Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

Whole mitochondrial genomes illuminate ancient intercontinental dispersals of grey wolves (Canis lupus )

(2016) Stephan Koblmüller et al.   JOURNAL OF BIOGEOGRAPHY

Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys , Nannosciurinae)

(2016) Melissa T.R. Hawkins et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates

(2015) Paul B Frandsen et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeography of vertebrates on the Sunda Shelf: a multi-species comparison

(2015) Jennifer A. Leonard et al.   JOURNAL OF BIOGEOGRAPHY

In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA

(2015) Melissa T. R. Hawkins et al.   Molecular Ecology Resources

Applying species-tree analyses to deep phylogenetic histories: Challenges and potential suggested from a survey of empirical phylogenetic studies

(2015) Hayley C. Lanier et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Mitochondrial Genomes Suggest Rapid Evolution of Dwarf California Channel Islands Foxes (Urocyon littoralis)

(2015) Courtney A. Hofman et al.   PLoS One

The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews

(2015) Thomas C. Giarla et al.   SYSTEMATIC BIOLOGY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

(2014) Patrick Kück et al.   Frontiers in Zoology

Each flying fox on its own branch: A phylogenetic tree for Pteropus and related genera (Chiroptera: Pteropodidae)

(2014) Francisca C. Almeida et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Snail Perspective on the Biogeography of Sulawesi, Indonesia: Origin and Intra-Island Dispersal of the Viviparous Freshwater Gastropod Tylomelania

(2014) Thomas von Rintelen et al.   PLoS One

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

The palaeogeography of Sundaland and Wallacea since the Late Jurassic

(2013) Robert Hall   JOURNAL OF LIMNOLOGY

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models

(2012) Ben Wielstra et al.   BMC EVOLUTIONARY BIOLOGY

THE BIOGEOGRAPHY OF SULAWESI REVISITED: IS THERE EVIDENCE FOR A VICARIANT ORIGIN OF TAXA ON WALLACE'S “ANOMALOUS ISLAND”?

(2012) Björn Stelbrink et al.   EVOLUTION

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation phylogenetics takes root

(2012) John E. McCormack et al.   MOLECULAR ECOLOGY

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

Birds of a feather

(2012) Robert E. Ricklefs et al.   NATURE

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Late Jurassic–Cenozoic reconstructions of the Indonesian region and the Indian Ocean

(2012) Robert Hall   TECTONOPHYSICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Multilocus Resolution of Phylogeny and Timescale in the Extant Adaptive Radiation of Hawaiian Honeycreepers

(2011) Heather R.L. Lerner et al.   CURRENT BIOLOGY

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

Ancient hybridization and underestimated species diversity in Asian striped squirrels (genusTamiops): inference from paternal, maternal and biparental markers

(2011) S.-W. Chang et al.   JOURNAL OF ZOOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

(2011) Brian J Knaus et al.   BMC ECOLOGY

Biogeography and conservation in Southeast Asia: how 2.7 million years of repeated environmental fluctuations affect today’s patterns and the future of the remaining refugial-phase biodiversity

(2010) David S. Woodruff   BIODIVERSITY AND CONSERVATION

Cryptic genetic diversity in “widespread” Southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated

(2010) David J. Lohman et al.   BIOLOGICAL CONSERVATION

Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

(2010) Guy G. Musser et al.   BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY

Nuclear copies of mitochondrial genes: another problem for ancient DNA

(2010) Robert-Jan den Tex et al.   GENETICA

Surface deformation and slab–mantle interaction during Banda arc subduction rollback

(2010) Wim Spakman et al.   Nature Geoscience

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

DO GEOLOGICAL OR CLIMATIC PROCESSES DRIVE SPECIATION IN DYNAMIC ARCHIPELAGOS? THE TEMPO AND MODE OF DIVERSIFICATION IN SOUTHEAST ASIAN SHREWS

(2009) Jacob A. Esselstyn et al.   EVOLUTION

Origin and status of the Great Lakes wolf

(2009) STEPHAN KOBLMÜLLER et al.   MOLECULAR ECOLOGY

The current refugial rainforests of Sundaland are unrepresentative of their biogeographic past and highly vulnerable to disturbance

(2009) C. H. Cannon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Multilocus phylogeography and phylogenetics using sequence-based markers

(2008) Patrícia H. Brito et al.   GENETICA

Ancient hybridization and mitochondrial capture between two species of chipmunks

(2008) JEFFREY M. GOOD et al.   MOLECULAR ECOLOGY

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

(2007) S. Stephen et al.   MOLECULAR BIOLOGY AND EVOLUTION