Universität zu Köln

Strütt, Stefan ORCID: 0000-0002-2785-2815 (2022). Inference of transitions to self-fertilization using haplotype genomic variation. PhD thesis, Universität zu Köln.

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Abstract

Mating systems play an essential role in the evolution of natural populations. The reproductive mode of a population affects the evolutionary forces and recombination. Shifts in mating systems change major evolutionary traits of natural populations and affect the life-history cycle on many different levels. Among all transitions of mating schemes, a shift from outcrossing to selfing is one of the major shifts in plants. Such shifts have repeatedly occurred on the phylogenetic level. Despite their importance, there were no published tools to estimate such transitions in natural populations using genetic data on a genome- wide level. Existing estimates rely on estimating the loss-of-function mutations of causal loci. However, such estimates rely on the knowledge of the underlying genetic mechanism to induce the shift from outcrossing to selfing. Thus, such estimates are restricted to be conducted on very few species. In this study, we investigated the genetic consequences of shifts from outcrossing to selfing (Chapter 1). We used extensive simulations of the forward- in-time Wright-Fisher model and the backward-in-time coalescent model. We found the previously described theoretical work on implementing partial selfing in the coalescent to suffice in simulating transitions to selfing. We developed an Approximate Bayesian Computation approach (tsABC) to identify and estimate the date of transitions from outcrossing to selfing using a pairwise comparison of genomes (Chapter2). Finally, in collaboration with Thibaut Sellinger, we introduced the modified PSMC’ (teSMC) to estimate piecewise-constant selfing rates through time jointly with piecewise-constant population sizes for single- population demographies and analyzed its accuracy (Chapter 3). Taken together, we provide not only an approximate Bayesian but also a maximum likelihood approach to identify and estimate transitions to selfing for single populations. We found tsABC to be a versatile tool to identify and estimate transitions to selfing. Under carefully made assumptions for the proposed models, transitions to selfing can be detected under a broad range of scenarios. Moreover, the assumed model in the teSMC method improved the estimates of demography and detected transitions to selfing at least as powerful as the tsABC. The automized parametrization of teSMC allows users with little expertise in scripting to use it. We used both methods to estimate the transition from outcrossing to selfing for three genetic clusters of Arabidopsis thaliana. Our results were consistent with each other and existing estimates from the literature. With our study, we not only contributed to the understanding of evolutionary processes that formed the genetic diversity of natural populations but also provided two powerful tools to investigate the demographic history of natural populations in the context of transitions to selfing. Recombination provides a molecular clock on a separate time scale compared to mutation that interacts with all the four evolutionary forces at various levels. Eventually, that will contribute to understanding the functions of genes and their relationship and interaction with the bearing individual, the population, and the environment. Taken together, selfing as a breeding scheme or reproductive strategy is a crucial trait that interferes and connects evolutionary forces, adaptive potential, and life- history traits of natural populations.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Strütt, Stefan stefan.struett@gmail.com orcid.org/0000-0002-2785-2815 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-651614
Date:	2022
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Außeruniversitäre Forschungseinrichtungen > MPI for Plant Breeding Research
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language Selfing; recombination; tsABC; teSMC; Arabidopsis thaliana English
Date of oral exam:	8 August 2022
Referee:	Name Academic Title Tsiantis, Miltos Prof. Dr. Krug, Joachim Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/65161