Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia 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 coexistence 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 quantitative trait loci (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.

Keywords: Daphnia; facultative sex; male production; population genomics; quantitative genetics.

Fig. 1.

Location and features of the focal ponds. (A) Location of D. pulex sampling sites. The left panel shows the location of the focal populations, Dorset, and two distant ponds in Wales. The middle panel zooms in on the Dorset region and shows a neighboring pond, D10, along with the focal metapopulation at the Kilwood Coppice Nature Reserve, situated just north of the Purbeck hills. The right panel shows the location of the focal ponds DCat, D8, and DBunk, as well as two additional sampled ponds, DOily and DMud at the Kilwood Coppice Nature Reserve. (B) Pictures depicting water level in the three focal ponds in February (2020) and July (2018), illustrating their variance in ephemerality. The outlined area in the July picture of D8 shows the borders of a remnant puddle. Map credits and references shown in the data accessibility statement.

Fig. 2.

Assignment of clonal identity via IBS. Pairwise IBS matrix generated using whole-genome sequence data. Matrix includes 498 diploid genomes from D10, DCat, D8, and DBunk. The largest clonal group identified in D8 is superclone A, the second largest is superclone C.

Fig. 3.

Inferred pedigree based on kinship and IBS₀. Each diamond is a superclone, with the size of the diamond proportional to the abundance of the superclone. Diamonds present across multiple years indicate superclones sampled across multiple time points. Vertical lines indicate within-clone mating, whereas question marks indicate inferred, unsampled clones.

Fig. 4.

Superclones A and C invest differently in asexual and sexual reproduction. Demographic data over time for A and C isofemale lines propagated in mesocosms. Line types correspond to different isofemale lines. Two isofemale lines were used for each superclones (A: D8–179, D8–349; C: D8–222, D8–515). (A) Total population size, (B) proportion of females reproducing asexually, (C) proportion of females reproducing sexually (producing ephippia), (D) proportion of males, (E) number of sexually produced embryos graphed on a log 10 scale, (F) male production of A and C females when exposed or not exposed to MF. Error bars represent 95% confidence intervals.

Fig. 5.

Genetic variation and mapping of variation in male production. Male production (A) rate and ephippial fill rate (B) in A, C, A×C F1s, and C×C F1s. Points represent isofemale lines and vertical lines represent 95% confidence intervals. (C) Male production rate versus the number of male⁺ alleles across the 14 QTL identified via Pool-Seq (see E) for both the A×C cross (red) and C×C cross (blue). Each point represents an isofemale line. See text for statistics on correlation between the number of male⁺ alleles and male production rate. (D) QTL mapping in A×C F1 hybrids for ephippial fill rate and male production identified multiple peaks for each trait. Black points represent QTL regions that pass chromosome level permutation threshold. (E) Mapping of male production using pooled field samples identified multiple peaks, with some overlap with the A×C F1 hybrid mapping. To visualize overlap, the pooled sequencing peaks are plotted on the A×C F1 hybrid mapping figure as dashed lines. Horizontal line is the 5% FDR (false discovery rate) threshold. Values above the zero line represent Pool-Seq replicate 1, and those below the zero line represent replicate 2. (F) Genotype for superclone A and C at each pooled sequencing QTL. (G) TMRCA for the 12 pooled sequencing QTL plotted against the genome-wide distribution. (H) RNA-seq identified many genes differentially expressed between superclones A and C, some of which are located near QTL peaks. Blue points are genes within 50 kb of QTL identified in the Pool-Seq, red points are all other genes, and genes that are near the Pool-Seq peaks and are in the top 10% of differential expression genome-wide are labeled with their corresponding QTL number. For both (G) and (H), the number in the boxes corresponds to the QTL number as identified in (E).

Fig. 6.

Attributes of QTL₁₂. (A) The proportion of male offspring versus dosage of the male+ alleles for the F1 offspring of the A×C and C×C cross, with the sign of allelic effect calculated from the Pool-Seq data. (B) Overall frequency of the QTL₁₂  male⁺ allele among ponds across sample years. (C) Expression of Daphnia00787, one of the genes within QTL₁₂ in A and C isofemale lines. The y-axis represents gene expression, normalized for library size. (D) A haplotype spanning network plot of Daphnia00787 with D. pulicaria and D. obtusa as outgroups. The male⁻ allele and male⁺ allele are labeled.