Search filters

List of works by Ludovic Orlando

"Adopt-a-Tissue" Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare

publication published on 26 March 2021

137 ancient human genomes from across the Eurasian steppes

scientific article published in Nature

A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered

scientific article

A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

article

A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability

scientific article

A new genus of horse from Pleistocene North America

scientific article

A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses

publication published on 13 December 2021

A southern African origin and cryptic structure in the highly mobile plains zebra

scientific article published in 2018

Accurate continuous geographic assignment from low- to high-density SNP data

scientific article

AdapterRemoval v2: rapid adapter trimming, identification, and read merging

scientific article

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

An Aboriginal Australian genome reveals separate human dispersals into Asia

scientific article (publication date: 7 October 2011)

An epigenetic window into the past?

scientific article (publication date: August 2014)

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

scientific article published on 11 February 2021

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

scientific article

Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages

scientific article

Ancient DNA analysis reveals woolly rhino evolutionary relationships

scientific article

Ancient DNA and human evolution

scientific article

Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time

scientific article published in November 2002

Ancient DNA clarifies the evolutionary history of American Late Pleistocene equids

scientific article

Ancient DNA refines taxonomic classification of Roman equids north of the Alps, elaborated with osteomorphology and geometric morphometrics

scientific article published in 2022

Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene

scientific article

Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics

scientific article published on 06 December 2019

Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

article

Ancient and modern environmental DNA

scientific article

Ancient genomes revisit the ancestry of domestic and Przewalski's horses

scientific article published on 22 February 2018

Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

scientific article published on 5 October 2017

Ancient genomic changes associated with domestication of the horse

scientific article

Ancient genomics

scientific article

Ancient hepatitis B viruses from the Bronze Age to the Medieval period

scientific article published in Nature

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

scientific article published in 2021

Ancient human genome sequence of an extinct Palaeo-Eskimo

scientific article

Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates

scientific article (publication date: 18 March 2015)

Animal domestication in the era of ancient genomics

scientific article published on 07 April 2020

Annotation of the Protein Coding Regions of the Equine Genome

scientific article published on 24 June 2015

Assessing DNA Sequence Alignment Methods for Characterizing Ancient Genomes and Methylomes

scientific article published in 2020

Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA

scientific article published in 2022

Authentication and Assessment of Contamination in Ancient DNA

scientific article published on 01 January 2019

Author Correction: 137 ancient human genomes from across the Eurasian steppes

scientific article published in Nature

Author Correction: Ancient hepatitis B viruses from the Bronze Age to the Medieval period

scientific article published in Nature

Author Correction: Late Quaternary dynamics of Arctic biota from ancient environmental genomics

correction of a scholarly article

Author Correction: Spotted phenotypes in horses lost attractiveness in the Middle Ages

scientific article published on 10 April 2020

Back to the roots and routes of dromedary domestication

scientific article

CASCADE: A Custom-Made Archiving System for the Conservation of Ancient DNA Experimental Data

scientific article published in 2020

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.

scientific article

Combining bleach and mild predigestion improves ancient DNA recovery from bones

scientific article

Comparative genomics reveals insights into avian genome evolution and adaptation

scientific article

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

scientific article published on 24 September 2015

Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads

scientific article

Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution

scientific article published on November 2007

Convergent genomic signatures of domestication in sheep and goats

scientific article published on 6 March 2018

Corrigendum

article published in 2014

DNA from extinct giant lemurs links archaeolemurids to extant indriids

scientific article published in 2008

DNA from soil mirrors plant taxonomic and growth form diversity

scientific article

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

scientific article published on 29 April 2019

Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years

scientific article published on 02 March 2020

DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage

article by Kristian Ebbesen Hanghøj et al published 1 April 2019 in GigaScience

Decline of genetic diversity in ancient domestic stallions in Europe

scientific article published on 18 April 2018

Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD.

scientific article published in June 2018

Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

scientific article published on 27 July 2017

Does the 43 bp sequence from an 800,000 year old cretan dwarf elephantid really rewrite the textbook on mammoths?

scientific article (publication date: 22 February 2007)

EPAS1 gain-of-function mutation contributes to high-altitude adaptation in Tibetan horses

scientific article published on 02 July 2019

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

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago

scientific article

Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan

scientific article published in PLoS ONE

Equids

scientific article published on October 2015

Erratum: Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition

scientific article published on 11 September 2019

Evaluating the impact of domestication and captivity on the horse gut microbiome.

scientific article published on 14 November 2017

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse

scientific article published on 22 September 2015

Evolutionary Patterns and Processes: Lessons from Ancient DNA.

scientific article

Experimental conditions improving in-solution target enrichment for ancient DNA.

scientific article

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX

scientific article

Fifty thousand years of Arctic vegetation and megafaunal diet

scientific article (publication date: 6 February 2014)

Filling Important Gaps in the Genomic History of Southwest Asia

scientific article published on 01 May 2020

First evidence of Equus asinus L. in the Chalcolithic disputes the Phoenicians as the first to introduce donkeys into the Iberian Peninsula

article

Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae

scientific article published on 30 September 2020

Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname.

scientific article published in November 2017

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

scientific article

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

scientific article (publication date: March 2014)

Genomic affinities of two 7,000-year-old Iberian hunter-gatherers

scientific article

Genomics and the Evolutionary History of Equids

scientific article published on 16 November 2020

Geographic distribution of an extinct equid (Equus hydruntinus: Mammalia, Equidae) revealed by morphological and genetical analyses of fossils

scientific article

Ginnerup Revisited. New Excavations at a Key Neolithic Site on Djursland, Denmark

Glacial survival of boreal trees in northern Scandinavia

scientific article published in March 2012

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

High-Throughput DNA sequencing of ancient wood

scientific article published on 7 February 2018

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

scientific article published in Nature Communications

Human evolution: a tale from ancient genomes.

scientific article

Improved de novo genomic assembly for the domestic donkey.

scientific article published on 4 April 2018

Improved reference genome for the domestic horse increases assembly contiguity and composition

article

Improving access to endogenous DNA in ancient bones and teeth

scientific article

Improving access to endogenous DNA in ancient bones and teeth

Improving ancient DNA read mapping against modern reference genomes

scientific article (publication date: 10 May 2012)

Improving the performance of true single molecule sequencing for ancient DNA

scientific article (publication date: 10 May 2012)

Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals

scientific article

Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding

scientific article

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples

scientific article published on 14 May 2019

Late Bronze Age cultural origins of dairy pastoralism in Mongolia

scientific article

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

scientific article

Late Quaternary horses in Eurasia in the face of climate and vegetation change

article

Less effective selection leads to larger genomes

scientific article

Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes

scientific article (publication date: 2013)

Major transitions in human evolution revisited: a tribute to ancient DNA.

scientific article published on 19 December 2014

Mammoth and Elephant Phylogenetic Relationships: <i>Mammut Americanum</i>, the Missing Outgroup

scientific article published in 2007

Mammoth and elephant phylogenetic relationships: Mammut americanum, the missing outgroup

scientific article (publication date: 29 March 2007)

Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity

scientific article

Mitochondrial Genetic Diversity of Eurasian Red Squirrels (Sciurus vulgaris) from Denmark

scientific article published on 30 October 2015

Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids

scientific article

Mitochondrial phylogenomics of modern and ancient equids

scientific article published in 2013

Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.).

scientific article published on 17 April 2012

Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats

scientific article

Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

scientific article (publication date: 10 March 2011)

Monitoring endangered freshwater biodiversity using environmental DNA.

scientific article

Morphological and genetic evidence for early Holocene cattle management in northeastern China.

scientific article published in January 2013

Morphological convergence in Hippidion and Equus (Amerhippus) South American equids elucidated by ancient DNA analysis

scientific article published in January 2003

Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland

scientific article published on 17 April 2020

Napoleon Bonaparte and the fate of an Amazonian rat: new data on the taxonomy of Mesomys hispidus (Rodentia: Echimyidae).

scientific article

Neanderthals in central Asia and Siberia

scientific article (publication date: 30 September 2007)

New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA.

scientific article published in December 2015

Next-generation sequencing offers new insights into DNA degradation

scientific article published on 17 April 2012

No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy

scientific article published on 01 April 2021

Oral health status in historic population: Macroscopic and metagenomic evidence.

scientific article published on 16 May 2018

Origin and Evolution of Deleterious Mutations in Horses

scientific article published on 28 August 2019

Out of the Pacific and back again: insights into the matrilineal history of Pacific killer whale ecotypes

scientific article published in 2011

Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years

scientific article

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

article

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

scientific article published on 23 February 2012

Performance and automation of ancient DNA capture with RNA hyRAD probes

scientific article published on 15 October 2021

Plankton-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

scientific article published in 2017

Planning tiger recovery: Understanding intraspecific variation for effective conservation

scientific article

Population Demography and Genetic Diversity in the Pleistocene Cave Lion

scholarly article by Erik Ersmark et al published 9 March 2015 in Open quaternary

Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA

scientific article published on 21 November 2016

Population genomics of Bronze Age Eurasia

scientific article published on June 2015

Population genomics of post-glacial western Eurasia

scientific article published on 10 January 2024

Population genomics of the Viking world

scientific article published on 16 September 2020

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

scientific article

Positive selection in the SLC11A1 gene in the family Equidae

scientific article published on 4 February 2016

Postglacial viability and colonization in North America's ice-free corridor.

scientific article

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

scientific article

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

scientific article

Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins

scientific article (publication date: 3 February 2012)

Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene

scientific article published on 11 May 2022

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

scientific article

Reconstructing ancient genomes and epigenomes

scientific article published on 9 June 2015

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.

scientific article

Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses

scientific article published on 21 December 2015

Revising the recent evolutionary history of equids using ancient DNA

scientific article

Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence

scientific article published in June 2006

Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics

scientific article published in July 2014

Sexing Viking Age horses from burial and non-burial sites in Iceland using ancient DNA

scholarly article by Heidi M. Nistelberger et al published January 2019 in Journal of Archaeological Science

Speciation with gene flow in equids despite extensive chromosomal plasticity

scientific article

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

scientific article (publication date: 2 November 2011)

Spotted phenotypes in horses lost attractiveness in the Middle Ages

scientific article

Statistical guidelines for detecting past population shifts using ancient DNA.

scientific article

Struct-f4: a Rcpp package for ancestry profile and population structure inference from <i>f</i>4-statistics

scientific article published in 2022

Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos)

scientific article (publication date: April 2008)

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

Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation

scientific article

Taming the Past: Ancient DNA and the Study of Animal Domestication

scientific article (publication date: 8 February 2017)

Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.

scientific article

The Effects of Captivity on the Mammalian Gut Microbiome

scientific article published in October 2017

The Evolutionary Origin and Genetic Makeup of Domestic Horses

scientific article

The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics

scientific article published on 22 September 2020

The ancestry and affiliations of Kennewick Man

scientific article

The derived FOXP2 variant of modern humans was shared with Neandertals

scientific article (publication date: November 2007)

The first aurochs genome reveals the breeding history of British and European cattle

scientific article

The first horse herders and the impact of early Bronze Age steppe expansions into Asia

scientific article

The genetic prehistory of the New World Arctic

scientific article

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

scientific article

The genomic history and global expansion of domestic donkeys

scientific article published on 9 September 2022

The microcephalin ancestral allele in a Neanderthal individual

scientific article

The origin of ambling horses.

scientific article published in August 2016

The origins and spread of domestic horses from the Western Eurasian steppes

The prehistoric peopling of Southeast Asia

scientific article

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

scientific article

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

scientific article published on 2 May 2019

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

scientific article

True single-molecule DNA sequencing of a pleistocene horse bone

scientific article (publication date: October 2011)

Twelve Years of Neandertal Genetic Discoveries: State-of-the-Art and Future Challenges

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

scientific article

Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

scientific article published in 2020

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

scientific article published on 02 March 2020

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

scientific article

Using Ancient DNA to Understand Evolutionary and Ecological Processes

article published in 2014

Using classical population genetics tools with heterochroneous data: time matters!

scientific article (publication date: 2009)

Using paleo-archives to safeguard biodiversity under climate change

scientific article

Variola virus in a 300-year-old Siberian mummy

scientific article published in November 2012

Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs

scientific article published on 19 February 2018

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

scientific article

Widespread horse-based mobility arose around 2,200 BCE in Eurasia

scientific article published on 6 June 2024

gargammel: a sequence simulator for ancient DNA

scientific article

mapDATAge: a ShinyR package to chart ancient DNA data through space and time

scientific article published in 2022

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

scientific article (publication date: July 2013)

mapDamage: testing for damage patterns in ancient DNA sequences

scientific article

metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data

scientific article

Paulina is supported by:

About Paulina

Help