The Strength of Selection against Neanderthal Introgression

Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought

Alzheimer's disease related genes during primate evolution

During primate evolution, the neuronal and cognition-related genes have evolved rapidly. These genes seem to induce neurological illnesses such as Alzheimer's disease (AD). In this study, we analyzed genes APOE, TOMM40, and PICALM known as the risk factors of AD. We performed bioinformatics analyses in relation to evolution, phylogeny, and protein structure for those genes in humans, Neanderthals, chimpanzees, bonobos, gorillas, orangutans, crab-eating monkeys, and rhesus monkeys. Cholesterol-related genes showed relatively rapid evolution toward a lower risk of AD. Neanderthals showed relatively higher polymorphism in genes APOE, TOMM40, and PICALM than humans did. Phylogeny indicated different topologies in the trichotomy of humans, chimpanzees, and gorillas in terms of genes APOE, TOMM40, and PICALM. These results provide to hominin-specific patterns in three genes, and give clues to the modern human-specific traits of AD and shed light on further functional research helping to understand AD

Evidence for archaic adaptive introgression in humans

As modern and ancient DNA sequence data from diverse human populations accumulate(1–4), evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments — a process, known as adaptive introgression (AI). Within the past couple of years, a series of studies(5–8) have identified genomic regions showing strong evidence for archaic adaptive introgression. In this Review, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans, and to determine whether positive selection has acted on these fragments. We discuss recently reported examples of adaptive introgression and consider the level of supporting evidence for each, grouped by selection pressure. We discuss challenges and recommendations for inferring selection on introgressed regions

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP-seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells required and increasing the resolution. Complementary experimental approaches – for example DNaseI hypersensitive site mapping and analysis of chromatin interactions mediated by particular proteins - provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins