Title: "Local ecology shapes the evolution of reproductive polymorphism in Daphnia pulex"

Abstract: Organisms living in temperate localities often experience changes in population size across seasons. These cyclic booms and busts have the potential to dramatically alter the genetic composition of populations through the joint action of natural selection and drift. We examine the genetic consequences of seasonal fluctuations in population size in the cyclic parthenogen, Daphnia pulex, living in a series of ponds in southern England. Using a combination of genomic, field, and lab-based approaches, we the focus on the evolutionary dynamics of Daphnia living in two focal ponds which differ in their degree of ephemerality. In a larger and more permanent pond we find Daphnia populations dominated by a limited number of clonal lineages which have persisted for multiple years and differ in their life-history: one clonal lineage is likely to engage in sex whereas the other invests more heavily in asexual reproduction. In a smaller pond, we find a diverse assemblage of recombinant lineages which are the product of frequent and recurrent sex. Using whole genome-sequencing of >500 clones, we document the evolutionary history of these Daphnia populations and link the persistence of genetic diversity within ponds to reproductive niche partitioning. We examine the demographic consequences of alternate reproductive strategies using laboratory mesocosm experiments and assess the seasonal dynamics of clonal turnover and sexual investment in the field through pooled-resequencing. We argue that reproductive niche partitioning is a mechanism of balancing selection leading to maintenance of genetic diversity across seasons as populations undergo periodic and population booms and busts.