Patterns of coding variation in the complete exomes of three Neandertals

Abstract

We present the DNA sequence of 17,367 protein-coding genes in two Neandertals from Spain and Croatia and analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia. Comparisons with present-day humans from Africa, Europe, and Asia reveal that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans. Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans. We also identify amino acid substitutions in Neandertals and present-day humans that may underlie phenotypic differences between the two groups. We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in behavior and pigmentation have changed more on the modern human lineage.ancient DNA | exome capture | site frequency spectra | paleogenetics A nalyses of the coding regions of multiple present-day human individuals have uncovered many amino acid-changing SNPs segregating at low frequency in present-day human populations (1-7). It also has been shown that Europeans carry a larger proportion than Africans of amino acid-changing SNPs inferred to alter the structure or function of proteins and thus to be potentially deleterious (4), a fact attributed to the bottleneck and subsequent expansion of human populations during and after the migration out of Africa (4). In contrast, little is known about the coding variation in Neandertals, an extinct hominin group closely related to presentday humans. The main reasons for this are the rarity of Neandertal remains and the fact that >99% of the DNA extracted from typical Neandertal bones is derived from microbes (8, 9), making shotgun sequencing of the endogenous DNA impractical.Here, we use a hybridization approach to enrich and sequence the protein-coding fractions of the genomes of two Neandertals from Spain and Croatia. We analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia (10) and show that the genetic diversity, pattern of coding variation, and genes that may underlie phenotypic changes in Neandertals are remarkably different from those in present-day humans. Results and DiscussionWe used densely tiled oligonucleotide probes (9) and a recently described protocol (11) to capture the protein-coding exons from 17,367 genes in a ∼49,000-y-old (12) (uncalibrated radiocarbon date) Neandertal from Spain (SD1253, El Sidrón Cave) and a ∼44,000-y-old (uncalibrated radiocarbon date) Neandertal from Croatia (Vi33.15, Vindija Cave). The DNA libraries from these two Neandertals contain 0.2% and 0.5% endogenous DNA, respectively, and the capture approach enriched the endogenous DNA 325-fold and 153-fold, resulting in an average coverage of 12.5-fold and 42.0-fold for the El Sidrón and Vindi...

Morphology and function of Neandertal and modern human ear ossicles

“…Here, Neandertals are consistently more derived than AMHs. This finding is concordant with genetic data that show that genes involved in skeletal morphology have changed more than previously thought in the line leading to Neandertals (57) and further adds to the distinctiveness of this archaic human species.…”

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

“…Using this approach, we confidently identify five proteins that contain a total of seven amino acid positions with nonsynonymous SNPs with both alleles at frequencies ≥1.0% in present-day humans (SI Appendix, Table S6). In six cases, we observed the ancestral Hominidae state in the proteome data, which is also present in Denisovan and Neandertal protein sequences (34). These include one position for which a majority of AMHs (93.5%) carry a derived substitution (COL28α1; dbSNP rs17177927) and where our data contain the ancestral position (amino acid P).…”

“…We used an error-tolerant search engine (PEAKS) against the human reference proteome and compared our protein sequence data against available amino acid sequence variations known through genomic research for modern humans (32), a Denisovan genome (33), and the coding regions of three Neandertals (34). Using this approach, we confidently identify five proteins that contain a total of seven amino acid positions with nonsynonymous SNPs with both alleles at frequencies ≥1.0% in present-day humans (SI Appendix, Table S6).…”

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

“…44 000 years ago for Vindija 33.15 and approx. 49 000 years ago for El Sidrón 1253), the homozygosity tracks longer than 200 kb almost double in about 5000 years [55]. In addition, the genetic differentiation among individuals is larger among Neanderthals than among present-day humans.…”

“…The recent advent of the high-coverage exomes of two Neanderthals, one from Vindija 33.15 (40X) in Croatia and the other from El Sidrón SD1253 in Spain (12X) [55] (figure 1), has allowed a start in addressing those subjects. Together with the exome regions of the Altai and the Denisovan genomes, the Neandertal exomes have been compared with the same regions from three modern individuals from Africa, Europe and Asia/Pacific.…”