Abnormalities in Pleistocene Homo

 

An excess of congenital defects is certainly compatible with high levels of inbreeding, and the publication of the Denisova genome clearly suggested "extremely low" genetic diversity in that Pleistocene human. It'll be interesting to see if more ancient DNA data will reveal high levels of inbreeding consistent with the abundance of genetic abnormalities evident in the anthropological record.

PLoS ONE 8(3): e59587. doi:10.1371/journal.pone.0059587
An Enlarged Parietal Foramen in the Late Archaic Xujiayao 11 Neurocranium from Northern China, and Rare Anomalies among Pleistocene Homo

Xiu-Jie Wu et al.

We report here a neurocranial abnormality previously undescribed in Pleistocene human fossils, an enlarged parietal foramen (EPF) in the early Late Pleistocene Xujiayao 11 parietal bones from the Xujiayao (Houjiayao) site, northern China. Xujiayao 11 is a pair of partial posteromedial parietal bones from an adult. It exhibits thick cranial vault bones, arachnoid granulations, a deviated posterior sagittal suture, and a unilateral (right) parietal lacuna with a posteriorly-directed and enlarged endocranial vascular sulcus. Differential diagnosis indicates that the perforation is a congenital defect, an enlarged parietal foramen, commonly associated with cerebral venous and cranial vault anomalies. It was not lethal given the individual’s age-at-death, but it may have been associated with secondary neurological deficiencies. The fossil constitutes the oldest evidence in human evolution of this very rare condition (a single enlarged parietal foramen). In combination with developmental and degenerative abnormalities in other Pleistocene human remains, it suggests demographic and survival patterns among Pleistocene Homo that led to an elevated frequency of conditions unknown or rare among recent humans.

Link

High-quality Neandertal genome online

The Max Planck institute has posted their high-coverage Neandertal genome on their site. The data can be downloaded from here. They had done the same with the high-quality Denisova genome, and it's great that they're making data available ahead of the official scientific publication, as this allows others to start using it much earlier.
From their site:

The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010.  The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).
DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.

It then appears that Neandertals occupied the same cave as the elusive Denisovans. When? I guess we'll have to wait to find out, but the preliminary genetic analysis shown on the figure (top-left) makes it clear that the "Altai" specimen marked in red which is the source of the high-coverage Neandertal genome does indeed group with other Neandertals, while Denisova is more related to Neandertals than to modern humans.
I've highlighted this before, but it bears repeating: divergence between Neandertals and Denisovans --who were in the same place (Denisova cave), perhaps some thousands of years apart-- seems to exceed that found between any two modern human groups which span the entire Earth.

Ancient DNA from Tianyuan Cave

Ancient DNA from Tianyuan Cave

Another new PNAS paper that hasn't yet appeared in the journal website. Still, from this description at ScienceNews this appears to be Very Important, as it pertains to a 40,000-year-old modern human, which, if I'm not mistaken is the oldest modern human tested so far:

Ancient DNA from cell nuclei and maternally inherited mitochondria indicates that this individual belonged to a population that eventually gave rise to many present-day Asians and Native Americans, says a team led by Qiaomei Fu and Svante Paabo, evolutionary geneticists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

The partial skeleton, unearthed in Tianyuan Cave near Beijing in 2003, carries roughly the same small proportions of Neandertal and Denisovan genes as living Asians do (SN: 8/25/12, p. 22), the scientists report online January 21 in the Proceedings of the National Academy of Sciences.

The Max Planck press release adds some information:

The genetic profile reveals that this early modern human was related to the ancestors of many present-day Asians and Native Americans but had already diverged genetically from the ancestors of present-day Europeans.

This is an important finding because some published demographic models had Europeans and East Eurasians diverging as recently as ~20 thousand years ago. It now appears that they did so already at around the time of the Upper Paleolithic revolution, when unambiguous evidence of modern humans across Eurasia exists.

UPDATE I: While we wait for this paper to appear on the PNAS website, it might be useful to wonder whether the Tianyuan sample might fall on the East Asian/Amerindian group or the more general "Ancestral South Indian" (ASI)/East Eurasian group.

According to current dating, haplogroup M itself is ~50 thousand years old, and most of the subclades therein coalesce to younger than 40ky times. It's possible that the Tianyuan sample dates from a period where ASI/East Asian differentiation had only just begun or was just about to begin.

The press release makes clear that Tianyuan was already "Asian" rather than generalized Eurasian, proving that East/West Eurasian differentiation had begun by ~40kya. It will be interesting to see whether it can be placed on a more specific "East Eurasian" group rather than a generalized "Asian" one.

UPDATE II: The paper is now online.

UPDATE III: From the paper:

Thus, it is related to the mtDNA that was ancestral to present-day haplogroup B (Fig. 1), which has been estimated to be around 50,000 y old (18) (50. 7 ka BP; 95% CI: 38.1–68.3 ka BP). We note that the age of the Tianyuan individual is compatible with this date.

So, it appears to be within macro-haplogroup N, with haplogroup B being, I think, a fairly unambiguously East Asian/Native American clade of the phylogeny. It will certainly be interesting to see how the much more successful -and younger- M subclades ended up dominating East Eurasia.

UPDATE IV: The TreeMix analysis clearly places Tianyuan within the Asian group, but does not resolve whether Papuans are an outgroup to East Asians/Tianyuan:

I guess that is expected (see my UPDATE I), since Tianyuan dates from a period where within-Asia differentiation had only just begun or was about to begin.

UPDATE V: With respect to sharing of alleles with archaic Eurasian hominins, the Tianyuan sample is within the modern range of variation.

PNAS doi: 10.1073/pnas.1221359110

DNA analysis of an early modern human from Tianyuan Cave, China

Qiaomei Fu et al.

Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (~30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.

Link

Mating between Modern Humans, Neanderthals and other Archaics (Waddell & Tan 2012)

Mating between Modern Humans, Neanderthals and other Archaics (Waddell & Tan 2012)

arXiv:1212.6820 [q-bio.GN]

New g%AIC, g%AICc, g%BIC, and Power Divergence Fit Statistics Expose Mating between Modern Humans, Neanderthals and other Archaics

Peter J. Waddell, Xi Tan

The purpose of this article is to look at how information criteria, such as AIC and BIC, relate to the g%SD fit criterion derived in Waddell et al. (2007, 2010a). The g%SD criterion measures the fit of data to model based on a normalized weighted root mean square percentage deviation between the observed data and model estimates of the data, with g%SD = 0 being a perfectly fitting model. However, this criterion may not be adjusting for the number of parameters in the model comprehensively. Thus, its relationship to more traditional measures for maximizing useful information in a model, including AIC and BIC, are examined. This results in an extended set of fit criteria including g%AIC and g%BIC. Further, a broader range of asymptotically most powerful fit criteria of the power divergence family, which includes maximum likelihood (or minimum G^2) and minimum X^2 modeling as special cases, are used to replace the sum of squares fit criterion within the g%SD criterion. Results are illustrated with a set of genetic distances looking particularly at a range of Jewish populations, plus a genomic data set that looks at how Neanderthals and Denisovans are related to each other and modern humans. Evidence that Homo erectus may have left a significant fraction of its genome within the Denisovan is shown to persist with the new modeling criteria.

Link

Introgression of archaic haplotype at OAS1 in Melanesians (Mendez et al. 2012)

Introgression of archaic haplotype at OAS1 in Melanesians (Mendez et al. 2012)

It seems that Michael Hammer was good on his promise that in 2012 "This year, we should be able to confirm what we found and go way beyond that."  In a new paper, conclusive evidence is presented about introgression of an archaic sequence into Melanesian populations. The argument is as follows:

• Melanesians are more diverse in that region than Africans.
• The common ancestor of the "archaic" and "African" haplotypes lived >3 million years ago.
• The "archaic" haplotype matches the ancient DNA from the Denisova hominin.
• Balancing selection (which can sometimes maintain extremely old polymorphism) is not reasonable in this case, because it would need to maintain both "archaic" and "African" haplotypes for a long time, but then (inexplicably) would continue to operate in Melanesia and cease to operate everywhere else.

Notice that once again, this is based on resequencing a small region of the genome. This is why I am all the more confident in my prediction that the advent of full genome sequencing will uncover more archaic admixture in humans. It may not always be able to use all the above listed criteria to confirm this admixture (since we do not and cannot have ancient DNA from all the archaic hominins that once roamed the planet), but all the remaining ones will suffice to make a very good case for introgression.

What I find particularly interesting, is that Mendez et al. re-iterate a few times that genomewide averages admit to different explanations:

Full genome comparisons of the Neandertal and Denisova draft genomes with modern human sequences have revealed different amounts of shared ancestry between each of these archaic forms and anatomically modern human (AMH) populations from different geographic regions. For example, a higher proportion of SNPs was shared between non-African and Neandertal, and between Melanesian and the Denisova genomes, than between either Neandertal or Denisova and extant African genomes (Green et al. 2010; Reich et al. 2010). An intriguing possibility is that these patterns result from introgression of archaic genes into AMH populations in Eurasia. However, this SNP sharing pattern could also be explained by ancestral population structure in Africa (i.e., without the need to posit introgression). For example, if non-Africans and the ancestors of Neandertals descend from the same deme in a subdivided African population, and this structure persisted with low levels of gene flow among African residents until the ancestors of non-Africans migrated into Eurasia, then we would expect more SNP sharing between non-Africans and Neandertals (Durand et al. 2011). 

... 

While genome-wide comparisons detect more sequence agreement between non-African and Neandertal genomes, and between Melanesian and Denisova genomes, the specific loci exhibiting these signals have not yet been identified. Furthermore, current analyses do not elucidate the relative roles of recent introgression versus long-term population structure in Africa in explaining these patterns.

The current paper does a good job at showing how in one particular region archaic introgression into Melanesians is indeed the best explanation for the evidence. But, the fact that the authors seem to re-iterate the possibility of African population structure and repeatedly caution against using patterns of genomewide sharing between modern and archaic humans is a strong hint that there are more things to come on the topic.

We should remember that the widely-circulated estimates of Neandertal->Eurasian introgression are based on genomewide averages. It is true that Reich et al. (2010) identified 13 regions of potential Neandertal introgression, which together make up a very small portion of the human genome. So, the jury is out on whether African population structure or Neandertal introgression is responsible for most of the genomewide pattern.

What you can be sure of is that many scientists are busy lining up full genomes from different human populations as we speak, and finding plenty of regions where haplotypes of extremely old divergence times co-exist in our species. We will probably learn more about such efforts during 2012.



Mol Biol Evol (2012)doi: 10.1093/molbev/msr301

Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations

Fernando L. Mendez, Joseph C. Watkins and Michael F. Hammer

Recent analysis of DNA extracted from two Eurasian forms of archaic human show that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. While these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene, OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We re-sequenced a 7 kb region encompassing the OAS1 gene in 88 individuals from 6 Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5' region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 million years, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

Link