Genetic Variation in Reproductive Investment Across an Ephemerality Gradient inDaphnia pulex

Abstract

Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. We studied the ecological and evolutionary dynamics of reproductive investment in the facultatively sexual model species, Daphnia pulex. We found that patterns of clonal diversity, but not genetic diversity varied among ponds consistent with the predicted relationship between ephemerality and clonal structure. Reconstruction of a multi-year pedigree demonstrated the co-existence of clones that differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative QTL underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.

Maternal control of spontaneous dormancy termination inDaphnia pulex

“…We assessed whether the maternal environment affected the early hatching rate as a function of mesocosm age. Over the 8 sample weeks, the density of individuals increased from 60 individuals to several thousand (Barnard-Kubow et al, 2022). To assess the early hatching rate of the two clonal lineages, we collected ephippia weekly from the mesocosms, and found that the rate of early hatching increased as mesocosms became older (df= 1, χ 2 =34.03 p=5.434e-09, Fig 1B, Model 1).…”

“…D. pulex were collected from a semi-permanent pond in Dorset, England in the Kilwood Nature Reserve (50.64, - 2.09) in the spring of 2017. Pond ephemerality was determined using trail cameras, and multi-year survey of the genetic composition of D. pulex (Barnard-Kubow et al, 2022). Live Daphnia samples were transported back to the University of Virginia, where clonal lineages were established from wild female isolates.…”

“…15 liter mesocosms filled with ASTM were established in the spring of 2019, and inoculated with one of either two D. pulex lineages (D8515, D8222), which were established from two separate field isolates of the same wild superclone lineage (superclone C, Barnard-Kubow et al, 2022). Clonal isolates D8515 and D8222 are nearly genetically identical, although there are a limited number of genetic differences that have arisen due to mutation accumulation and gene conversion (Barnard-Kubow et al, 2022). The mesocosms were seeded with ~60 adult females, and were placed in a Percival incubator (Model Number: 1166NL) at 18C 18:6 light:dark conditions using LED lights (~1500 lux, Royal Pacific 4311WH).…”

“…Although we demonstrate that diapause termination is likely under maternal control, we cannot rule out genetic variation as an additional source of variation. Lineages were maintained under laboratory conditions for two years prior to starting the mesocosm cultures and mesocosms were initiated with multiple females from each clonal lineage (Barnard-Kubow et al, 2022). This might have been ample time for novel mutations to appear prior to the 10 start of the mesocosm or during the multigeneration mesocosm experiment itself (Flynn et al, 2017;Keith et al, 2016).…”

Balancing selection and the functional effects of shared polymorphism in crypticDaphniaspecies

“…Next, we show that North American and European D. pulex possess tens of thousands of shared polymorphisms, whose abundance cannot be explained by incomplete lineage sorting, Leinonen et al, 2011). We incorporated wild-sequenced or isogenic female lineages (Barnard-Kubow et al, 2022;Lynch et al, 2017;Xu et al, 2015;Ye et al, 2022), and excluded samples that were from mutation accumulation studies. Species identity for these samples was based on annotations provided in each SRA record.…”