Latest Articles
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Evolutionary Biology
Bimodal breeding phenology in the Parsley Frog Pelodytes punctatus as a bet-hedging strategy in an unpredictable environment despite strong priority effects
10.24072/pcjournal.176 - Peer Community Journal, Volume 2 (2022), article no. e57.
Get full text PDFWhen environmental conditions are unpredictable, expressing alternative phenotypes spreads the risk of failure, a mixed strategy called bet-hedging. In the southern part of its range, the Parsley Frog Pelodytes punctatus breeds both in autumn and in spring. Our aim was to study the breeding phenology and reproductive success associated with the use of those two seasonal niches to understand how this breeding strategy can be maintained. Field surveys revealed that breeding phenology was typically bimodal with a higher breeding effort in autumn. More importantly, in spring, the survival rate of offspring was severely reduced by the presence of autumn tadpoles, indicating a clear priority effect. However, the autumn cohort often failed to survive over winter, in which case spring cohorts were often successful. Based on those results, we constructed a model in which females can allocate a variable portion of eggs to each season and added a priority effect. We conclude that the existence of the two breeding seasons may indeed constitute a bet-hedging strategy.
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Genomics
EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes
10.24072/pcjournal.173 - Peer Community Journal, Volume 2 (2022), article no. e56.
Get full text PDFEukProt is a database of published and publicly available predicted protein sets selected to represent the breadth of eukaryotic diversity, currently including 993 species from all major supergroups as well as orphan taxa. The goal of the database is to provide a single, convenient resource for gene-based research across the spectrum of eukaryotic life, such as phylogenomics and gene family evolution. Each species is placed within the UniEuk taxonomic framework in order to facilitate downstream analyses, and each data set is associated with a unique, persistent identifier to facilitate comparison and replication among analyses. The database is regularly updated, and all versions will be permanently stored and made available via FigShare. The current version has a number of updates, notably ‘The Comparative Set’ (TCS), a reduced taxonomic set with high estimated completeness while maintaining a substantial phylogenetic breadth, which comprises 196 predicted proteomes. A BLAST web server and graphical displays of data set completeness are available at http://evocellbio.com/eukprot/. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, with the goal of building a collaborative resource that will promote research to understand eukaryotic diversity and diversification.
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Animal Science
Detecting dairy cows' lying behaviour using noisy 3D ultra-wide band positioning data
10.24072/pcjournal.167 - Peer Community Journal, Volume 2 (2022), article no. e55.
Get full text PDFIn precision livestock farming, technology-based solutions are used to monitor and manage livestock and support decisions based on on-farm available data. In this study, we developed a methodology to monitor the lying behaviour of dairy cows using noisy spatial positioning data, thereby combining time-series segmentation based on statistical changepoints and a machine learning classification algorithm using bagged decision trees. Position data (x, y, z -coordinates) collected with an ultra-wide band positioning system from 30 dairy cows housed in a freestall barn were used. After the data pre-processing and selection, statistical changepoints were detected per cow-day (no. included = 331) in normalized 'distance from the centre of the barn' and (z) time series. Accelerometer-based lying bout data were used as a practical ground truth. For the segmentation, changepoint detection was compared with getting-up or lying-down events as indicated by the accelerometers. For the classification of segments into lying or non-lying behaviour, two data splitting techniques resulting in 2 different training and test sets were implemented to train and evaluate performance: one based on the data collection day and one based on cow identity. In 85.5% of the lying-down or getting-up events a changepoint was detected in a window of 5 minutes. Of the events where no detection had taken place, 86.2% could be associated with either missing data (large gaps) or a very short lying or non-lying bout. Overall classification and lying behaviour prediction performance was above 91% in both independent test sets, with a very high consistency across cow-days. Per cow-day, the average error in the estimation of the lying durations were 7.1% and 7.8% for the cow-identity and time-based data splits respectively. This resulted in sufficient accuracy for automated quantification of lying behaviour in dairy cows, for example for health or welfare monitoring purposes.
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Evolutionary Biology
Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?
10.24072/pcjournal.172 - Peer Community Journal, Volume 2 (2022), article no. e54.
Get full text PDFHuman-mediated introductions are reshuffling species distribution on a global scale. Consequently, an increasing number of allopatric taxa are now brought into contact, promoting introgressive hybridization between incompletely isolated species and new adaptive gene transfer. The broadcast spawning marine species, Ciona robusta, has been recently introduced in the native range of its sister taxa, Ciona intestinalis, in the English Channel and North-East Atlantic. These sea squirts are highly divergent, yet hybridization has been reported by crossing experiments and genetic studies in the wild. Here, we examined the consequences of secondary contact between C. intestinalis and C. robusta in the English Channel. We produced genomes phased by transmission to infer the history of divergence and gene flow, and analyzed introgressed genomic tracts. Demographic inference revealed a history of secondary contact with a low overall rate of introgression. Introgressed tracts were short, segregating at low frequency, and scattered throughout the genome, suggesting traces of past contacts during the last 30 ky. However, we also uncovered a hotspot of introgression on chromosome 5, characterized by several hundred kb-long C. robusta haplotypes segregating in C. intestinalis, that introgressed during contemporary times the last 75 years. Although locally more frequent than the baseline level of introgression, C. robusta alleles are not fixed, even in the core region of the introgression hotspot. Still, linkage-disequilibrium patterns and haplotype-based tests suggest this genomic region is under recent positive selection. We further detected in the hotspot an over-representation of candidate SNPs lying on a cytochrome P450 gene with a high copy number of tandem repeats in the introgressed alleles. Cytochromes P450 are a superfamily of enzymes involved in detoxifying exogenous compounds, constituting a promising avenue for functional studies. These findings support that introgression of an adaptive allele is possible between very divergent genomes and that anthropogenic hybridization can provide the raw material for adaptation of native lineages in the Anthropocene.
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