Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa

Background and AimsDioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY₁Y₂ sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes.MethodsWe flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons.Key ResultsWe identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes.ConclusionsThe X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage.     

Surprisingly long survival of premature conclusions about naked mole-rat biology

Naked mole-rats express many unusual traits for such a small rodent. Their morphology, social behaviour, physiology, and ageing have been well studied over the past half-century. Many early findings and speculations about this subterranean species persist in the literature, although some have been repeatedly questioned or refuted. While the popularity of this species as a natural-history curiosity, and oversimplified story-telling in science journalism, might have fuelled the perpetuation of such misconceptions, an accurate understanding of their biology is especially important for this new biomedical model organism. We review 28 of these persistent myths about naked mole-rat sensory abilities, ecophysiology, social behaviour, development and ageing, and where possible we explain how these misunderstandings came about.     

Embryo ecology: Developmental synchrony and asynchrony in the embryonic development of wild annual fish populations

Embryo–environment interactions are of paramount importance during the development of all organisms, and impacts during this period can echo far into later stages of ontogeny. African annual fish of the genus Nothobranchius live in temporary pools and their eggs survive the dry season in the dry bottom substrate of the pools by entering a facultative developmental arrest termed diapause. Uniquely among animals, the embryos (encased in eggs) may enter diapause at three different developmental stages. Such a system allows for the potential to employ different regulation mechanisms for each diapause. We sampled multiple Nothobranchius embryo banks across the progressing season, species, and populations. We present important baseline field data and examine the role of environmental regulation in the embryonic development of this unique system. We describe the course of embryo development in the wild and find it to be very different from the typical development under laboratory conditions. Development across the embryo banks was synchronized within and across the sampled populations with all embryos entering diapause I during the rainy season and diapause II during the dry season. Asynchrony occurred at transient phases of the habitat, during the process of habitat desiccation, and at the end of the dry season. Our findings reveal the significance of environmental conditions in the serial character of the annual fish diapauses.     

Is sampling subjectivity a distorting factor in surveys for vegetation diversity?

Sampling design has long been a key methodology issue of vegetation science. There are still unsolved problems, amongst which the influence of the positioning (spatial arrangement) of plots remains a basic one. Random sampling is considered the only statistically valid option, along with its amendment by stratifying. However, huge amounts of plot-sample data originated from using subjective plot positioning, involving a great deal of the author’s judgement, experience and bias. Field studies examining the role of subjectivity within a larger area (a landscape) are lacking. In the presented case-study, datasets sampled using computer-based geographically stratified random (R) and field-based subjective (S) designs are compared. In 1999–2000, 120 R and 244 S plots were spread across some 270 km². Their properties are compared regarding the differences in vegetation variability by ordination, and diversity by rarefaction. Although the differences are not conspicuous, both datasets partly contain different vegetation types and the S dataset contains at least some species-richer plots. The number of R plots had been clearly underrated while the expected species diversity values were nearly reached by the S. More R than S plots would probably be needed to reach the expected diversity maximum.     

Evaluation of potential deer browsing impact on sunflower (<Emphasis Type="Italic">Helianthus annus</Emphasis>)

Large herbivores are the key species for game management in the Central Europe. Analyses of factors affecting the feeding behaviour of herbivores and consequences of their browsing are therefore highly important both for farmers and for game managers as the protective measurements should be focused on the most threatened fields. The influence of fallow (Dama dama) and roe deer (Capreolus capreolus) browsing during vegetation period on sunflower production was studied. The experiment was carried out in 2006 on a field located near a forest complex. We marked out pairs of paired permanent plots and monitored deer impact regularly from the emergence of plants until the harvest. Herbivores damaged the sunflower intensively immediately after the emergence at the height of 1 to 2 cm above the ground. When the plants had reached approximately 15-40 cm in height, deer browsed the top shoots and as the plants grew higher the browsing was restricted to leaves or to substitute stems of the previously browsed plants. Sunflower ceased to attract big herbivores in flowering stage. Browsing significantly affected the yield of seeds. Approximately one half of the plants that had been damaged in early stage died as well as 12.5% of plants that had been damaged at second term; the rest produced substitute stems. Almost 33% of the substitute stems did not form disc florets; the second third of them formed disc florets with a diameter of 6-8 cm, and the last third set disc florets with a diameter of 8-10 cm.     

Reactions to disturbances in the context of antipredatory behaviour in a solitary subterranean rodent

We investigated reactions of free-living silvery mole-rats (Heliophobius argenteocinereus) to anthropogenic disturbances. Mole-rats detected soil vibrations caused by man carefully walking at a distance of up to 6 m (proved by radio-telemetry). Occasionally, mole-rats encountered outside a nest retreated there after this type of disturbance. After having their burrows broken into, the mole-rats retreated into deep tunnels, separating themselves from the rest of the burrows by soil plugs. Trapping success of silvery mole-rats using live traps for subterranean rodents was low, which contrasts with data so far published on social bathyergids. Antipredatory function of examined behaviours is discussed.