The problems of molecular phylogenetics with the example of squamate reptiles: Mitochondrial DNA markers

Bioinformatics Analysis the Complete Sequences of Cytochrome b of Takydromus sylvaticus and Modeling the Tertiary Structure of Encoded Protein

(2012) Qi-Long CHEN et al.   International Journal of Biological Sciences

Numts help to reconstruct the demographic history of the ocellated lizard (Lacerta lepida) in a secondary contact zone

(2012) ANDREIA MIRALDO et al.   MOLECULAR ECOLOGY

What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodonsalamanders and 13 other vertebrate clades

(2011) M Caitlin Fisher-Reid et al.   BMC EVOLUTIONARY BIOLOGY

Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination

(2011) Svenja Sammler et al.   BMC GENOMICS

Evolutionary Patterns of the Mitochondrial Genome in Metazoa: Exploring the Role of Mutation and Selection in Mitochondrial Protein–Coding Genes

(2011) S. Castellana et al.   Genome Biology and Evolution

Neutral mitochondrial heteroplasmy and the influence of aging

(2011) Neal Sondheimer et al.   HUMAN MOLECULAR GENETICS

Extensive Phylogeographic and Morphological Diversity in Diporiphora nobbi (Agamidae) Leads to a Taxonomic Review and a New Species Description

(2011) Danielle L. Edwards et al.   JOURNAL OF HERPETOLOGY

Repeated DNA sequences as an engine of biological diversification

(2011) V. V. Grechko   MOLECULAR BIOLOGY

Molecular differentiation and taxonomy of the sunwatcher toad-headed agama species complex Phrynocephalus superspecies helioscopus (Pallas 1771) (Reptilia: Agamidae)

(2011) E. N. Solovyeva et al.   RUSSIAN JOURNAL OF GENETICS

Phylogeography of Psammodromus algirus (Lacertidae) revisited: systematic implications

(2010) Joaquín Verdú-Ricoy et al.   AMPHIBIA-REPTILIA

Genome Evolution in Reptilia, the Sister Group of Mammals

(2010) Daniel E. Janes et al.   Annual Review of Genomics and Human Genetics

Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications

(2010) Yasuhisa Okajima et al.   BMC EVOLUTIONARY BIOLOGY

Nuclear mitochondrial pseudogenes

(2010) A. I. Gaziev et al.   MOLECULAR BIOLOGY

In defence of model-based inference in phylogeography

(2010) MARK A. BEAUMONT et al.   MOLECULAR ECOLOGY

Coalescent-based, maximum likelihood inference in phylogeography

(2010) ALAN R. TEMPLETON   MOLECULAR ECOLOGY

Lizards as model organisms for linking phylogeographic and speciation studies

(2010) ARLEY CAMARGO et al.   MOLECULAR ECOLOGY

Divergence times and colonization of the Canary Islands by Gallotia lizards

(2010) Siobhan C. Cox et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary origins and diversification of dragon lizards in Australia’s tropical savannas

(2010) J. Melville et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Detection of Heteroplasmic Mitochondrial DNA in Single Mitochondria

(2010) Joseph E. Reiner et al.   PLoS One

Bayesian species delimitation using multilocus sequence data

(2010) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

Progressive colonization and restricted gene flow shape island-dependent population structure in Galápagos marine iguanas (Amblyrhynchus cristatus)

(2009) Sebastian Steinfartz et al.   BMC EVOLUTIONARY BIOLOGY

WHY DOES A METHOD THAT FAILS CONTINUE TO BE USED? THE ANSWER

(2009) Alan R. Templeton   EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Examining the utility of categorical models and alleviating artifacts in phylogenetic reconstruction of the Squamata (Reptilia)

(2009) D.A. Douglas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Historical biogeography, phylogenetic relationships and intraspecific diversity of agamid lizards in the Central Asian deserts of Kazakhstan and Uzbekistan

(2009) Jane Melville et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeography’s past, present, and future: 10 years after Avise, 2000

(2009) M.J. Hickerson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species trees for spiny lizards (Genus Sceloporus): Identifying points of concordance and conflict between nuclear and mitochondrial data

(2009) Adam D. Leaché   MOLECULAR PHYLOGENETICS AND EVOLUTION

Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)

(2009) A. D. Leache et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for an ancient adaptive episode of convergent molecular evolution

(2009) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Heuristic Methods for Joint Species Delimitation and Species Tree Inference

(2009) Brian C. O'Meara   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

Python phylogenetics: inference from morphology and mitochondrial DNA

(2008) LESLEY H. RAWLINGS et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Documenting the advantages and limitations of different classes of molecular markers in a well-established phylogeographic context: lessons from the Iberian endemic Golden-striped salamander, Chioglossa lusitanica (Caudata: Salamandridae)

(2008) FERNANDO SEQUEIRA et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Using supernetworks to distinguish hybridization from lineage-sorting

(2008) Barbara R Holland et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny And Systematics Of Squamata (Reptilia) Based On Morphology

(2008) Jack L. Conrad   BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY

The molecular evolutionary tree of lizards, snakes, and amphisbaenians

(2008) Nicolas Vidal et al.   COMPTES RENDUS BIOLOGIES

WHY DOES A METHOD THAT FAILS CONTINUE TO BE USED?

(2008) L. Lacey Knowles   EVOLUTION

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data

(2008) Eva M. Albert et al.   GENE

Timing of a mtDNA gene rearrangement and intercontinental dispersal of varanid lizards

(2008) Sayed A. M. Amer et al.   GENES & GENETIC SYSTEMS

An integrated Assessment of a group with complex systematics: the Iberomaghrebian lizard genusPodarcis(Squamata, Lacertidae)

(2008) Miguel A. CARRETERO   Integrative Zoology

Phylogeny, Recombination, and Mechanisms of Stepwise Mitochondrial Genome Reorganization in Mantellid Frogs from Madagascar

(2008) A. Kurabayashi et al.   MOLECULAR BIOLOGY AND EVOLUTION

The limits of mtDNA phylogeography: complex patterns of population history in a highly structured Iberian lizard are only revealed by the use of nuclear markers

(2008) R. GODINHO et al.   MOLECULAR ECOLOGY

Mitochondrial DNA under siege in avian phylogeography

(2008) ROBERT M. ZINK et al.   MOLECULAR ECOLOGY

In situ genetic differentiation in a Hispaniolan lizard (Ameiva chrysolaema): A multilocus perspective

(2008) Matthew E. Gifford et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

(2008) A ECKERT et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogeny of three Mesalina (Reptilia: Lacertidae) species (M. guttulata, M. brevirostris and M. bahaeldini) from North Africa and the Middle East: Another case of paraphyly?

(2008) P. Kapli et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Diversification patterns of pebble-mimic dragons are consistent with historical disruption of important habitat corridors in arid Australia

(2008) L.P. Shoo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Systematic and phylogeographical assessment of the Acanthodactylus erythrurus group (Reptilia: Lacertidae) based on phylogenetic analyses of mitochondrial and nuclear DNA

(2008) Miguel M. Fonseca et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny, evolutionary history, and biogeography of Oriental–Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences

(2007) Michael E. Alfaro et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION