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List of works by Beth Shapiro

863 genomes reveal the origin and domestication of chicken

scientific article published on 25 June 2020

A Bayesian phylogenetic method to estimate unknown sequence ages

scientific article

A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation

preprint

A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius)

scientific article

A detailed life history of a pleistocene steppe bison (Bison priscus) skeleton unearthed in Arctic Alaska

scientific article

A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA

scientific article

A late Pleistocene steppe bison (Bison priscus) partial carcass from Tsiigehtchic, Northwest Territories, Canada

article

A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos

scientific article published on 27 December 2019

A method for positive forensic identification of samples from extremely low-coverage sequence data

scientific article

A middle Holocene steppe bison and paleoenvironments from the Versleuce Meadows, Whitehorse, Yukon, Canada

article

A mummified Pleistocene gray wolf pup

scientific article published on 01 December 2020

A new genus of horse from Pleistocene North America

scientific article

A novel NGS library preparation method to characterize native termini of fragmented DNA

scientific article published on 29 February 2020

A paleogenomic perspective on evolution and gene function: new insights from ancient DNA.

scientific article

A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears

scientific article published in 2022

A probable prehistoric case of meningococcal disease from San Francisco Bay: Next generation sequencing of Neisseria meningitidis from dental calculus and osteological evidence

scientific article published on 25 May 2018

A review of the dodo and its ecosystem: insights from a vertebrate concentration Lagerstätte in Mauritius

scientific article published on 19 November 2015

A revised evolutionary history of armadillos (Dasypus) in North America based on ancient mitochondrial DNA

AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data

scientific article

Accommodating the effect of ancient DNA damage on inferences of demographic histories

scientific article

Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns

An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus

scientific article published on 01 July 2021

An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis

scientific article published on 18 February 2020

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes

scientific article published in 2021

An ancient bison from the mouth of the Rauchua River (Chukotka, Russia)

Analysis of ancient human genomes: using next generation sequencing, 20-fold coverage of the genome of a 4,000-year-old human from Greenland has been obtained

scientific article published in May 2010

Ancient DNA Resolves the History of Tetragnatha (Araneae, Tetragnathidae) Spiders on Rapa Nui.

scientific article published on 20 December 2017

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics

scientific article (publication date: 23 March 2010)

Ancient DNA analysis indicates the first English lions originated from North Africa

scientific article published in 2008

Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?

scientific article

Ancient DNA confirms a local origin of domesticated chenopod in eastern North America

Ancient DNA provides new insights into the evolutionary history of New Zealand's extinct giant eagle

scientific article published in January 2005

Ancient DNA supports southern survival of Richardson's collared lemming (Dicrostonyx richardsoni) during the last glacial maximum

scientific article published on 18 March 2013

Ancient DNA typing of archaeological pig remains corroborates historical records

scholarly article by James Haile published in January 2010

Ancient DNA-based sex determination of bison hide moccasins indicates Promontory cave occupants selected female hides for footwear

scientific article published in 2022

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

scientific article

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

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

article published in the Proceedings of the National Academy of Sciences of the United States of America

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

scientific article published in 2021

Ancient hyaenas highlight the old problem of estimating evolutionary rates.

scientific article published in February 2014

Ancient hybridization and an Irish origin for the modern polar bear matriline

scientific article

Ancient hybridization with an unknown population facilitated high altitude adaptation of canids

scientific article published on 08 May 2020

Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe

scientific article

Ancient mitochondrial DNA from hair

scientific article published in June 2004

Ancient mitogenomes of Argentine Patagonia (6070-310 YBP) reveal the early contribution of lineages not previously found in South America

article

Ancient papillomavirus-host co-speciation in Felidae

scientific article (publication date: 2007)

Ancient plant DNA reveals High Arctic greening during the Last Interglacial

scientific article published in 2021

Author Correction: 863 genomes reveal the origin and domestication of chicken

scientific article published on 20 July 2020

Author Correction: Puma genomes from North and South America provide insights into the genomic consequences of inbreeding

scientific article published on 21 November 2019

Bayesian Estimation of Sequence Damage in Ancient DNA

scientific article published in 2007

Bayesian coalescent inference of past population dynamics from molecular sequences

scientific article

Bayesian estimation of sequence damage in ancient DNA.

scientific article published on 29 March 2007

Bayesian estimation of substitution rates from ancient DNA sequences with low information content

scientific article published on 4 February 2011

Beringia as an Ice Age genetic museum

Bermuda 2.0: reflections from Santa Cruz

scientific article published on December 2016

Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada

scientific article

Brown bear (Ursus arctos) (9880 ± 35 BP) from late-glacial Champlain Sea deposits at Saint-Nicolas, Quebec, Canada, and the dispersal history of brown bears

article

Case study: ancient DNA recovered from pleistocene-age remains of a Florida armadillo

scientific article published on January 2012

Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon

scientific article

Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences

article

Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100.

scientific article

Climate-driven ecological stability as a globally shared cause of Late Quaternary megafaunal extinctions: the Plaids and Stripes Hypothesis

scientific article published on 22 August 2018

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"

scientific article (publication date: 4 January 2008)

Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs ⬇️

Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs

scientific article

Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation

scientific article

Complex Admixture Preceded and Followed the Extinction of Wisent in the Wild

scientific article

Conservation of biodiversity in the genomics era

scientific article published on 11 September 2018

Conserving intraspecific variation for nature’s contributions to people

scientific article

Correlating Bayesian date estimates with climatic events and domestication using a bovine case study

scientific article (publication date: 23 August 2008)

Deep-time paleogenomics and the limits of DNA survival

scientific article published on 11 October 2023

Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic

Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic

scientific article published on 13 November 2023

Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic

preprint dated 30 October 2023

Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic

preprint dated 12 July 2023

Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic

preprint dated 14 March 2023

Demographic reconstruction from ancient DNA supports rapid extinction of the great auk

scientific article published on 26 November 2019

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (Ursus maritimus)

scientific article published on 19 July 2019

Detecting hybridization using ancient DNA.

scientific article published on 30 January 2016

Dire wolves were the last of an ancient New World canid lineage

scientific article

Discovery of lost diversity of paternal horse lineages using ancient DNA.

scientific article published on 23 August 2011

Discovery of the skull of Stephanorhinus kirchbergensis (Jäger, 1839) above the Arctic Circle

article published in 2017

Diverse plant and animal genetic records from Holocene and Pleistocene sediments

scientific article (publication date: 2 May 2003)

Dynamics of Pleistocene population extinctions in Beringian brown bears

scientific article

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

scientific article published on 11 September 2019

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

scholarly article published 10 September 2018

Early cave art and ancient DNA record the origin of European bison

scientific article

Early dispersal of domestic horses into the Great Plains and northern Rockies

scientific article published on 31 March 2023

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA

scientific article

Engineered polymerases amplify the potential of ancient DNA.

scientific article published on 24 April 2008

Environmental <scp>DNA</scp> reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication

scientific article published in 2023

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

Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo

scientific article published in October 2007

Evidence for time dependency of molecular rate estimates

scientific article (publication date: June 2007)

Evolutionary constraint and innovation across hundreds of placental mammals

scientific article published on 28 April 2023

Experimental Investigation of the Dietary Ecology of the Extinct Passenger Pigeon, Ectopistes migratorius

scientific article published in 2018

Flight of the dodo

scientific article (publication date: March 2002)

Fossil and genomic evidence constrains the timing of bison arrival in North America.

scientific article

Genetic relatedness in two-tiered plains zebra societies suggests that females choose to associate with kin

Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius

scientific article

Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species

scientific article

Genomic Data from Extinct North American Camelops Revise Camel Evolutionary History

scientific article

Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation

scientific article

Genomic basis for skin phenotype and cold adaptation in the extinct Steller’s sea cow

scientific article published on 04 February 2022

Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution

scientific article published in 2013

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

scientific article published on 5 February 2015

Genomic evidence of widespread admixture from polar bears into brown bears during the last ice age.

scientific article published on 20 February 2018

Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions

scientific article published on 16 June 2022

Grevy's zebra conservation: overcoming threats of isolation, genetic hybridization and demographic instability

Grey wolf genomic history reveals a dual ancestry of dogs

scientific article published on 29 June 2022

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France

Highly accurate long-read HiFi sequencing data for five complex genomes

scientific article published on 17 November 2020

Homotherium serumandCervalcesfrom the Great Lakes Region, USA: geochronology, morphology and ancient DNA

article

Horseshoe-based bayesian nonparametric estimation of effective population size trajectories

scientific article published on 11 April 2020

How to Clone a Mammoth

book by Beth Shapiro

Human evolution: turning back the clock

scientific article

Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci

scientific article (publication date: March 2013)

Improving societies' harassment policies

scientific article published on 01 September 2018

Improving the performance of true single molecule sequencing for ancient DNA

scientific article (publication date: 10 May 2012)

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

scientific article

Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2

scientific article

Is amino acid racemization a useful tool for screening for ancient DNA in bone?

scientific article (publication date: 22 August 2009)

Is the endangered Grevy's zebra threatened by hybridization?

Late Pleistocene northward-dispersing Bison antiquus from the Bighill Creek Formation, Gallelli Gravel Pit, Alberta, Canada, and the fate of Bison occidentalis

article

Life and extinction of megafauna in the ice-age Arctic

scientific article

Life as We Made It

2021 non-fiction book by Beth Shapiro

Lifetime mobility of an Arctic woolly mammoth

scientific article

Mammoth 2.0: will genome engineering resurrect extinct species?

scientific article

Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography, and Introgression

scientific article (publication date: 26 April 2016)

Metabarcoding meiofauna biodiversity assessment in four beaches of Northern Colombia: effects of sampling protocols and primer choice

scholarly article

Mid-Holocene vertebrate bone Concentration-Lagerstätte on oceanic island Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus)

scientific article published in January 2009

Million-year-old DNA sheds light on the genomic history of mammoths

scientific article published in March 2021

Minimizing polymerase biases in metabarcoding

scientific article published on 24 May 2018

Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs

scientific article (publication date: 7 June 2007)

Mitochondrial phylogenomics of modern and ancient equids

scientific article published in 2013

Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands

scientific article published on 20 March 2019

Mitogenomics of the Extinct Cave Lion, Panthera spelaea (Goldfuss, 1810), Resolve its Position within the Panthera Cats

Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon

scientific article published on 23 February 2010

Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus

scientific article

Morphological and genetic identification and isotopic study of the hair of a cave lion (Panthera spelaea Goldfuss, 1810) from the Malyi Anyui River (Chukotka, Russia)

scholarly article

Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients

scientific article published on 25 January 2008

Multiple losses of flight and recent speciation in steamer ducks

scientific article (publication date: 22 June 2012)

Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

scientific article

New middle chapter in the story of human evolution

scientific article published on 01 September 2019

No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.).

scientific article published on 26 May 2006

Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons

scientific article

Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution

scientific article

Partial genetic turnover in neandertals: continuity in the East and population replacement in the West

scientific article published on 23 February 2012

Pathways to de-extinction: how close can we get to resurrection of an extinct species?

article

Pattern of extinction of the woolly mammoth in Beringia

scholarly article

Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages.

scientific article published on 3 October 2012

Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity

scientific article

Population-level genotyping of coat colour polymorphism in woolly mammoth (Mammuthus primigenius)

scholarly article

Post-glacial dispersal patterns of Northern pike inferred from an 8800 year old pike (Esox cf. lucius) skull from interior Alaska

scholarly article by Matthew J. Wooller et al published July 2015 in Quaternary Science Reviews

Post-mortem DNA damage hotspots in Bison (Bison bison) provide evidence for both damage and mutational hotspots in human mitochondrial DNA

article

Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros

scientific article published on 30 July 2020

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

scientific article

Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch

scientific article

Pros and cons of methylation-based enrichment methods for ancient DNA

scientific article

Protocols for sampling viral sequences to study epidemic dynamics

scientific article

Puma genomes from North and South America provide insights into the genomic consequences of inbreeding

scientific article published on 18 October 2019

Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change ⬇️

scientific article published on 02 June 2020

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

scientific article

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form

scientific article

Rejoinder for discussion on "Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories"

scientific article published on 07 May 2020

Relict permafrost preserves megafauna, insects, pollen, soils and pore-ice isotopes of the mammoth steppe and its collapse in central Yukon

scientific article published in 2023

Response to Hohenlohe et al.

scientific article

Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis

scientific article

Rise and fall of the Beringian steppe bison

scientific article (publication date: 26 November 2004)

Sedimentary DNA and molecular evidence for early human occupation of the Faroe Islands

scholarly article

Sequence preservation of osteocalcin protein and mitochondrial DNA in bison bones older than 55 ka

scientific article

Setting Up an Ancient DNA Laboratory

scientific article published on 01 January 2019

Shotgun microbial profiling of fossil remains

scientific article

Skyline-plot methods for estimating demographic history from nucleotide sequences

scientific article published on 06 February 2011

Species-specific responses of Late Quaternary megafauna to climate and humans

scientific article (publication date: 2 November 2011)

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

scientific article published on 24 October 2017

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics

scientific article published on 2 January 2007

Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA

scientific article published on 01 January 2019

Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course

scientific article published on 16 October 2020

The California Environmental DNA "CALeDNA" Program

The Climate Book

2022 book by Greta Thunberg

The Late Pleistocene distribution of vicuñas (Vicugna vicugna) and the “extinction” of the gracile llama (“Lama gracilis”): New molecular data

scholarly article

The Zhenya Mammoth ( Mammuthus primigenius (Blum.)): Taphonomy, geology, age, morphology and ancient DNA of a 48,000 year old frozen mummy from western Taimyr, Russia

scholarly article by Evgeny N. Maschenko et al published July 2017 in Quaternary International

The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections

scientific article published on 23 December 2019

The contribution of historical processes to contemporary extinction risk in placental mammals ⬇️

The earliest evidence for anatomically modern humans in northwestern Europe

scientific article

The effect of inappropriate calibration: three case studies in molecular ecology

scientific article (publication date: 20 February 2008)

The effects of demineralisation and sampling point variability on the measurement of glutamine deamidation in type I collagen extracted from bone

scientific article published in May 2016

The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis

scientific article

The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography

scientific article (publication date: 8 December 2009)

The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis

scientific article

The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants

scientific article

The southern coastal Beringian land bridge: cryptic refugium or pseudorefugium for woody plants during the Last Glacial Maximum?

article

Time-dependent estimates of molecular evolutionary rates: evidence and causes

scientific article published in December 2015

Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska

scientific article

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

scientific article published on 2 May 2019

Transoceanic drift and the domestication of African bottle gourds in the Americas.

scientific article published on 10 February 2014

True single-molecule DNA sequencing of a pleistocene horse bone

scientific article (publication date: October 2011)

Using ancient DNA and coalescent-based methods to infer extinction

scientific article published on February 2016

Using ancient DNA techniques to identify the origin of unprovenanced museum specimens, as illustrated by the identification of a 19th century lion from Amsterdam

scientific article published in 2007

Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses

scientific article

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

scientific article

How to Clone a Mammoth ⬇️

hardcover edition (en)

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