Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution

Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.

Vineyards, but not cities, are associated with lower presence of a generalist bird, the Common Blackbird (Turdus merula), in Western France

Background Land-use change is one of the main drivers of the global erosion of biodiversity. In that context, it is crucial to understand how landscape characteristics drive the presence of rare endangered species. Nevertheless, it is also important to study common species in multiple habitats, because they represent a large proportion of biodiversity and are essential to maintain ecological functions. Interestingly, some habitats, as farmlands with permanent crops (e.g. vineyards), have been overlooked in the literature. Methods In this study, we investigated the distribution of a widespread and common bird species, the Common Blackbird (Turdus merula), within and between the three main habitats of our study area (rural Western France). We specifically focused on (1) woodlands, (2) farmlands with a high vineyard coverage, and (3) moderately urbanized areas. Specifically, we aimed to assess the beneficial and detrimental effects of these habitats and their fine-scale composition on the presence of a common bird species, relying on a survey by point counts (nearly 100 locations). We studied the effects of habitats and gradients of fine-scale habitat composition on blackbird presence using logistic regression analyses. Results Blackbirds were present in all studied habitats. However, their presence varied between habitats, being lower in vineyards than in woodlands and cities. In woodlands and cities, fine-scale analyses did not reveal any component driving the species’ presence. However, we found that shrub and tree vegetation cover had a significant positive effect on blackbird presence in vineyards. Conclusions Our results are in agreement with the definition of a generalist species. Interestingly, species distribution varied between habitats. The high presence of blackbirds in urban areas suggests that medium-sized cities, despite their artificialization, do not constrain the settlement of this former forest specialist and that green spaces may allow blackbirds to thrive in medium-sized cities. On the contrary, we found an impoverished presence of blackbirds in vineyards and a positive effect of vegetation on their presence in these landscapes. This suggests that permanent crops, and more generally farmlands, may impose important constraints to common species. Future studies should examine how to enhance biodiversity through agricultural management policies, especially in vineyards.

Light and territoriality : A preliminary report on a capture-recapture study of common Blackbird (Turdus Merula)

The natural light conditions and the artificial lighting of the habitats affect the quality of bird territories and the territorial behaviour of birds. However, we know almost nothing about the evolutionary consequences of light on birds. In the biomonitoring part of the project entitled “ Development of international research environment for light pollution studies”, which is carried on in Bárdudvarnok in Somogy county, Hungary, we study the apparent survival probability, adaptive morphological characteristics and area fidelity in Common Blackbird populations living in territories under different light conditions. In this preliminary report, we also describe the methods of our studies - individual marking of birds, capture and recapture, measurement of body weight, wing length and other ecomorphological parameters - and the types of data collected. Based on the outcomes of the data collection planned to continue for several years, we can formulate proposals for the design and application of artificial lighting resulting in the reduction of the adverse effects of light pollution.

Hedgehogs, Squirrels, and Blackbirds as Sentinel Hosts for Active Surveillance of Borrelia miyamotoi and Borrelia burgdorferi Complex in Urban and Rural Environments

Lyme borreliosis (LB), caused by spirochetes of the Borrelia burgdorferi sensu lato (s.l.) complex, is one of the most common vector-borne zoonotic diseases in Europe. Knowledge about the enzootic circulation of Borrelia pathogens between ticks and their vertebrate hosts is epidemiologically important and enables assessment of the health risk for the human population. In our project, we focused on the following vertebrate species: European hedgehog (Erinaceus europaeus), Northern white-breasted hedgehog (E. roumanicus), Eurasian red squirrel (Sciurus vulgaris), and Common blackbird (Turdus merula). The cadavers of accidentally killed animals used in this study constitute an available source of biological material, and we have confirmed its potential for wide monitoring of B. burgdorferi s.l. presence and genospecies diversity in the urban environment. High infection rates (90% for E. erinaceus, 73% for E. roumanicus, 91% for S. vulgaris, and 68% for T. merula) were observed in all four target host species; mixed infections by several genospecies were detected on the level of individuals, as well as in particular tissue samples. These findings show the usefulness of multiple tissue sampling as tool for revealing the occurrence of several genospecies within one animal and the risk of missing particular B. burgdorferi s.l. genospecies when looking in one organ alone.

Nest use of common blackbird Turdus merula Linnaeus 1758 by the Eurasian collared-dove Streptopelia decaocto Frivaldsky 1838 in an urban habitat

Se reporta un episodio de uso de un nido de mirlo Turdus merula por parte de una pareja de tórtola turca Streptopelia decaocto, el cual modificaron agregándole una plataforma, en una zona residencial en la ciudad de Madrid (España) durante mayo de 2018. El nido fue construido por el mirlo durante un periodo de unos 5 días, y 13 días después fue usado por una pareja de tórtola turca, donde la hembra colocó dos huevos, eclosionando dos semanas después. Este constituye el primer reporte de uso de nido de mirlo por parte de la tórtola turca. The use by the Eurasian collared-dove Streptopelia decaocto of a nest of common blackbird Turdus merula is reported, which was modified by adding a platform, in an urban area in Madrid (Spain) in May 2018. The nest was constructed by Blackbirds, and thirteen days later was used by a pair of a Eurasian collared-dove, where the female laid two eggs. This represents the first record of interspecific nest use by Eurasian collared-dove.

High susceptibility of the laboratory-reared biting midges Culicoides nubeculosus to Haemoproteus infections, with review on Culicoides species that transmit avian haemoproteids

Haemosporidian parasites belonging to Haemoproteus cause avian diseases, however, vectors remain unidentified for the majority of described species. We used the laboratory-reared biting midges Culicoides nubeculosus to determine if the sporogonic development of three widespread Haemoproteus parasites completes in this insect. The midges were reared and fed on one common blackbird, white wagtail and thrush nightingale naturally infected with Haemoproteus minutus, Haemoproteus motacillae and Haemoproteus attenuatus, respectively. The engorged females were dissected in order to follow their sporogonic development. Microscopic examination was used to identify sporogonic stages. Bayesian phylogeny based on partial cytochrome b gene was constructed in order to determine phylogenetic relationships among Culicoides species-transmitted haemoproteids. All three parasites completed sporogony. Phylogenetic analysis placed Culicoides species transmitted haemoproteids in one well-supported clade, proving that such analysis readily indicates groups of dipteran insects transmitting avian haemoproteids. Available data show that 11 species of Culicoides have been proved to support complete sporogony of 18 species of avian haemoproteids. The majority of Culicoides species can act as vectors for many Haemoproteus parasites, indicating the low specificity of these parasites to biting midges, whose are globally distributed. This calls for control of haemoproteid infections during geographical translocation of infected birds.

Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula)

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.