Development and application of computational tools for ancient DNA analysis

Keywords: Ancient DNA, Bioinformatics, Phylogenetic Placement, Read Alignment

Research Outline

Ancient DNA sample placement into reference phylogenies using pathPhynder (in Martiniano et al., 2020 biorXiv).

Ancient DNA data is highly degraded, and this poses great challenges for population genetic analyses and inference. One of the focus of my group is to develop ancient DNA-aware computational methods from maximizing the information that can be extracted from ancient DNA data and minimize error and bias. Examples of past work include the improvement of phylogenetic placement of ancient DNA samples into reference phylogenies (Martiniano et al., 2020 biorXiv) and removing reference bias in ancient DNA read alignment using variation graphs.

Ancient DNA read mapping using Variation Graphs (in Martiniano et al., 2020 Genome Biology).

We use various computational approaches to elucidate different aspects of the genetic history of our species, including:

  • The impact of past migrations and admixture processes in the formation of past and present-day genetic diversity:
  • The effect of natural selection on various human traits during prehistory.


Other Projects involving Rui Martiniano

Ancient Human Genomics

Our research group focuses on generating and analysing ancient DNA sequence data from ancient remains in order to study past migration and population history. We currently have several ongoing projects dedicated to different archaeological sites around the world, including Arabia, the Iberian Peninsula and Britain.

Click here to find out more…

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