Showing papers by "Matthias Meyer published in 2017"
TL;DR: The genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, is sequenced to ~30-fold genomic coverage, allowing 10 to 20% more Ne andertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
Abstract: 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 ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
473 citations
Harvard University1, Emory University2, Radcliffe Institute for Advanced Study3, Max Planck Society4, University College Dublin5, University of Cape Town6, Broad Institute7, University of Tübingen8, Howard Hughes Medical Institute9, California State Polytechnic University, Pomona10, University of Queensland11, University of Wisconsin–La Crosse12, University College London13, Canterbury Archaeological Trust14, University of Bristol15, McDonald Institute for Archaeological Research16, University of Pretoria17, Leiden University18, Garvan Institute of Medical Research19, University of Sydney20, Pennsylvania State University21, University of Vienna22
TL;DR: The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others.
272 citations
Max Planck Society1, University of Oviedo2, Pompeu Fabra University3, Spanish National Research Council4, Leiden University5, Bournemouth University6, University of Liège7, Altai State University8, Russian Academy of Sciences9, University of Wollongong10, Australian Research Council11, Croatian Academy of Sciences and Arts12
TL;DR: Using targeted enrichment of mitochondrial DNA, it is shown that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no Hominin remains have been discovered.
Abstract: Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave, we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains are found.
248 citations
TL;DR: It is found that single-stranded library preparation increases library yields from tissues stored in formalin for many years by several orders of magnitude and is less costly and better compatible with automation.
Abstract: DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3΄ biotinylated donor oligonucleotide. A thorough evaluation of this ligation scheme shows that single-stranded DNA can be ligated to adapter oligonucleotides in higher concentration than with CircLigase (an RNA ligase that was previously chosen for end-to-end ligation in single-stranded library preparation) and that biases in ligation can be minimized when choosing splinters with 7 or 8 random nucleotides. We show that ssDNA2.0 tolerates higher quantities of input DNA than CircLigase-based library preparation, is less costly and better compatible with automation. We also provide an in-depth comparison of library preparation methods on degraded DNA from various sources. Most strikingly, we find that single-stranded library preparation increases library yields from tissues stored in formalin for many years by several orders of magnitude.
191 citations
TL;DR: The Tianyuan individual is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split.
151 citations
TL;DR: It is shown that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction, and the combination of DNA extraction and library preparation techniques described here substantially increases the yield of DNA sequences from ancient remains and provides access to a yet unexploited source of highly degraded DNA fragments.
Abstract: The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than ∼35 base pairs (bp). Here, we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction. We present a refined silica-based DNA extraction method that not only enables efficient recovery of molecules as short as 25 bp but also doubles the yield of sequences from longer fragments due to improved recovery of molecules with single-strand breaks. Furthermore, we present strategies for monitoring inefficiencies in library preparation that may result from co-extraction of inhibitory substances during DNA extraction. The combination of DNA extraction and library preparation techniques described here substantially increases the yield of DNA sequences from ancient remains and provides access to a yet unexploited source of highly degraded DNA fragments. Our work may thus open the door for genetic analyses on even older material.
79 citations
TL;DR: The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined as mentioned in this paper.
Abstract: The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada's Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195-135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45-21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.
73 citations
TL;DR: The view that Denisovans were likely to have been present in the vicinity of Denisova Cave over an extended time period is reinforced, and it is shown that the level of nuclear DNA sequence diversity found among Denisovan is within the lower range of that of present-day human populations.
Abstract: The presence of Neandertals in Europe and Western Eurasia before the arrival of anatomically modern humans is well supported by archaeological and paleontological data. In contrast, fossil evidence for Denisovans, a sister group of Neandertals recently identified on the basis of DNA sequences, is limited to three specimens, all of which originate from Denisova Cave in the Altai Mountains (Siberia, Russia). We report the retrieval of DNA from a deciduous lower second molar (Denisova 2), discovered in a deep stratigraphic layer in Denisova Cave, and show that this tooth comes from a female Denisovan individual. On the basis of the number of "missing substitutions" in the mitochondrial DNA determined from the specimen, we find that Denisova 2 is substantially older than two of the other Denisovans, reinforcing the view that Denisovans were likely to have been present in the vicinity of Denisova Cave over an extended time period. We show that the level of nuclear DNA sequence diversity found among Denisovans is within the lower range of that of present-day human populations.
71 citations
Max Planck Society1, Harvard University2, University of Potsdam3, University of York4, University of Basel5, Danube Private University6, University of Illinois at Urbana–Champaign7, Naturalis8, Weimar Institute9, Howard Hughes Medical Institute10, Broad Institute11, University of California, Santa Cruz12
TL;DR: Recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils demonstrate that the current picture of elephant evolution is in need of substantial revision and suggests that Loxodonta has not been constrained to Africa.
Abstract: The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods ~120 and ~244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.
43 citations
05 May 2017
TL;DR: This work proposes and discusses methods to obtain an accurate polarizability model by combining absorption spectrum measurements, Kramers–Kronig tranformations, and density functional theory (DFT) calculations, and introduces simple KK-consistent analytic functions based on the theory of critical points as a much more accurate approach to model dye polarizabilities.
Abstract: The wavelength-dependent complex linear polarizability of a dye is a crucial input for the modeling of the optical properties of dye-containing systems. We here propose and discuss methods to obtain an accurate polarizability model by combining absorption spectrum measurements, Kramers–Kronig (KK) tranformations, and density functional theory (DFT) calculations. We focus, in particular, on the real part of the polarizability and its link with static polarizability. In addition, we introduce simple KK-consistent analytic functions based on the theory of critical points as a much more accurate approach to model dye polarizabilities compared with existing models based on Lorentz oscillators. Accurate polarizability models based on critical points and DFT calculations of the static polarizability are derived for five commonly used dyes: Rhodamine 6G, Rhodamine 700, Crystal Violet, Nile Blue A, and Methylene Blue. Finally, we demonstrate explicitly, using examples of Mie Theory calculations of nanoparticle–dye...
31 citations
TL;DR: The first direct radiocarbon date for the Darra-i-Kur specimen is reported and the genetic analyses of DNA extracted and sequenced from two areas of the bone suggest that the specimen is younger than previously thought.
Max Planck Society1, Harvard University2, University of Potsdam3, University of York4, Danube Private University5, University of Basel6, University of Illinois at Urbana–Champaign7, Naturalis8, Weimar Institute9, Howard Hughes Medical Institute10, Broad Institute11, University of California, Santa Cruz12
Patent•
11 Oct 2017
TL;DR: In this paper, a combination of light inlet ports P 1, P 2 and light outlet ports P 3, P 4 are provided to receive light from at least one light source and to deliver light to a spectrometer.
Abstract: A spectrometer apparatus ( 1 ) is provided for measuring spectra of a liquid sample, such as a beverage such as wine. The apparatus ( 1 ) comprises an integrating cavity ( 3 ) comprising a reflective inner wall or walls ( 5 ), configured to receive a cuvette ( 7 ) containing the liquid sample within the integrating cavity ( 5 ). A combination of light inlet ports P 1, P 2 and light outlet ports P 3, P 4 are provided to receive light from at least one light source ( 9 ) and to deliver light to a spectrometer ( 11 ). A light path adjuster ( 13, 13 B) is configured to selectively adjust a light path through the integrating cavity ( 5 ) such that at least two distinct light paths are provided; wherein when the light path adjuster ( 13, 13 B) is in a first configuration, the apparatus ( 1 ) is in a transmission mode in which light from the light source follows a first light path ( 15 ) from the or one of the light inlet port(s) to the liquid sample such that the light from the light source irradiates the liquid sample directly before the light transmitted by the sample is transmitted through the or one of the light outlet port(s) and received by the spectrometer ( 11 ) for wavelength analysis of the light to provide an extinction spectrum of the liquid sample; and when the light path adjuster ( 13, 13 B) is in a second configuration, the apparatus is in a diffusely reflecting mode in which light from the light source follows a second light path ( 17 ) from the or one of the inlet port(s) into the integrating cavity, is incident onto the reflective inner wall or walls of the integrating cavity and is diffusely reflected within the integrating cavity, such that the light from the light source irradiates the liquid sample before being transmitted through the or one of the light outlet port(s) and received by the spectrometer ( 11 ) for wavelength analysis of the light to provide an absorbance spectrum of the liquid sample contained in the liquid sample.