Repertoire-wide gene structure analyses : a case study comparing automatically predicted and manually annotated gene models

Background The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative. Results Our results show that the subset of genes chosen for manual annotation by a research community (3.5–7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species’ gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities. Conclusions In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative

The role of the triangle singularity in Λ(1405)\Lambda(1405) production in the π−p→K0πΣ\pi^-p\rightarrow K^0\pi\Sigma and pp→pK+πΣpp\rightarrow pK^+\pi\Sigma processes

We have investigated the cross section for the $\pi^-p\rightarrow K^0\pi\Sigma$ and $pp\rightarrow pK^+\pi\Sigma$ reactions paying attention to a mechanism that develops a triangle singularity. The triangle diagram is realized by the decay of a $N^*$ to $K^*\Sigma$ and the $K^*$ decay into $\pi K$, and the $\pi\Sigma$ finally merges into $\Lambda(1405)$. The mechanism is expected to produce a peak around $2140$ MeV in the $K\Lambda(1405)$ invariant mass. We found that a clear peak appears around $2100$ MeV in the $K\Lambda(1405)$ invariant mass which is about $40$ MeV lower than the expectation, and that is due to the resonance peak of a $N^*$ resonance which plays a crucial role in the $K^*\Sigma$ production. The mechanism studied produces the peak of the $\Lambda(1405)$ around or below 1400 MeV, as is seen in the $pp\rightarrow pK^+\pi\Sigma$ HADES experiment.Comment: 12 pages, 9 figure

Eurasian Blackbirds (<i>Turdus merula</i>) and their gastrointestinal parasites : A role for parasites in life-history decisions?

Parasites are increasingly being recognized as potent agents of selection. Gastrointestinal parasites, however, have largely been ignored. The aim of the present thesis was to contribute to the still scarce knowledge about gastrointestinal parasites in ecological, evolutionary and behavioural studies and to critically elucidate methodological aspects of indirect parasitic assays. Fecal samples were collected from an urban, individually marked population of Eurasian Blackbirds (Turdus merula L.,1758) and were examined for eggs and oocysts of gastrointestinal parasites. Four parasitic taxa commonly occurred in the population: protozoans of the genus Isospora, nematodes of the genus Capillaria, cestodes and acanthocephalans. Isospora spp. and Capillaria spp. were the most frequent parasites, infecting 53 % and 56 % of birds, respectively. These results markedly differed from a similar study conducted 35 years ago (Binder 1971) and explicitly demonstrate, that the parasite communities and prevalences assessed from single populations can not be taken as representative for the whole species, as has repeatedly been done in the past. It was investigated whether these parasites impose fitness costs on their hosts. It is a central assumption of life-history theory that the availability of energy or resources is limited. Thus, the investment in one costly trait can only occur at the expense of another costly trait (Stearns 1992). In adult male blackbirds I found a cost of parasitism. Males that had invested more heavily in the feeding of nestlings, were also more likely to be infected with gastrointestinal parasites. Female infection prevalence was very high (95%) and significantly higher than in males. Since females are alone responsible for nest building, egg laying and incubating they probably incur high reproductive costs already prior to the nestling feeding stage. In nestlings no direct cost of parasitism on aspects of somatic growth could be found. Quite on the contrary, nestling size, measured as tarsus length and wing length were positively associated with prevalence of coccidian infection. I conclude that infections with Isospora spp. do not impose the predicted trade-off on blackbird nestlings. Rather, infections with Isopora spp. seem to be a function of feeding rate. Thus, an alternative trade-off, namely between energy intake and risk of infection seems to become of primary importance for blackbird nestlings. It is a still commonly practised method to assess a bird’s infection status by the examination of a single sample, although it is known that the failure to find parasitic stages does not reliably indicate the absence of an infection. Several properties of the host and of the parasites potentially influence the probability to detect parasitic stages in samples. One such property is the temporal fluctuation of oocyst or egg shedding by parasites. In fecal samples of adult and nestling blackbirds I found oocysts of Isospora spp. to be shedded more frequently and at higher intensities in the afternoon. This periodic phenomenon, the diurnal shedding of isosporan oocysts in the feces, is in congruence with results on Isospora oocyst shedding in other bird species. In order to give future investigators a tool to estimate the quality of their indirect method, I developed a model in which the calculation of the parameter pinf determines the probabilty to falsely denote an infected individual as “not infected” if no parasites can be found in n samples collected from this individual. The model showed that in the blackbird population it was not possible to reliably (with a probability of 95%) denote an individual as not infected after the evaluation of a single fecal sample. These results suggest that great consciousness and caution have to be used in the methodological planning of studies involving indirect parasitic assays

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.Peer reviewe

The importance of biobanking in molecular taxonomy, with proposed definitions for vouchers in a molecular context

Volume: 365Start Page: 67End Page: 7

Equivariant Neural Tangent Kernels

Equivariant neural networks have in recent years become an important technique for guiding architecture selection for neural networks with many applications in domains ranging from medical image analysis to quantum chemistry. In particular, as the most general linear equivariant layers with respect to the regular representation, group convolutions have been highly impactful in numerous applications. Although equivariant architectures have been studied extensively, much less is known about the training dynamics of equivariant neural networks. Concurrently, neural tangent kernels (NTKs) have emerged as a powerful tool to analytically understand the training dynamics of wide neural networks. In this work, we combine these two fields for the first time by giving explicit expressions for NTKs of group convolutional neural networks. In numerical experiments, we demonstrate superior performance for equivariant NTKs over non-equivariant NTKs on a classification task for medical images.Comment: 13 pages + 5 pages appendice