Casper-Emil Tingskov Pedersen:
Demographic inferences from large-scale NGS data

Date: 31-08-2017    Supervisor: Anders Albrechtsen

The development of Next Generation Sequencing (NGS) methods have revolutionized the speed and cost of doing large-scale genomic analyses. Furthermore, the quantity of sequences produced facilitate analyses of a number of non-model organisms as well as deeper and more theoretical predictions for e.g. human genetics. In this thesis, the three papers presented demonstrate the advantages of NGS data in the framework of population genetics for elucidating demographic inferences, important for understanding conservation efforts, selection and mutational burdens.

In the first whole-genome study of waterbucks, we investigated the divergence process in a large African mammal. The African mammals are known for their high species and withinspecies diversity, probably driven by environmental fluctuations. Our results showed that the population structure conformed to two isolated subspecies, but we also found that there has been historical gene flow in certain parts of the species range. We also found a lack of recent gene flow within one of the subspecies even across short distances, which suggests an anthropogenic effect on the waterbuck population connectivity and therefore possibly nearfuture conservation concerns.

Investigating the plains zebra, we disentangle the complex genetic structure across a large geographical area and further provide detailed insights into the past phylogeography of this species, including finding a likely plains zebra “cradle” from which all plains zebra populations arose some 367kya. The genetic structure identified in the plains zebra is also different from what has been found using morphometrics, which supports the use of genomic information to supplement morphology-based management decisions.

From a study of exomic sites in the Inuit population, we show that the demographic history of the Inuit is the most extreme in terms of population size, of any human population. We identify a slight increase in the number of deleterious alleles because of this demographic history and support our results using simulations. We use this to show that the reduction in population size experienced by the Inuit will improve mapping of disease-alleles, which are uncommon in populations with larger population size.