS OF CROTAPHYTID LIZARDS
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THE COMBINED EFFECTS OF RIVERS AND REFUGIA GENERATE EXTREME CRYPTIC FRAGMENTATION WITHIN THE COMMON GROUND SKINK (SCINCELLA LATERALIS)
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PHYLOGENETIC INFERENCE OF NUPTIAL TRAIT EVOLUTION IN THE CONTEXT OF ASYMMETRICAL INTROGRESSION IN NORTH AMERICAN DARTERS (TELEOSTEI)
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seqphase : a web tool for interconverting phase input/output files and fasta sequence alignments
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Use of allele‐specific sequencing primers is an efficient alternative to PCR subcloning of low‐copy nuclear genes
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No evidence for nuclear introgression despite complete mt DNA replacement in the C arpathian newt ( L issotriton montandoni)
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Multilocus phylogeographic assessment of the C alifornia M ountain K ingsnake ( L ampropeltis zonata) suggests alternative patterns of diversification for the C alifornia F loristic P rovince
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The advantages of going large: genome‐wide SNP s clarify the complex population history and systematics of the threatened western pond turtle
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Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs
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Powerful methods for detecting introgressed regions from population genomic data
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Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage
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An age constraint on Gulf of California rifting from the Santa Rosalia basin, Baja California Sur, Mexico
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Thick evaporites and early rifting in the Guaymas Basin, Gulf of California
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PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
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Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling
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Simulating gene trees under the multispecies coalescent and time-dependent migration
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BEAST: Bayesian evolutionary analysis by sampling trees
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Chapter 11
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Relaxed Phylogenetics and Dating with Confidence
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Species Tree Inference by Minimizing Deep Coalescences
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Adaptive Introgression across Species Boundaries in Heliconius Butterflies
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Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
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Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution
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Impact of Deep Coalescence on the Reliability of Species Tree Inference from Different Types of DNA Markers in Mammals
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Amphibians and Reptiles of Baja California, Including Its Pacific Islands and the Islands in the Sea of Cortés
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PREDICTING NUCLEAR GENE COALESCENCE FROM MITOCHONDRIAL DATA: THE THREE-TIMES RULE
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A NEW BAT (CHIROPTERA: NATALIDAE) FROM THE EARLY MIOCENE OF FLORIDA, WITH COMMENTS ON NATALID PHYLOGENY
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Revision of the anguine lizard Pseudopus laurillardi (Squamata, Anguidae) from the Miocene of Europe, with comments on paleoecology
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Phylogenetic Placement of the Pygmy Alligator Lizard Based on Mitochondrial DNA
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Botta's Visit to California
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A Shift of Specific Names in the Genus Gerrhonotus
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New Alligator Lizards from the Pacific Coast
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Handbuch der Paläoherpetologie: Part 10 A, Sauria Terrestria, Amphisbaenia
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Phylogenetic Relationships among Gerrhonotine Lizards. An Analysis of External Morphology
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Allocation and Status of the Garter Snake Names Coluber infernalis Blainville, Eutaenia sirtalis tetrataenia Cope and Eutaenia imperialis Coues and Yarrow
inferredcites →https://doi.org/10.2307/2411967openalex-snapshot
Evolution of a Peninsular Herpetofauna
inferredcites →https://doi.org/10.2307/2420638openalex-snapshot
A Systematic Account of the Alligator Lizards (Gerrhonotus) in the Western United States and Lower California
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The Genera of Gerrhonotine Lizards
inferredcites →https://doi.org/10.2307/3670661openalex-snapshot
A New Gerrhonotus (Lacertilia: Anguidae) from the Sierra Madre Oriental, Nuevo Leon, Mexico
inferredcites →https://doi.org/10.5962/bhl.part.12884openalex-snapshot
Remarks upon the natural history of Gerrhonotus panamintinus Stebbins
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Herpeto Fauna Of The Pacific Coast Of North Central Baja-California Mexico With A Description Of A New Subspecies Of Phyllodactylus-Xanti
inferredcites →https://doi.org/10.5962/bhl.part.15521openalex-snapshot
The significance of the scale characteristics in evaluation of the lizard genera Gerrhonotus, Elgaria, and Barisia

What points at this work

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

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Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
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Novel placental structure in the Mexican gerrhonotine lizard, Mesaspis viridiflava (Lacertilia; Anguidae)
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Developmental morphology and evolution of extraembryonic membranes of lizards and snakes (Reptilia, Squamata)
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Genetic structure and environmental niche modeling confirm two evolutionary and conservation units within the western spadefoot (Spea hammondii)
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Common lizards break Dollo’s law of irreversibility: Genome-wide phylogenomics support a single origin of viviparity and re-evolution of oviparity
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Introgression obscures lineage boundaries and phylogeographic history in the western banded gecko, Coleonyx variegatus (Squamata: Eublepharidae)
inferred← citeshttps://doi.org/10.1101/342048openalex-snapshot
What is the Best Available Science?: Conservation Status of Two California Desert Vertebrates
inferred← citeshttps://doi.org/10.1111/ecog.07391openalex-snapshot
Habitat quality or quantity? Niche marginality across 21 plants and animals suggests differential responses between highland and lowland species to past climatic changes
inferred← citeshttps://doi.org/10.1111/jbi.14511openalex-snapshot
Near‐shore island lizard fauna shaped by a combination of human‐mediated and natural dispersal
inferred← citeshttps://doi.org/10.1111/mec.16624openalex-snapshot
Phylogeography and population genetics of a widespread cold‐adapted ant, Prenolepis imparis
inferred← citeshttps://doi.org/10.1111/zsc.12294openalex-snapshot
Phylogeography of the Northern Alligator Lizard (Squamata, Anguidae): Hidden diversity in a western endemic
inferred← citeshttps://doi.org/10.1186/s12862-019-1503-3openalex-snapshot
Multiple convergent events created a nominal widespread species: Triplophysa stoliczkae (Steindachner, 1866) (Cobitoidea: Nemacheilidae)
inferred← citeshttps://doi.org/10.1186/s12862-020-01718-0openalex-snapshot
DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau
inferred← citeshttps://doi.org/10.1186/s12862-021-01912-8openalex-snapshot
A new extinct species of alligator lizard (Squamata: Elgaria) and an expanded perspective on the osteology and phylogeny of Gerrhonotinae
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007341openalex-snapshot
Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia
inferred← citeshttps://doi.org/10.1371/journal.pone.0199584openalex-snapshot
The skull of the gerrhonotine lizard Elgaria panamintina (Squamata: Anguidae)
inferred← citeshttps://doi.org/10.1515/mammalia-2018-0191openalex-snapshot
Phylogeography and niche modelling: reciprocal enlightenment
inferred← citeshttps://doi.org/10.1515/mammalia-2020-0068openalex-snapshot
A new species of Cynomops (Chiroptera: Molossidae) from the northwestern slope of the Andes
inferred← citeshttps://doi.org/10.22541/au.171386928.89423307/v1openalex-snapshot
Habitat quality or quantity? Changes in niche marginality across 21 species of plant and animal suggest differential responses between highland and lowland species to past climatic changes
inferred← citeshttps://doi.org/10.23880/izab-16000569openalex-snapshot
Molecular Markers and Taxonomic Explosion in Herpetology: More or Less Robust Taxonomy? True and False Advantages of DNA Markers
inferred← citeshttps://doi.org/10.26879/837openalex-snapshot
The earliest known occurrence of Elgaria (Squamata: Anguidae) and a minimum age for crown Gerrhonotinae: Fossils from the Split Rock Formation, Wyoming, USA
inferred← citeshttps://doi.org/10.3897/zookeys.1166.86986openalex-snapshot
An updated list of the Mexican herpetofauna: with a summary of historical and contemporary studies
inferred← citeshttps://doi.org/10.6084/m9.figshare.13233183openalex-snapshot
Additional file 1 of DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau
inferred← citeshttps://doi.org/10.6084/m9.figshare.16703233openalex-snapshot
Additional file 1 of A new extinct species of alligator lizard (Squamata: Elgaria) and an expanded perspective on the osteology and phylogeny of Gerrhonotinae
inferred← citeshttps://doi.org/10.69905/v867s883openalex-snapshot
Inventario de la Herpetofauna de México 2023
inferred← citeshttps://doi.org/10.7287/peerj.6744v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Introgressive hybridization in a Spiny-Tailed Iguana, Ctenosaura pectinata, and its implications for taxonomy and conservation (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.6744v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Introgressive hybridization in a Spiny-Tailed Iguana, Ctenosaura pectinata, and its implications for taxonomy and conservation (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.6744v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Introgressive hybridization in a Spiny-Tailed Iguana, Ctenosaura pectinata, and its implications for taxonomy and conservation (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.11602openalex-snapshot
Variation in the skulls of Elgaria and Gerrhonotus (Anguidae, Gerrhonotinae) and implications for phylogenetics and fossil identification
inferred← citeshttps://doi.org/10.7717/peerj.6744openalex-snapshot
Introgressive hybridization in a Spiny-Tailed Iguana, Ctenosaura pectinata , and its implications for taxonomy and conservation
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.