Robust bacterial co-occurence community structures are independent of r- and K-selection history

Selection for bacteria which are K-strategists instead of r-strategists has been shown to improve fish health and survival in aquaculture. We considered an experiment where microcosms were inoculated with natural seawater and the selection regime was switched from K-selection (by continuous feeding) to r-selection (by pulse feeding) and vice versa. We found the networks of significant co-occurrences to contain clusters of taxonomically related bacteria having positive associations. Comparing this with the time dynamics, we found that the clusters most likely were results of similar niche preferences of the involved bacteria. In particular, the distinction between r- or K-strategists was evident. Each selection regime seemed to give rise to a specific pattern, to which the community converges regardless of its prehistory. Furthermore, the results proved robust to parameter choices in the analysis, such as the filtering threshold, level of random noise, replacing absolute abundances with relative abundances, and the choice of similarity measure. Even though our data and approaches cannot directly predict ecological interactions, our approach provides insights on how the selection regime affects the composition of the microbial community, providing a basis for aquaculture experiments targeted at eliminating opportunistic fish pathogens.

Balanced polymorphisms and their divergence in a Heliconius butterfly

The evolution of mimicry in similarly defended prey is well described by Müllerian mimicry theory, which predicts the convergence of warning patterns in order to gain the most protection from predators. However, despite this prediction, we can find great diversity of color patterns amongst Müllerian mimics such as Heliconius butterflies in the neotropics. Furthermore, some species have evolved the ability to maintain multiple distinct warning patterns in single populations, a phenomenon known as polymorphic mimicry. The adaptive benefit of these polymorphisms is questionable since variation from the most common warning patterns is expected to be disadvantageous as novel signals are punished by predators naive to them. In this study, we use artificial butterfly models throughout Central and South America to characterize the selective pressures maintaining polymorphic mimicry in Heliconius doris. Our results highlight the complexity of positive frequency-dependent selection, the principal selective pressure driving convergence amongst Müllerian mimics, and its impacts on interspecific variation of mimetic warning colouration. We further show how this selection regime can both limit and facilitate the diversification of mimetic traits.

Balanced polymorphisms and their divergence in a Heliconius butterfly

The evolution of mimicry in similarly defended prey is well described by Müllerian mimicry theory, which predicts the convergence of warning patterns in order to gain the most protection from predators. However, despite this prediction, we can find great diversity of color patterns amongst Müllerian mimics such as Heliconius butterflies in the neotropics. Furthermore, some species have evolved the ability to maintain multiple distinct warning patterns in single populations, a phenomenon known as polymorphic mimicry. The adaptive benefit of these polymorphisms is questionable since variation from the most common warning patterns is expected to be disadvantageous as novel signals are punished by predators naive to them. In this study, we use artificial butterfly models throughout Central and South America to characterize the selective pressures maintaining polymorphic mimicry in Heliconius doris. Our results highlight the complexity of positive frequency-dependent selection, the principal selective pressure driving convergence amongst Müllerian mimics, and its impacts on interspecific variation of mimetic warning colouration. We further show how this selection regime can both limit and facilitate the diversification of mimetic traits.

Robust bacterial co-occurence community structures are independent of r- and K-selection history

Selection for bacteria which are K-strategists instead of r-strategists has been shown to improve fish health and survival in aquaculture. We considered an experiment where microcosms were inoculated with natural seawater and the selection regime was switched from K-selection (by continuous feeding) to r-selection (by pulse feeding) and vice versa. We found the networks of significant co-occurrences to contain clusters of taxonomically related bacteria having positive associations. Comparing this with the time dynamics, we found that the clusters most likely were results of similar niche preferences of the involved bacteria. In particular, the distinction between r- or K-strategists was evident. Each selection regime seemed to give rise to a specific pattern, to which the community converges regardless of its prehistory. Furthermore, the results proved robust to parameter choices in the analysis, such as the filtering threshold, level of random noise, replacing absolute abundances with relative abundances, and the choice of similarity measure. Even though our data and approaches cannot directly predict ecological interactions, our approach provides insights on how the selection regime affects the composition and workings of the microbial community, providing a basis for aquaculture experiments targeted at eliminating opportunistic fish pathogens.

The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime

Background Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence, which combines advantages of experimental evolution such as time series, replicate populations, and controlled environmental conditions, with whole genome sequencing. Recent analysis of replicate populations from two different Drosophila simulans founder populations, which were adapting to the same novel hot environment, uncovered very different architectures—either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. Results Here, we expose the founder population from Portugal to a cold temperature regime. Although almost no selection targets are shared between the hot and cold selection regime, the adaptive architecture was similar. We identify a moderate number of targets under strong selection (19 selection targets, mean selection coefficient = 0.072) and parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. Conclusions These observations will have broad implications for the correct interpretation of the genomic responses to a changing climate in natural populations.

The adaptive architecture is shaped by population ancestry and not by selection regime

Understanding the genetic architecture of adaptive phenotypes is a key question in evolutionary biology. One particularly promising approach is Evolve and Resequence (E&R), which combines advantages of experimental evolution such as time series, replicate populations and controlled environmental conditions, with whole genome sequencing. The recent analysis of replicate populations from two different Drosophila simulans founder populations, which were adapting to the same novel hot environment, uncovered very different architectures - either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. Here, we exposed the founder population from Portugal to a cold temperature regime. Although almost no selection targets were shared between the hot and cold selection regime, the adaptive architecture was similar: we identified a moderate number of loci under strong selection (19 selected alleles, mean selection coefficient = 0.072) and very parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. These observations have a pronounced impact on our understanding of adaptation in natural populations.

Quantifying the selection regime in a natural Chironomus riparius population

SummaryWhile the evolutionary fitness of natural populations is affected by a multitude of environmental factors, theory predicts that selective responses are in principle limited. However, we lack empirical knowledge on the magnitude of different selection pressures natural populations adaptively track. Here, we developed a framework to investigate the quantitative and qualitative complexity of the effectively acting selection regime using population genomic time series data. We applied the approach to a natural population of the multivoltine midge Chironomus riparius. Using six seasonal samples over three years from the same natural population, we could show with fitness experiments that the population continuously evolved in response to a highly variable environment. Analyses of genome-wide allele-frequencies revealed that tens of thousands of haplotypes responded at least once to selection during the monitored period. Clustering the temporal haplotype frequency trajectories revealed 46 different patterns, i.e. selection pressures. Some of these co-varied with measured environmental variables known to be selective factors for the species. Our results demonstrate that 1) adaptive tracking of multiple fluctuating selection pressures occurs in natural populations, 2) the estimated minimum number of simultaneously acting selective pressures is quite high but appears to be limited and 3) changes in intensity and direction of selective responses can be frequent. This shows that adaptation in natural populations can be rapid, pervasive and complex