The stable isotopic composition of Daphnia ephippia reflects changes in d13C and d18O values of food and water

The stable isotopic composition of fossil resting eggs (ephippia) of Daphnia spp. is being used to reconstruct past environmental conditions in lake ecosystems. However, the underlying assumption that the stable isotopic composition of the ephippia reflects the stable isotopic composition of the parent Daphnia, of their diet and of the environmental water have yet to be confirmed in a controlled experimental setting. We performed experiments with Daphnia pulicaria cultures, which included a control treatment conducted at 12 °C in filtered lake water and with a diet of fresh algae and three treatments in which we manipulated the stable carbon isotopic composition (?13C value) of the algae, stable oxygen isotopic composition (?18O value) of the water and the water temperature, respectively. The stable nitrogen isotopic composition (?15N value) of the algae was similar for all treatments. At 12 °C, differences in algal ?13C values and in ?18O values of water were reflected in those of Daphnia. The differences between ephippia and Daphnia stable isotope ratios were similar in the different treatments (?13C: +0.2 ± 0.4 ‰ (standard deviation); ?15N: ?1.6 ± 0.4 ‰; ?18O: ?0.9 ± 0.4 ‰), indicating that changes in dietary ?13C values and in ?18O values of water are passed on to these fossilizing structures. A higher water temperature (20 °C) resulted in lower ?13C values in Daphnia and ephippia than in the other treatments with the same food source and in a minor change in the difference between ?13C values of ephippia and Daphnia (to ?1.3 ± 0.3 ‰). This may have been due to microbial processes or increased algal respiration rates in the experimental containers, which may not affect Daphnia in natural environments. There was no significant difference in the offset between ?18O and ?15N values of ephippia and Daphnia between the 12 and 20 °C treatments, but the ?18O values of Daphnia and ephippia were on average 1.2 ‰ lower at 20 °C than at 12 °C. We conclude that the stable isotopic composition of Daphnia ephippia provides information on that of the parent Daphnia and of the food and water they were exposed to, with small offsets between Daphnia and ephippia relative to variations in Daphnia stable isotopic composition reported from downcore studies. However, our experiments also indicate that temperature may have a minor influence on the ?13C, ?15N and ?18O values of Daphnia body tissue and ephippia. This aspect deserves attention in further controlled experiment

Natural selection and genetic diversity in the butterfly heliconius melpomene

A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila. A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. © 2016 by the Genetics Society of America

PSMC results

[12 files] PSMC results for twelve selected samples

PCA results

Results of Eigenstrat PCA analysis

simulated_error_rates

[20 files] Counts of paires of actual and inferred genotype patterns for simulated data at different percentage divergences and sequence coverage depths. Foer example "counts_01_00" refers to the number of sites at which the actual genotype was 0/1 and the inferred genotype was 0/0

Genotypes Intergenic Part 1 of 3

Genotype calls for all individuals at intergenic sites. Part 1 of 3