A high-coverage Neandertal genome from Vindija Cave in Croatia

Abstract

To date the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50 thousand years ago from Vindija Cave, Croatia to ~30-fold genomic coverage. She carried 1.6 differences per ten thousand base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10-20% more Neandertal DNA to be identified in present-day humans, including variants involved in LDL cholesterol levels, schizophrenia and other diseases.

Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture

“…In individual populations, coverage ranges from 382 Mb in Peruvians (PEL) to 655 Mb in Bengalis (BEB), and the average proportion of haplotypes carrying a detected segment at a position ranges from 0.80% in Puerto Ricans (PUR) to 1.23% in Han Chinese (CHB and CHS) (Figure 3). These detection rates are around half of the estimated introgression proportions obtained using f 4 -ratio statistics (Prufer et al, 2017). This is in line with the simulation results, in which half the introgressed material can be detected, while the other introgressed segments are too short for confident detection.…”

“…High coverage reference genomes for the Altai Neanderthal, Altai Denisovan and Vindija 33.19 Neanderthal (Prufer et al, 2017) were obtained from http://cdna.eva.mpg.de/neandertal/Vindija/. Most of the analyses in this study were conducted prior to the publication of the Vindija 33.19 genome, and hence most Neanderthal-based analyses use the Altai Neanderthal rather than the Vindija 33.19 Neanderthal.…”

“…Most of the analyses in this study were conducted prior to the publication of the Vindija 33.19 genome, and hence most Neanderthal-based analyses use the Altai Neanderthal rather than the Vindija 33.19 Neanderthal. These three genomes have been called with snpAD, an ancient DNA damage-aware genotyper (Prufer et al, 2017). When comparing putative introgressed alleles with an archaic genome, we applied the masks provided with these data and downloaded from http://cdna.eva.mpg.de/neandertal/Vindija/FilterBed/ which filter sites with coverage depth below 10, or mapping quality below 25, or that are within tandem repeats or indels, or that have poor mappability (Li and Durbin, 2011).…”

No Evidence for Recent Selection at FOXP2 among Diverse Human Populations

“…In all cases save for rs115978361, the SNPs in the ROI are uniquely derived in humans as compared to other primates and archaic hominins, and are present in more than one individual in the 1000G and HGDP data (Table 2). No SNPs are present in the ROI in a sample of 10 chimpanzees (Auton et al, 2012) and no fixed substitutions are present compared to three archaic hominins (Meyer et al, 2012; Prüfer et al, 2014, 2017) across the entire 2251 bp region. There is one fully derived site in our human samples that is heterozygous in the Altai Neanderthal (chr7:114288583) and 9 fixed differences compared to the PanMap chimps (Table S1).…”

Something old, something borrowed: Admixture and adaptation in human evolution

“…A few years later, a high coverage genome sequence from a Neanderthal found in the Altai mountains allowed researchers to pin down the proportion of Neanderthal ancestry in non-Africans to be ~2% [4] . In 2017, a second high coverage genome sequence from a Neanderthal in Croatia showed that this individual was more closely related to the introgressing Neanderthal population than the Altai Neanderthal, allowing researchers to detect even slightly higher levels of Neanderthal DNA [5] . In 2018, low-coverage genomes of five additional Neanderthals living between 39,000 and 47,000 years ago allowed a first glimpse at population structure in Neanderthals and showed indications of population turnover in late Neanderthal history [6] .…”