Inferring recent demography from spatial genetic structure Dissertation Thesis

Author(s): Ringbauer, Harald
Advisor(s): Barton, Nicholas
Committee Chair(s): Kolmogorov, Vladimir
Committee Member(s): Lampert, Christoph
Title: Inferring recent demography from spatial genetic structure
Affiliation IST Austria
Abstract: This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.
Publication Title: IST Dissertation
Degree Granting Institution: IST Austria  
Degree: PhD
Degree Date: 2018-02-21
Start Page: 1
Total Pages: 146
DOI: 10.15479/AT:ISTA:th_963
Notes: Finishing a PhD has been the hardest, but also the most productive undertaking of my life so far. There are many people which made it possible that I completed this rough journey. It would have been impossible to make it alone, and I am really grateful for all the support I have received. Most of all I am indebted to my parents for their continuous support throughout my studies, and also to the rest of my family: My grandparents, my fun sister and furry Kitty, as well as my cousins and their significant others - and by now also Lorenz, the very definition of a best friend. I was also lucky to have an amazing group of friends - thanks to Dominik, Christoph, David, Johannes and Mato for all the fun game and cinema nights. I also want to thank Julia, who supported me when I needed it the most, and was the best thing that happened to me in the last years. I also want to thank my support group at IST. It is impossible to list all the great connections I made. But I try to pick out a few shining examples. Anton, with whom I have set out on so many adventures and ski trips. To give just one example: Right now, I am on the way to meet him in Istanbul and heading for a powder adventure in Hokkaido. Alex K., my great table soccer sparring partner who pushed my game to the next level. He made many of my days much more fun (fist pump man). Michal, my man for the enjoyable nights out at ...classic Viennese places and deep after-football conversations. And last but not least, Jamie and Alex Z., for countless fun pub quiz, sports bar and table soccer nights. I have also been lucky to be part of an amazing research group. Maria, who grew a close friend, and David, whom I had so many great discussions about Science Fiction with, deserve a special mentioning. So do also Himani, Barbora, Gemma and Katka, for all the interesting lunch conversations, and for giving me a lot of perspective which hopefully helped me grow. I also want to thank the Coop lab. Visiting them for two months in California has been a truly fun experience, and it was also a very productive time. And most importantly, I want to express my gratitude towards my supervisor, Nick, for the freedom to explore my own interests, and for giving me a lot of flexibility throughout my PhD.
Open access: yes (repository)