Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

(2013) Wei Wang et al.   Journal of Zhejiang University-SCIENCE B

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

(2013) Zhuo Wang et al.   NATURE GENETICS

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

(2013) H Bradley Shaffer et al.   GENOME BIOLOGY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus)

(2012) Hilary C Miller et al.   BMC GENOMICS

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia

(2012) Jonathan J. Fong et al.   PLoS One

Parallel Evolution of Auditory Genes for Echolocation in Bats and Toothed Whales

(2012) Yong-Yi Shen et al.   PLoS Genetics

MicroRNAs support a turtle + lizard clade

(2011) T. R. Lyson et al.   Biology Letters

Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles

(2011) X.-X. Shen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates

(2011) Andrew H. Moeller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

(2011) Athanasia C Tzika et al.   EvoDevo

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Natural Selection on Functional Modules, a Genome-Wide Analysis

(2011) François Serra et al.   PLoS Computational Biology

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

Transitional fossils and the origin of turtles

(2010) T. R. Lyson et al.   Biology Letters

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Proopiomelanocortin (POMC) and testing the phylogenetic position of turtles (Testudines)

(2010) Rosemary E. Becker et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

(2010) A. M. Heimberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of the Turtle Body Plan by the Folding and Creation of New Muscle Connections

(2009) H. Nagashima et al.   SCIENCE

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE