Targeted retrieval and analysis of five neandertal mtDNA genomes (2009)
Briggs, Adrian W., Good, Jeffrey M., Green, Richard E., Krause, Johannes, Maricic, Tomislav, Stenzel, Udo, ...
4 pages, 2 figures, 1 table.-- Supporting information available (Materials and Methods, Suppl. figs S1-S14, Suppl. tables S1-S8, Suppl refs, 1 appendix, 37 pages) at:...
A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice (2009)
Enard, Wolfgang, Gehre, Sabine, Hammerschmidt, Kurt, Hölter, Sabine M., Blass, Torsten, Somel, Mehmet, ...
It has been proposed that two amino acid substitutions in the transcription factor FOXP2 have been positively selected during human evolution due to effects on aspects of speech and language. Here,...
Metabolic changes in schizophrenia and human brain evolution (2008)
Khaitovich, Philipp, Lockstone, Helen E, Wayland, Matthew T, Tsang, Tsz M, Jayatilaka, Samantha D, Guo, Arfu J, ...
Abstract Background Despite decades of research, the molecular changes responsible for the evolution of human cognitive abilities remain unknown. Comparative evolutionary studies provide detailed...
Krause, Johannes, Unger, Tina, Noçon, Aline, Malaspinas, Anna-Sapfo, Kolokotronis, Sergios-Orestis, Stiller, Mathias, ...
Abstract Background Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear....
Aging and Gene Expression in the Primate (2008)
Hunter B. Fraser, Joshua B. Plotkin, Svante Pääbo, Michael B. Eisen
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Albert, Frank W., Shchepina, Olesya, Winter, Christine, Römpler, Holger, Teupser, Daniel, Palme, Rupert, ...
Meyer, Matthias, Briggs, Adrian W., Maricic, Tomislav, Höber, Barbara, Höffner, Barbara, Krause, Johannes, ...
Groszer, Matthias, Keays, David A., Deacon, Robert M.J., De Bono, Joseph P., Prasad-Mulcare, Shweta, Gaub, Simone, ...
A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing (2008)
Green, Richard E., Malaspinas, Anna-Sapfo, Krause, Johannes, Briggs, Adrian W., Johnson, Philip L. F., Uhler, Caroline, ...
Farkas, Lila M., Haffner, Christiane, Giger, Thomas, Khaitovich, Philipp, Nowick, Katja, Birchmeier, Carmen, ...
Krause, Johannes, Unger, Tina, Noçon, Aline, Malaspinas, Anna-Sapfo, Kolokotronis, Sergios-Orestis, Stiller, Matthias, ...
Suggested guidelines for invasive sampling of hominid remains (2008)
Hublin, Jena-Jacques, Pääbo, Svante, Derevianko, Anatoly P., Doronichev, Vladimir B., Golovanova, Liubov V., Friess, Martin, ...
Metabolic changes in schizophrenia and human brain evolution (2008)
Khaitovich, Philipp, Lockstone, Helen E., Wayland, Matthew T., Tsang, Tsz M., Jayatilaka, Samantha D., Guo, Arfu J., ...
Human and Chimpanzee Gene Expression Differences Replicated in Mice Fed Different Diets (2008)
Somel, Mehmet, Creely, Hilliary, Franz, Henriette, Mueller, Uwe, Lachmann, Michael, Khaitovich, Philipp, ...
Meyer, Matthias, Briggs, Adrian W., Maricic, Tomislav, Höber, Barbara, Höffner, Barbara, Krause, Johannes, ...
Current efforts to recover the Neandertal and mammoth genomes by 454 DNA sequencing demonstrate the sensitivity of this technology. However, routine 454 sequencing applications still require...
Prüfer, Kay, Muetzel, Bjoern, Do, Hong-Hai, Weiss, Gunter, Khaitovich, Philipp, Rahm, Erhard, ...
Abstract Background Genome-wide expression, sequence and association studies typically yield large sets of gene candidates, which must then be further analysed and interpreted. Information about...
Sudden replacement of cave bear mitochondrial DNA in the late Pleistocene (2007)
Hofreiter, Michael, Münzel, Susanne, Conard, Nicholas J., Pollack, Joshua, Slatkin, Montgomery, Weiss, Gunter, ...
Patterns of damage in genomic DNA sequences from a Neandertal (2007)
Briggs, Adrian W., Stenzel, Udo, Johnson, Philip L. F., Green, Richard E., Kelso, Janet, Prüfer, Kay, ...
Neanderthals in central Asia and Siberia (2007)
Krause, Johannes, Orlando, Ludivic, Serre, David, Bence, Viola, Prüfer, Kay, Richards, Michael P., ...
The Joint Allele-Frequency Spectrum in Closely Related Species (2007)
Chen, Hua, Green, Richard E., Pääbo, Svante, Slatkin, Montgomery
The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals (2007)
Krause, Johannes, Lalueza-Fox, Carles, Ludovic, Orlando, Enard, Wolfgang, Green, Richard E., Burbano, Hernán A., ...
The Complex Evolutionary History of Gorillas: Insights from Genomic Data (2007)
Thalmann, Olaf, Fischer, Anne, Lankester, F. H., Pääbo, Svante, Vigilant, Linda
The Complex Evolutionary History of Gorillas (2007)
Vigilant, Linda, Thalmann, Olaf, Fischer, Anne, Pääbo, Svante
Molecular breeding of polymerases for amplification of ancient DNA (2007)
D'Abbadie, Marc, Hofreiter, Michael, Vaisman, Alexandra, Loakes, David, Gasparutto, Didier, Cadet, Jean, ...
Comparison of Protein and mRNA Expression Evolution in Humans and Chimpanzees (2007)
Fu, Ning, Drinnenberg, Ines, Kelso, Janet, Wu, Jia-Rui, Pääbo, Svante, Zeng, Rong, ...
Sequencing and analysis of Neanderthal genomic DNA (2006)
Coop, Graham, Kudaravalli, Sridhar, Smith, Doug, Krause, Johannes, Alessi, Joe, ...
Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe...
Functionality of Intergenic Transcription: An Evolutionary Comparison (2006)
Philipp Khaitovich, Janet Kelso, Henriette Franz, Johann Visagie, Thomas Giger, Sabrina Joerchel, ...
Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression...
Functionality of Intergenic Transcription: An Evolutionary Comparison (2006)
Philipp Khaitovich, Janet Kelso, Henriette Franz, Johann Visagie, Thomas Giger, Sabrina Joerchel, ...
Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression...
Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae (2006)
Krause, Johannes, Dear, Paul H., Pollack, Joshua L., Slatkin, Montgomery, Spriggs, Helen, Barnes, Ian, ...
Evolution of primate gene expression (2006)
Khaitovich, Philipp, Enard, Wolfgang, Lachmann, Michael, Pääbo, Svante
Functionality of Intergenic Transcription : an Evolutionary Comparison (2006)
Khaitovich, Philipp, Kelso, Janet, Franz, Henriette, Visagie, Johann, Giger, Thomas, Joerchel, Sabrina, ...
Accelerated Evolution of Conserved Noncoding Sequences in Humans (2006)
Prabhakar, Shyam, Noonan, James, Pääbo, Svante, Rubin, Edward M.
The Complex Evolutionary History of Gorillas : Insights from Genomic Data (2006)
Thalmann, Olaf, Fischer, Anne, Lankester, F., Pääbo, Svante, Vigilant, Linda
Aspm specifically maintains symmetric proliferative divisions of neuroepithelial cells (2006)
Fish, Jennifer L., Kosodo, Yoichi, Enard, Wolfgang, Pääbo, Svante, Huttner, Wieland B.
Demographic History and Genetic Differentiation in Apes (2006)
Fischer, Anne, Pollack, Joshua, Thalmann, Olaf, Nickel, Birgit, Pääbo, Svante
Positive selection on gene expression in the human brain (2006)
Khaitovich, Philipp, Tang, Kun, Franz, Henriette, Kelso, Janet, Hellmann, Ines, Enard, Wolfgang, ...
Gene expression becomes heterogeneous with age (2006)
Somel, Mehmet, Khaitovich, Philipp, Bahn, Sabine, Pääbo, Svante, Lachmann, Michael
Analysis of one million base pairs of Neanderthal DNA (2006)
Green, Richard E., Krause, Johannes, Ptak, Susan E., Briggs, Adrian W., Ronan, Michael T., Simons, Jan F., ...
Sequencing and analysis of Neanderthal genomic DNA (2006)
Noonan, J.P., Coop, G., Kudaravalli, S., Smith, D., Krause, Johannes, Alessi, J., ...
No evidence of Neanderthal mtDNA contribution to early modern humans (2006)
Serre, David, Langaney, A., Chech, M., Teschler-Nicola, M., Paunovic, M., Mennecier, P., ...
Structure of the forkhead domain of FOXP2 bound to DNA (2006)
Stroud, J. C., Wu, Y. Q., Bates, D. L., Han, A. D., Nowick, Katja, Pääbo, Svante, ...
Systematic analysis of gene expression in human brains before and after death (2005)
Franz, Henriette, Ullmann, Claudia, Becker, Albert, Ryan, Margaret, Bahn, Sabine, Arendt, Thomas, ...
Abstract Background Numerous studies have employed microarray techniques to study changes in gene expression in connection with human disease, aging and evolution. The vast majority of human samples...
Aging and Gene Expression in the Primate Brain (2005)
Hunter B. Fraser, Philipp Khaitovich, Joshua B. Plotkin, Svante Pääbo, Michael B. Eisen
Transcriptional profiles in human and chimpanzee reveal a diversity of aging patterns present within the human brain, as well as how rapidly genome-wide patterns of aging can evolve between species.
Aging and Gene Expression in the Primate Brain (2005)
Hunter B. Fraser, Philipp Khaitovich, Joshua B. Plotkin, Svante Pääbo, Michael B. Eisen
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Functional analysis of human and chimpanzee promoters (2005)
Heissig, Florian, Krause, Johannes, Bryk, Jaroslaw, Khaitovich, Philipp, Enard, Wolfgang, Pääbo, Svante
Abstract Background It has long been argued that changes in gene expression may provide an additional and crucial perspective on the evolutionary differences between humans and chimpanzees. To...
Chris T. Yohn, Zhaoshi Jiang, Sean D. McGrath, Karen E. Hayden, Philipp Khaitovich, Matthew E. Johnson, ...
Comparison of human and other primate genomes provides evidence for a retroviral infection that bombarded the genomes of chimpanzees and gorillas 3-4 million years ago.
Chris T. Yohn, Zhaoshi Jiang, Sean D. McGrath, Karen E. Hayden, Philipp Khaitovich, Matthew E. Johnson, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Fine-scale recombination patterns differ between chimpanzees and humans (2005)
Ptak, Susan E., Hinds, David A., Koehler, Kathrin, Nickel, Birgit, Patil, Nila, Ballinger, Dennis G., ...
Yohn, Chris T., Jiang, Zhaoshi, McGrath, Sean D., Hayden, Karen E., Khaitovich, Philipp, Johnson, Matthew E., ...
Genomic sequencing of Pleistocene Cave Bears (2005)
Noonan, James P., Hofreiter, Michael, Smith, Doug, Priest, James R., Rohland, Nadin, Rabeder, Gernot, ...
Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries...
Functional analysis of human and chimpanzee promoters (2005)
Heissig, Florian, Krause, Johannes, Bryk, Jaroslaw, Khaitovich, Philipp, Enard, Wolfgang, Pääbo, Svante
Aging and Gene Expression in the Primate Brain (2005)
Fraser, Hunter B., Khaitovich, Philipp, Plotkin, Joshua B., Pääbo, Svante, Eisen, Michael B.
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Systematic analysis of gene expression in human brains before and after death (2005)
Franz, H., Ullmann, C., Becker, A., Ryan, M., Bahn, S., Arendt, T., ...
BACKGROUND: Numerous studies have employed microarray techniques to study changes in gene expression in connection with human disease, aging and evolution. The vast majority of human samples...
The rise and fall of the chemoattractant receptor GPR33 (2005)
Römpler, H., Schulz, A., Pitra, C., Coop, G., Przeworski, Molly, Pääbo, Svante, ...
Chemokine and chemoattractant receptors are members of the large superfamily of G protein- coupled receptors ( GPCR), which control leukocyte chemotaxis. In addition to their physiological role,...
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
The population history of extant and extinct hyenas (2005)
Rohland, Nadin, Pollack, J. L., Nagel, D., Beauval, C., Airvaux, J., Pääbo, Svante, ...
Why do human diversity levels vary at a megabase scale? (2005)
Hellmann, Ines, Prüfer, Kai, Ji, H. K., Zody, M. C., Pääbo, Svante, Ptak, Susan E.
A late Neandertal femur from Les Rochers-de-Villeneuve, France (2005)
Beauval, C., Maureille, B., Lacrampe-Cuyaubere, F., Serre, D., Peressinotto, D., Bordes, J. G., ...
A genome-wide comparison of recent chimpanzee and human segmental duplications (2005)
Cheng, Z., Ventura, M., She, X. W., Khaitovich, Philipp, Graves, T., Osoegawa, K., ...
We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (>94% sequence identity) are not...
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees (2005)
Khaitovich, Philipp, Hellmann, Ines, Enard, Wolfgang, Nowick, Katja, Leinweber, M., Franz, H., ...
The Population History of Extant and Extinct Hyenas (2005)
Rohland, Nadin, Pollack, Joshua L., Nagel, Doris, Beauval, Cédric, Airvaux, Jean, Pääbo, Svante, ...
We have analyzed partial DNA sequences of the mitochondrial (mt) cytochrome-B gene from extant striped, brown and spotted hyenas as well as from Pleistocene cave hyenas. Sequences of the Pleistocene...
The Population History of Extant and Extinct Hyenas (2005)
Rohland, Nadin, Pollack, Joshua L., Nagel, Doris, Beauval, Cédric, Airvaux, Jean, Pääbo, Svante, ...
We have analyzed partial DNA sequences of the mitochondrial cytochrome b gene from extant striped, brown, and spotted hyenas as well as from Pleistocene cave hyenas. Sequences of the Pleistocene cave...
Evolution of Bitter Taste Receptors in Humans and Apes (2005)
Fischer, Anne, Gilad, Yoav, Man, Orna, Pääbo, Svante
Bitter taste perception is crucial for the survival of organisms because it enables them to avoid the ingestion of potentially harmful substances. Bitter taste receptors are encoded by a gene family...
The Population History of Extant and Extinct Hyenas (2005)
Rohland, Nadin, Pollack, Joshua L., Nagel, Doris, Beauval, Cédric, Airvaux, Jean, Pääbo, Svante, ...
We have analyzed partial DNA sequences of the mitochondrial (mt) cytochrome-B gene from extant striped, brown and spotted hyenas as well as from Pleistocene cave hyenas. Sequences of the Pleistocene...
A late Neandertal femur from Les Rochers-de-Villeneuve, France (2005)
Beauval, Cédric, Maureille, Bruno, Lacrampe-Cuyaubère, François, Serre, David, Peressinotto, David, Bordes, Jean-Guillaume, ...
In 2002, a Neandertal partial femoral diaphysis was discovered at Les Rochers-de-Villeneuve (Vienne, France). Radiocarbon dated to +/- 40,700 14C years before present, this specimen is one of the...
A late Neandertal femur from Les Rochers-de-Villeneuve, France (2005)
Beauval, Cédric, Maureille, Bruno, Lacrampe-Cuyaubère, François, Serre, David, Peressinotto, David, Bordes, Jean-Guillaume, ...
In 2002, a Neandertal partial femoral diaphysis was discovered at Les Rochers-de-Villeneuve (Vienne, France). Radiocarbon dated to +/- 40,700 14C years before present, this specimen is one of the...
Absence of the TAP2 Human Recombination Hotspot in Chimpanzees (2004)
Susan E. Ptak, Amy D. Roeder, Matthew Stephens, Yoav Gilad, Svante Pääbo, Molly Przeworski
The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees, with important implications for association studies, the HapMap project and understanding fine-scale...
Absence of the TAP2 Human Recombination Hotspot in Chimpanzees (2004)
Susan E. Ptak, Amy D. Roeder, Matthew Stephens, Yoav Gilad, Svante Pääbo, Molly Przeworski
Recent experiments using sperm typing have demonstrated that, in several regions of the human genome, recombination does not occur uniformly but instead is concentrated in “hotspots” of 1–2 kb....
A Neutral Model of Transcriptome Evolution (2004)
Philipp Khaitovich, Gunter Weiss, Michael Lachmann, Ines Hellmann, Wolfgang Enard, Bjoern Muetzel, ...
Analysis of differences in gene expression between primate species suggests that the majority of them are selectively neutral and likely to have little or no functional consequences.
A Neutral Model of Transcriptome Evolution (2004)
Philipp Khaitovich, Gunter Weiss, Michael Lachmann, Ines Hellmann, Wolfgang Enard, Bjoern Muetzel, ...
Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for...
No Evidence of Neandertal mtDNA Contribution to Early Modern Humans (2004)
David Serre, André Langaney, Mario Chech, Maria Teschler-Nicola, Maja Paunovic, Philippe Mennecier, ...
Analysis of mitochondrial DNA from four Neandertal fossils and five "modern human" contemporaries excludes any large genetic contribution of Neandertals to the gene pool of modern humans.
No Evidence of Neandertal mtDNA Contribution to Early Modern Humans (2004)
David Serre, André Langaney, Mario Chech, Maria Teschler-Nicola, Maja Paunovic, Philippe Mennecier, ...
The retrieval of mitochondrial DNA (mtDNA) sequences from four Neandertal fossils from Germany, Russia, and Croatia has demonstrated that these individuals carried closely related mtDNAs that are not...
Yoav Gilad, Victor Wiebe, Molly Przeworski, Doron Lancet, Svante Pääbo
Examination of olfactory receptor genes in 19 primate species suggests that the olfactory repertoire lost complexity as our ancestors acquired full-color vision.
Yoav Gilad, Victor Wiebe, Molly Przeworski, Doron Lancet, Svante Pääbo
Olfactory receptor (OR) genes constitute the molecular basis for the sense of smell and are encoded by the largest gene family in mammalian genomes. Previous studies suggested that the proportion of...
Differences in DNA methylation patterns between humans and chimpanzees (2004)
Enard, Wolfgang, Fassbender, Anne, Model, Fabian, Adorján, Péter, Pääbo, Svante, Olek, Alexander
Evidence for reproductive isolation between cave bear populations (2004)
Hofreiter, Michael, Rabeder, G., Jänicke-Despres, Viviane, Withalm, G., Nagel, D., Paunovic, M., ...
Evidence for a Complex Demographic History of Chimpanzees (2004)
Fischer, Anne, Wiebe, Victor, Pääbo, Svante, Przeworski, Molly
Regional Patterns of Gene Expression in Human and Chimpanzee Brains (2004)
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
Lack of phylogeography in European mammals before the last glaciation (2004)
Hofreiter, Michael, Serre, David, Nadin, Rohland, Rabeder, Gernot, Nagel, Doris, Conard, Nicholas, ...
DNA sequence and comparative analysis of chimpanzee chromosome 22 (2004)
Watanabe, H., Fujiyama, A., Hattory, M., Taylor, T. D., Toyoda, A., Kuroki, Y., ...
Genetic analyses from ancient DNA (2004)
Pääbo, Svante, Poinar, Hendrik, Serre, David, Jaenicke-Després, Viviane, Hebler, Juliane, Rohland, Nadin, ...
Gilad, Yoav, Wiebe, Victor, Przeworski, Molly, Lancet, Doron, Pääbo, Svante
Olfactory receptor (OR) genes constitute the molecular basis for the sense of smell and are encoded by the largest gene family in mammalian genomes. Previous studies suggested that the proportion of...
No evidence of Neandertal mtDNA contribution to early modern humans (2004)
Serre, David, Langaney, A., Chell, M., Teschler-Nicola, M., Paunovic, M., Mennecier, P., ...
The retrieval of mitochondrial DNA (mtDNA) sequences from four Neandertal fossils from Germany, Russia, and Croatia has demonstrated that these individuals carried closely related mtDNAs that are not...
A Neutral Model of Transcriptome Evolution (2004)
Khaitovich, Phillip, Weiss, Gunter, Lachmann, Michael, Hellmann, Ines, Enard, Wolfgang, Muetzel, Bjoern, ...
Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for...
Absence of the TAP2 Human Recombination Hotspot in Chimpanzees (2004)
Ptak, Susan E., Roeder, Amy D., Stephens, Matthew, Gilad, Yoav, Pääbo, Svante, Przeworski, Molly
Recent experiments using sperm typing have demonstrated that, in several regions of the human genome, recombination does not occur uniformly but instead is concentrated in “hotspots” of 1–2 kb....
Evidence for a Complex Demographic History of Chimpanzees (2004)
Fischer, Anne, Wiebe, Victor, Pääbo, Svante, Przeworski, Molly
To characterize patterns of genomic variation in central chimpanzees (Pan troglodytes troglodytes) and gain insight into their evolution, we sequenced nine unlinked, intergenic regions, representing...
Evolution of Bitter Taste Receptors in Humans and Apes (2004)
Fischer, Anne, Gilad, Yoav, Man, Orna, Pääbo, Svante
Bitter taste perception is crucial for the survival of organisms since it enables them to avoid the ingestion of potentially harmful substances. Bitter taste receptors are encoded by a gene family...
Regional Patterns of Gene Expression in Human and Chimpanzee Brains (2004)
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each...
Evidence for a Complex Demographic History of Chimpanzees (2004)
Fischer, Anne, Wiebe, Victor, Pääbo, Svante, Przeworski, Molly
To characterize patterns of genomic variation in central chimpanzees (Pan troglodytes troglodytes) and gain insight into their evolution, we sequenced nine unlinked, intergenic regions, representing...
Evidence for a Complex Demographic History of Chimpanzees (2004)
Fischer, Anne, Wiebe, Victor, Pääbo, Svante, Przeworski, Molly
To characterize patterns of genomic variation in central chimpanzees (Pan troglodytes troglodytes) and gain insight into their evolution, we sequenced nine unlinked, intergenic regions, representing...
Evolution of Bitter Taste Receptors in Humans and Apes (2004)
Fischer, Anne, Gilad, Yoav, Man, Orna, Pääbo, Svante
Bitter taste perception is crucial for the survival of organisms since it enables them to avoid the ingestion of potentially harmful substances. Bitter taste receptors are encoded by a gene family...
Otte, K., Kranz, H., Kober, I., Thompson, P., Hoefer, M., Haubold, B., ...
Selection on human genes as revealed by comparisons to chimpanzee cDNA (2003)
Hellmann, Ines, Zöllner, Sebastian, Enard, Wolfgang, Ebersberger, Ingo, Nickel, Birgit, Pääbo, Svante
Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees (2003)
Gilad, Yoav, Bustamante, Carlos D., Lancet, Doron, Pääbo, Svante
Gene Diversity Patterns at 10 X-Chromosomal Loci in Humans and Chimpanzees (2003)
Kitano, Takashi, Schwarz, Carsten, Nickel, Birgit, Pääbo, Svante
Early Allelic Selection in Maize as Revealed by Ancient DNA (2003)
Jänicke-Després, Viviane, Buckler, Ed S., Smith, Bruce D., Gilbert, M. T., Cooper, Alan, Doebley, John, ...
Nuclear gene sequences from a late Pleistocene sloth coprolite (2003)
Poinar, Hendrik, Kuch, M., McDonald, G., Martin, P., Pääbo, Svante
Gene Diversity Patterns at Ten X-Chromosomal Loci in Humans and Chimpanzees (2003)
Kitano, Takashi, Schwarz, Carsten, Nickel, Birgit, Pääbo, Svante
We have investigated the pattern and extent of nucleotide diversity in 10 X-chromosomal genes where mutations are known to cause mental retardation in humans. For each gene, we sequenced the entire...
Motz, Michael, Sagner, Gregor, Pääbo, Svante, Kilger, Christian
Sequential DEXAS (direct exponential amplification and sequencing), a one step amplification and sequencing procedure that allows accurate, inexpensive and rapid DNA sequence determination directly...
Gene Diversity Patterns at 10 X-Chromosomal Loci in Humans and Chimpanzees (2003)
Kitano, Takashi, Schwarz, Carsten, Nickel, Birgit, Pääbo, Svante
We have investigated the pattern and extent of nucleotide diversity in 10 X-chromosomal genes where mutations are known to cause mental retardation in humans. For each gene, we sequenced the entire...
Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA (2003)
Hellmann, Ines, Zöllner, Sebastian, Enard, Wolfgang, Ebersberger, Ingo, Nickel, Birgit, Pääbo, Svante
To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from the chimpanzee and compared them to their human counterparts. In conjunction with...
Gene Diversity Patterns at Ten X-Chromosomal Loci in Humans and Chimpanzees (2003)
Kitano, Takashi, Schwarz, Carsten, Nickel, Birgit, Pääbo, Svante
We have investigated the pattern and extent of nucleotide diversity in 10 X-chromosomal genes where mutations are known to cause mental retardation in humans. For each gene, we sequenced the entire...
Chou, H. H., Hayakawa, T., Diaz, S., Krings, M., Indriati, E., Leakey, M., ...
Humans are genetically deficient in the common mammalian sialic acid N-glycolylneuraminic acid (Neu5Gc) because of an Alu- mediated inactivating mutation of the gene encoding the enzyme...
Hofreiter, Michael, Capelli, C., Krings, M., Waits, L., Conard, N., Munzel, S., ...
Cave bears (Ursus spelaeus) existed in Europe and western Asia until the end of the last glaciation some 10,000 years ago. To investigate the genetic diversity, population history, and relationship...
Schmitz, R. W., Serre, David, Bonani, G., Feine, S., Hillgruber, F., Krainitzki, H., ...
The 1856 discovery of the Neandertal type specimen (Neandertal 1) in western Germany marked the beginning of human paleontology and initiated the longest-standing debate in the discipline: the role...
Molecular evolution of FOXP2, a gene involved in speech and language (2002)
Enard, Wolfgang, Przeworski, Molly, Fisher, S. E., Lai, C. S. L., Wiebe, Victor, Kitano, T., ...
Language is a uniquely human trait likely to have been a prerequisite for the development of human culture. The ability to develop articulate speech relies on capabilities, such as fine control of...
Genomewide comparison of DNA sequences between humans and chimpanzees (2002)
Ebersberger, Ingo, Metzler, D., Schwarz, Carsten, Pääbo, Svante
A total of 8,859 DNA sequences encompassing similar to1.9 million base pairs of the chimpanzee genome were sequenced and compared to corresponding human DNA sequences. Although the average sequence...
Intra- and interspecific variation in primate gene expression patterns (2002)
Enard, Wolfgang, Khaitovich, Phillip, Klose, Joachim, Zöllner, Sebastian, Heissig, Florian, Giavalisco, P., ...
Although humans and their closest evolutionary relatives, the chimpanzees, are 98.7% identical in their genomic DNA sequences, they differ in many morphological, behavioral, and cognitive aspects....
Extensive linkage disequilibrium in small human populations in Eurasia (2002)
Kaessmann, Henrik, Zöllner, Sebastian, Gustafsson, A. C., Wiebe, Victor, Laan, M., Lundeberg, J., ...
The extent of linkage disequilibrium (LD) was studied in two small food-gathering populations-Evenki and Saami- and two larger food-producing populations-Finns and Swedes-in northern Eurasia. In...
The genetical history of humans and the great apes (2002)
Kaessmann, Henrik, Pääbo, Svante
When and where did modern humans evolve? How did our ancestors spread over the world? Traditionally, answers to questions such as these have been sought in historical, archaeological, and fossil...
Functional genomics in the chimpanzee (2002)
Enard, Wolfgang, Ebersberger, Ingo, Fischer, Anne, Heissig, Florian, Hellmann, Ines, Höffner, Barbara, ...
Die neue Taxonomy der Höhlenbären (2002)
Rabeder, G., Hofreiter, Michael, Nagel, D., Pääbo, Svante, Withalm, G.
Hofreiter, Michael, Capelli, Cristian, Krings, Matthias, Waits, Lisette, Conard, Nicholas, Münzel, Susanne, ...
Cave bears (Ursus spelaeus) existed in Europe and western Asia until the end of the last glaciation some 10,000 years ago. To investigate the genetic diversity, population history, and relationship...
A molecular phylogeny of two extinct sloths. (2001)
Greenwood, A. D., Castresana, J., Feldmaier-Fuchs, G., Pääbo, Svante
Great ape DNA sequences reveal a reduced diversity and an expansion in humans. (2001)
Kaessmann, Henrik, Wiebe, Victor, Weiss, Gunter, Pääbo, Svante
A molecular analysis of dietary diversity for three archaic Native Americans. (2001)
Poinar, Hendrick, Kuch, Melanie, Sobolik, K. D., Barnes, I., Stankiewicz, A. B., Kuder, T., ...
Decreased aminoacylation of mutant tRNAs in MELAS but not in MERRF patients. (2000)
Börner, G. V., Zeviani, M., Tiranti, V., Carrara, F., Hoffmann, S., Gerbitz, K. D., ...
Mitochondrial DNA sequences in prehistoric human remains from the Alps. (2000)
Di Benedetto, G., Nasidze, Ivan, Stenico, M., Nigro, L., Krings, M., Lanzinger, M., ...
Mitochondrial DNA sequences in prehistoric human remains from the Alps. (2000)
Di Benedetto, G., Nasidze, Ivan, Stenico, M., Nigro, L., Krings, M., Lanzinger, M., ...
A molecular analysis of ground sloth diet through the last glaciation. (2000)
Hofreiter, Michael, Poinar, Hendrik, Spaulding, W. G., Bauer, K., Martin, P. S., Possnert, G., ...
Mitochondrial genome variation and the origin of modern humans. (2000)
Ingman, M., Kaessmann, Henrik, Pääbo, Svante, Gyllensten, U.
A view of Neandertal genetic diversity. (2000)
Krings, M., Capelli, C., Tschentscher, F., Geisert, H., Meyer, Sonja, Haeseler, Arndt Von, ...
Decreased aminoacylation of mutant tRNAs in MELAS but not in MERRF patients (2000)
Börner, G. Valentin, Zeviani, Massimo, Tiranti, Valeria, Carrara, Franco, Hoffmann, Sabine, Gerbitz, Klaus Dieter, ...
Mutations in human mitochondrial tRNA genes are associated with a number of multisystemic disorders. Using an assay that combines tRNA oxidation and circularization we have determined the relative...
Erlandsson, Rikard, Wilson, James F., Pääbo, Svante
We sequenced the genomic region containing the human Y-linked zinc finger gene (ZFY). Comparison of ZFY to the related region on the X chromosome (ZFX) and to autosomal sequences reveals a...
DNA sequence variation in a non-coding region of low recombination on the human X chromosome (1999)
Kaessmann, Henrik, Heißig, Florian, Haeseler, Arndt Von, Pääbo, Svante
DNA Sequence of the Mitochondrial Hypervariable Region II from the Neandertal Type Specimen (1999)
Krings, Matthias, Geisert, Helga, Schmitz, Ralf W., Krainitzki, Heike, Pääbo, Svante
MtDNA Analysis of Nile River Valley Populations: A Genetic Corridor or aBarrier to Migration? (1999)
Krings, Matthias, Salem, Abd-el Halim, Bauer, Karin, Geisert, Helga, Malek, Adel K., Chaix, Louis, ...
Yokobori, Shin-ichi, Ueda, Takuya, Feldmaier-Fuchs, Gertraud, Pääbo, Svante, Kondow, Akiko, Nishikawa, Kazuya, ...
Cao, Ying, Janke, Axel, Waddell, Peter J., Westermann, Michael, Takenaka, Osamu, Murata, Shigenori, ...
Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis (1998)
Poinar, Hendrik N., Hofreiter, Michael, Spaulding, W. Geoffrey, Martin, Paul S., Stankiewicz, B. Artur, Bland, Helen, ...
Neandertal DNA Sequences and the Origin of Modern Humans (1997)
Krings, Matthias, Stone, Anne, Schmitz, Ralf W., Krainitzki, Heike, Stoneking, Mark, Pääbo, Svante
RNA editing in metazoan mitochondria: staying fit without sex (1997)
Börner, Valentin, Yokobori, Shin-Ichi, Mörl, Mario, Pääbo, Svante
Mörl, Mario, Dörner, Marion, Pääbo, Svante
In marsupial mitochondria, the nucleotide residue at the second position of the anticodon of the tRNA for aspartic acid is changed post-transcriptionally such that the translational machinery...
Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition (1993)
RNA editing has been described for organellar genes of protozoa and plants as well as in three cases for nuclear transcipts of mammals. The mitochondrial tRNA for aspartic acid is encoded in the...
Kocher, Thomas D., Thomas, W. Kelley, Meyer, Axel, Edwards, Scott V., Pääbo, Svante, Villablanca, Francis X., ...
With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including...
Mitochondrial DNA sequences from a 7000-year old brain (1988)
Pääbo, Svante, Gifford, John A., Wilson, Allan C.
Pieces of mitochondrial DNA from a 7000-year-old human brain were amplified by the polymerase chain reaction and sequenced. Albumin and high concentrations of polymerase were required to overcome a...
Codon reassignment and amino acid composition in hemichordate mitochondria
Castresana, Jose, Feldmaier-Fuchs, Gertraud, Pääbo, Svante
In the mitochondrial genome of the hemichordate Balanoglossus carnosus, the codon AAA, which is assigned to lysine in most metazoans but to asparagine in echinoderms, is absent. Furthermore, the...
DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen
Krings, Matthias, Geisert, Helga, Schmitz, Ralf W., Krainitzki, Heike, Pääbo, Svante
The DNA sequence of the second hypervariable region of the mitochondrial control region of the Neandertal type specimen, found in 1856 in central Europe, has been determined from 92 clones derived...
A molecular analysis of dietary diversity for three archaic Native Americans
Poinar, Hendrik N., Kuch, Melanie, Sobolik, Kristin D., Barnes, Ian, Stankiewicz, Artur B., Kuder, Tomasz, ...
DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans,...
Evidence for Import of a Lysyl-tRNA into Marsupial Mitochondria
Dörner, Marion, Altmann, Markus, Pääbo, Svante, Mörl, Mario
The mitochondrial tRNA gene for lysine was analyzed in 11 different marsupial mammals. Whereas its location is conserved when compared with other vertebrate mitochondrial genomes, its primary...
Hofreiter, Michael, Jaenicke, Viviane, Serre, David, Haeseler, Arndt Von, Pääbo, Svante
We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C→T and G→A substitutions. These...
Schmitz, Ralf W., Serre, David, Bonani, Georges, Feine, Susanne, Hillgruber, Felix, Krainitzki, Heike, ...
The 1856 discovery of the Neandertal type specimen (Neandertal 1) in western Germany marked the beginning of human paleontology and initiated the longest-standing debate in the discipline: the role...
Identification of Farnesoid X Receptor β as a Novel Mammalian Nuclear Receptor Sensing Lanosterol
Otte, Kerstin, Kranz, Harald, Kober, Ingo, Thompson, Paul, Hoefer, Michael, Haubold, Bernhard, ...
Nuclear receptors are ligand-modulated transcription factors. On the basis of the completed human genome sequence, this family was thought to contain 48 functional members. However, by mining human...
Human specific loss of olfactory receptor genes
Gilad, Yoav, Man, Orna, Pääbo, Svante, Lancet, Doron
Olfactory receptor (OR) genes constitute the basis for the sense of smell and are encoded by the largest mammalian gene superfamily of >1,000 genes. In humans, >60% of these are pseudogenes. In...
Sequential DEXAS: a method for obtaining DNA sequences from genomic DNA and blood in one reaction
Motz, Michael, Sagner, Gregor, Pääbo, Svante, Kilger, Christian
Sequential DEXAS (direct exponential amplification and sequencing), a one step amplification and sequencing procedure that allows accurate, inexpensive and rapid DNA sequence determination directly...
Gilad, Yoav, Wiebe, Victor, Przeworski, Molly, Lancet, Doron, Pääbo, Svante
Olfactory receptor (OR) genes constitute the molecular basis for the sense of smell and are encoded by the largest gene family in mammalian genomes. Previous studies suggested that the proportion of...
No Evidence of Neandertal mtDNA Contribution to Early Modern Humans
Serre, David, Langaney, André, Chech, Mario, Teschler-Nicola, Maria, Paunovic, Maja, Mennecier, Philippe, ...
The retrieval of mitochondrial DNA (mtDNA) sequences from four Neandertal fossils from Germany, Russia, and Croatia has demonstrated that these individuals carried closely related mtDNAs that are not...
A Neutral Model of Transcriptome Evolution
Khaitovich, Philipp, Weiss, Gunter, Lachmann, Michael, Hellmann, Ines, Enard, Wolfgang, Muetzel, Bjoern, ...
Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for...
Absence of the TAP2 Human Recombination Hotspot in Chimpanzees
Ptak, Susan E, Roeder, Amy D, Stephens, Matthew, Gilad, Yoav, Pääbo, Svante, Przeworski, Molly
Recent experiments using sperm typing have demonstrated that, in several regions of the human genome, recombination does not occur uniformly but instead is concentrated in “hotspots” of 1–2 kb....
Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA
Hellmann, Ines, Zöllner, Sebastian, Enard, Wolfgang, Ebersberger, Ingo, Nickel, Birgit, Pääbo, Svante
To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from the chimpanzee and compared them to their human counterparts. In conjunction with...
Regional Patterns of Gene Expression in Human and Chimpanzee Brains
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each...
Evidence for Gradients of Human Genetic Diversity Within and Among Continents
Genetic variation in humans is sometimes described as being discontinuous among continents or among groups of individuals, and by some this has been interpreted as genetic support for “races.” A...
Lack of phylogeography in European mammals before the last glaciation
Hofreiter, Michael, Serre, David, Rohland, Nadin, Rabeder, Gernot, Nagel, Doris, Conard, Nicholas, ...
In many extant animal and plant species in Europe and North America a correlation exists between the geographical location of individuals and the genetic relatedness of the mitochondrial (mt) DNA...
Yohn, Chris T, Jiang, Zhaoshi, McGrath, Sean D, Hayden, Karen E, Khaitovich, Philipp, Johnson, Matthew E, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
A late Neandertal femur from Les Rochers-de-Villeneuve, France
Beauval, Cédric, Maureille, Bruno, Lacrampe-Cuyaubère, François, Serre, David, Peressinotto, David, Bordes, Jean-Guillaume, ...
In 2002, a Neandertal partial femoral diaphysis was discovered at Les Rochers-de-Villeneuve (Vienne, France). Radiocarbon dated to ≈40,700 14C years before present, this specimen is one of the most...
Functional analysis of human and chimpanzee promoters
Heissig, Florian, Krause, Johannes, Bryk, Jaroslaw, Khaitovich, Philipp, Enard, Wolfgang, Pääbo, Svante
Twelve promoters of genes differentially expressed between humans and chimpanzees were tested for expression activity in culture cells. Seven promoters showed a significant difference in expression...
Aging and Gene Expression in the Primate Brain
Fraser, Hunter B, Khaitovich, Philipp, Plotkin, Joshua B, Pääbo, Svante, Eisen, Michael B
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Systematic analysis of gene expression in human brains before and after death
Franz, Henriette, Ullmann, Claudia, Becker, Albert, Ryan, Margaret, Bahn, Sabine, Arendt, Thomas, ...
Comparison of the gene expression profiles of pre- and post-mortem human brains suggests that post-mortem human brain samples are suitable for investigating general gene-expression patterns.
Laan, Maris, Wiebe, Victor, Khusnutdinova, Elza, Remm, Maido, Pääbo, Svante
Linkage disequilibrium structure is still unpredictable because the interplay of regional recombination rate and demographic history is poorly understood. We have compared the distribution of LD...
Why do human diversity levels vary at a megabase scale?
Hellmann, Ines, Prüfer, Kay, Ji, Hongkai, Zody, Michael C., Pääbo, Svante, Ptak, Susan E.
Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of...
Toward a Neutral Evolutionary Model of Gene Expression
Khaitovich, Philipp, Pääbo, Svante, Weiss, Gunter
We introduce a stochastic model that describes neutral changes of gene expression over evolutionary time as a compound Poisson process where evolutionary events cause changes of expression level...
Functionality of Intergenic Transcription: An Evolutionary Comparison
Khaitovich, Philipp, Kelso, Janet, Franz, Henriette, Visagie, Johann, Giger, Thomas, Joerchel, Sabrina, ...
Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression...
Codon reassignment and amino acid composition in hemichordate mitochondria
Castresana, Jose, Feldmaier-Fuchs, Gertraud, Pääbo, Svante
In the mitochondrial genome of the hemichordate Balanoglossus carnosus, the codon AAA, which is assigned to lysine in most metazoans but to asparagine in echinoderms, is absent. Furthermore, the...
DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen
Krings, Matthias, Geisert, Helga, Schmitz, Ralf W., Krainitzki, Heike, Pääbo, Svante
The DNA sequence of the second hypervariable region of the mitochondrial control region of the Neandertal type specimen, found in 1856 in central Europe, has been determined from 92 clones derived...
A molecular analysis of dietary diversity for three archaic Native Americans
Poinar, Hendrik N., Kuch, Melanie, Sobolik, Kristin D., Barnes, Ian, Stankiewicz, Artur B., Kuder, Tomasz, ...
DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans,...
Evidence for Import of a Lysyl-tRNA into Marsupial Mitochondria
Dörner, Marion, Altmann, Markus, Pääbo, Svante, Mörl, Mario
The mitochondrial tRNA gene for lysine was analyzed in 11 different marsupial mammals. Whereas its location is conserved when compared with other vertebrate mitochondrial genomes, its primary...
Hofreiter, Michael, Jaenicke, Viviane, Serre, David, Haeseler, Arndt Von, Pääbo, Svante
We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C→T and G→A substitutions. These...
Schmitz, Ralf W., Serre, David, Bonani, Georges, Feine, Susanne, Hillgruber, Felix, Krainitzki, Heike, ...
The 1856 discovery of the Neandertal type specimen (Neandertal 1) in western Germany marked the beginning of human paleontology and initiated the longest-standing debate in the discipline: the role...
Identification of Farnesoid X Receptor β as a Novel Mammalian Nuclear Receptor Sensing Lanosterol
Otte, Kerstin, Kranz, Harald, Kober, Ingo, Thompson, Paul, Hoefer, Michael, Haubold, Bernhard, ...
Nuclear receptors are ligand-modulated transcription factors. On the basis of the completed human genome sequence, this family was thought to contain 48 functional members. However, by mining human...
Human specific loss of olfactory receptor genes
Gilad, Yoav, Man, Orna, Pääbo, Svante, Lancet, Doron
Olfactory receptor (OR) genes constitute the basis for the sense of smell and are encoded by the largest mammalian gene superfamily of >1,000 genes. In humans, >60% of these are pseudogenes. In...
Sequential DEXAS: a method for obtaining DNA sequences from genomic DNA and blood in one reaction
Motz, Michael, Sagner, Gregor, Pääbo, Svante, Kilger, Christian
Sequential DEXAS (direct exponential amplification and sequencing), a one step amplification and sequencing procedure that allows accurate, inexpensive and rapid DNA sequence determination directly...
Gilad, Yoav, Wiebe, Victor, Przeworski, Molly, Lancet, Doron, Pääbo, Svante
Olfactory receptor (OR) genes constitute the molecular basis for the sense of smell and are encoded by the largest gene family in mammalian genomes. Previous studies suggested that the proportion of...
No Evidence of Neandertal mtDNA Contribution to Early Modern Humans
Serre, David, Langaney, André, Chech, Mario, Teschler-Nicola, Maria, Paunovic, Maja, Mennecier, Philippe, ...
The retrieval of mitochondrial DNA (mtDNA) sequences from four Neandertal fossils from Germany, Russia, and Croatia has demonstrated that these individuals carried closely related mtDNAs that are not...
Genomewide Comparison of DNA Sequences between Humans and Chimpanzees
Ebersberger, Ingo, Metzler, Dirk, Schwarz, Carsten, Pääbo, Svante
A total of 8,859 DNA sequences encompassing ∼1.9 million base pairs of the chimpanzee genome were sequenced and compared to corresponding human DNA sequences. Although the average sequence...
Extensive Linkage Disequilibrium in Small Human Populations in Eurasia
Kaessmann, Henrik, Zöllner, Sebastian, Gustafsson, Anna C., Wiebe, Victor, Laan, Maris, Lundeberg, Joakim, ...
The extent of linkage disequilibrium (LD) was studied in two small food-gathering populations—Evenki and Saami—and two larger food-producing populations—Finns and Swedes—in northern Eurasia....
A Neutral Model of Transcriptome Evolution
Khaitovich, Philipp, Weiss, Gunter, Lachmann, Michael, Hellmann, Ines, Enard, Wolfgang, Muetzel, Bjoern, ...
Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for...
Absence of the TAP2 Human Recombination Hotspot in Chimpanzees
Ptak, Susan E, Roeder, Amy D, Stephens, Matthew, Gilad, Yoav, Pääbo, Svante, Przeworski, Molly
Recent experiments using sperm typing have demonstrated that, in several regions of the human genome, recombination does not occur uniformly but instead is concentrated in “hotspots” of 1–2 kb....
Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA
Hellmann, Ines, Zöllner, Sebastian, Enard, Wolfgang, Ebersberger, Ingo, Nickel, Birgit, Pääbo, Svante
To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from the chimpanzee and compared them to their human counterparts. In conjunction with...
Regional Patterns of Gene Expression in Human and Chimpanzee Brains
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each...
Evidence for Gradients of Human Genetic Diversity Within and Among Continents
Genetic variation in humans is sometimes described as being discontinuous among continents or among groups of individuals, and by some this has been interpreted as genetic support for “races.” A...
Lack of phylogeography in European mammals before the last glaciation
Hofreiter, Michael, Serre, David, Rohland, Nadin, Rabeder, Gernot, Nagel, Doris, Conard, Nicholas, ...
In many extant animal and plant species in Europe and North America a correlation exists between the geographical location of individuals and the genetic relatedness of the mitochondrial (mt) DNA...
Yohn, Chris T, Jiang, Zhaoshi, McGrath, Sean D, Hayden, Karen E, Khaitovich, Philipp, Johnson, Matthew E, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
A late Neandertal femur from Les Rochers-de-Villeneuve, France
Beauval, Cédric, Maureille, Bruno, Lacrampe-Cuyaubère, François, Serre, David, Peressinotto, David, Bordes, Jean-Guillaume, ...
In 2002, a Neandertal partial femoral diaphysis was discovered at Les Rochers-de-Villeneuve (Vienne, France). Radiocarbon dated to ≈40,700 14C years before present, this specimen is one of the most...
Functional analysis of human and chimpanzee promoters
Heissig, Florian, Krause, Johannes, Bryk, Jaroslaw, Khaitovich, Philipp, Enard, Wolfgang, Pääbo, Svante
Twelve promoters of genes differentially expressed between humans and chimpanzees were tested for expression activity in culture cells. Seven promoters showed a significant difference in expression...
A Neutral Explanation for the Correlation of Diversity with Recombination Rates in Humans
Hellmann, Ines, Ebersberger, Ingo, Ptak, Susan E., Pääbo, Svante, Przeworski, Molly
One of the most striking findings to emerge from the study of genomic patterns of variation is that regions with lower recombination rates tend to have lower levels of intraspecific diversity but not...
Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees
Gilad, Yoav, Bustamante, Carlos D., Lancet, Doron, Pääbo, Svante
The olfactory receptor (OR) genes constitute the largest gene family in mammalian genomes. Humans have >1,000 OR genes, of which only ∼40% have an intact coding region and are therefore putatively...
Aging and Gene Expression in the Primate Brain
Fraser, Hunter B, Khaitovich, Philipp, Plotkin, Joshua B, Pääbo, Svante, Eisen, Michael B
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Why do human diversity levels vary at a megabase scale?
Hellmann, Ines, Prüfer, Kay, Ji, Hongkai, Zody, Michael C., Pääbo, Svante, Ptak, Susan E.
Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of...
Systematic analysis of gene expression in human brains before and after death
Franz, Henriette, Ullmann, Claudia, Becker, Albert, Ryan, Margaret, Bahn, Sabine, Arendt, Thomas, ...
Comparison of the gene expression profiles of pre- and post-mortem human brains suggests that post-mortem human brain samples are suitable for investigating general gene-expression patterns.
Toward a Neutral Evolutionary Model of Gene Expression
Khaitovich, Philipp, Pääbo, Svante, Weiss, Gunter
We introduce a stochastic model that describes neutral changes of gene expression over evolutionary time as a compound Poisson process where evolutionary events cause changes of expression level...
Functionality of Intergenic Transcription: An Evolutionary Comparison
Khaitovich, Philipp, Kelso, Janet, Franz, Henriette, Visagie, Johann, Giger, Thomas, Joerchel, Sabrina, ...
Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression...
Aspm specifically maintains symmetric proliferative divisions of neuroepithelial cells
Fish, Jennifer L., Kosodo, Yoichi, Enard, Wolfgang, Pääbo, Svante, Huttner, Wieland B.
The ASPM (abnormal spindle-like microcephaly-associated) protein has previously been implicated in the determination of human cerebral cortical size, but the cell biological basis of this regulation...
Comparison of Protein and mRNA Expression Evolution in Humans and Chimpanzees
Fu, Ning, Drinnenberg, Ines, Kelso, Janet, Wu, Jia-Rui, Pääbo, Svante, Zeng, Rong, ...
Even though mRNA expression levels are commonly used as a proxy for estimating functional differences that occur at the protein level, the relation between mRNA and protein expression is not well...
FUNC: a package for detecting significant associations between gene sets and ontological annotations
Prüfer, Kay, Muetzel, Bjoern, Do, Hong-Hai, Weiss, Gunter, Khaitovich, Philipp, Rahm, Erhard, ...
The Joint Allele-Frequency Spectrum in Closely Related Species
Chen, Hua, Green, Richard E., Pääbo, Svante, Slatkin, Montgomery
We develop the theory for computing the joint frequency spectra of alleles in two closely related species. We allow for arbitrary population growth in both species after they had a common ancestor....
Human and Chimpanzee Gene Expression Differences Replicated in Mice Fed Different Diets
Somel, Mehmet, Creely, Hilliary, Franz, Henriette, Mueller, Uwe, Lachmann, Michael, Khaitovich, Philipp, ...
Although the human diet is markedly different from the diets of closely related primate species, the influence of diet on phenotypic and genetic differences between humans and other primates is...
Meyer, Matthias, Briggs, Adrian W., Maricic, Tomislav, Höber, Barbara, Höffner, Barbara, Krause, Johannes, ...
Current efforts to recover the Neandertal and mammoth genomes by 454 DNA sequencing demonstrate the sensitivity of this technology. However, routine 454 sequencing applications still require...
Patterns of damage in genomic DNA sequences from a Neandertal
Briggs, Adrian W., Stenzel, Udo, Johnson, Philip L. F., Green, Richard E., Kelso, Janet, Prüfer, Kay, ...
High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a...
Krause, Johannes, Unger, Tina, Noçon, Aline, Malaspinas, Anna-Sapfo, Kolokotronis, Sergios-Orestis, Stiller, Mathias, ...
Metabolic changes in schizophrenia and human brain evolution
Khaitovich, Philipp, Lockstone, Helen E, Wayland, Matthew T, Tsang, Tsz M, Jayatilaka, Samantha D, Guo, Arfu J, ...
Human cognitive evolution involved genes implicated in energy metabolism and energy-expensive brain functions that are also altered in schizophrenia, suggesting that human brains may have reached...
Transcriptional neoteny in the human brain
Somel, Mehmet, Franz, Henriette, Yan, Zheng, Lorenc, Anna, Guo, Song, Giger, Thomas, ...
In development, timing is of the utmost importance, and the timing of developmental processes often changes as organisms evolve. In human evolution, developmental retardation, or neoteny, has been...
Genetic Architecture of Tameness in a Rat Model of Animal Domestication
Albert, Frank W., Carlborg, Örjan, Plyusnina, Irina, Besnier, Francois, Hedwig, Daniela, Lautenschläger, Susann, ...
A common feature of domestic animals is tameness—i.e., they tolerate and are unafraid of human presence and handling. To gain insight into the genetic basis of tameness and aggression, we studied...
The Neandertal genome and ancient DNA authenticity
Green, Richard E, Briggs, Adrian W, Krause, Johannes, Prüfer, Kay, Burbano, Hernán A, Siebauer, Michael, ...
Recent advances in high-thoughput DNA sequencing have made genome-scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the...