Properties of consensus methods for inferring species trees from gene trees

Consensus methods provide a useful strategy for summarizing information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical properties of consensus trees that would be obtained from large numbers of loci evolving according to a basic evolutionary model, we construct consensus trees from rooted gene trees that occur in proportion to gene-tree probabilities derived from coalescent theory. We consider majority-rule, rooted triple (R(*)), and greedy consensus trees obtained from known, rooted gene trees, both in the asymptotic case as numbers of gene trees approach infinity and for finite numbers of genes. Our results show that for some combinations of species-tree branch lengths, increasing the number of independent loci can make the rooted majority-rule consensus tree more likely to be at least partially unresolved. However, the probability that the R(*) consensus tree has the species-tree topology approaches 1 as the number of gene trees approaches infinity. Although the greedy consensus algorithm can be the quickest to converge on the correct species-tree topology when increasing the number of gene trees, it can also be positively misleading. The majority-rule consensus tree is not a misleading estimator of the species-tree topology, and the R(*) consensus tree is a statistically consistent estimator of the species-tree topology. Our results therefore suggest a method for using multiple loci to infer the species-tree topology, even when it is discordant with the most likely gene tree.

A coherent synchrotron X-ray microradiology investigation of bubble and droplet coalescence

A quantitative application of microradiology with coherent X-rays to the real-time study of microbubble and microdroplet coalescence phenomena, with specific emphasis on the size relations in three-body events, is presented. The results illustrate the remarkable effectiveness of coherent X-ray imaging in delineating interfaces in multiphase systems, in accurately measuring their geometric properties and in monitoring their dynamics.

Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters

Large-scale sequencing of short mtDNA fragments for biodiversity inventories ('DNA barcoding') indicates that sequence variation in animal mtDNA is highly structured and partitioned into discrete genetic clusters that correspond broadly to species-level entities. Here we explore how the migration rate, an important demographic parameter that is directly related to population isolation, might affect variation in the strength of mtDNA clustering among taxa. Patterns of mtDNA variation were investigated in two groups of beetles that both contain lineages occupying habitats predicted to select for different dispersal abilities: predacious diving beetles (Dytiscidae) in the genus Bidessus from lotic and lentic habitats across Europe and darkling beetles (Tenebrionidae) in the genus Eutagenia from sand and other soil types in the Aegean Islands. The degree of genetic clustering was determined using the recently developed 'mixed Yule coalescent' (MYC) model that detects the transition from between-species to within-population branching patterns. Lineages from presumed stable habitats, and therefore displaying lower dispersal ability and migration rates, showed greater levels of mtDNA clustering and geographical subdivision than their close relatives inhabiting ephemeral habitats. Simulations of expected patterns of mtDNA variation under island models showed that MYC clusters are only detected when the migration rates are much lower than the value of Nm=1 typically used to define the threshold for neutral genetic divergence. Therefore, discrete mtDNA clusters provide strong evidence for independently evolving populations or species, but their formation is suppressed even under very low levels of dispersal.

Drug-loaded nano/microbubbles for combining ultrasonography and targeted chemotherapy

A new class of multifunctional nanoparticles that combine properties of polymeric drug carriers, ultrasound imaging contrast agents, and enhancers of ultrasound-mediated drug delivery has been developed. At room temperature, the developed systems comprise perfluorocarbon nanodroplets stabilized by the walls made of biodegradable block copolymers. Upon heating to physiological temperatures, the nanodroplets convert into nano/microbubbles. The phase state of the systems and bubble size may be controlled by the copolymer/perfluorocarbon volume ratio. Upon intravenous injections, a long-lasting, strong and selective ultrasound contrast is observed in the tumor volume indicating nanobubble extravasation through the defective tumor microvasculature, suggesting their coalescence into larger, highly echogenic microbubbles in the tumor tissue. Under the action of tumor-directed ultrasound, microbubbles cavitate and collapse resulting in a release of the encapsulated drug and dramatically enhanced intracellular drug uptake by the tumor cells. This effect is tumor-selective; no accumulation of echogenic microbubbles is observed in other organs. Effective chemotherapy of the MDA MB231 breast cancer tumors has been achieved using this technique.

DEMOGRAPHIC CONSEQUENCES OF COALESCENCE IN SPORELING POPULATIONS OF MAZZAELLA LAMINARIOIDES (GIGARTINALES, RHODOPHYTA)(1)

Coalescing macroalgae are ecologically important members of intertidal and shallow subtidal communities. However, we still lack quantitative information on the demographic consequences of coalescence. Using demographic models developed for modular invertebrates, we studied the demography of settlement and early recruitment in the coalescing macroalga Mazzaella laminarioides (Bory) Fredericq. Permanently marked microscopic fields on laboratory-incubated and field-incubated plates were monitored regularly (at 15, 30, 45, and 60 d) using image analysis techniques to evaluate the relative importance of settler abundance, mortality, coalescence (fusion), and fission on the changes in size and numbers of recruits. On the plates, spores settled individually or in groups. Over time, spores in close proximity may coalesce, resulting in a mixture of unisporic and multisporic crusts. When new spores arrive, they may or may not coalesce with previously settled crusts. Coalescence and mortality reduce the number of sporelings, but coalescence increases the size of the sporelings, thereby reducing further probability of sporeling mortality. Crust fissions are negligible in frequency, while the frequency of coalescence increases from ∼25% after only 3 d, to ∼75% after 60 d. Thus, as a result of variable settlement, mortality, and coalescence, any area colonized by M. laminarioides would contain a mixture of crusts of different sizes, ages, and genetic constitution. The interactions between the above three processes create a more complex survivorship curve than the ones known for unitary organisms.