Intro
How much % of Neanderthal DNA was found in the genomes of present-day people outside of Africa? (range)
1-4%
What is the type of genetic sequencing and analysis, performed on fossils, crucial for reconstructing Neanderthal genomes?
Ancient DNA sequencing and analysis
Which specific gene, encompassing a Neanderthal introgressed haplotype at high frequency in Europeans, is associated with skin pigmentation and freckling?
BNC2
What is the phenomenon by which some Neanderthal genetic variants, introduced into the modern human gene pool through interbreeding, increased in frequency due to this evolutionary process, ultimately aiding human survival in new environments?
Adaptive introgression
Fossil records, genomic predictions
What year was the first draft of the Neanderthal genome was published?
2010
What are the computational approaches, such as S* and the Conditional Random Field (CRF), developed to detect and map the traces of archaic DNA within modern human genomes, called?
Analytical framework
A Neanderthal-derived haplotype in this gene, involved in lipid metabolism in the liver, is a common risk factor for type 2 diabetes in Mexico.
SLC16A11
What is the hybrid incompatibilities known as and on which chromosome did these preferentially accumulate?
Dobzhansky-Muller incompatibilities (DMIs), X chromosome
What two methods are used to study both Neaderthal remains and live modern humans to map the gentic factors affecting skull shape?
Computated tomography (CT) and Magnetic resonance imaging (MRI)
Besides Neanderthals, what other archaic hominin group, discovered in a Siberian cave, also contributed to the genomes of modern humans, particularly in Oceania and East/Southeast Asia?
Denisovans
What are the large genomic regions, identified in modern human genomes, that show a significant depletion of Neanderthal ancestry?
Introgression deserts
Which part of the immune system are genes OAS1, 2, and 3 key components of and form a cluster showing evidence of Neanderthal adaptive introgression?
Innate immune system
Which bodily system is the introgression of Neanderthal alleles related to, particularly antiviral responses, highlighted as a key example of adaptive introgression?
Immunity
The advent of what kind of technology promises to massively expand the catalog of human structional variants?
Third-generation seuqencing technology
What is the approximate time range that Neanderthals likely admixed with modern human contemporaries, according to the first draft of the Neanderthal genome?
40-50 kya
What is the type of large-scale study that compares genotypes across the genome to phenotypes of interest to find associations, including those involving Neanderthal variants?
Genome-Wide Association Studies (GWAS)
Studies using MRI scans linked Neanderthal alleles to a reduction in which aspect of brain shape in modern humans?
Endocranial globularity
What is the evolutionary force that drove the removal of Neanderthal introgressed variation from introgession deserts?
Negative selection
What are some limitations of GWAS and PheWAS?
Individual genetic loci contributing to the phenotype need to have a fairly large effect in order to be detected; alleles contributing to the phenotype must be sufficiently common in the population for their effect to be detected; the effects of different genetic loci are often assumed to be independent.
What is the sequencing of the specific high-coverage Neanderthal genome, named after the cave where the specimen was found in Russia, that significantly catalyzed research into Neanderthal introgression called?
Altai Neanderthal genome
These direct experimental techniques allowed researchers to identify the causal roles of specific Neanderthal genetic variants on modern human traits by measuring the activity of gene regulatory elements or precisely altering the genome in model systems.
In vitro functional assays (Massively Parallel Reporter Assays (MPRAs) and CRISPER/Cas9-based genome engineering)
An early study suggested that the proportion of Neanderthal ancestry in ancient modern humans showed what kind of trend over time, although later research refined this finding?
Decreased linearity through time
What is a consequence of negative selection acting against Neanderthal introgressed alleles?
Neanderthal ancestry proportion would decrease over time.
Future research aims to further investigate introgression from these populations, beyond Neanderthals and Denisovans, often referred to as "ghost" lineages.
Other archaic hominins