Effects of cold winters and roost site stability on population development of non-native Asian ring-necked parakeets (Alexandrinus manillensis) in temperate Central Europe – Results of a 16-year census

Asian ring-necked parakeets (Alexandrinus manillensis, formerly Psittacula krameri, hereafter RNP) first bred in Germany in 1969. Since then, RNP numbers increased in all three major German subpopulations (Rhineland, Rhine-Main, Rhine-Neckar) over the period 2003–2018. In the Rhine-Neckar region, the population increased to more than fivefold within only 15 years. Interestingly, there was no significant breeding range expansion of  RNP in the period 2010–2018. In 2018, the total number of RNP in Germany amounted to >16,200 birds. Differences in RNP censuses between years were evident. Surprisingly, cold winters (extreme value, −13.7 °C) and cold weather conditions in the breeding season (coldest month average, −1.36 °C) were not able to explain between-year variation. This finding suggests that in general winter mortality is low – with exceptions for winters 2008/2009 and 2009/2010, and a population-relevant loss of broods is low in our study population. Surprisingly, the social behaviour in terms of spatio-temporal stability of roost sites could well explain positive and negative population trends. Years of spatially stable and regularly used roost sites seem to correlate with increasing population sizes. In contrast, known shifts of RNP among different roost sites or the formations of new roost sites by split are related to population stagnation or a decrease in numbers. Climate change may lead to further range expansion as cities not suitable yet for RNP may become so in the near future.

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

Data from: Contrasting heterozygosity-fitness correlations across life in a long-lived seabird

Selection is a central force underlying evolutionary change and can vary in strength and direction, for example across time and space. The fitness consequences of individual genetic diversity have often been investigated by testing for multi-locus heterozygosity-fitness correlations (HFCs), but few studies have been able to assess HFCs across life stages and in both sexes. Here, we test for HFCs using a 26-year longitudinal individual-based dataset from a large population of a long-lived seabird (the common tern, Sterna hirundo), where 7974 chicks and breeders of known age were genotyped at 15 microsatellite loci and sampled for life-history traits over the complete life cycle. Heterozygosity was not correlated with fledging or post-fledging prospecting probabilities, but was positively correlated with recruitment probability. For breeders, annual survival was not correlated with heterozygosity, but annual fledgling production was negatively correlated with heterozygosity in males and highest in intermediately heterozygous females. The contrasting HFCs among life stages and sexes indicate differential selective processes and emphasize the importance of assessing fitness consequences of traits over complete life histories

Psittinus Blyth 1842

Psittinus Blyth Type species: Psittacus malaccensis Latham = Psittacus cyanurus J. R. Forster Morphology/distribution: red bend of wing and red underwing coverts; small size, very short tail; sexually dichromatic; yellow edging on wing coverts; males with bluish head, otherwise predominantly green head; red upper mandible, females with brown head and bill. Distribution: Malay Peninsula to Borneo and Sumatra. Psittinus, which is represented by nominate cyanurus in our dataset, is sister to a clade formed by Tanygnathus, Belocercus and Psittacula s.s. It represents a long branch within the Psittacula s.l. group, which together with its distinct morphological traits supports its status as a separate genus.Published as part of Braun, Michael P., Datzmann, Thomas, Arndt, Thomas, Reinschmidt, Matthias, Schnitker, Heinz, Bahr, Norbert, Sauer-Gürth, Hedwig & Wink, Michael, 2019, A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, † Mascarinus) with taxonomic implications, pp. 547-562 in Zootaxa 4563 (3) on pages 557-558, DOI: 10.11646/zootaxa.4563.3.8, http://zenodo.org/record/260147

Belocercus S. Muller 1847

Belocercus S. Müller Type species: Psittacus barbatulatus Bechstein = Psittacus longicauda Boddaert Morphology/distribution: no red shoulder patch; medium size, very long tail; male with black lores, horizontal black beard stripe, green crown and rose-coloured cheeks, not encircling hindneck; upper mandible red, lower mandible brown; females duller with completely dark-brown bill and shorter tail. Distribution: Malay Peninsula to Borneo and Sumatra. Several subspecies exist within the B. longicauda complex, and further investigation is required to resolve the evolutionary history and taxonomy of Belocercus, which shares a common ancestor with Psittacula s.s. Based on its unclear phylogenetic position, with low support values, and morphological differences from this clade, however, we regard it as a separate genus.Published as part of Braun, Michael P., Datzmann, Thomas, Arndt, Thomas, Reinschmidt, Matthias, Schnitker, Heinz, Bahr, Norbert, Sauer-Gürth, Hedwig & Wink, Michael, 2019, A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, † Mascarinus) with taxonomic implications, pp. 547-562 in Zootaxa 4563 (3) on page 558, DOI: 10.11646/zootaxa.4563.3.8, http://zenodo.org/record/260147

New Microsatellite Markers for the Common Tern (Sterna hirundo) Developed with 454 Shot-Gun Pyrosequencing

Long term studies, focusing on population- and socio-biology research, require the unequivocal identification of individuals. DNA studies with Short Tandem Repeats (STR loci) became a widespread tool in population genetics. We used the next-generation sequencing (NGS) approach with 454 shot-gun pyrosequencing to identify 13 new polymorphic STR loci for the Common Tern, Sterna hirundo. To enlarge the marker set we added two more loci originally developed for Black-legged Kittiwake (Rissa tridactyla) and Red-billed Gull (Chroicocephalus scopulinus) and arranged these 15 loci into three multiplex PCR panels for high throughput genotyping. Loci characterization demonstrated that our marker set is of high quality. A PIC value of about 0.67 and a power of exclusion value of 0.99 were reached. Deviation from Hardy-Weinberg expectations of some loci and low frequencies for null alleles are interpreted as a result of inbreeding and founder effect in the investigated tern colony. We used a test data set of this well-studied breeding colony of Common Tern at Banter Lake, Wilhelmshaven, Germany, to perform a parentage test. Parent-chick relationships, known from the social pedigree of that colony, were compared with genetically calculated ones. In order to test our markers and the used parentage program COLONY, we conducted six competing data sets with varying completeness of included parental genotypes. By including fully sampled parent pairs of known family assignment, results were correct for nest mates, single parents and parent pairs. Our marker set provides a powerful tool to investigate life-time reproductive success and other issues of population and socio-biology for Common Terns, e.g. in the aforementioned colony monitored for decades

A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, † Mascarinus) with taxonomic implications

Braun, Michael P., Datzmann, Thomas, Arndt, Thomas, Reinschmidt, Matthias, Schnitker, Heinz, Bahr, Norbert, Sauer-Gürth, Hedwig, Wink, Michael (2019): A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, † Mascarinus) with taxonomic implications. Zootaxa 4563 (3): 547-562, DOI: https://doi.org/10.11646/zootaxa.4563.3.

Palaeornis Vigors 1825

Palaeornis Vigors Type species: Psittacus eupatria Linnaeus fixed here according to Art. 70.3 of the Code (ICZN 1999), misidentified in the original description by Vigors as Psittacus alexandri Linnaeus. Morphology/distribution: red shoulder patch; large size, long tail, very large bill; predominantly green colour; sexual dimorphism; males with broad neck collar and green-bluish head pattern, females without collar. Distribution: S Asia, Seychelles. This genus includes large species of the Psittacula s.l. clade and appears to be closely related to the morphologically similar Alexandrinus parakeets. The most basal taxon within this clade, according to the dataset used, is the extinct † P. wardi E. Newton from the Seychelles. The next taxon that splits off is P. e. magnirostris Ball from the Andaman Islands. The taxon P. e. siamensis Kloss from SE Asia is sister to P. eupatria from the southern Indian subcontinent.Published as part of Braun, Michael P., Datzmann, Thomas, Arndt, Thomas, Reinschmidt, Matthias, Schnitker, Heinz, Bahr, Norbert, Sauer-Gürth, Hedwig & Wink, Michael, 2019, A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, † Mascarinus) with taxonomic implications, pp. 547-562 in Zootaxa 4563 (3) on page 557, DOI: 10.11646/zootaxa.4563.3.8, http://zenodo.org/record/260147

Tanygnathus Wagler 1832

Tanygnathus Wagler Type species: Tanygnathus macrorhynchus Wagler = Psittacus megalorynchos Boddaert Morphology/distribution: no red shoulder patch; medium to large size; very large bills; medium sized, rounded tails; sexual dimorphism weak or absent; yellow edging on wing coverts; black lore and blue crown only in T. gramineus, otherwise predominantly green head, red upper and lower mandible, juveniles duller. Distribution only on islands of the Philippines and Wallacea. The genus Tanygnathus clusters within the former genus Psittacula with high support values. Tanygnathus forms a clade with Psittacula s.s. and Belocercus. Its morphological characters (bill size, tail length and shape, no sexual dimorphism in two of the four species) apparently evolved quite quickly away from the general pattern in Psittacula. The monophyletic clade of T. megalorynchos and T. sumatranus clusters together with Psittinus, Belocercus longicauda, and the Psittacula s.s. clade in our dataset..Published as part of Braun, Michael P., Datzmann, Thomas, Arndt, Thomas, Reinschmidt, Matthias, Schnitker, Heinz, Bahr, Norbert, Sauer-Gürth, Hedwig & Wink, Michael, 2019, A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, † Mascarinus) with taxonomic implications, pp. 547-562 in Zootaxa 4563 (3) on page 558, DOI: 10.11646/zootaxa.4563.3.8, http://zenodo.org/record/260147

Psittacula Braun & Datzmann & Arndt & Reinschmidt & Schnitker & Bahr & Sauer-Gürth & Wink 2019, s.s.

Psittacula s.s. Cuvier Type species: Psittacus alexandri Linnaeus Morphology/distribution: no red shoulder patch; medium to large size; sexual dimorphism; yellow patch on wing coverts in most taxa; males with red upper mandibles; unique grey to bluish head pattern with bold black lores and bold black stripe on lower cheeks. Distribution: Southern Asia to Bali. Based on high support values, only three other taxa, P. derbiana Fraser, P. a. abbotti Oberholser, and P. a. fasciata Statius Müller, remain in core Psittacula. Based on morphology, P. caniceps Blyth (for details see Arndt 2008; Forshaw 2010), which was not genetically sampled, should also remain in Psittacula s.s. The taxon fasciata is currently treated as a subspecies of P. alexandri, but based on genetic distance and morphology, separate species status should be considered. The taxon abbotti is also in need of further taxonomic investigation. If only monophyletic groups are considered species, P. alexandri should be split into two distinct species: P. alexandri with completely red bill in both sexes and P. fasciata with black bill in females and red upper and black lower mandible in males. Further investigations using more individuals and sampling of all wild populations are needed for deeper insights into the evolutionary history of this species complex. between the clades alexandri and fasciata / abbotti. CYTB p-distance values are a measure of divergence time (MYA).Published as part of Braun, Michael P., Datzmann, Thomas, Arndt, Thomas, Reinschmidt, Matthias, Schnitker, Heinz, Bahr, Norbert, Sauer-Gürth, Hedwig & Wink, Michael, 2019, A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, † Mascarinus) with taxonomic implications, pp. 547-562 in Zootaxa 4563 (3) on pages 558-559, DOI: 10.11646/zootaxa.4563.3.8, http://zenodo.org/record/260147