A global catalog of whole-genome diversity from 233 primate species

The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

(2022) Lucie A Bergeron et al.   eLife

205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

(2022) Mareike C. Janiak et al.   MOLECULAR ECOLOGY

The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

(2022) Stéphane Peyrégne et al.   eLife

The inflated significance of neutral genetic diversity in conservation genetics

(2021) João C. Teixeira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment

(2021) Cleber A. Trujillo et al.   SCIENCE

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Earliest Palaeocene purgatoriids and the initial radiation of stem primates

(2021) Gregory P. Wilson Mantilla et al.   Royal Society Open Science

COMBINE: a coalesced mammal database of intrinsic and extrinsic traits

(2021) Carmen D. Soria et al.   ECOLOGY

Evolutionary and biomedical insights from a marmoset diploid genome assembly

(2021) Chentao Yang et al.   NATURE

Reduced purine biosynthesis in humans after their divergence from Neandertals

(2021) Vita Stepanova et al.   eLife

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

(2021) Lucie A Bergeron et al.   GigaScience

The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates

(2021) David Marjanović   Frontiers in Genetics

Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution

(2021) Hans P. Püschel et al.   Nature Ecology & Evolution

HuConTest: Testing Human Contamination in Great Ape Samples

(2021) Martin Kuhlwilm et al.   Genome Biology and Evolution

Biotic community and landscape changes around the Eocene–Oligocene transition at Shapaja, Peruvian Amazonia: Regional or global drivers?

(2021) Pierre-Olivier Antoine et al.   GLOBAL AND PLANETARY CHANGE

An Early Oligocene age for the oldest known monkeys and rodents of South America

(2021) Kenneth E. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population

(2020) Michael D. Kessler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the mutation rate across primates

(2020) Manjusha Chintalapati et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Branching out: what omics can tell us about primate evolution

(2020) Lukas FK Kuderna et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A high-coverage Neandertal genome from Chagyrskaya Cave

(2020) Fabrizio Mafessoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing sex-biased admixture origin of macaque species using autosomal and X-chromosomal genomic sequences

(2020) Naoki Osada et al.   Genome Biology and Evolution

New Middle Miocene Ape (Primates: Hylobatidae) from Ramnagar, India fills major gaps in the hominoid fossil record

(2020) Christopher C. Gilbert et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?

(2020) Daniel M Portik et al.   SYSTEMATIC BIOLOGY

A comparison of humans and baboons suggests germline mutation rates do not track cell divisions

(2020) Felix L. Wu et al.   PLOS BIOLOGY

Biogeographic mechanisms involved in the colonization of Madagascar by African vertebrates: Rifting, rafting and runways

(2020) Judith C. Masters et al.   JOURNAL OF BIOGEOGRAPHY

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

(2020) Dan Vanderpool et al.   PLOS BIOLOGY

Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation

(2020) William J. Murphy et al.   Annual Review of Animal Biosciences

The Diversity of Primates: From Biomedicine to Conservation Genomics

(2020) Joseph D. Orkin et al.   Annual Review of Animal Biosciences

Visualization in Bayesian workflow

(2019) Jonah Gabry et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

Direct estimation of mutations in great apes reconciles phylogenetic dating

(2019) Søren Besenbacher et al.   Nature Ecology & Evolution

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

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

Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction

(2019) Jacqueline A. Robinson et al.   Science Advances

MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees

(2019) Mark N Puttick   BIOINFORMATICS

The rodents from Santpedor-2 (Ebro Basin, NE Spain) confirm the Oligocene age of the latest primates from the Paleogene of Europe

(2019) Monique Vianey-Liaud et al.   GEOBIOS

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins

(2019) Martin Kuhlwilm et al.   Scientific Reports

The presence and impact of reference bias on population genomic studies of prehistoric human populations

(2019) Torsten Günther et al.   PLoS Genetics

Congruence, fossils and the evolutionary tree of rodents and lagomorphs

(2019) Robert J. Asher et al.   Royal Society Open Science

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

(2019) Suha Naser-Khdour et al.   Genome Biology and Evolution

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

The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets

(2019) Tom van der Valk et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

(2019) Lu Wang et al.   GigaScience

Admixture in Mammals and How to Understand Its Functional Implications

(2019) Claudia Fontsere et al.   BIOESSAYS

Paleogene mammalian fauna exchanges and the paleogeographic pattern in Asia

(2019) Xijun Ni et al.   Science China-Earth Sciences

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

(2019) Michael R McGowen et al.   SYSTEMATIC BIOLOGY

Genomic Mechanisms of Physiological and Morphological Adaptations of Limestone Langurs to Karst Habitats

(2019) Zhijin Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

The soft explosive model of placental mammal evolution

(2018) Matthew J. Phillips et al.   BMC EVOLUTIONARY BIOLOGY

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

Mitochondrial DNA Analyses of Cercopithecus Monkeys Reveal a Localized Hybrid Origin for C. mitis doggetti in Gombe National Park, Tanzania

(2018) Kate M. Detwiler   INTERNATIONAL JOURNAL OF PRIMATOLOGY

How many species of mammals are there?

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

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

Ancient hybridization and admixture in macaques (genus Macaca ) inferred from whole genome sequences

(2018) Zhenxin Fan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

(2018) Mario Dos Reis et al.   SYSTEMATIC BIOLOGY

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

(2018) Daniele Silvestro et al.   SYSTEMATIC BIOLOGY

R 2s for Correlated Data: Phylogenetic Models, LMMs, and GLMMs

(2018) Anthony R Ives   SYSTEMATIC BIOLOGY

Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar’s aye-aye

(2018) Gregg F. Gunnell et al.   Nature Communications

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas

(2018) Tom van der Valk et al.   CURRENT BIOLOGY

New fossils, systematics, and biogeography of the oldest known crown primate Teilhardina from the earliest Eocene of Asia, Europe, and North America

(2018) Paul E. Morse et al.   JOURNAL OF HUMAN EVOLUTION

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

(2017) Jacob A. Esselstyn et al.   Genome Biology and Evolution

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

New infant cranium from the African Miocene sheds light on ape evolution

(2017) Isaiah Nengo et al.   NATURE

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

Genes and molecular pathways underpinning ciliopathies

(2017) Jeremy F. Reiter et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

(2017) Liang Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multispecies coalescent delimits structure, not species

(2017) Jeet Sukumaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

(2017) Rachel C. M. Warnock et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier

(2017) Ben J. Evans et al.   Royal Society Open Science

Impending extinction crisis of the world’s primates: Why primates matter

(2017) Alejandro Estrada et al.   Science Advances

Primate brain size is predicted by diet but not sociality

(2017) Alex R. DeCasien et al.   Nature Ecology & Evolution

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

(2016) D. R. Schrider et al.   GENETICS

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

The population genomics of rhesus macaques ( Macaca mulatta ) based on whole-genome sequences

(2016) Cheng Xue et al.   GENOME RESEARCH

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

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

Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation

(2016) Li Yu et al.   NATURE GENETICS

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

Oligocene primates from China reveal divergence between African and Asian primate evolution

(2016) X. Ni et al.   SCIENCE

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

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

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

(2015) Brant C. Faircloth   BIOINFORMATICS

Climate change modifies risk of global biodiversity loss due to land-cover change

(2015) Chrystal S. Mantyka-Pringle et al.   BIOLOGICAL CONSERVATION

The position of tree shrews in the mammalian tree: Comparing multi-gene analyses with phylogenomic results leaves monophyly of Euarchonta doubtful

(2015) Xuming ZHOU et al.   Integrative Zoology

The systematics and evolution of New World primates – A review

(2015) Horacio Schneider et al.   MOLECULAR PHYLOGENETICS AND 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

Constraints on the timescale of animal evolutionary history

(2015) MJ Benton et al.   PALAEONTOLOGIA ELECTRONICA

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

(2015) Y. Xue et al.   SCIENCE

Geomolecular Dating and the Origin of Placental Mammals

(2015) Matthew J. Phillips   SYSTEMATIC BIOLOGY

The Human Condition—A Molecular Approach

(2014) Svante Pääbo   CELL

The red island and the seven dwarfs: body size reduction in Cheirogaleidae

(2014) Judith C. Masters et al.   JOURNAL OF BIOGEOGRAPHY

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

(2014) Luca Pozzi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

A partial hominoid innominate from the Miocene of Pakistan: Description and preliminary analyses

(2014) Michèle E. Morgan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel episodes of phyletic dwarfism in callitrichid and cheirogaleid primates

(2013) S. H. Montgomery et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The westernmost tarsier: A new genus and species from the Miocene of Pakistan

(2013) Jelle S. Zijlstra et al.   JOURNAL OF HUMAN EVOLUTION

Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate

(2013) Jiannan Lin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Phylogenetic signal in primate behaviour, ecology and life history

(2013) J. M. Kamilar et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Imperfect Isolation: Factors and Filters Shaping Madagascar’s Extant Vertebrate Fauna

(2013) Karen E. Samonds et al.   PLoS One

A Mitogenomic Phylogeny of Living Primates

(2013) Knut Finstermeier et al.   PLoS One

Early cercopithecid monkeys from the Tugen Hills, Kenya

(2013) J. B. Rossie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) M. A. O'Leary et al.   SCIENCE

Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids

(2013) Gerrit Hartig et al.   Scientific Reports

Generation length for mammals

(2013) Moreno Di Marco et al.   Nature Conservation-Bulgaria

INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION

(2012) Graham J. Slater et al.   EVOLUTION

The bonobo genome compared with the chimpanzee and human genomes

(2012) Kay Prüfer et al.   NATURE

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

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

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

Spatial and temporal arrival patterns of Madagascar's vertebrate fauna explained by distance, ocean currents, and ancestor type

(2012) K. E. Samonds et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drift-barrier hypothesis and mutation-rate evolution

(2012) W. Sung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys

(2011) Christian Roos et al.   BMC EVOLUTIONARY BIOLOGY

Genomic data reject the hypothesis of a prosimian primate clade

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

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

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

Stepwise evolution of stable sociality in primates

(2011) Susanne Shultz et al.   NATURE

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mammalian biodiversity on Madagascar controlled by ocean currents

(2010) Jason R. Ali et al.   NATURE

Late middle Eocene epoch of Libya yields earliest known radiation of African anthropoids

(2010) Jean-Jacques Jaeger et al.   NATURE

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

A new Middle Miocene tarsier from Thailand and the reconstruction of its orbital morphology using a geometric-morphometric method

(2010) Y. Chaimanee et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

The new framework for understanding placental mammal evolution

(2009) Robert J. Asher et al.   BIOESSAYS

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

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

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

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

(2009) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY