The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics

Species list of the European herpetofauna – 2020 update by the Taxonomic Committee of the Societas Europaea Herpetologica

(2020) Jeroen Speybroeck et al.   AMPHIBIA-REPTILIA

Multigene phylogeny, phylogeography and population structure of Podarcis cretensis species group in south Balkans

(2019) Loukia Spilani et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

Podarcis vaucheri (Sauria: Lacertidae) far away from home: a new invasive species in Greece

(2018) Loukia Spilani et al.   AMPHIBIA-REPTILIA

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system

(2018) Nikolaos Psonis et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes

(2018) Ricardo Betancur‐R. et al.   EVOLUTION

Structure_threader : An improved method for automation and parallelization of programs structure , fastStructure and MavericK on multicore CPU systems

(2017) Francisco Pina-Martins et al.   Molecular Ecology Resources

Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity

(2017) Adrián Nieto-Montes de Oca et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hidden diversity in the Podarcis tauricus (Sauria, Lacertidae) species subgroup in the light of multilocus phylogeny and species delimitation

(2017) Nikolaos Psonis et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The effects of historical fragmentation on major histocompatibility complex class II β and microsatellite variation in the Aegean island reptile, Podarcis erhardii

(2017) Trent Santonastaso et al.   Ecology and Evolution

Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae)

(2017) Xueqin Wang et al.   Scientific Reports

Genome-wide data reveal cryptic diversity and genetic introgression in an Oriental cynopterine fruit bat radiation

(2016) Balaji Chattopadhyay et al.   BMC EVOLUTIONARY BIOLOGY

ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: Analyses of two avian genera with contrasting histories

(2016) Jeffrey M. DaCosta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evaluating the phylogenetic signal limit from mitogenomes, slow evolving nuclear genes, and the concatenation approach. New insights into the Lacertini radiation using fast evolving nuclear genes and species trees

(2016) Joana Mendes et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

(2015) Adam D. Leaché et al.   Genome Biology and Evolution

Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

(2015) Naama M. Kopelman et al.   Molecular Ecology Resources

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

(2015) Jeffrey W. Streicher et al.   SYSTEMATIC BIOLOGY

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock

(2014) Tetsumi Takahashi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Correction: Variability of the mc1r Gene in Melanic and Non-Melanic Podarcis lilfordi and Podarcis pityusensis from the Balearic Archipelago

(2013) Joana M. Buades et al.   PLoS One

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast radiation of the subfamily Lacertinae (Reptilia: Lacertidae): History or methodical artefact?

(2009) Mihaela Pavlicev et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Effects of fragmentation on genetic diversity in island populations of the Aegean wall lizard Podarcis erhardii (Lacertidae, Reptilia)

(2009) H. Hurston et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

(2008) G. Aguileta et al.   SYSTEMATIC BIOLOGY

Two new species ofPodarcis(Squamata; Lacertidae) from Greece

(2008) P. Lymberakis et al.   SYSTEMATICS AND BIODIVERSITY