Biology subjects

Schroeder, J.

Publications and source records attributed to Schroeder, J..

5 recordsLinked to original sources

bioRxiv2018

A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses

The identification of homologous genes with functional overlap in forward genetic screens is severely limited. Here we report the generation of over 14,000 amiRNA-expressing plants that enable screens of the functionally redundant gene space in Arabidopsis. A protocol is developed here for isolating robust and reproducible amiRNA-mutants. Examples of validation approaches and essential controls are presented for two new amiRNA mutants that exhibit genetically redundant phenotypes and circumvent double mutant lethality. In a forward genetic screen for abscisic acid (ABA)-mediated inhibition of seed germination, amiRNAs that target combinations of known redundant ABA receptor and SnRK2 kinase genes were rapidly isolated, providing a strong proof of principle for this approach. A new ABA insensitive amiRNA line is isolated, which targets three genes encoding avirulence-induced gene2-like (AIG2) genes. A thermal imaging screen for plants with impaired stomatal opening in response to low CO2 exposure led here to isolation of a new amiRNA targeting two essential proteasomal subunits, PAB1 and PAB2. The seed library of 14,000 T2 amiRNA lines generated here provides a new platform for forward genetic screens and is being made available to the Arabidopsis Biological Resource Center (ABRC) and optimized procedures for amiRNA screening and controls are described.\n\nHighlightThe generation of over 14,000 amiRNA-expressing plants is reported that are being made publicly available enabling screens of redundant genes in Arabidopsis. Identification of known and new genes is reported.

plant biology↗

bioRxiv2018

Meta-analysis challenges a textbook example of status signalling: evidence for publication bias

The status signalling hypothesis aims to explain conspecific variation in ornamentation by suggesting that some ornaments signal dominance status. Here, we use multilevel meta-analytic models to challenge the textbook example of this hypothesis, the black bib of house sparrows (Passer domesticus). We conducted a systematic review, and obtained raw data from published and unpublished studies to test whether dominance rank is positively associated with bib size across studies. Contrary to previous studies, our meta-analysis did not support this prediction. Furthermore, we found several biases in the literature that further question the support available for the status signalling hypothesis. First, the overall effect size of unpublished studies was zero, compared to the medium effect size detected in published studies. Second, the effect sizes of published studies decreased over time, and recently published effects were, on average, no longer distinguishable from zero. We discuss several explanations including pleiotropic, population- and context-dependent effects. Our findings call for reconsidering this established textbook example in evolutionary and behavioural ecology, raise important concerns about the validity of the current scientific publishing culture, and should stimulate renewed interest in understanding within-species variation in ornamental traits.

evolutionary biology↗

bioRxiv2017

Male age is associated with extra-pair paternity, but not with extra-pair mating behaviour

Extra-pair paternity is the result of copulation between a female and a male other than her social partner. In socially monogamous birds, old males are most likely to sire extra-pair offspring. The male manipulation and female choice hypotheses predict that age-specific male mating behaviour could explain this old-over-young male advantage. These hypotheses have been difficult to test because copulations and the individuals involved are hard to observe. Here, we studied the mating behaviour and pairing contexts of captive house sparrows, Passer domesticus. Our set-up mimicked the complex social environment experienced by wild house sparrows. We found that middle-aged males, that would be considered old in natural populations, gained most extra-pair paternity. However, both female solicitation behaviour and subsequent extra-pair matings were unrelated to male age. Further, copulations were more likely when solicited by females than those initiated by males (i.e. unsolicited copulations), and unsolicited within-pair copulations were more common than unsolicited extrapair copulations. To conclude, our results did not support either hypotheses regarding age-specific male mating behaviour. Instead, female choice, independent of male age, governed copulation success, especially in an extra-pair context and post-copulatory mechanisms might determine why older males sire more extra-pair offspring.

evolutionary biology↗

bioRxiv2017

A practical guide for inferring reliable dominance hierarchies and estimating their uncertainty

Many animal social structures are organized hierarchically, with dominant individuals monopolizing resources. Dominance hierarchies have received great attention from behavioural and evolutionary ecologists. As a result, there are many methods for inferring hierarchies from social interactions. Yet, there are no clear guidelines about how many observed dominance interactions (i.e. sampling effort) are necessary for inferring reliable dominance hierarchies, nor are there any established tools for quantifying their uncertainty. In this study, we simulated interactions (winners and losers) in scenarios of varying steepness (the probability that a dominant defeats a subordinate based on their difference in rank). Using these data, we (1) quantify how the number of interactions recorded and hierarchy steepness affect the performance of three methods, (2) propose an amendment that improves the performance of a popular method, and (3) suggest two easy procedures to measure uncertainty in the inferred hierarchy. First, we found that the ratio of interactions to individuals required to infer reliable hierarchies is surprisingly low, but depends on the hierarchy steepness and method used. We then show that Davids score and our novel randomized Elo-rating are the two best methods, whereas the original Elo-rating and the recently described ADAGIO perform less well. Finally, we propose two simple methods to estimate uncertainty at the individual and group level. These uncertainty measures further allow to differentiate non-existent, very flat and highly uncertain hierarchies from intermediate, steep and certain hierarchies. Overall, we find that the methods for inferring dominance hierarchies are relatively robust, even when the ratio of observed interactions to individuals is as low as 10 to 20. However, we suggest that implementing simple procedures for estimating uncertainty will benefit researchers, and quantifying the shape of the dominance hierarchies will provide new insights into the study organisms.\n\nHighlightsO_LIDavids score and the randomized Elo-rating perform best.\nC_LIO_LIMethod performance depends on hierarchy steepness and sampling effort.\nC_LIO_LIGenerally, inferring dominance hierarchies requires relatively few observations.\nC_LIO_LIThe R package \"aniDom\" allows easy estimation of hierarchy uncertainty.\nC_LIO_LIHierarchy uncertainty provides insights into the shape of the dominance hierarchy.\nC_LI

animal behavior and cognition↗

bioRxiv2017

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

The identification of genomic rearrangements, particularly in cancers, with high sensitivity and specificity using massively parallel sequencing remains a major challenge. Here, we describe the Genome Rearrangement IDentification Software Suite (GRIDSS), a high-speed structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph assembler. By combining assembly, split read and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line and patient tumour data, recently winning SV sub-challenge #5 of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods. GRIDSS identifies non-template sequence insertions, micro-homologies and large imperfect homologies, and supports multi-sample analysis. GRIDSS is freely available at https://github.com/PapenfussLab/gridss.

bioinformatics↗