Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species

Oil palm plantations in Peninsular Malaysia: Determinants and constraints on expansion

(2019) Varada S. Shevade et al.   PLoS One

Presbytis neglectus or P. femoralis, Colobine Molecular Phylogenies, and GenBank Submission of Newly Generated DNA Sequences

(2019) Vincent Nijman   FOLIA PRIMATOLOGICA

Boosting natural history research via metagenomic clean-up of crowdsourced feces

(2019) Amrita Srivathsan et al.   PLOS BIOLOGY

How many species of mammals are there?

(2018) Connor J Burgin et al.   JOURNAL OF MAMMALOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces

(2018) Kenneth L. Chiou et al.   Scientific Reports

Taxonomy based on science is necessary for global conservation

(2018) Scott A. Thomson et al.   PLOS BIOLOGY

Is Malaysia’s banded langur, Presbytis femoralis femoralis, actually Presbytis neglectus neglectus? Taxonomic revision with new insights on the radiation history of the Presbytis species group in Southeast Asia

(2018) Muhammad Abu Bakar Abdul-Latiff et al.   PRIMATES

Expansion of Industrial Plantations Continues to Threaten Malayan Tiger Habitat

(2017) Varada S. Shevade et al.   Remote Sensing

Scientific research on animal biodiversity is systematically biased towards vertebrates and temperate regions

(2017) Mark A. Titley et al.   PLoS One

Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate

(2016) Amrita Srivathsan et al.   Frontiers in Zoology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

(2014) Amrita Srivathsan et al.   Molecular Ecology Resources

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

True lemurs…true species - species delimitation using multiple data sources in the brown lemur complex

(2013) Matthias Markolf et al.   BMC EVOLUTIONARY BIOLOGY

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic Relationships among the Colobine Monkeys Revisited: New Insights from Analyses of Complete mt Genomes and 44 Nuclear Non-Coding Markers

(2012) Xiao Ping Wang et al.   PLoS One

Geographical and taxonomic biases in research on biodiversity in human-modified landscapes

(2012) Morgan J. Trimble et al.   Ecosphere

On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature

(2011) Amrita Srivathsan et al.   CLADISTICS

Phylogenetic relationships of leaf monkeys (Presbytis; Colobinae) based on cytochrome b and 12S rRNA genes

(2011) V.F. Vun et al.   GENETICS AND MOLECULAR RESEARCH

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

Mitochondrial phylogeny of leaf monkeys (genus Presbytis, Eschscholtz, 1821) with implications for taxonomy and conservation

(2011) Dirk Meyer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Soils on exposed Sunda Shelf shaped biogeographic patterns in the equatorial forests of Southeast Asia

(2011) J. W. F. Slik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

(2010) Gaurav Vaidya et al.   CLADISTICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

(2010) A. C. Stone et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Monkeys of the Genera Pithecus (or Presbytis) and Pygulhrix found to the East of the Bay of Bengal.

(2010) R. I. Pocock   PROCEEDINGS OF THE ZOOLOGICAL SOCIETY OF LONDON

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Establishing the foundation for an applied molecular taxonomy of otters in Southeast Asia

(2008) Klaus-Peter Koepfli et al.   CONSERVATION GENETICS

The need for specifying species concepts: How many species of silvered langurs (Trachypithecus cristatus group) should be recognized?

(2008) Tan Siew Hoong Denise et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Mitochondrial phylogeny, taxonomy and biogeography of the silvered langur species group (Trachypithecus cristatus)

(2008) Christian Roos et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION