Australia: The Land Where Time Began

A biography of the Australian continent 

Neanderthal from Chagyrskaya Cave – a High-Coverage Genome

The genome of a Neanderthal from Chagyrskaya Cave in the Altai Mountains, Russia, was sequenced by Mafessoni et al. (2020) to 27-fold genomic coverage. It was shown by the results of this study that female Neanderthal was more closely related to Neanderthals from western Eurasia Prüfer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018) than to Neanderthals who lived earlier in Denisova Cave [Prüfer et al., Nature 505, 43-49 (2014), which is located about 100 km from Denisova Cave. Homozygous regions between 2.5 and 10 centiMorgans (cM) long span about 12.9% of the Chagyrskaya genome. According to Mafessoni et al., this is consistent with the fact that in Siberia Neanderthals lived in populations that were relatively isolated of 60 individuals. Contrasting with this, a Neanderthal from Europe, a Denisovan from the Altai Mountains and ancient modern humans seem to have lived in larger populations. A view of genetic features that were unique to Neanderthals and that are likely to have been at high frequency among them has been allowed by the availability of 3 Neanderthal genomes that were of high quality. Mafessoni et al. found that genes that were highly expressed in the striatum in the basal ganglia of the brain carry more amino acid-changing substitutions than genes that were expressed elsewhere in the brain, which suggests that in Neanderthals the striatum may have evolved unique functions.

Evolutionarily, Neanderthals and Denisovans are the closest relatives of humans of the present. It was shown by analysis of their genomes that they contributed to people of the present outside sub-Saharan Africa. To date, however, there are only 2 Neanderthal and 1 Denisovan genomes that have been sequenced to high quality. Of these Neanderthal genomes (Vindija 33.19) was recovered from an individual that was found in Vindija Cave in Croatia (Prüfer et al., 2014), whereas the other Neanderthal genome (Denisova 5, or “Altai Neanderthal”) (Green et al., 2010) and the Denisovan genome (Denisova 3) (Reich et al., 2010) both are from specimens that were recovered from Denisova Cave, in the Altai Mountains in Siberia.

Additional insights into Neanderthal history have been yielded by a number of archaic genomes of moderate quality (1 to 3-fold genomic coverage). Genome sequences from 5 late Neanderthals from Europe have shown that that they carried little genome variation (Mayer et al., 2012; Prüfer, snpAD) and were related more closely to the Vindija 33.19 than to the Denisova 5 Neanderthal. A genome sequence that was from a bone that was morphologically undiagnostic from Denisova Cave, Denisova 11, was from a direct offspring from a Neanderthal mother and a Denisovan father (Slon et al., 2018), which indicated that the 2 groups met in the Altai region. The Neanderthal mother of Denisova 11 was related more closely to Vindija 33.19 than to Denisova 5, which indicates that a replacement of Neanderthal populations in the Altai Mountains occurred (Slon et al., 2018).

In this paper Mafessoni et al. present a high coverage genome sequence of a Neanderthal from Chagyrskaya Cave that is 106 km west of Denisova Cave (Rudaya et al., 2017; Kolobova et al., 2020; Kolobova et al., 2019; Roberts, Jacob & Li, 2018). Insights into the population structure and history of Neanderthals and allows identification of genome features that are unique to Neanderthals.

Modern day non-African humans carry ~2% (Prüfer et al., 2016; Hajdinjak, 2018) Neanderthal ancestry resulting from gene flow from Neanderthals that took place between 50 and 90 Ka (Prüfer et al., 2017; Sankararaman et al., 2012).

Relationship with modern humans

Chagyrskaya 8 shares more alleles, genomewide, non-African humans of the present than does Denisova 5, a similar proportion of alleles as Vindija 33.19. If the analysis was restricted to Neanderthal haplotypes that were detected previously introgressed into humans of the present (Skov et al., 2018), however, or to derived alleles that occur at low frequencies in nun-African populations and that therefore are more likely to be introgressed from Neanderthals, Vindija 33.19 share more alleles with populations of the present than does Chagyrskaya 8. Vindija 33.19 is related more closely than Chagyrskaya 8 to populations of Neanderthals that contributed the majority of DNA to populations of the present.

In order to test if any populations of modern humans carry an additional contribution from Neanderthals that are related more closely to Chagyrskaya 8  than to Vindija 33.19, Mafessoni et al. used haplotypes that had been published previously that were inferred to come from Neanderthals that are presently found exclusively in East Asia, Europe, India or Oceania. Among 300 genomes from the Simons Genome Diversity Panel (Mallick et al., 2016) and 89 Papuan genomes (Vernot et al., 2016; Malaspinas et al., 2016), the proportions of alleles that were shared with Chagyrskaya 8 and with Vindija 33.19 contributed to the populations that were tested. Therefore they concluded that within the limits of the resolution of these analyses populations of Neanderthals contributed to the genomes of different populations of modern humans in different proportions (Vernot & Akey, 2015; Villanea & Schraiber, 2019), these Neanderthal populations were similarly related to Chagyrskaya 8 and Vindija.

Small population size and inbreeding

Denisova 5, the Neanderthal genome that was recovered from Denisova Cave, carries a high proportion of long tracts that are homozygous by descent (HBD tracts) (Green et al., 2010). Tracts between 2.5 cM and 10 cM indicate that the population from which Denisova 5 comes was of small size over ~100 generations before the individual lived (S1 Appendix 8), whereas tracts that are more than 10 cM long indicate that the parents of Denisova 5 were closely related.

The Chagyrskaya 8 genome carries fewer HBD tacts that are longer than 10 cM compared to Denisova 5, but more HBD tracts of intermediate length (SI Appendix 8). In fact, all 3 high-coverage genomes of Neanderthals that are available carry more HBD tracts of intermediate size than almost all present day and prehistoric modern human genomes, as well as the Denisovan genome (Denisova 3). It has been shown by Mafessoni et al. by coalescent simulations that this cannot be explained by an overall small though panmictic population. It suggests, rather, the populations of Neanderthals were subdivided (SI Appendix 8). They infer by coalescent modelling that Chagyrskaya 8 and Denisova 5 may have lived in subpopulations of 60 or fewer individuals. Contrasting with this, current and past modern human populations as well as Denisovans (Based on the genome of Denisova 3) lived in subpopulations of more than 100 individuals, if it is assumed there was a migration rate between populations of 1% or less. According to Mafessoni et al. it is interesting the Vindija 33.19 seems to have lived in a subpopulation of larger size than the 2 Siberian Neanderthals, though this difference is only marginally statistically significant when the proportion of the genomes that are covered by all HBD tracts that are longer than 25 cM is considered (likelihood-ratio test, P = 0.05).

Derived genomic features in Neanderthals

Mafessoni et al. identified, by the use of the 3 high-coverage Neanderthal genomes, biological pathways where protein-coding genes showed more derived nonsynonymous substitutions fixed in the 3 Neanderthals than was expected from the polymorphic and silent changes. They identified 993 substitutions that were nonsynonymous among 899 genes, and 2,952 nonsynonymous substitutions in the 3 Neanderthals. No groups of genes that are associated with known biological functions or phenotypes (Köhler et al., 2014) show a higher ratio of nonsynonymous to synonymous fixed changes relative to the ratio of nonsynonymous to synonymous polymorphic changes (MacDonald-Kreitman ratio) (McDonald & Kreitman, 1991), compared to other groups of genes (family-wise error rate > 0.1) (Prüfer et al., 2007).

Mafessoni et al. found, however, that genes that were expressed in the striatum in individuals that were 12 – 19 yr of age show a higher MacDonald-Kreitman ratio (1.02, familywise error rate = 0.029) than genes that were expressed in other regions of the brain and at other ages (0.53-0.83), when they analysed genes that were expressed preferentially in different regions of the brain according to the Allen Bain Atlas (Grot, Prüfer, Kelso & Dannemann, 2016; Hawrylycz et al., 2012). It may be indicated by this that negative selection in genes that are expressed in the striatum was relaxed in Neanderthals. Some of the proteins that are encoded by these genes might have, alternatively, been the target of positive selection. Also, genes that are expressed in the prenatal striatum carry more substitutions in their regions that are untranslated than genes that are expressed elsewhere (familywise error rate = 0.049) and at other times. Among genes that are expressed in the striatum, those that carry fixed nonsynonymous changes in Neanderthals and present more often in genomic regions that carry little or no DNA that is introgressed from Neanderthals than striatal genes that do not carry such changes (Fisher’s exact test P = 0.026). This pattern in not observed for all genes that carry fixed nonsynonymous substitutions in Neanderthals (P>0.1), which suggests that in Neanderthal striatal genes there are some substitutions might have been negatively selected in modern humans. As well as in the striatum, genes that are expressed prenatally in the posterior parietal cortex, in the ventrolateral prefrontal cortex, and in the primary somatosensory cortex carry more fixed substitutions in their regulatory regions in Neanderthals than genes that are expressed in other regions of the brain and at other times.

Mafessoni et al. performed the Hudson, Kreitman, Aguadé (HKA) test (Hudson, Kreitman and Aguadé, 1987), and the population branch statistic (PBS) (Yi et al., 2010) in 25-kb sliding windows across the genome, in a further attempt to detect positive selection along the Neanderthal lineage. They estimated the probability of obtaining the observed values of the different statistics by coalescence simulations, and retained windows that had a false discovery rate of <5%. They identified a total of 35 separate candidate regions on the autosomes. Of these candidate regions, they identified by PBS a region that was 75 kb long on chromosome 5 that overlaps 2 separate windows that were identified by HKA. This overlap is lower than it would have been expected to have been by chance (P value <4 x 10^-4 and SI Appendix 10). The candidate regions that were identified overlap genes that are involved in neural development (EXOC6B), immunity, and wound healing (HTN1, EVPLL) and mitochondrial functions (NSUN3, TIMM20). They found that for both statistics there was an overlap with genomic regions that had been identified previously as being positively selected in modern humans (Peyrégne, Boyle, Dannemann & Prüfer, 2017) (enrichment test, P values = 0.010 and 0.056) for HKA and PBS, respectively).

Discussion

Chagyrskaya 8 is related more closely to Vindija 33.19 and other late Neanderthals in western Eurasia than to the Denisova 5 Neanderthal who lived in the Altai Mountains at an earlier time. Therefore Chagyrskaya 8 is related to populations of Neanderthals that moved east at some time between 120 and 80 Ka (Peyrégne et al., 2019). It is interesting that the artefacts that were found at Chagyrskaya Cave display similarities to artefact assemblages in central and eastern Europe (Kolobova et al., 2020), which suggests that Neanderthal populations that moved from Eurasia to Siberia may have brought their material culture with them (Kolobova et al., 2020; Derevianko et al., 2018). Local populations of Denisovans were encountered by the incoming Neanderthals, as is shown by Denisova 11, who had a Denisovan father and a Neanderthal mother who was related to the population in which the Chagyrskaya 8 lived.

It is interesting in this regard that Chagyrskaya 8 and Denisova 5 lived in smaller populations than the Vindija 33.19 Neanderthal in Croatia, the Denisovan Denisova 3 and modern humans (Sikora et al., 2017). The Altai region was on the periphery of the geographical distribution of Neanderthals and it was suggested that this may have been the reason that the Neanderthals in the Altai region lived in smaller and more isolated populations and may have been an area where Denisovans may have been present more continuously. Mafessoni et al. suggest more detailed studies of the population history of Denisova Cave will be necessary to clarify this.

The number of changes that were expressed in the striatum during adolescence stands out when analysing genetic changes on the Neanderthal lineage using the 3 Neanderthal genomes. There is a possibility that these changes accumulated in the Neanderthals as a result of the small size of their populations, perhaps in combination with a relaxation of selection on genes expressed in the striatum. Genes that are expressed in the striatum overlap more frequently than expected in genomic regions where Neanderthal introgressed fragments in modern genomes are rare. It is speculated by Mafessoni et al. that the       striatal genes may carry changes that are Neanderthal-specific that were disadvantageous when introduced into modern humans. As well as positive selection for changes in the modern lineage, this may underlie so-called Neanderthal deserts in genomes of modern human genomes, i.e., regions that are depleted in Neanderthal ancestry     (Vernot et al., 2016; Sankararaman et al., 2014).

According to Mafessoni et al. it will become possible to explore genes and groups of genes that carried functionally relevant changes in Neanderthals more comprehensively as more high-quality Neanderthal genomes become available. There is currently suggestive evidence that such findings may be forthcoming. E.g., as well as genes that are expressed in the striatum, regions that are untranslated and promoters of genes that are expressed in posteroventral (inferior) parietal cortex, a region of the brain that has been associated with speech and mathematical cognition (Wu et al., 2009), carry more changes in the 3 Neanderthals than would be expected by chance. Also, among the top phenotypes that are associated with changes in the regulatory regions in Neanderthals that are abnormalities in parts of the skeleton where Neanderthal morphology stand out, such as the nasal bridge and the rib cage (e.g., Weaver, 2009).

Mafessoni, F., et al. (2020). "A high-coverage Neandertal genome from Chagyrskaya Cave." Proceedings of the National Academy of Sciences 117(26): 15132-15136.