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Background In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed. Methods Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R. Results Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found. Discussion Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype.

Previous studies detected an influence of urban characteristics on song traits in passerine birds, that is, song adjustments to ambient noise in urban areas. Several studies already described the effect of weather conditions on the behavior of birds, but not the effect on song traits. We investigate, if song trait variability changes along a continuous urbanity gradient in Frankfurt am Main, Germany. We examined, for the first time on a larger scale, the influence of weather on song parameters. We made song recordings of three common passerine species: the blue and great tit (Cyanistes caeruleus (Linnaeus, 1758) and Parus major Linnaeus, 1758) and the European blackbird (Turdus merula Linnaeus, 1758). We measured different song traits and performed statistical analyses and modeling on a variety of variables—among them urbanity and weather parameters. Remarkably, we found only few cases of a significant influence of urbanity parameters on song traits. The influence of weather parameters (air pressure, atmospheric humidity, air and soil temperatures) on song traits was highly significant. Birds in Frankfurt face high noise pollution and might show different adaptations to high noise levels. The song trait variability of the investigated species is affected more by weather conditions than by urban characteristics in Frankfurt. However, the three species react differently to specific weather parameters. Smaller species seem to be more affected by weather than larger species.

Intraspecific variation of passerine song may influence mate choice and consequently provides a potential mechanism for premating reproductive isolation in birds. Notable geographic variation of songs is particularly common in widespread bird species, such as the coal tit Periparus ater (Aves, Passeriformes, Paridae) having a large trans-Palearctic distribution range including allopatric populations. In this study, measurement and analysis of 16 song parameters from different Western Palearctic populations showed a relatively uniform song in all continental European and the island populations of Corsica and Sardinia. Song variation among and within these populations seems so variable that there is a broad geographical overlap of acoustic parameters between populations. However, songs from northwest African and Cypriot populations had lowest minimum frequencies and were thus significantly different from continental European, Corsican and Sardinian populations. To test for intraspecific species recognition and potential acoustic isolation of different Palearctic populations, we carried out field playback experiments on Central European coal tit males with songs from populations of the Eurasian (Germany, Latvia, Russian Far East, Japan) and the Mediterranean region (northwest Africa, Cyprus, Corsica, Sardinia). Eurasian song types elicited similar strong territorial reactions in Central European coal tits as local control songs. In contrast, none of the Mediterranean songs evoked any notable reaction. Thus, there is geographic variation in coal tit song across continents that coincides with reduced species recognition between Central European and Mediterranean populations.

Songs in passerine birds are important for territory defense and mating. Speciation rates in oscine passerines are so high, due to cultural evolution, that this bird lineage makes up half of the extant bird species. Leaf warblers are a speciose Old-World passerine family of limited morphological differentiation, so that songs are even more important for species delimitation. We took 16 sonographic traits from song recordings of 80 leaf warbler taxa and correlated them with 15 potentially explanatory variables, pairwise, and in linear models. Based on a well-resolved molecular phylogeny of the same taxa, all pairwise correlations were corrected for relatedness with phylogenetically independent contrasts and phylogenetic generalized linear models were used. We found a phylogenetic signal for most song traits, but a strong one only for the duration of the longest and of the shortest element, which are presumably inherited instead of learned. Body size of a leaf warbler species is a constraint on song frequencies independent of phylogeny. At least in this study, habitat density had only marginal impact on song features, which even disappeared through phylogenetic correction. Maybe most leaf warblers avoid the deterioration through sound propagation in dense vegetation by singing from exposed perches. Latitudinal (and longitudinal) extension of the breeding ranges was correlated with most song features, especially verse duration (longer polewards and westwards) and complexity (lower polewards). Climate niche or expansion history might explain these correlations. The number of different element types per verse decreases with elevation, possibly due to fewer resources and congeneric species at higher elevations.

Der Fang von Vögeln zu wissenschaftlichen Zwecken in den Tropen und Subtropen stellt eine Herausforderung für Ornithologen dar. Probleme aufgrund rechtlicher sowie sozioökonomischer und soziokultureller Rahmenbedingungen lassen sich oft durch eine intensive Vorbereitung und Kooperationen mit lokalen Partnern vermeiden oder reduzieren. Beim eigentlichen Fang sind logistische Herausforderungen wie die Materialbeschaffung vor Ort, aber auch die Ökologie einiger überwiegend tropischer Vogelgruppen zu berücksichtigen. Hier wie auch bei der Probennahme und -lagerung beeinflussen die herrschenden Umweltbedingungen die Arbeit, insbesondere extreme Witterung. Problemlösungenlassen sich jedoch teilweise nur schwer verallgemeinern. Wir unterstreichen die Bedeutung lokaler und regionaler Besonderheiten anhand zahlreicher Beispiele aufgrund eigener Erfahrungen. Capturing birds for scientific purposes in tropical and subtropical areas is particularly challenging. Problems due to general judicial, socio-economic and socio-cultural conditions can often be avoided or reduced by an intensive prearrangement and cooperation with local partners. When actually capturing birds, logistical challenges, differences in predation and the ecology of specific tropical bird groups need to be considered. In this respect and also for sampling and sample storage, environmental conditions, especially extreme weather conditions, are factors to be considered. Troubleshooting and resolving issues related to ornithology in the tropical biomes is not always straightforward. Here we emphasize the importance of local and regional peculiarities by numerous examples based on our own experiences.

Kurzfassung der Dissertation an der Johannes Gutenberg-Universität Mainz, Fachbereich Biologie, Institut für Zoologie (2007), betreut durch Prof. Dr. Jochen Martens.

Die mit der Fortpflanzung verbundenen Lautäußerungen der Vögel sind meist artspezifisch, so dass sie als taxonomische Merkmale verwendet werden können. Besondere Relevanz kommt ihnen dabei zu, wenn bei Vögeln, die Gesang erlernen können, Artbildungsprozesse beschleunigt ablaufen. Nach dem biologischen Artkonzept sind Arten Fortpflanzungsgemeinschaften. Ob zwei am selben Ort vorkommende Formen Arten sind, lässt sich also unschwer feststellen. Überlappen ihre Verbreitungsgebiete jedoch nicht, kann ein Aufeinandertreffen mit Hilfe von Klangattrappenversuchen simuliert werden. Ansonsten bleibt – auch auf überartlichem Niveau – nur der Vergleich homologer Lautäußerungen: Er kann deskriptiv nach Höreindruck oder auf Grund der Visualisierung (Sonagramm) oder statistisch mit Hilfe verschiedener dem Sonagramm entnommener Parameter erfolgen. Sofern eine (molekulare) Phylogenie der betreffenden Gattung oder Familie vorliegt, sollten die herangezogenen Parameter auf phylogenetisches Signal hin getestet werden, um rein adaptive Merkmale auszuschließen. Bird vocalizations connected to reproduction are mostly species-specific, hence they may be used as taxonomic characters. They have special relevance when in bird species which are able to learn song speciation processes at an accelerated pace. According to the biological species concept, species are populations which are reproductively isolated from other populations. Thus it can easily be decided, if two forms occurring in the same place are species. But if their distributions do not overlap, a contact can be simulated by means of playback experiments. Otherwise homologous vocalizations have to be compared – like on a supra-specific level: Such comparisons may be performed descriptively according to auditory impression, or based on the visualization (sonagram), or statistically on parameters measured from the sonagram. In case a (molecular) phylogeny of the genus or family under investigation is available, the analyzed parameters should be tested for phylogenetic signal to exclude merely adaptive characters.