Note: The reference list may be incomplete. This list contains all references that BIP software was able to retrieve.
The Black Rat
Extinctions and Invasions · 2010
       
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
PLoS Genetics · 2012
       
Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes
Molecular Phylogenetics and Evolution · 2008
       
EAGER: efficient ancient genome reconstruction
Genome Biology · 2016
       
Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies
BioEssays · 2020
       
Versatile And Open Software For Comparing Large Genomes
Genome Biology · 2004
       
Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets
PLOS ONE · 2017
       
Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region
BMC Evolutionary Biology · 2012
       
jModelTest 2: more models, new heuristics and parallel computing
Nature Methods · 2012
       
Eagle owl (Bubo bubo) pellets from Roman Sagalassos (SW Turkey): distinguishing the prey remains from nest and roost sites
International Journal of Osteoarchaeology · 2009
       
Cooling and societal change during the Late Antique Little Ice Age from 536 to around 660 AD
Nature Geoscience · 2016
       
Inference of human population history from individual whole-genome sequences
Nature · 2011
       
Improving SNP discovery by base alignment quality
Bioinformatics · 2011
       
A High-CoverageYersinia pestisGenome from a Sixth-Century Justinianic Plague Victim
Molecular Biology and Evolution · 2016
       
Mitochondrial DNA evidence for the spread of Pacific rats through Oceania
Biological Invasions · 2008
       
Phylogeography of the introduced speciesRattus rattusin the western Indian Ocean, with special emphasis on the colonization history of Madagascar
Journal of Biogeography · 2010
       
Modeling the Justinianic Plague: Comparing hypothesized transmission routes
PLOS ONE · 2020
       
A history of British mammals
N/A · 1910
       
Early colonization of Mediterranean islands by Rattus rattus: a review of zooarcheological data
Biological Invasions · 2010
       
Marine20—The Marine Radiocarbon Age Calibration Curve (0–55,000 cal BP)
Radiocarbon · 2020
       
What Disease was Plague?
N/A · 2010
       
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
The American Journal of Human Genetics · 2007
       
The Pacific Rat Race to Easter Island: Tracking the Prehistoric Dispersal of Rattus exulans Using Ancient Mitochondrial Genomes
Frontiers in Ecology and Evolution · 2017
       
Identifying Rattus species using mitochondrial DNA
Molecular Ecology Notes · 2007
       
Phylogeography of the black rat Rattus rattus in India and the implications for its dispersal history in Eurasia
Biological Invasions · 2018
       
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Bioinformatics · 2015
       
From Africa to Ifrīqiya: Settlement and Society in Early Medieval North Africa (650–800)
Al-Masāq · 2013
       
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Genome Research · 2010
       
Ancient pathogen genomics as an emerging tool for infectious disease research
Nature Reviews Genetics · 2019
       
Urban rats have less variable, higher protein diets
Proceedings of the Royal Society B: Biological Sciences · 2018
       
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments
Proceedings of the National Academy of Sciences · 2013
       
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
Genome Research · 2016
       
An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data
Genome Research · 2015
       
Genetic tracking of mice and other bioproxies to infer human history
Trends in Genetics · 2013
       
Rats, Communications, and Plague: Toward an Ecological History
The Journal of Interdisciplinary History · 2003
       
Dispersal in house mice
Biological Journal of the Linnean Society · 2005
       
Fast and accurate short read alignment with Burrows-Wheeler transform
Bioinformatics · 2009
       
Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats
PLoS ONE · 2011
       
The Sequence Alignment/Map format and SAMtools
Bioinformatics · 2009
       
Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis
The Lancet Infectious Diseases · 2014
       
Rodent-borne diseases and their risks for public health
Critical Reviews in Microbiology · 2009
       
Rats cannot have been intermediate hosts for Yersinia pestis during medieval plague epidemics in Northern Europe
Journal of Archaeological Science · 2013
       
Improved DNA extraction from ancient bones using silica-based spin columns
American Journal of Physical Anthropology · 1998
       
Framing the Early Middle Ages
N/A · 2005
       
Unwelcome companions: ancient rats reviewed
Antiquity · 1994
       
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Bioinformatics · 2014
       
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
PLoS ONE · 2011
       
Recent Evolution inRattus norvegicusIs Shaped by Declining Effective Population Size
Molecular Biology and Evolution · 2015
       
Approaches to Estimating Marine Protein in Human Collagen for Radiocarbon Date Calibration
Radiocarbon · 2010
       
Human ectoparasites and the spread of plague in Europe during the Second Pandemic
Proceedings of the National Academy of Sciences · 2018
       
Small Mammal Fossil Assemblages as Indicators of Environmental Change in Northern Corsica during the Last 2500 Years
Journal of Archaeological Science · 1996
       
“1st century BCE occurrence of chicken, house mouse and black rat in Morocco: Socio-economic changes around the reign of Juba II on the site of Rirha”
Journal of Archaeological Science: Reports · 2020
       
Yersinia pestis--etiologic agent of plague
Clinical Microbiology Reviews · 1997
       
The Chronology of Roman Trade in the Indian Ocean from Augustus to Early Third Century ce
Journal of the Economic and Social History of the Orient · 2015
       
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
Nucleic Acids Research · 2011
       
Single‐tube library preparation for degraded DNA
Methods in Ecology and Evolution · 2017
       
Human Dispersal and Species Movement
N/A · 2017
       
Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication
Proceedings of the National Academy of Sciences · 2010
       
The transition from late antiquity to early Middle Ages in Italy. A zooarchaeological perspective
Quaternary International · 2019
       
The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0–55 cal kBP)
Radiocarbon · 2020
       
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
Bioinformatics · 2013
       
Rating the rat: global patterns and research priorities in impacts and management of rodent pests
Mammal Review · 2014
       
Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA
Nature Protocols · 2020
       
Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species
Molecular Biology and Evolution · 2017
       
Barn Owls and Black Rats from a Rural Roman Villa at Gatehampton, South Oxfordshire
Environmental Archaeology · 2019
       
Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
Genome Biology · 2015
       
On the trail of Neolithic mice and men towards Transcaucasia: zooarchaeological clues from Nakhchivan (Azerbaijan)
Biological Journal of the Linnean Society · 2013
       
Bayesian inference of ancient human demography from individual genome sequences
Nature Genetics · 2011
       
Ancient Admixture in Human History
Genetics · 2012
       
Invasion facilitates hybridization with introgression in theRattus rattusspecies complex
Molecular Ecology · 2012
       
Cryptic genetic diversity in Rattus of the San Francisco Bay region, California
Biological Invasions · 2012
       
Rethinking ruralization in terms of resilience: Subsistence strategies in sixth-century Caričin Grad in the light of plant and animal bone finds
Quaternary International · 2019
       
Tandem repeats finder: a program to analyze DNA sequences
Nucleic Acids Research · 1999
       
On the lack of bones of the ship rat Rattus rattus from Dark Age York
Journal of Zoology · 1991
       
Mitochondrial phylogeography of the black rat supports a single invasion of the western Mediterranean basin
Biological Invasions · 2015
       
On the history of the spread of the black rat (Rattus rattus L., 1758) in northwestern Russia
Biology Bulletin · 2011
       
The Under-Appreciated Rodent: Harbingers of Plague From the Middle Ages to the Twenty-First Century
The Journal of Interdisciplinary History · 2019
       
Improving access to endogenous DNA in ancient bones and teeth
Scientific Reports · 2015
       
Uluburun shipwreck stowaway house mouse: molar shape analysis and indirect clues about the vessel's last journey
Journal of Archaeological Science · 2008
       
Proto-globalisation and biotic exchange in the Old World
Human Dispersal and Species Movement · 2017
       
Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries
BMC Evolutionary Biology · 2010
       
Historic black rat invasions into Sri Lanka lead to hybridization forming two sub-lineages in the <em>Rattus rattus</em> species complex
Ceylon Journal of Science · 2020
       
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Molecular Biology and Evolution · 2013
       
An Ecological and Evolutionary Framework for Commensalism in Anthropogenic Environments
Trends in Ecology & Evolution · 2016
       
ANGSD: Analysis of Next Generation Sequencing Data
BMC Bioinformatics · 2014
       
Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions
Proceedings of the National Academy of Sciences · 2016
       
Karyotypes and serum transferrin patterns of hybrids between Asian and Oceanian black rats, Rattus rattus
Chromosoma · 1971
       
Partial uracil–DNA–glycosylase treatment for screening of ancient DNA
Philosophical Transactions of the Royal Society B: Biological Sciences · 2015
       
Tracking the Near Eastern origins and European dispersal of the western house mouse
Scientific Reports · 2020
       
The Biology and Behaviour of a Free-Living Population of Black Rats (Rattus rattus)
Animal Behaviour Monographs · 1971
       
Roman Grain Pests in Britain: Implications for Grain Supply and Agricultural Production
Britannia · 2011
       
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Nucleic Acids Research · 2004
       
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
BMC Research Notes · 2016
       
Origins and dispersals of Pacific peoples: Evidence from mtDNA phylogenies of the Pacific rat
Proceedings of the National Academy of Sciences · 2004
       
Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)
Proceedings of the National Academy of Sciences · 2019