Paleo genomics
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Developing ancient Ancestry Informative Markers (aAIMs)
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In this paper (Esposito et al. 2016) define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories. |
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Dating Y chromosomal "Adam"
is the name of the most ancient Y chromosome ever found. In 2013, Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal
position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent
common ancestor (TMRCA) for the Y tree to be 338 000 years ago (95% CI:237 000-581 000). Such an extraordinarily early
estimate contradicts all previous estimates in the literature and is over a 100,000 years older than the earliest fossils of
anatomically modern humans.
We led the effort to examine Mendez et al.'s claims (watch the movie on your right). In Elhaik et al. (2014a), We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208 300 (95% CI:163,900-260,200) years ago. In Elhaik et al. (2014c) we have responded to Mednez et al. continuous misunderstanding of their erroneous analysis. This work was widely covered by the media (see Press). We have also published the first Youtube video that summarizes a scineitifc paper. |
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Human origin and its relationship with related hominins
is one of the most fascinated questions in paleogenomics.
Our review paper (Morozova et al. 2016) aims to improve our understanding of ancient DNA: What is it? When it was first extracted? How many and which samples were studied so far? What are the advances and pitfalls of studying ancient DNA? And what are the future perspectives of this exciting field. My lab is leading an effort to re-examine the data published in the literature. Together with our collaborators, we are developing a new theory to the origin of man. |