Paleogenomics is crushing it right now

It’s only Valentine’s Day, and already early 2014/late 2013 have provided several fascinating, high profile studies of ancient DNA (all been published in Nature). Forecasting this deluge, last year closed with the announcement of sequenced mtDNA from a ≥400,000 year old human fossil from Sima de los Huesos, Spain (Meyer et al., 2013). This is the oldest DNA obtained for any human fossil, and among the oldest of any animal.Meyer title copy 2

Shortly thereafter, Prüfer and pals (2014) published the complete genome of a Neandertal from the infamous Denisova cave. This study revealed extensive inbreeding in Siberian Neandertals; the fossil individual’s high level of homozygosity is consistent with their parents being half-siblings.  Furthermore, comparison of the genome of this inbred Neandertal with modern humans’ allowed researchers to identify many mutations that have become fixed (shared by all people) by natural selection since the divergence of our and Neandertals’ ancestors. Uncovering these human-specific variants can help us understand the genetic bases for many of humans’ remarkable traits.Prufer title

In January, Olalde y coautores published a genomic analysis of a 7,000 hunter-gatherer from Spain. This ancient genome contained ancestral variants for genes relating to skin pigmentation (SLC45A2, SLC45A5MC1R, TYR, and KILTG), meaning this Mesolithic European most probably had dark skin. This individual also had a derived variant of the HERC-OCA2 locus, associated with blue eye color in present day people. This suggests that the relatively novel phenotype of non-brown eyes may have increased in frequency more quickly than light skin color in ancient Europe. This guy also had many derived loci associated with immune function, indicating that the rise of agriculture is not solely responsible for the evolution of immune function in present day Europeans.

Olalde title

Around the same time, Sankararamen and team published an analysis of the distribution of Neandertal genes in living people. Whereas previous studies had already shown that Neandertals contributed ≤4% on average to the genomes of living people, this study examined where in modern people’s genomes this Neandertal ancestry tends to be located. One of the most interesting findings is that Neandertal genes are not uniformly or randomly distributed across the modern human genome. Rather, some regions appear to be especially devoid of Neandertal ancestry, implying natural selection acted strongly against Neandertal genes. These Neander-nude areas are preferentially found on the the X chromosome and in genes expressed in the testes, a finding consistent with reduced fertility in hybrid males. Although the genetic contribution of Neandertals to modern humans means that the two belonged to the same species, Sankararaman et al’s findings suggest the two groups were on their way to becoming different species.sanakararaman

Finally, this past week Rasmussen and rascals have published an analysis of a 12,000 year old human from the Anzick site in Montana, associated with the Clovis stone tool culture. I don’t know much about this time period save for what I learned in a class on North American archaeology taught by Dr. John Speth, back when I was a young, bright-eyed graduate student. One thing I recall from this class, when we were going over Clovis, was that this tool industry was found all over the United States at the beginning of the Holocene, but I was always disappointed by the dearth of bones complementing the copious lithics. Turns out, the DNA analyzed by Rasmussen et al. comes from the only known burial from this time period. This lone burial provides compelling genetic evidence that indigenous Americans have descended largely from a single ancestral population that separated into the North and South American populations prior to the Clovis period. This ancestral population was definitely not from Europe, as a minority of researchers have argued. Check out the SEAC Underground blog for more on the archaeology and ethics of the Anzick analyses.rasmussen

So, paleogenomics is really crushing it right now. There have been many of recent advances in sampling and sequencing poorly-preserved ancient DNA, and as we’re seeing now, lots of ancient bones (and teeth) are bringing awesome new, genetic insights into recent human evolution. If this is how well we’re doing so early in 2014, you can bet that the rest of the year promises many more exciting discoveries.


2 thoughts on “Paleogenomics is crushing it right now

  1. Pingback: Dawn of Paleoepigenomics | Lawn Chair Anthropology

  2. Pingback: Driving nails into the 2014 Lawn Chair | Lawn Chair Anthropology

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