Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories

Animal domestication in the era of ancient genomics

(2020) Laurent A. F. Frantz et al.   NATURE REVIEWS GENETICS

The spatiotemporal spread of human migrations during the European Holocene

(2020) Fernando Racimo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Anders Bergström et al.   SCIENCE

The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East

(2019) Lehti Saag et al.   CURRENT BIOLOGY

Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave

(2019) Hannes Schroeder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring whole-genome histories in large population datasets

(2019) Jerome Kelleher et al.   NATURE GENETICS

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Human origins in a southern African palaeo-wetland and first migrations

(2019) Eva K. F. Chan et al.   NATURE

The International Genome Sample Resource (IGSR) collection of open human genomic variation resources

(2019) Susan Fairley et al.   NUCLEIC ACIDS RESEARCH

Genetic contributions to variation in human stature in prehistoric Europe

(2019) Samantha L. Cox et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinship-based social inequality in Bronze Age Europe

(2019) Alissa Mittnik 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

Ancient Human Genomics: The First Decade

(2018) Pontus Skoglund et al.   Annual Review of Genomics and Human Genetics

Estimating genetic kin relationships in prehistoric populations

(2018) Jose Manuel Monroy Kuhn et al.   PLoS One

The genomic history of southeastern Europe

(2018) Iain Mathieson et al.   NATURE

Understanding 6th-century barbarian social organization and migration through paleogenomics

(2018) Carlos Eduardo G. Amorim et al.   Nature Communications

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots

(2018) Daniel J. Lawson et al.   Nature Communications

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

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

Harnessing ancient genomes to study the history of human adaptation

(2017) Stephanie Marciniak et al.   NATURE REVIEWS GENETICS

Holocene fluctuations in human population demonstrate repeated links to food production and climate

(2017) Andrew Bevan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating mobility using sparse data: Application to human genetic variation

(2017) Liisa Loog et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods

(2017) Rui Martiniano et al.   PLoS Genetics

Identifying Bird Remains Using Ancient DNA Barcoding

(2017) Love Dalén et al.   Genes

Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum

(2017) Henrik B. Hansen et al.   PLoS One

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe

(2016) Cosimo Posth et al.   CURRENT BIOLOGY

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Genomic analyses inform on migration events during the peopling of Eurasia

(2016) Luca Pagani et al.   NATURE

Late Pleistocene climate drivers of early human migration

(2016) Axel Timmermann et al.   NATURE

Early farmers from across Europe directly descended from Neolithic Aegeans

(2016) Zuzana Hofmanová et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds

(2015) Pontus Skoglund et al.   CURRENT BIOLOGY

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

(2015) Eleftheria Palkopoulou et al.   CURRENT BIOLOGY

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective

(2015) Anna-Sapfo Malaspinas   MOLECULAR ECOLOGY

Genome-wide patterns of selection in 230 ancient Eurasians

(2015) Iain Mathieson et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Visualizing spatial population structure with estimated effective migration surfaces

(2015) Desislava Petkova et al.   NATURE GENETICS

Genomic evidence for the Pleistocene and recent population history of Native Americans

(2015) M. Raghavan et al.   SCIENCE

Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference

(2015) Lucy van Dorp et al.   PLoS Genetics

Investigating Population History Using Temporal Genetic Differentiation

(2014) Pontus Skoglund et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes

(2014) Adrien Rieux et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Iosif Lazaridis et al.   NATURE

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

(2014) Morten Rasmussen et al.   NATURE

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

(2014) Iñigo Olalde et al.   NATURE

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y

(2014) Sandra Wilde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Storytelling and story testing in domestication

(2014) P. Gerbault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Cristina Gamba et al.   Nature Communications

Genome Sequencing Highlights the Dynamic Early History of Dogs

(2014) Adam H. Freedman et al.   PLoS Genetics

Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach

(2013) S. Sheehan et al.   GENETICS

Accurate sex identification of ancient human remains using DNA shotgun sequencing

(2013) Pontus Skoglund et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

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

Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs

(2013) O. Thalmann et al.   SCIENCE

Regional population collapse followed initial agriculture booms in mid-Holocene Europe

(2013) Stephen Shennan et al.   Nature Communications

Approximate Bayesian Computation

(2013) Mikael Sunnåker et al.   PLoS Computational Biology

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Reconstructing the origin and spread of horse domestication in the Eurasian steppe

(2012) V. Warmuth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

(2012) A. Eriksson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Late Pleistocene climate change and the global expansion of anatomically modern humans

(2012) A. Eriksson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

(2011) M. Currat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination

(2010) Nicolas Ray et al.   BIOINFORMATICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians

(2009) Helena Malmström et al.   CURRENT BIOLOGY

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Statistical inferences in phylogeography

(2009) RASMUS NIELSEN et al.   MOLECULAR ECOLOGY

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe's First Farmers

(2009) B. Bramanti et al.   SCIENCE

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

USING CIRCUIT THEORY TO MODEL CONNECTIVITY IN ECOLOGY, EVOLUTION, AND CONSERVATION

(2008) Brad H. McRae et al.   ECOLOGY

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

(2008) J. Z. Li et al.   SCIENCE

Geographic Patterns of Genome Admixture in Latin American Mestizos

(2008) Sijia Wang et al.   PLoS Genetics

Wild or domesticated? An ancient DNA approach to canid species identification in South Africa's Western Cape Province

(2007) K. Ann Horsburgh   JOURNAL OF ARCHAEOLOGICAL SCIENCE