4.8 Article

Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

Jazmin Ramos-Madrigal et al.

Summary: The extant genetic diversity of Canis lupus can be grouped into three distinct clades: Eurasian wolves, American wolves, and domestic dogs. Genetic studies suggest that these groups trace their origins back to a wolf population that expanded during the last glacial maximum and replaced local wolf populations. Ancient genomes from Siberia provide evidence of at least one extinct wolf lineage. Previous studies on Pleistocene Siberian canids have shown two morphological groups, but it is unknown if this classification represents distinct genetic groups. Resequencing of genomes from four Pleistocene canids in Northeast Siberia shows they are genetically more similar to Eurasian wolves, branching off the lineage that gave rise to present-day wolves and dogs. The two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.

CURRENT BIOLOGY (2021)

Article Multidisciplinary Sciences

Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshu

Jonas Niemann et al.

Summary: The Honshu wolf, a distinct grey wolf subspecies endemic to islands in Japan, was revered as a guardian but persecuted and driven to extinction in the early 20th century due to a rabies epidemic. Research showed a close relationship between the Honshu wolf and a lineage of Siberian wolves, with significant gene flow between Japanese dogs and the Honshu wolf.

ISCIENCE (2021)

Article Multidisciplinary Sciences

Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages

Takahiro Segawa et al.

Summary: The biogeography of brown bears in the Japanese Archipelago was significantly affected by sea-level fluctuations, with evidence showing at least two migration events from the Eurasian continent to Honshu. Glacial-age sea-level falls may have facilitated mammalian migrations more frequently than previously thought, impacting ecosystem dynamics on these isolated islands.

ROYAL SOCIETY OPEN SCIENCE (2021)

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)

Editorial Material Biochemistry & Molecular Biology

Illuminating the mysteries of wolf history

Rena M. Schweizer et al.

MOLECULAR ECOLOGY (2020)

Article Multidisciplinary Sciences

Arctic-adapted dogs emerged at the Pleistocene-Holocene transitiond

Mikkel-Holger S. Sinding et al.

SCIENCE (2020)

Article Agriculture, Dairy & Animal Science

A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves

V Jagannathan et al.

ANIMAL GENETICS (2019)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Evolutionary Biology

Inferring Phylogenetic Networks Using PhyloNet

Dingqiao Wen et al.

SYSTEMATIC BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

Shyam Gopalakrishnan et al.

CURRENT BIOLOGY (2018)

Article Virology

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Marc A. Suchard et al.

VIRUS EVOLUTION (2018)

Article Biochemistry & Molecular Biology

A new model for ancient DNA decay based on paleogenomic meta-analysis

Logan Kistler et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Geochemistry & Geophysics

METHODS FOR SUMMARIZING RADIOCARBON DATASETS

Christopher Bronk Ramsey

RADIOCARBON (2017)

Article Biochemical Research Methods

BCFtools/csq: haplotype-aware variant consequences

Petr Danecek et al.

BIOINFORMATICS (2017)

Article Multidisciplinary Sciences

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

Wei Shen et al.

PLOS ONE (2016)

Article Biochemistry & Molecular Biology

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

Pontus Skoglund et al.

CURRENT BIOLOGY (2015)

Review Geography, Physical

Isotopic tracking of large carnivore palaeoecology in the mammoth steppe

Herve Bocherens

QUATERNARY SCIENCE REVIEWS (2015)

Article Multidisciplinary Sciences

Improving access to endogenous DNA in ancient bones and teeth

Peter B. Damgaard et al.

SCIENTIFIC REPORTS (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

Reconstructing the colonization history of lost wolf lineages by the analysis of the mitochondrial genome

Shuichi Matsumura et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2014)

Article Biochemical Research Methods

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

Hakon Jonsson et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

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

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Geochemistry & Geophysics

INTCAL13 AND MARINE13 RADIOCARBON AGE CALIBRATION CURVES 0-50,000 YEARS CAL BP

Paula J. Reimer et al.

RADIOCARBON (2013)

Article Genetics & Heredity

Ancient Admixture in Human History

Nick Patterson et al.

GENETICS (2012)

Article Geography, Physical

Timing of megafaunal extinction in the late Late Pleistocene on the Japanese Archipelago

Akira Iwase et al.

QUATERNARY INTERNATIONAL (2012)

Article Genetics & Heredity

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

Joseph K. Pickrell et al.

PLOS GENETICS (2012)

Article Ecology

Are inland wolf-ungulate systems influenced by marine subsidies of Pacific salmon?

Layne G. Adams et al.

ECOLOGICAL APPLICATIONS (2010)

Article Geography, Physical

The nature of megafaunal extinctions during the MIS 3-2 transition in Japan

Christopher J. Norton et al.

QUATERNARY INTERNATIONAL (2010)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Genetics & Heredity

Mitochondrial genome of the Tibetan wolf

Chao Meng et al.

MITOCHONDRIAL DNA (2009)

Article Genetics & Heredity

A Bayesian evaluation of human mitochondrial substitution rates

Phillip Endicott et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2008)

Article Biochemistry & Molecular Biology

Megafaunal extinctions and the disappearance of a specialized wolf ecomorph

Jennifer A. Leonard et al.

CURRENT BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Application of phylogenetic networks in evolutionary studies

DH Huson et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Multidisciplinary Sciences

Modelled atmospheric temperatures and global sea levels over the past million years

R Bintanja et al.

NATURE (2005)

Article Biochemistry & Molecular Biology

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

SYW Ho et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Biochemistry & Molecular Biology

Neighbor-Net: An agglomerative method for the construction of phylogenetic networks

D Bryant et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Biochemical Research Methods

Constructing splits graphs

AWM Dress et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2004)