Qiaomei Fu

Qiaomei Fu
Chinese Academy of Sciences | CAS · ancient DNA lab

PhD

About

121
Publications
169,015
Reads
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17,337
Citations
Citations since 2017
50 Research Items
13058 Citations
201720182019202020212022202305001,0001,5002,0002,500
201720182019202020212022202305001,0001,5002,0002,500
201720182019202020212022202305001,0001,5002,0002,500
201720182019202020212022202305001,0001,5002,0002,500
Additional affiliations
January 2016 - present
Institute of Vertebrate Paleontology and Paleoanthropology,Chinese Academy of Sciences
Position
  • Professor, head of the ancient DNA lab
July 2015 - present
Max Planck Institute for Evolutionary Anthropology
Position
  • Researcher
February 2014 - December 2015
Harvard Medical School
Position
  • PostDoc Position

Publications

Publications (121)
Article
Full-text available
Neanderthals are thought to have disappeared in Europe approximately 39,000-41,000 years ago but they have contributed 1-3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000-42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strateg...
Article
Full-text available
We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order...
Article
Full-text available
We present the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segme...
Article
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We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG),...
Article
Full-text available
Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Bei...
Article
Ancient DNA (aDNA) techniques applied to human genomics have significantly advanced in the past decade, enabling large-scale aDNA research, sometimes independent of human remains. This commentary reviews the major milestones of aDNA techniques and explores future directions to expand the scope of aDNA research and insights into present-day human he...
Article
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Shimao City is considered an important political and religious center during the Late Neolithic Longshan period of the Middle Yellow River basin. The genetic history and population dynamics among the Shimao and other ancient populations, especially the Taosi-related populations, remain unknown. Here, we sequenced 172 complete mitochondrial genomes,...
Article
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The Xinjiang region in northwest China is a historically important geographical passage between East and West Eurasia. By sequencing 201 ancient genomes from 39 archaeological sites, we clarify the complex demographic history of this region. Bronze Age Xinjiang populations are characterized by four major ancestries related to Early Bronze Age cultu...
Article
Although the first ancient DNA molecules were extracted more than three decades ago, the first ancient nuclear genomes could only be characterized after high-throughput sequencing was invented. Genome-scale data have now been gathered from thousands of ancient archaeological specimens, and the number of ancient biological tissues amenable to genome...
Article
Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generated 42 complete mitochondri...
Article
Full-text available
The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000–2800 bc from the Dzungarian Basin and 13 individuals dating to around 2100–1700 bc from the Tarim Basin, representi...
Article
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We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommenda...
Article
Recent advancements in DNA sequencing technologies and laboratory preparation protocols have rapidly expanded the scope of ancient DNA research over the past decade, both temporally and geographically. Discoveries include interactions between archaic and modern humans as well as modern human population dynamics, including those coinciding with the...
Article
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While Uzbekistan and Central Asia are known for the well-studied Bronze Age civilization of Bactria-Margiana Archaeological Complex (BMAC), the lesser-known Iron Age was also a dynamic period that resulted in increased interaction and admixture among different cultures from this region. To broaden our understanding of events which impacted the demo...
Article
Southern East Asia, including Guangxi and Fujian provinces in China, is home to diverse ethnic groups, languages, and cultures. Previous studies suggest a high complexity regarding population dynamics and the history of southern East Asians. However, large-scale genetic studies on ancient populations in this region are hindered by limited sample pr...
Article
Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest human...
Article
Full-text available
DNA studies of endangered or extinct species often rely on ancient or degraded remains. The majority of ancient DNA (aDNA) extraction protocols focus on skeletal elements, with skin and hair samples rarely explored. Similar to that found in bones and teeth, DNA extracted from historical or ancient skin and fur samples is also extremely fragmented w...
Article
Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6–3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the...
Article
Full-text available
Modern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 a...
Article
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Xinjiang is a key region in northwestern China, connecting East and West Eurasian populations and cultures for thousands of years. To understand the genetic history of Xinjiang, we sequenced 237 complete ancient human mitochondrial genomes from the Bronze Age through Historical Era (41 archaeological sites). Overall, the Bronze Age Xinjiang populat...
Article
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Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population hist...
Article
Full-text available
The snub-nosed monkey genus ( Rhinopithecus ) comprises five closely related species ( R. avunculus, R. bieti, R. brelichi, R. roxellana , and R. strykeri ). All are among the world's rarest and most endangered primates. However, the genomic impact associated with their population decline remains unknown. We analyzed population genomic data of all...
Article
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A timeline of cave dwellers in sediment Two archaic lineages overlapped with modern humans outside of Africa: the well-studied Neanderthals and their more mysterious cousins, the Denisovans. Denisovan remains are rare, being limited to Denisovan Cave in Siberia and a putative, undated jaw from Tibet. However, there is evidence for multiple introgre...
Article
Y chromosome evolution in Neanderthals The genomes of archaic hominins have been sequenced and compared with that of modern humans. However, most archaic individuals with high-quality sequences available have been female. Petr et al. performed targeted sequencing of the paternally inherited Y chromosomes from three Neanderthals and two Denisovans (...
Article
The genetic history of Southern East Asians is not well-known, especially prior to the Neolithic period. To address this, we successfully sequenced two complete mitochondrial genomes of 11,000-year-old human individuals from Southern China, thus generating the oldest ancient DNA sequences from this area. Integrating published mitochondrial genomes,...
Article
A hominin bone fragment from Denisova Cave (Russia) was identified among very few archaic human specimens (i.e., Neanderthals and Denisovans) as being the first-generation offspring of a Neanderthal mother and a Denisovan father. The ancient genomic study of this individual, together with previous evidence of interbreeding, suggests that admixture...
Article
Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia—some with no subst...
Article
Full-text available
A genetic history of China The history of human movements into and within China has been difficult to determine solely from archaeological investigations or genetic studies of contemporary peoples. Yang et al. sequenced DNA from 26 individuals from 9500 to 300 years ago from locations within China. Analyses of these individuals, along with previous...
Article
The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogr...
Preprint
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The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000-to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wolf and 26 domestic dogs) from the...
Preprint
Full-text available
Ancient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, comprehensive studies of Y chromosomes of Denisovans and Neandertals have not yet been possible. Here we present sequences of the first...
Article
Full-text available
The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000 to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wolf and 26 domestic dogs) from the...
Conference Paper
We report a high-power, mid-infrared OP-GaAs OPO with controllable pulse repetition rates (100 MHz – 1 GHz) and adjustable pulse durations (~95 ps – ~1.1 ns). The highest average output power of 13.7 W was achieved from the OPO with 9.2 W signal (3.3 μm) and 4.5 W idler (4.9 μm).
Article
Full-text available
Although gray wolves (Canis lupus) are one of the most widely distributed terrestrial mammals, their origins in China are not well understood. We sequenced six specimens from wolf skins, showing that gray wolves from Southern China (SC) derive from a single lineage, distinct from gray wolves from the Tibetan Plateau and Northern China, suggesting t...
Article
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Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex populati...
Article
Full-text available
Denisovans are members of a hominin group who are currently only known directly from fragmentary fossils, the genomes of which have been studied from a single site, Denisova Cave1–3 in Siberia. They are also known indirectly from their genetic legacy through gene flow into several low-altitude East Asian populations4,5 and high-altitude modern Tibe...
Conference Paper
We report an idler-resonant, watt-level, picosecond OP-GaAs OPO with a tuning range of 4394-6102 nm (idler) and 2997-3661 nm (signal), and diffraction-limited idler beam.
Preprint
Despite being one of the most widely distributed terrestrial mammals, the history of gray wolves (Canis lupus) in China is not well understood as their habitats have been destroyed with growing economic development. Using six specimens from wolf skins in Chinese Natural History museums, we sequenced their genome using a modified ancient DNA procedu...
Preprint
Full-text available
Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we report 34 ancient genome sequences, including two fr...
Article
We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migr...
Conference Paper
Supercontinuum generation from 750 nm to 5 μm, with an output power of 1.76 W and a 3-dB spectral-bandwidth of 1870 nm, was achieved by pumping a 10-m-long fluoroindate-fiber with a 2-µm picosecond fiber MOPA.
Article
Present-day giant pandas (Ailuropoda melanoleuca) are estimated to have diverged from their closest relatives, all other bears, ∼20 million years ago, based on molecular data [1]. With fewer than 2,500 individuals living today [2], it is unclear how well genetic data from extant and historical giant pandas [3] reflect the past [3]. To date, there h...
Conference Paper
We demonstrate a narrow-linewidth, mid-infrared OP-GaAs cascaded OPG-OPA with a widely tunable output of 2552-2960 nm (signal) and 5733-8305 nm (idler), and with a maximum peak power of 11.1 kW (signal) and 4.5 kW (idler).
Article
With the emergence and advancements in ancient DNA experimental methods and high-throughput sequencing technology, it is increasingly possible to directly extract and retrieve genetic materials from ancient human fossils. This has led to a series of breakthroughs in the genomic research of archaic humans, including reconstructing the past interacti...
Article
Full-text available
Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retriev...
Article
The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations...
Article
Full-text available
Background Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~400...
Article
To date the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50 thousand years ago from Vindija Cave, Croatia to ~30-fold genomic coverage. She carried 1.6 differences per ten thousand base pairs between the two copies of her genome,...
Article
By at least 45,000 years before present, anatomically modern humans had spread across Eurasia [1-3], but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide da...
Article
Full-text available
The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from...
Article
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumu...
Article
Full-text available
We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 BCE, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separat...
Preprint
Full-text available
We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated f...
Article
Full-text available
Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection ag...
Article
Significance We report a method for dating ancient human samples that uses the recombination clock. To infer the age of ancient genomes, we take advantage of the shared history of Neanderthal gene flow into non-Africans that occurred around 50,000 y ago and measure the amount of “missing evolution” in terms of recombination breakpoints in the ancie...
Article
Full-text available
The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple...
Data
List of genic alleles in the DAnc European tail. Union of alleles in the tails of all European DAnc (YRI, P2, Ust'-Ishim) distribution (P2: GBR, FIN, TSI, or CEU) including the genomic position (hg19), rs ID (dbSNP b138), and gene overlapping the SNP position. Table published alongside the manuscript as a tsv file.
Data
Supplementary Figures, Supplementary Tables, Supplementary Notes and Supplementary References Supplementary Figures 1-31, Supplementary Tables 1-2, Supplementary Notes 1-2 and Supplementary References
Data
Zip archive containing the shell and R code used for all major analyses. A tarball is also available on our website (https://bioinf.eva.mpg.de/download/PopDiff_aDNA_study/).