No abstract

Maximum likelihood analyses based on the internal transcribed spacer region of nuclear ribosomal DNA and the chloroplast protein coding gene rps4 were conducted to investigate phylogenetic relationships among species of Plagiochila and to reconstruct the ranges of natural species groups within the genus. Based on the results of the molecular analyses and on morphological evidence, the tropical African species of Plagiochila are assigned to the sections Arrectae, Cucullatae, Hylacoetes, Rutilantes, Vagae, and the new sect. Africanae ( P. barteri, P. colorans ). With the exception of Africanae, all sections possess intercontinental ranges; their centers of diversity are in the tropics. Clade and species diversity in Africa is lower than in other parts of the tropics and may reflect drought periods of the Pleistocene. Intercontinental ranges at specific level exist between tropical America and Africa whereas similarities between tropical Asia and Africa were only recovered at the sectional level. ITS sequence sets were used to test the monophyly of species with intercontinental ranges and to explore the development of the Afro‐American range of P. boryana. A well supported clade with accessions of P. boryana from Bolivia and Uganda is nested in the robust neotropical Hylacoetes. This topology and the low genetic distance of the different P. boryana accessions provide some evidence for long‐range dispersal of P. boryana eastwards across the Atlantic, originating from the Neotropics. An African origin of the Vagae clade which includes neotropical and paleotropical taxa is suggested by the clustering of accessions from the East African Islands at the base of this clade. In addition, the presented data support the hypothesis of several switches from Africa to Asia and vice versa. A derived clade within Vagae includes accessions from the African mainland and the Neotropics. Our results seem to indicate that the extant tropical African Plagiochila flora is a mixture of old elements and rather recent immigrants.

Background DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n = 6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled. Results We simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10 kb up- and downstream regions adjacent to the gene body. Conclusion Temporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.

Epigenetic mechanisms can alter gene expression without a change in the nucleotide sequence and are increasingly recognized as important mechanisms that can generate phenotypic diversity. Most of our current knowledge regarding the origin and role of epigenetic variation comes from research on plants or mammals, often in controlled rearing conditions. Epigenetic research on birds in their natural habitats is still in its infancy, but is needed to answer questions regarding the origin of epigenetic marks and their role in phenotypic variation and evolution. Here we review the potential for studying epigenetic variation in natural bird systems. We aim to provide insights into (1) the origin of epigenetic variation, (2) the relationship between epigenetic variation and trait variation, and (3) the possible role of epigenetic variation in adaptation to changing environments. As there is currently little research on epigenetics in wild birds, we examine how findings on other taxa such as plants and mammals relate to birds. We also examine some of the pros and cons of the most commonly used methods to study patterns of DNA methylation in birds, and suggest some topics we believe need to be addressed to develop the field of wild avian epigenetics further. Zusammenfassung Anwendung von Epigenetik an freilebenden VögelnEpigenetische Mechanismen sind in der Lage die Aktivität eines Gens zu beeinflussen ohne die DNA-Sequenz zu veränderen und werden zunehmend als wichtige Mechanismen erkannt um phänotypische Diversität generieren zu können. Der größte Teil unseres derzeitigen Wissens über den Ursprung und die Rolle epigenetischer Variationen stammt aus der Erforschung von Pflanzen oder Säugetieren, oft unter kontrollierten Aufzuchtbedingungen. Die epigenetische Forschung an Vögeln in ihren natürlichen Lebensräumen steckt noch in den Kinderschuhen, ist jedoch erforderlich, um Fragen zur Herkunft der epigenetischen Merkmale und ihrer Rolle bei der Variation und Evolution des Phänotyps zu beantworten. Hier untersuchen wir das Potenzial zur Untersuchung der epigenetischen Variation in natürlichen Vogelsystemen. Wir möchten Einblicke geben in Communicated by M. Wink.