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

The root of the East African cichlid radiations

<p>Abstract</p> <p>Background</p> <p>For decades cichlid fishes (Perciformes: Cichlidae) of the East African cichlid radiations (Teleostei: Cichlidae) have served as natural experimental subjects for the study of speciation processes and the search for potential speciation key factors. Despite numerous phylogenetic studies dealing with their intragroup relationships, surprisingly little is known about the phylogenetic placement and time of origin of this enigmatic group. We used multilocus DNA-sequence data from five nuclear and four mitochondrial genes and refined divergence time estimates to fill this knowledge gap.</p> <p>Results</p> <p>In concordance with previous studies, the root of the East African cichlid radiations is nested within the so called "Tilapias", which is a paraphyletic assemblage. For the first time, we clarified tilapiine intragroup relationships and established three new monophyletic groups:"Oreochromini", "Boreotilapiini" and a group with a distribution center in East/Central Africa, the "Austrotilapiini". The latter is the founder lineage of the East African radiations and emerged at the Miocene/Oligocene boundary at about 14 to 26 mya.</p> <p>Conclusion</p> <p>Our results provide the first resolved hypothesis for the phylogenetic placement of the megadiverse East African cichlid radiations as well as for the world's second most important aquaculture species, the Nile Tilapia, <it>Oreochromis niloticus</it>. Our analyses constitute not only a robust basis for African cichlid phylogenetics and systematics, but provide a valid and necessary framework for upcoming comparative phylogenomic studies in evolutionary biology and aquaculture.</p

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

Signatures o DNA Methylation across Insects Suggest Reduced DNA Methylation Levels in Holometabola

It has been experimentally shown that DNA methylation is involved in the regulation of gene expression and the silencing of transposable element activity in eukaryotes. The variable levels of DNA methylation among different insect species indicate an evolutionarily flexible role of DNA methylation in insects, which due to a lack of comparative data is not yet well-substantiated. Here, we use computational methods to trace signatures of DNA methylation across insects by analyzing transcriptomic and genomic sequence data from all currently recognized insect orders. We conclude that: 1) a functional methylation system relying exclusively on DNA methyltransferase 1 is widespread across insects. 2) DNA methylation has potentially been lost or extremely reduced in species belonging to springtails (Collembola), flies and relatives (Diptera), and twisted-winged parasites (Strepsiptera). 3) Holometabolous insects display signs of reduced DNA methylation levels in protein-coding sequences compared with hemimetabolous insects. 4) Evolutionarily conserved insect genes associated with housekeeping functions tend to display signs of heavier DNA methylation in comparison to the genomic/transcriptomic background. With this comparative study, we provide the much needed basis for experimental and detailed comparative analyses required to gain a deeper understanding on the evolution and function of DNA methylation in insects

Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny)

Background: Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significant background data. Not knowing how reliable traditional knowledge is, a crucial question concerns the quality of newly produced molecular data. The information content of DNA alignments is rarely discussed, as quality statements are mostly restricted to the statistical support of clades. Here we present a case study of a recently published mollusk phylogeny that contains surprising groupings, based on five genes and 108 species, and we apply new or rarely used tools for the analysis of the information content of alignments and for the filtering of noise (masking of random-like alignment regions, split decomposition, phylogenetic networks, quartet mapping). Results: The data are very fragmentary and contain contaminations. We show that that signal-like patterns in the data set are conflicting and partly not distinct and that the reported strong support for a "rather surprising result" (monoplacophorans and chitons form a monophylum Serialia) does not exist at the level of primary homologies. Split-decomposition, quartet mapping and neighbornet analyses reveal conflicting nucleotide patterns and lack of distinct phylogenetic signal for the deeper phylogeny of mollusks. Conclusion: Even though currently a majority of molecular phylogenies are being justified with reference to the 'statistical' support of clades in tree topologies, this confidence seems to be unfounded. Contradictions between phylogenies based on different analyses are already a strong indication of unnoticed pitfalls. The use of tree-independent tools for exploratory analyses of data quality are highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed

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