Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

The comparative genomics and complex population history of Papio baboons

(2019) Jeffrey Rogers et al.   Science Advances

Large ancestral effective population size explains the difficult phylogenetic placement of owl monkeys

(2019) Carlos G. Schrago et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Ancient admixture from an extinct ape lineage into bonobos

(2019) Martin Kuhlwilm et al.   Nature Ecology & Evolution

The perils of intralocus recombination for inferences of molecular convergence

(2019) Fábio K. Mendes et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs

(2019) Rachel C. Williams et al.   HEREDITY

The radiation of macaques out of Africa: Evidence from mitogenome divergence times and the fossil record

(2019) Christian Roos et al.   JOURNAL OF HUMAN EVOLUTION

Asymmetric Distribution of Gene Trees Can Arise Under Purifying Selection if Differences in Population Size Exist

(2019) Chong He et al.   MOLECULAR BIOLOGY AND EVOLUTION

ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets

(2019) Mark S Springer et al.   JOURNAL OF HEREDITY

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

(2018) Diep Thi Hoang et al.   BMC EVOLUTIONARY BIOLOGY

A phylogenomic perspective on the robust capuchin monkey ( Sapajus ) radiation: First evidence for extensive population admixture across South America

(2018) Marcela G.M. Lima et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Early arrival and climatically-linked geographic expansion of New World monkeys from tiny African ancestors

(2018) Daniele Silvestro et al.   SYSTEMATIC BIOLOGY

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

(2018) et al.   Genes

Reconstructing the phylogeny of New World monkeys (Platyrrhini): evidence from multiple non-coding loci

(2018) Xiaoping Wang et al.   Current Zoology

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

1.9-million- and 2.4-million-year-old artifacts and stone tool–cutmarked bones from Ain Boucherit, Algeria

(2018) Mohamed Sahnouni et al.   SCIENCE

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

(2017) Hannes Svardal et al.   NATURE GENETICS

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Why Concatenation Fails Near the Anomaly Zone

(2017) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons

(2016) Jeffrey D. Wall et al.   MOLECULAR ECOLOGY

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree

(2016) James P. Herrera et al.   SYSTEMATIC BIOLOGY

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

(2016) Andrej Kuritzin et al.   PLoS Computational Biology

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

(2016) V. C. Mason et al.   Science Advances

Assessment of the hybridization between rhesus (Macaca mulatta) and long-tailed macaques (M. fascicularis) based on morphological characters

(2015) Yuzuru Hamada et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

(2015) K. R. Veeramah et al.   GENETICS

Comparative and population mitogenomic analyses of Madagascar's extinct, giant ‘subfossil’ lemurs

(2015) Logan Kistler et al.   JOURNAL OF HUMAN EVOLUTION

The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis

(2015) Natalie M. Jameson Kiesling et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Eocene primates of South America and the African origins of New World monkeys

(2015) Mariano Bond et al.   NATURE

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History

(2014) Zhenxin Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history

(2014) Xuming Zhou et al.   NATURE GENETICS

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Pliocene–Pleistocene climate of the northern margin of Saharan–Arabian Desert recorded in speleothems from the Negev Desert, Israel

(2013) A. Vaks et al.   EARTH AND PLANETARY SCIENCE LETTERS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Palaeontological evidence for an Oligocene divergence between Old World monkeys and apes

(2013) Nancy J. Stevens et al.   NATURE

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Divergence Times and the Evolutionary Radiation of New World Monkeys (Platyrrhini, Primates): An Analysis of Fossil and Molecular Data

(2013) S. Ivan Perez et al.   PLoS One

Were Rivers Flowing across the Sahara During the Last Interglacial? Implications for Human Migration through Africa

(2013) Tom J. Coulthard et al.   PLoS One

Dynamics of Green Sahara Periods and Their Role in Hominin Evolution

(2013) Juan C. Larrasoaña et al.   PLoS One

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

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

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

Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids

(2013) Gerrit Hartig et al.   Scientific Reports

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

The bonobo genome compared with the chimpanzee and human genomes

(2012) Kay Prüfer et al.   NATURE

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

(2012) Mark S. Springer et al.   PLoS One

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome

(2012) Atsunori Higashino et al.   GENOME BIOLOGY

Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)

(2011) Gloria L Fawcett et al.   BMC GENOMICS

Genomic data reject the hypothesis of a prosimian primate clade

(2011) Natalie M. Jameson et al.   JOURNAL OF HUMAN EVOLUTION

Erratum: A map of human genome variation from population-scale sequencing

(2011)   NATURE

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

(2011) Guangmei Yan et al.   NATURE BIOTECHNOLOGY

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

A Molecular Phylogeny of Living Primates

(2011) Polina Perelman et al.   PLoS Genetics

Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta

(2010) NAOKI OSADA et al.   MOLECULAR ECOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the External Characters of the Lemurs and of Tarsius

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

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data

(2010) Richard D. Wilkinson et al.   SYSTEMATIC BIOLOGY

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genetic analysis of hybridization and introgression between wild mongoose and brown lemurs

(2009) Jennifer Pastorini et al.   BMC EVOLUTIONARY BIOLOGY

Estimating the phylogeny and divergence times of primates using a supermatrix approach

(2009) Helen J Chatterjee et al.   BMC EVOLUTIONARY BIOLOGY

The presence of a large cercopithecine (cf. Theropithecus sp.) in the ‘Ubeidiya formation (Early Pleistocene, Israel)

(2009) Miriam Belmaker   JOURNAL OF HUMAN EVOLUTION

Hybridization between mouse lemurs in an ecological transition zone in southern Madagascar

(2009) M. GLIGOR et al.   MOLECULAR ECOLOGY

What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?

(2009) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Phylogenetic Analysis in the Anomaly Zone

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

New Analytic Results for Speciation Times in Neutral Models

(2008) Tanja Gernhard   BULLETIN OF MATHEMATICAL BIOLOGY

Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees

(2008) M. Slatkin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Theropithecus and ‘Out of Africa’ dispersal in the Plio-Pleistocene

(2007) John K. Hughes et al.   JOURNAL OF HUMAN EVOLUTION