The causes and consequences of asexuality in Daphnia: insights into the evolution of sex

Understanding the causes and consequences of asexuality is essential for addressing the question why sexual reproduction is predominant in nature. Here I used Daphnia as a model system to investigate causes and genetic consequences of asexual reproduction. First I used Daphnia mutation-accumulation (MA) lines to show the high frequency of large-scale deletions during asexual reproduction (6.7 × 10 -5 locus -1 * generation -1 ) and significant amount of ameiotic crossing over and gene conversion (3.3 × 10 -5 locus -1 * generation -1 ). The high rate of deletions suggests the genomic instability and irreversible process of mutation accumulation. However, it remains unclear how ameiotic recombination can affect the evolution of asexual taxa. Furthermore, I investigated the mitochondrial DNA mutation rates and spectra for the MA lines originated from asexual and sexual ancestors to test the theoretical predication that loss of sex would result in a much higher mutation rate. The nearly complete mitochondrial genome sequences of 82 sexual and 47 asexual MA lines reveal high mtDNA mutation rate of 1.37 × 10 -7 and 1.73 × 10 -7 per nucleotide per generation, respectively. Maximum-likelihood estimates of the Daphnia mitochondrial effective population size revealed that between five and ten copies of mitochondrial genomes are transmitted per female per generation. However, there was no statistical significant difference between the mutation rates in sexual and asexual MA lines and the mutation spectra are highly similar. Lastly, I use microsatellite data to examine the roles of hybridization and meiosis suppression in the origin of obligately asexual D. pulex that are thought to be the hybrids of D. pulex and D. pulicaria. The results of phylogenetic analyses and Bayesian estimates of ancestry based on nine microsatellite loci strongly support that these hybrids originate from the crossing of F1 progeny with D. pulex males produced by obligately parthenogenetic clones carrying genetic elements conferring meiosis suppression. Overall, this thesis improves our understanding of how abandoning sex can affect the genomic stability and mutation rate in asexual taxa and provides a solid framework for future investigations on the cellular mechanisms and genetic consequences of obligate asexuality in Daphnia

On the Convergence of (Stochastic) Gradient Descent with Extrapolation for Non-Convex Optimization

Extrapolation is a well-known technique for solving convex optimization and variational inequalities and recently attracts some attention for non-convex optimization. Several recent works have empirically shown its success in some machine learning tasks. However, it has not been analyzed for non-convex minimization and there still remains a gap between the theory and the practice. In this paper, we analyze gradient descent and stochastic gradient descent with extrapolation for finding an approximate first-order stationary point in smooth non-convex optimization problems. Our convergence upper bounds show that the algorithms with extrapolation can be accelerated than without extrapolation