Showing papers by "Kay Prüfer published in 2016"

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

Abstract: A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.

Natural Selection in the Great Apes.

Abstract: Natural selection is crucial for the adaptation of populations to their environments Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies) Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population size Thus, even the modest differences in population size among the closely related Hominidae lineages have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments Most signatures of balancing and positive selection are species-specific, with signatures of balancing selection more often being shared among species We also identify loci with evidence of positive selection across several lineages Notably, we detect signatures of positive selection in several genes related to brain function, anatomy, diet and immune processes Our results contribute to a better understanding of human evolution by putting the evidence of natural selection in humans within its larger evolutionary context The global map of natural selection in our closest living relatives is available as an interactive browser at http://tinyurlcom/nf8qmzh

ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain

Abstract: We present ABAEnrichment, an R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas. We validate ABAEnrichment by successfully recovering the origin of gene sets identified in specific brain cell-types and developmental stages. AVAILABILITY AND IMPLEMENTATION ABAEnrichment was implemented as an R package and is available under GPL (≥ 2) from the Bioconductor website (http://bioconductor.org/packages/3.3/bioc/html/ABAEnrichment.html). CONTACTS steffi_grote@eva.mpg.de, kelso@eva.mpg.de or michael_dannemann@eva.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.

Detecting ancient positive selection in humans using extended lineage sorting

Abstract: Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 genomes dataset, we find evidence for ancient selective sweeps favoring regulatory changes in the brain and present a list of genomic regions that are predicted to underlie positively selected human specific traits.