Showing papers by "Matthias Meyer published in 2014"
Max Planck Society1, University of California, Berkeley2, Broad Institute3, Harvard University4, University of Washington5, National Institutes of Health6, University of California, Santa Cruz7, Ludwig Maximilian University of Munich8, Emory University9, Fondation Jean Dausset Centre d'Etude du Polymorphisme Humain10, Allen Institute for Brain Science11, Russian Academy of Sciences12, Howard Hughes Medical Institute13
TL;DR: It is shown that interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene and a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans is established.
Abstract: We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
1,691 citations
Broad Institute1, Harvard University2, University of Tübingen3, Max Planck Society4, University of Mainz5, University of Washington6, University of California, Berkeley7, Massachusetts Institute of Technology8, Stockholm University9, University of Adelaide10, The Heritage Foundation11, National Museum of Natural History12, Sultan Qaboos University13, University of Edinburgh14, University of Costa Rica15, University of Antioquia16, Rambam Health Care Campus17, University of Pécs18, Al Akhawayn University19, Catholic University of the Sacred Heart20, University of Oxford21, Belgorod State University22, University of Toronto23, University of Buenos Aires24, University of Bern25, Russian Academy of Sciences26, Paul Sabatier University27, North-Eastern Federal University28, University of Chicago29, University of Arizona30, Stony Brook University31, University of Bergen32, Illumina33, Sofia Medical University34, Bashkir State University35, University of Cambridge36, Vilnius University37, Estonian Biocentre38, University of Strasbourg39, University College London40, Amgen41, Gladstone Institutes42, University of Tartu43, University of Oulu44, Muhimbili University of Health and Allied Sciences45, University of Palermo46, University of Chile47, University of Tarapacá48, Academy of Sciences of Uzbekistan49, Armenian National Academy of Sciences50, University of North Texas51, University of Santiago de Compostela52, University of Kharkiv53, Higher University of San Andrés54, Novosibirsk State University55, Leidos56, Lebanese American University57, University of Split58, University of Pennsylvania59, Banaras Hindu University60, Centre for Cellular and Molecular Biology61, Estonian Academy of Sciences62, Pompeu Fabra University63, Howard Hughes Medical Institute64
TL;DR: It is shown that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians; and early European farmers, who were mainly of Near Eastern origin but also harboured west Europeanhunter-gatherer related ancestry.
Abstract: 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 analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
1,077 citations
Chinese Academy of Sciences1, Harvard University2, Columbia University3, University of California, Berkeley4, Russian Academy of Sciences5, Emory University6, Max Planck Society7, University of California, Davis8, University of Cape Town9, University of British Columbia10, University of Oxford11, Howard Hughes Medical Institute12
TL;DR: The high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia 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.
Abstract: 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 segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 3 10 29 to 0.6 3 10 29 per site per year, a Y chromosomal mutation rate of 0.7 3 10 29 to 0.9 3 10 29 per site per year based on the additional substitutions that have occurred in present-day nonAfricans compared to this genome, and a mitochondrial mutation rate of 1.8 3 10 28 to 3.2 3 10 28 per site per year based on the age of the bone.
814 citations
Harvard University1, Broad Institute2, University of Tübingen3, Max Planck Society4, University of Mainz5, University of Washington6, University of California, Berkeley7, Massachusetts Institute of Technology8, Stockholm University9, University of Adelaide10, The Heritage Foundation11, National Museum of Natural History12, Sultan Qaboos University13, University of Edinburgh14, University of Costa Rica15, University of Antioquia16, Rambam Health Care Campus17, University of Pécs18, Al Akhawayn University19, Catholic University of the Sacred Heart20, University of Oxford21, Belgorod State University22, University of Toronto23, University of Buenos Aires24, University of Bern25, Russian Academy of Sciences26, Paul Sabatier University27, North-Eastern Federal University28, University of Chicago29, University of Arizona30, Stony Brook University31, University of Bergen32, Illumina33, Sofia Medical University34, Bashkir State University35, University of Cambridge36, Vilnius University37, Estonian Biocentre38, University of Strasbourg39, University College London40, Amgen41, Gladstone Institutes42, University of Tartu43, University of Oulu44, Muhimbili University of Health and Allied Sciences45, University of Palermo46, University of Tarapacá47, University of Chile48, Academy of Sciences of Uzbekistan49, Armenian National Academy of Sciences50, University of North Texas51, University of Santiago de Compostela52, University of Kharkiv53, Higher University of San Andrés54, Novosibirsk State University55, Leidos56, Lebanese American University57, University of Split58, University of Pennsylvania59, Banaras Hindu University60, Centre for Cellular and Molecular Biology61, Estonian Academy of Sciences62, Pompeu Fabra University63, Howard Hughes Medical Institute64
TL;DR: The authors showed that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunters-gatherer related ancestry.
Abstract: 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 analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
442 citations
TL;DR: An almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos is determined and it is shown that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals.
Abstract: Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest
assemblage of Middle Pleistocene hominin fossils2,3, onsisting of at least 28 individuals4 dated to over 300,000 years ago5. The skeletal remains share a number of morphological features with fossils classifieds Homo heidelbergensis and also display distinct neanderthalderived traits6–8. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of enisovans 9,10, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
414 citations
TL;DR: This study based on transcriptomic data comprising 68,750-170,497 amino acid sites from 305 to 622 proteins resolves annelid relationships, including Chaetopteridae, Amphinomidae, Sipuncula, Oweniidae, and Magelonidae in the basal part of the tree.
Abstract: Annelida is one of three animal groups possessing segmentation and is central in considerations about the evolution of different character traits. It has even been proposed that the bilaterian ancestor resembled an annelid. However, a robust phylogeny of Annelida, especially with respect to the basal relationships, has been lacking. Our study based on transcriptomic data comprising 68,750-170,497 amino acid sites from 305 to 622 proteins resolves annelid relationships, including Chaetopteridae, Amphinomidae, Sipuncula, Oweniidae, and Magelonidae in the basal part of the tree. Myzostomida, which have been indicated to belong to the basal radiation as well, are now found deeply nested within Annelida as sister group to Errantia in most analyses. On the basis of our reconstruction of a robust annelid phylogeny, we show that the basal branching taxa include a huge variety of life styles such as tube dwelling and deposit feeding, endobenthic and burrowing, tubicolous and filter feeding, and errant and carnivorous forms. Ancestral character state reconstruction suggests that the ancestral annelid possessed a pair of either sensory or grooved palps, bicellular eyes, biramous parapodia bearing simple chaeta, and lacked nuchal organs. Because the oldest fossil of Annelida is reported for Sipuncula (520 Ma), we infer that the early diversification of annelids took place at least in the Lower Cambrian.
265 citations
TL;DR: It is shown that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans.
Abstract: We present the DNA sequence of 17,367 protein-coding genes in two Neandertals from Spain and Croatia and analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia. Comparisons with present-day humans from Africa, Europe, and Asia reveal that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans. Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans. We also identify amino acid substitutions in Neandertals and present-day humans that may underlie phenotypic differences between the two groups. We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in behavior and pigmentation have changed more on the modern human lineage.
224 citations
TL;DR: A pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change is found, however, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats.
Abstract: Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.
180 citations
Harvard University1, Broad Institute2, University of Tübingen3, Max Planck Society4, University of Mainz5, University of Washington6, University of California, Berkeley7, Massachusetts Institute of Technology8, Stockholm University9, University of Adelaide10, The Heritage Foundation11, National Museum of Natural History12, American Museum of Natural History13, University of Edinburgh14, National Scientific and Technical Research Council15, University of Costa Rica16, University of Antioquia17, Rambam Health Care Campus18, University of Pécs19, Al Akhawayn University20, Catholic University of the Sacred Heart21, University of Oxford22, Belgorod State University23, University of Toronto24, University of Buenos Aires25, Russian Academy26, University of Bern27, Paul Sabatier University28, North-Eastern Federal University29, University of Chicago30, Russian Academy of Sciences31, University of Arizona32, Stony Brook University33, University of Bergen34, Illumina35, Sofia Medical University36, University of Illinois at Chicago37, University of Cambridge38, Vilnius University39, Estonian Biocentre40, University of Strasbourg41, Amgen42, Gladstone Institutes43, University of Tartu44, University of Oulu45, Muhimbili University of Health and Allied Sciences46, University of Palermo47, University of Tarapacá48, Academy of Sciences of Uzbekistan49, University of Helsinki50, University of Santiago de Compostela51, University of Kharkiv52, Higher University of San Andrés53, Leidos54, Armenian National Academy of Sciences55, Lebanese American University56, University of Split57, University College London58, University of Pennsylvania59, Centre for Cellular and Molecular Biology60, Pompeu Fabra University61
TL;DR: It is shown that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE); and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry.
Abstract: We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had ~44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.
134 citations
Journal Article•
TL;DR: This paper used 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species, and found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change.
Abstract: Marsupials exhibit great diversity in ecology and morphology. However, compared to their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene, and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.
110 citations
TL;DR: A new molecular method is described, U selection, which exploits one of the most distinctive features of ancient DNA--the presence of deoxyuracils--for selective enrichment of endogenous DNA against a complex background of contamination during DNA library preparation, showing that the fraction of useful sequence information increases ∼ 10-fold and that the resulting sequences are more efficiently depleted of human contamination than when using purely computational approaches.
Abstract: .Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA—the presence of deoxyuracils—for selective enrichment of endogenous DNA against a complex background of contamination during DNA library preparation. By applying the method to Neanderthal DNA extracts that are heavily contaminated with present-day human DNA, we show that the fraction of useful sequence information increases ~10-fold and that the resulting sequences are more efficiently depleted of human contamination than when using purely computational approaches. Furthermore, we show that U selection can lead to a four- to fivefold increase in the proportion of endogenous DNA sequences relative to those of microbial contaminants in some samples. U selection may thus help to lower the costs for ancient genome sequencing of nonhuman samples also. [Supplemental material is available for this article.]
TL;DR: It is proposed that the trap is a Frenkel exciton state formed much below the main exciton band edge due to an environmentally induced heavy-tailed Lévy disorder, which points to disorder engineering as a new avenue in controlling light-harvesting in molecular ensembles.
Abstract: Using fluorescence super-resolution microscopy we studied simultaneous spectral, spatial localization, and blinking behavior of individual 1D J-aggregates. Excitons migrating 100 nm are funneled to a trap appearing as an additional red-shifted blinking fluorescence band. We propose that the trap is a Frenkel exciton state formed much below the main exciton band edge due to an environmentally induced heavy-tailed Levy disorder. This points to disorder engineering as a new avenue in controlling light-harvesting in molecular ensembles.
TL;DR: This work sequenced the exome of 20 humans, 20 chimpanzees and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 million years of independent evolution, and uncovered one coding trSNP in LAD1, a gene that encodes for Ladinin-1, an autoantigen responsible for linear IgA disease.
Abstract: Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo-Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 million years of independent evolution. While the majority of these trSNPs were found in three genes of the MHC cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1. All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here we focus on the trSNP in LAD1, a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1.
TL;DR: In this article, a collision between two conjugated polymer (CP) molecules in solution leads to simultaneous rupture of both chains, and the catalytic effect of the chain bending is also enhanced by a prolonged interaction between the chains owing to their entanglement.
Abstract: While collision theory successfully describes the kinetics of chemical reactions, very little is known about the processes at the molecular level, especially if the reacting molecules are large. In this study, using single-molecule spectroscopy, we visually observed that collision between two conjugated polymer (CP) molecules in solution leads to simultaneous rupture of both chains. In addition to opening up the possibility of monitoring chemical processes in solution at the single-molecule level, these results demonstrate that mechanical bending of two stiff conjugated backbones against each other (the effect of leverage) by Brownian motion can weaken the chemical bond and markedly accelerate photochemical oxygen-induced chain scission by at least 20 times. The catalytic effect of the chain bending is also enhanced by a prolonged interaction between the chains owing to their entanglement. These findings are important for the solution processing of CPs in their application in organic electronics, for understanding the degradation mechanisms in CPs and for the development of new catalysts based on mechanical interactions with target molecules.
TL;DR: In this article, the orientation of transition dipole moments of conjugated polymer-fullerene blends was analyzed using two-dimensional polarization imaging to obtain a detailed understanding of the local charge transfer (CT) states.
Abstract: Photoexcitation of conjugated polymer–fullerene blends results in population of a local charge transfer (CT) state at the interface between the two materials. The competition between recombination and dissociation of this interfacial state limits the generation of fully separated free charges. Therefore, a detailed understanding of the CT states is critical for building a comprehensive picture of the organic solar cells operation. We applied a new fluorescence microscopy method called two-dimensional polarization imaging to gain insight into the orientation of the transition dipole moments of the CT states, and the associated excitation energy transfer processes in TQ1:PCBM blend films. The polymer phase was oriented mechanically to relate the polymer dipole moment orientation to that of the CT states. CT state formation was observed to be much faster than energy transfer in the polymer phase. However, after being formed an emissive CT state does not exchange excitation energy with other CT states, sugges...
TL;DR: This morphotype, referred to here as ‘flat-toothed’ and which in several respects resembles the offshore form in the North Pacific and the Type 1 form inThe North Atlantic, does not seem to have been recorded previously from the Southern Hemisphere.
Abstract: Killer whales Orcinus orca occur worldwide in a number of morphotypes that differ in size, pigmentation, acoustic behaviour, food type and genetics – some may indeed warrant subspecific or even specific status. Until recently, all killer whales in South African waters were referred to a single morphotype, Type A, but three individuals (two males and one female) that have stranded since 1969 differ in several respects from other killer whales examined from the region. Adult length is some 1–1.5 m smaller, appendages such as dorsal fin and flippers tend to be relatively larger, and tooth wear is excessive. Although dietary information is scant, one stomach contained the remains of several elasmobranchs, identified from a DNA subsample as blue sharks Prionace glauca, a dietary item that, if habitual, might account for the tooth wear. This morphotype, referred to here as ‘flat-toothed’ and which in several respects resembles the offshore form in the North Pacific and the Type 1 form in the North Atlantic, doe...