Placing Ancient DNA Sequences into Reference Phylogenies

Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data

(2021) Hao Chen et al.   BMC BIOINFORMATICS

Genomic insights into the formation of human populations in East Asia

(2021) Chuan-Chao Wang et al.   NATURE

Environmental genomics of Late Pleistocene black bears and giant short-faced bears

(2021) Mikkel Winther Pedersen et al.   CURRENT BIOLOGY

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

(2021) Yucheng Wang et al.   NATURE

Ancient West African foragers in the context of African population history

(2020) Mark Lipson et al.   NATURE

Insights into human genetic variation and population history from 929 diverse genomes

(2020) Anders Bergström et al.   SCIENCE

A Southeast Asian origin for present-day non-African human Y chromosomes

(2020) Pille Hallast et al.   HUMAN GENETICS

Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

(2020) Ke Wang et al.   Science Advances

HaploGrouper: A generalized approach to haplogroup classification

(2020) Anuradha Jagadeesan et al.   BIOINFORMATICS

Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America

(2019) Pavel Flegontov et al.   NATURE

The population history of northeastern Siberia since the Pleistocene

(2019) Martin Sikora et al.   NATURE

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

(2019) Mary E. Prendergast et al.   SCIENCE

Ancient DNA sheds light on the genetic origins of early Iron Age Philistines

(2019) Michal Feldman et al.   Science Advances

Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan

(2019) Chao Ning et al.   CURRENT BIOLOGY

The formation of human populations in South and Central Asia

(2019) Vagheesh M. Narasimhan et al.   SCIENCE

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

(2019) Liisa Loog et al.   MOLECULAR ECOLOGY

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

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Yleaf: Software for Human Y-Chromosomal Haplogroup Inference from Next-Generation Sequencing Data

(2018) Arwin Ralf et al.   MOLECULAR BIOLOGY AND EVOLUTION

137 ancient human genomes from across the Eurasian steppes

(2018) Peter de Barros Damgaard et al.   NATURE

Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe

(2018) Rosa Fregel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

(2018) Marieke van de Loosdrecht et al.   SCIENCE

The first horse herders and the impact of early Bronze Age steppe expansions into Asia

(2018) Peter de Barros Damgaard et al.   SCIENCE

The genomic history of southeastern Europe

(2018) Iain Mathieson et al.   NATURE

The study of human Y chromosome variation through ancient DNA

(2017) Toomas Kivisild   HUMAN GENETICS

Female exogamy and gene pool diversification at the transition from the Final Neolithic to the Early Bronze Age in central Europe

(2017) Corina Knipper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

(2017) Carina M. Schlebusch et al.   SCIENCE

Archaeogenomic evidence reveals prehistoric matrilineal dynasty

(2017) Douglas J. Kennett et al.   Nature Communications

Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

(2017) Verena J. Schuenemann et al.   Nature Communications

Reconstructing genetic history of Siberian and Northeastern European populations

(2016) Emily H.M. Wong et al.   GENOME RESEARCH

Genomic insights into the origin of farming in the ancient Near East

(2016) Iosif Lazaridis et al.   NATURE

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

(2016) G David Poznik et al.   NATURE GENETICS

Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent

(2015) Beniamino Trombetta et al.   Genome Biology and Evolution

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

(2015) Monika Karmin et al.   GENOME RESEARCH

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

(2015) Hannes Schroeder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa

(2015) M. Gallego Llorente et al.   SCIENCE

Upper Palaeolithic genomes reveal deep roots of modern Eurasians

(2015) Eppie R. Jones et al.   Nature Communications

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

Genome flux and stasis in a five millennium transect of European prehistory

(2014) Cristina Gamba et al.   Nature Communications

An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

(2013) Fernando L. Mendez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

(2013) G. D. Poznik et al.   SCIENCE

Ancient DNA Damage

(2013) J. Dabney et al.   Cold Spring Harbor Perspectives in Biology

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Computational challenges in the analysis of ancient DNA

(2010) Kay Prüfer et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa

(2008) B. M. Henn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA