Biology subjects

Barata, C.

Publications and source records attributed to Barata, C..

3 recordsLinked to original sources

bioRxiv2022

Selection on the fly: short term adaptation to an altered sexual selection regime in Drosophila pseudoobscura

Experimental evolution studies are powerful approaches to unveil the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations genomes at multiple time points. Here, we analyse allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size - Ne - between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants on E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, only more marked in E and restricted to chromosome arm XR in M. Ne is lower on the X at the start of the experiment, which might indicate a swift adaptive response at the onset of selection. Additionally, we show that the third chromosome was also affected by elevated polyandry. Its distal end harbours a region showing a strong signal of adaptive divergence in E lines.

evolutionary biology↗

bioRxiv2020

Bait-ER: a Bayesian method to detect targets of selection in Evolve-and-Resequence experiments

For over a decade, experimental evolution has been combined with high-throughput sequencing techniques in so-called Evolve-and-Resequence (E&R) experiments. This allows testing for selection in populations kept in the laboratory under given experimental conditions. However, identifying signatures of adaptation in E&R datasets is far from trivial, and it is still necessary to develop more efficient and statistically sound methods for detecting selection in genome-wide data. Here, we present Bait-ER - a fully Bayesian approach based on the Moran model of allele evolution to estimate selection coefficients from E&R experiments. The model has overlapping generations, a feature that describes several experimental designs found in the literature. We tested our method under several different demographic and experimental conditions to assess its accuracy and precision, and it performs well in most scenarios. Nevertheless, some care must be taken when analysing trajectories where drift largely dominates and starting frequencies are low. We compare our method with other available software and report that ours has generally high accuracy even for trajectories whose complexity goes beyond a classical sweep model. Furthermore, our approach avoids the computational burden of simulating an empirical null distribution, outperforming available software in terms of computational time and facilitating its use on genome-wide data. We implemented and released our method in a new open-source software package that can be accessed at https://github.com/mrborges23/Bait-ER.

evolutionary biology↗

bioRxiv2020

Improving water quality does not guarantee fish health: effects of ammonia pollution on the behaviour of wild-caught pre-exposed fish.

Ammonia is a pollutant frequently found in aquatic ecosystems. In fish, ammonia can cause physical damage, alter its behaviour and even cause death. Exposure to ammonia also increases fish physiological stress, which can be measured through biomarkers. In this study, we analysed the effect of sublethal ammonia concentrations on the behaviour and the oxidative stress of Barbus meridionalis that had been pre-exposed to this compound in the wild. Wild-caught fish from a polluted site (pre-exposed fish) and from an unpolluted site (non-pre-exposed fish) were exposed, under experimental conditions, to total ammonia concentrations (TAN) of 0, 1, 5 and 8 mg/L. Swimming activity, feeding behaviour and oxidative stress response based on biomarkers were analysed. Pre-exposed fish showed both an altered behaviour and an altered oxidative stress response in the control treatment (0 mg/L). Differences in swimming activity were also found as pre-exposed fish swam less. Lower feeding activity (voracity and satiety) and altered response to oxidative stress were also observed at [≥] 1 mg/L TAN. Biomarker results confirmed pre-exposed fish suffer from a reduction in their antioxidant defences and, hence, showed increased oxidative tissue damage. In summary, pre-exposed fish showed more sensitivity to ammonia exposure than fish from a pristine site.

animal behavior and cognition↗