Locus-aware decomposition of gene trees with respect to polytomous species trees

Background

Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values.

Results

We investigate the locus tree inference problem as a possible alternative that combines the advantages of both approaches. We present several algorithms to solve the problem in the parsimony framework. We introduce a novel tree mapping, which allows us to obtain a heuristic solution to the problems of locus tree inference and duplication classification.

Conclusions

Our approach allows for faster comparisons of gene and species trees and improves known algorithms for duplication inference in the presence of polytomies in the species trees. We have implemented our algorithms in a software tool available at https://github.com/mciach/LocusTreeInference.

     

Do Antarctic populations represent local or widespread phylogenetic and ecological lineages? Complicated fate of bipolar moss concepts with <Emphasis Type="Italic">Drepanocladus longifolius</Emphasis> as a case study

Bipolar moss species, extreme examples of large and disjunctive geographical ranges, belong to the most important components of the vegetation cover in Antarctica. Their appropriate taxonomic interpretations are essential for fine-scale biogeographical considerations but our knowledge on their phylogenetic affinities still remains limited. Here, we address the history of the Antarctic populations of Drepanocladus longifolius, a moss species widely considered a bipolar taxon. First, based on a worldwide sampling, we verify its assumed bipolar status. Then, we ask whether its current Antarctic populations have persisted throughout at least the last major glaciation in situ or, alternatively, are they a recent, postglacial element. Phylogenetic analyses together with investigation of morphological characters were used to infer relationships among accessions representing the whole distribution range of the taxon. Morphological and phylogenetic data strictly segregated specimens from the Southern and the Northern Hemisphere, with an exception of Australian populations that were included in the latter group. The Antarctic, sub-Antarctic and South American populations belong to a single clade and are treated as D. longifolius s. str., which consequently is not a bipolar taxon. All Northern Hemisphere populations and the ones from Australia represent D. capillifolius, a lately neglected taxon, which thus displays a true bipolar distribution pattern but not comprising the Antarctic and South American populations. These results provide a sound example of key importance of a detailed taxonomical and phylogenetic treatment as a basis for biogeographical studies. In D. longifolius s. str., a homogeneity in all non-coding nuclear and plastid regions was observed throughout the whole range. It contrasted with the presence of one missense mutation in the rps4 gene in all examined Antarctic populations, which correlated with their distinct ecological situation. While identity of non-coding sequences in D. longifolius populations indicates a postglacial recruitment of extant Antarctic populations from extra-regional locations rather than a long-term in situ survival, the mutation in the rps4 gene may be hypothesised to reflect an adaptive response of plants to the Antarctic environment.     

Contrasting patterns of molecular diversity and Wolbachia infection in bisexual and parthenogenetic Strophosoma weevils (Coleoptera: Curculionidae)

It has been postulated that parthenogenesis in weevil species is of hybrid origin, but some have speculated that Wolbachia infection plays a role through the modification of host breeding systems. Here we focus on Strophosoma weevils, which are known to be pests in young forest stands. Using molecular data, we investigated the diversity of the two most common Strophosoma species in Europe: S. capitatum, which reproduces bisexually, and S. melanogrammum, which is parthenogenetic. Also researched were their associations with the endosymbiotic bacterium Wolbachia. These species of weevil were found to be clearly distinguishable based on their mitochondrial DNA, with the bisexual taxa being more diverse. However, the nuclear DNA divergence of the two species was very low, and the parthenogenetic taxon was found to be heterozygous. Wolbachia infection was detected in all individuals of the S. melanogrammum populations and less than half of the S. capitatum populations. Moreover, multiple Wolbachia strains were found in both taxa (two in the former and three in the latter). The results of this research suggest that parthenogenesis in this genus is of hybrid origin and that Wolbachia could have played a role in speciation of these weevils.     

Mathematical interpretation of dose-response curves

The dose-response of an individual organism can be described by a step functions if the organism survives when the dose is below a certain lethal level and dies when this level is exceeded. If, in a population of organism, the lethal dose for an individual has a unimodal distribution, the latter's properties will determine the shape of the population's response in the following manner. If the distribution is symmetric the dose-response curve has a symmetric sigmoid shape when plotted on linear coordinates. The location of the inflection point and the curve's slope around it are determined by the distribution's mode and variance. When the distribution is skewed, the dose-response curve has an asymmetric sigmoid shape which becomes reminiscent of an exponential decay when the distribution is strongly skewed to the right. The population's dose-response curve can be constructed by integration of the step changes over the distribution range. The step function representing the dose-response of an individual organism can be approximate by a Fermi function, and the distribution of an lethal doses can be represented by the Weibull distribution function. When the two functions are combined, the resulting dose-response of the populationS(X)), which is the fraction of survivors after exposure to a doseX, is given by:S(X)=∫ ₀ ¹ [1/{+exp{(X-X _c (φ))/a _i ]}]dω whereX _c (ω)={(1/b)[-ln(1-ω)]}^(1/n),n andb being the constants of the Weibull distribution anda _i an arbitrarily small number, i.e.a _i ≪[X−X _c (ϕ)], whose actual magnitude is of little significance. This model can be used to determine the underlying distributions of experimental dose-response relationship. It was applied to published survival data of microorganisms exposed to pulsed electric field, X-ray radiation and ozone to show that the different observed shapes of the dose-response curve, and shifts between them, can be expressed in terms of the correponding distribution parameters, namely the mode, variance and skewness.     

Photothermal control of the imposition of summer dormancy in Poabulbosa, a perennial grass geophyte

Poa bulbosa L., like many other Mediterranean geophytes, grows in the winter and enters a phase of summer dormancy in the spring. Summer dormancy enables these plants to survive the hot and dry summer. Long days are the main environmental factor active in the induction of summer dormancy in P . bulbosa and elevated temperatures accelerate dormancy development. P . bulbosa becomes dormant earlier than most other species that grow actively in the winter. Previous studies suggested that pre-exposure of P . bulbosa to short days and low temperatures during the autumn and early winter increased its sensitivity to photoperiodic induction in late winter, and thus enabled the early imposition of dormancy. To study this hypothesis, experiments were carried out under controlled photothermal conditions in the phytotron, under natural daylight extended with artificial lighting. The critical photoperiod for induction of summer dormancy at an optimal temperature (22/17°C day/night) was between 11 and 12 h. Photoperiods shorter than 12 h were noninductive, while 14- and 16-h days were fully inductive. A night break of 1 h of light given at the middle of the dark period of an 8-h photoperiod also resulted in full induction of dormancy. Pre-exposure to either low temperature (chilling at 5°C) or to short days of 8 h (SD) enhanced the inductive effect of subsequent 16-h long days (LD). The enhancing effect of chilling and SD increased with longer duration, i.e. fewer LDs were required to impose dormancy. However, the day-length during the low-temperature pretreatment had no effect on the level of induction at the following LD. Chilling followed by SD did not induce dormancy. The relevance of these responses to the development and survival of P . bulbosa in its natural habitat is discussed.     

Ischemic preconditioning and superoxide dismutase protect against endothelial dysfunction and endothelium glycocalyx disruption in the postischemic guinea-pig hearts

The effect of ischemic preconditioning and superoxide dismutase (SOD) on endothelial glycocalyx and endothelium-dependent vasodilation in the postischemic isolated guinea-pig hearts was examined. Seven groups of hearts were used: group 1 underwent sham aerobic perfusion; group 2 was subjected to 40 min global ischemia without reperfusion; group 3, 40 min ischemia followed by 40 min reperfusion; group 4 was preconditioned with three cycles of 5 min global ischemia followed by 5 min of reperfusion (IPC), prior to 40 min ischemia; group 5 was subjected to IPC prior to standard ischemia/reperfusion; group 6 underwent standard ischemia/reperfusion and SOD infusion (150 U/ml) was begun 5 min before 40 min ischemia and continued during the initial 5 min of the reperfusion period; group 7 was subjected to 80 min aerobic perfusion with NO-synthase inhibitor, L-NAME, to produce a model of endothelial dysfunction independent from the ischemia/reperfusion. Coronary flow responses to acetylcholine (ACh) and sodium nitroprusside (SNP) were used as measures of endothelium-dependent and endothelium-independent vascular function, respectively. Reduction in coronary flow caused by NO-synthase inhibitor, L-NAME, served as a measure of a basal endothelium-dependent vasodilator tone. After completion of each experimental protocol, the hearts were stained with ruthenium red or lanthanum chloride for electron microscopy evaluation of the endothelial glycocalyx. While ischemia led only to a slightly flocculent appearance of the glycocalyx, in ischemia/reperfused hearts the glycocalyx was disrupted, suggesting that it is the reperfusion injury which leads to the glycocalyx injury. Moreover, the coronary flow responses to ACh and L-NAME were impaired, while the responses to SNP were unchanged in the ischemia/reperfused hearts. The disruption of the glycocalyx and the deterioration of ACh and L-NAME responses was prevented by IPC. In addition, the alterations in the glycocalyx and the impairment of ACh responses were prevented by SOD. The glycocalyx appeared to be not changed in the hearts subjected to 80 min aerobic perfusion with L-NAME. In conclusion: (1) the impairment of the endothelium-dependent coronary vasodilation is paralleled by the endothelial glycocalyx disruption in the postischemic guinea-pig hearts; (2) both these changes are prevented by SOD, suggesting the role of free radicals in the mechanism of their development; (3) both changes are prevented by IPC. We hypothesize, therefore, that alterations in the glycocalyx contribute to the mechanism of the endothelial dysfunction in the postischemic hearts.     

Mechanistic determinants of MBNL activity

Muscleblind-like (MBNL) proteins are critical RNA processing factors in development. MBNL activity is disrupted in the neuromuscular disease myotonic dystrophy type 1 (DM1), due to the instability of a non-coding microsatellite in the DMPK gene and the expression of CUG expansion (CUG^exp) RNAs. Pathogenic interactions between MBNL and CUG^exp RNA lead to the formation of nuclear complexes termed foci and prevent MBNL function in pre-mRNA processing. The existence of multiple MBNL genes, as well as multiple protein isoforms, raises the question of whether different MBNL proteins possess unique or redundant functions. To address this question, we coexpressed three MBNL paralogs in cells at equivalent levels and characterized both specific and redundant roles of these proteins in alternative splicing and RNA foci dynamics. When coexpressed in the same cells, MBNL1, MBNL2 and MBNL3 bind the same RNA motifs with different affinities. While MBNL1 demonstrated the highest splicing activity, MBNL3 showed the lowest. When forming RNA foci, MBNL1 is the most mobile paralog, while MBNL3 is rather static and the most densely packed on CUG^exp RNA. Therefore, our results demonstrate that MBNL paralogs and gene-specific isoforms possess inherent functional differences, an outcome that could be enlisted to improve therapeutic strategies for DM1.     

Timber stacks: potential ecological traps for an endangered saproxylic beetle,the Rosalia longicorn <Emphasis Type="Italic">Rosalia alpina</Emphasis>

Ecological traps are serious, anthropogenic threats to animal populations. However, in certain cases it is difficult to determine whether they really act in the expected manner. This applies to the harmful effects of beech timber stacked in forests on the endangered saproxylic beetle Rosalia longicorn Rosalia alpina, which have been mentioned in numerous scientific articles, conservation action plans and similar publications. The aim of this paper is to determine whether beech timber stacks meet the criteria of an ecological trap for the Rosalia longicorn. Two basic criteria of such a trap are analysed: the attractiveness of timber stacks and the impossibility of complete larval development. The results show that beech timber stacks are highly attractive to Rosalia longicorn imagines. Moreover, the time during which the timber is stacked is shown to be significantly shorter than the species’ larval development period. These results suggest that timber stacks can be treated as operative ecological traps for the Rosalia longicorn, even though the extent of their influence on the demographic parameters of this beetle’s population has not been estimated. Forest management practices, i.e. increasing amounts and shifts in timing of wood storage, could intensify this threat.