4.6 Review

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

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

Susan Fairley et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

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

Liisa Loog et al.

MOLECULAR ECOLOGY (2020)

Article Multidisciplinary Sciences

The spatiotemporal spread of human migrations during the European Holocene

Fernando Racimo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

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

Anders Bergstrom et al.

SCIENCE (2020)

Review Genetics & Heredity

Animal domestication in the era of ancient genomics

Laurent A. F. Frantz et al.

NATURE REVIEWS GENETICS (2020)

Article Biochemistry & Molecular Biology

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

Lehti Saag et al.

CURRENT BIOLOGY (2019)

Article Multidisciplinary Sciences

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

Hannes Schroeder et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Genetics & Heredity

Inferring whole-genome histories in large population datasets

Jerome Kelleher et al.

NATURE GENETICS (2019)

Article Genetics & Heredity

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

Leo Speidel et al.

NATURE GENETICS (2019)

Article Multidisciplinary Sciences

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

Eva K. F. Chan et al.

NATURE (2019)

Article Multidisciplinary Sciences

Genetic contributions to variation in human stature in prehistoric Europe

Samantha L. Cox et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Kinship-based social inequality in Bronze Age Europe

Alissa Mittnik et al.

SCIENCE (2019)

Article Biochemistry & Molecular Biology

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

Benjamin C. Haller et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Review Genetics & Heredity

Ancient Genomics of Modern Humans: The First Decade

Pontus Skoglund et al.

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, VOL 19 (2018)

Article Multidisciplinary Sciences

Estimating genetic kin relationships in prehistoric populations

Jose Manuel Monroy Kuhn et al.

PLOS ONE (2018)

Article Multidisciplinary Sciences

The genomic history of southeastern Europe

Iain Mathieson et al.

NATURE (2018)

Article Multidisciplinary Sciences

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

Carlos Eduardo G. Amorim et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

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

Daniel J. Lawson et al.

NATURE COMMUNICATIONS (2018)

Review Genetics & Heredity

Harnessing ancient genomes to study the history of human adaptation

Stephanie Marciniak et al.

NATURE REVIEWS GENETICS (2017)

Article Multidisciplinary Sciences

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

Andrew Bevan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Multidisciplinary Sciences

Estimating mobility using sparse data: Application to human genetic variation

Liisa Loog et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Genetics & Heredity

Identifying Bird Remains Using Ancient DNA Barcoding

Love Dalen et al.

Article Multidisciplinary Sciences

Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum

Henrik B. Hansen et al.

PLOS ONE (2017)

Article Psychology, Biological

Genetic evidence of assortative mating in humans

Matthew R. Robinson et al.

NATURE HUMAN BEHAVIOUR (2017)

Review Biochemistry & Molecular Biology

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

Anna-Sapfo Malaspinas

MOLECULAR ECOLOGY (2016)

Article Genetics & Heredity

Visualizing spatial population structure with estimated effective migration surfaces

Desislava Petkova et al.

NATURE GENETICS (2016)

Article Multidisciplinary Sciences

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

Swapan Mallick et al.

NATURE (2016)

Article Multidisciplinary Sciences

Genomic analyses inform on migration events during the peopling of Eurasia

Luca Pagani et al.

NATURE (2016)

Article Multidisciplinary Sciences

Late Pleistocene climate drivers of early human migration

Axel Timmermann et al.

NATURE (2016)

Article Multidisciplinary Sciences

Early farmers from across Europe directly descended from Neolithic Aegeans

Zuzana Hofmanova et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Biochemical Research Methods

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

Jerome Kelleher et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

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

Eleftheria Palkopoulou et al.

CURRENT BIOLOGY (2015)

Article Multidisciplinary Sciences

Genome-wide patterns of selection in 230 ancient Eurasians

Iain Mathieson et al.

NATURE (2015)

Article Multidisciplinary Sciences

A global reference for human genetic variation

David M. Altshuler et al.

NATURE (2015)

Article Multidisciplinary Sciences

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

Maanasa Raghavan et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

Investigating Population History Using Temporal Genetic Differentiation

Pontus Skoglund et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Biochemistry & Molecular Biology

Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes

Adrien Rieux et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Multidisciplinary Sciences

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

Iosif Lazaridis et al.

NATURE (2014)

Article Multidisciplinary Sciences

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

Morten Rasmussen et al.

NATURE (2014)

Article Genetics & Heredity

Inferring human population size and separation history from multiple genome sequences

Stephan Schiffels et al.

NATURE GENETICS (2014)

Article Multidisciplinary Sciences

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

Sandra Wilde et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Storytelling and story testing in domestication

Pascale Gerbault et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

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

Cristina Gamba et al.

NATURE COMMUNICATIONS (2014)

Article Genetics & Heredity

Genome Sequencing Highlights the Dynamic Early History of Dogs

Adam H. Freedman et al.

PLOS GENETICS (2014)

Article Anthropology

Accurate sex identification of ancient human remains using DNA shotgun sequencing

Pontus Skoglund et al.

JOURNAL OF ARCHAEOLOGICAL SCIENCE (2013)

Article Multidisciplinary Sciences

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

Jesse Dabney et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

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

Stephen Shennan et al.

NATURE COMMUNICATIONS (2013)

Article Biochemical Research Methods

Approximate Bayesian Computation

Mikael Sunnaker et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Genetics & Heredity

Robust Demographic Inference from Genomic and SNP Data

Laurent Excoffier et al.

PLOS GENETICS (2013)

Article Genetics & Heredity

Ancient Admixture in Human History

Nick Patterson et al.

GENETICS (2012)

Article Multidisciplinary Sciences

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

Vera Warmuth et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

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

Anders Eriksson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

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

Anders Eriksson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Genetics & Heredity

Inference of Population Structure using Dense Haplotype Data

Daniel John Lawson et al.

PLOS GENETICS (2012)

Article Multidisciplinary Sciences

Inference of human population history from individual whole-genome sequences

Heng Li et al.

NATURE (2011)

Article Genetics & Heredity

Bayesian inference of ancient human demography from individual genome sequences

Ilan Gronau et al.

NATURE GENETICS (2011)

Article Multidisciplinary Sciences

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

Mathias Currat et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

A Draft Sequence of the Neandertal Genome

Richard E. Green et al.

SCIENCE (2010)

Article Biochemistry & Molecular Biology

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

Helena Malmstrom et al.

CURRENT BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Fast model-based estimation of ancestry in unrelated individuals

David H. Alexander et al.

GENOME RESEARCH (2009)

Review Biochemistry & Molecular Biology

Statistical inferences in phylogeography

Rasmus Nielsen et al.

MOLECULAR ECOLOGY (2009)

Article Multidisciplinary Sciences

Reconstructing Indian population history

David Reich et al.

NATURE (2009)

Article Genetics & Heredity

A Genealogical Interpretation of Principal Components Analysis

Gil McVean

PLOS GENETICS (2009)

Article Multidisciplinary Sciences

Genes mirror geography within Europe

John Novembre et al.

NATURE (2008)

Article Multidisciplinary Sciences

Worldwide human relationships inferred from genome-wide patterns of variation

Jun Z. Li et al.

SCIENCE (2008)

Article Genetics & Heredity

Geographic patterns of genome admixture in Latin American mestizos

Sijia Wang et al.

PLOS GENETICS (2008)

Article Multidisciplinary Sciences

Circuit theory predicts gene flow in plant and animal populations

Brad H. McRae et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

Staying out in the cold:: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears

Cristina E. Valdiosera et al.

MOLECULAR ECOLOGY (2007)

Article Multidisciplinary Sciences

Ancient DNA, pig domestication, and the spread of the Neolithic into Europe

Greger Larson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Ancient biomolecules from deep ice cores reveal a forested Southern Greenland

Eske Willerslev et al.

SCIENCE (2007)

Article Multidisciplinary Sciences

Absence of the lactase-persistence-associated allele in early Neolithic Europeans

J. Burger et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics

Jody Hey et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemical Research Methods

Ancient DNA extraction from bones and teeth

Nadin Rohland et al.

NATURE PROTOCOLS (2007)

Article Genetics & Heredity

A geographically explicit genetic model of worldwide human-settlement history

Hua Liu et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2006)

Article Multidisciplinary Sciences

Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa

S Ramachandran et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Review Biochemistry & Molecular Biology

The incomplete natural history of mitochondria

JWO Ballard et al.

MOLECULAR ECOLOGY (2004)

Review Genetics & Heredity

Genealogical trees, coalescent theory and the analysis of genetic polymorphisms

NA Rosenberg et al.

NATURE REVIEWS GENETICS (2002)

Article Genetics & Heredity

The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations

PA Underhill et al.

ANNALS OF HUMAN GENETICS (2001)