Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

Background: A number of the deeper divergences in the placental mammal tree are still inconclusively resolved despite extensive phylogenomic analyses. A recent analysis of 200 kbp of protein coding sequences yielded only limited support for the relationships among Laurasiatheria (cow, dog, bat and shrew), probably because the divergences occurred only within a few million years from each other. It is generally expected that increasing the amount of data and improving the taxon sampling enhance the resolution of narrow divergences. Therefore these and other difficult splits were examined by phylogenomic analysis of the hitherto largest sequence alignment. The increasingly complete genome data of placental mammals also allowed developing a novel and stringent data search method. Results: The rigorous data handling, recursive BLAST, successfully removed the sequences from gene families, including those from well-known families hemoglobin, olfactory, myosin and HOX genes, thus avoiding alignment of possibly paralogous sequences. The current phylogenomic analysis of 3,012 genes (2,844,615 nucleotides) from a total of 22 species yielded statistically significant support for most relationships. While some major clades were confirmed using genomic sequence data, the placement of the treeshrew, bat and the relationship between Boreoeutheria, Xenarthra and Afrotheria remained problematic to resolve despite the size of the alignment. Phylogenomic analysis of divergence times dated the basal placental mammal splits at 95–100 million years ago. Many of the following divergences occurred only a few (2–4) million years later. Relationships with narrow divergence time intervals received unexpectedly limited support even from the phylogenomic analyses. Conclusion: The narrow temporal window within which some placental divergences took place suggests that inconsistencies and limited resolution of the mammalian tree may have their natural explanation in speciation processes such as lineage sorting, introgression from species hybridization or hybrid speciation. These processes obscure phylogenetic analysis, making some parts of the tree difficult to resolve even with genome data

Degeneracy: a design principle for achieving robustness and evolvability

Robustness, the insensitivity of some of a biological system's functionalities to a set of distinct conditions, is intimately linked to fitness. Recent studies suggest that it may also play a vital role in enabling the evolution of species. Increasing robustness, so is proposed, can lead to the emergence of evolvability if evolution proceeds over a neutral network that extends far throughout the fitness landscape. Here, we show that the design principles used to achieve robustness dramatically influence whether robustness leads to evolvability. In simulation experiments, we find that purely redundant systems have remarkably low evolvability while degenerate, i.e. partially redundant, systems tend to be orders of magnitude more evolvable. Surprisingly, the magnitude of observed variation in evolvability can neither be explained by differences in the size nor the topology of the neutral networks. This suggests that degeneracy, a ubiquitous characteristic in biological systems, may be an important enabler of natural evolution. More generally, our study provides valuable new clues about the origin of innovations in complex adaptive systems.Comment: Accepted in the Journal of Theoretical Biology (Nov 2009

Selective nonresonant excitation of vibrational modes in suspended graphene via vibron-plasmon interaction

We theoretically study a doped graphene ribbon suspended over a trench and subject to an ac-electrical field polarized perpendicularly to the graphene plane. In such a system, the external ac-field is coupled to the relatively slow mechanical vibrations via plasmonic oscillations in the isolated graphene sheet. We show that the electrical field generates an effective pumping of the mechanical modes. It is demonstrated that in the case of underdamped plasma oscillation, a peculiar kind of geometrical resonance of the mechanical and plasma oscillations appear. Namely the efficiency of pumping significantly increases when the wave number of the mechanical mode is in close agreement with the wave number of the plasma waves. The intensity of the pumping increases with the wave number of the mode. This phenomenon allows selective actuation of different mechanical modes although the driving field is homogeneous

Coherent Resonat millenial-scale climate transitions triggered by massive meltwater pulses

The role of mean and stochastic freshwater forcing on the generation of millennial-scale climate variability in the North Atlantic is studied using a low-order coupled atmosphere–ocean–sea ice model. It is shown that millennial-scale oscillations can be excited stochastically, when the North Atlantic Ocean is fresh enough. This finding is used in order to interpret the aftermath of massive iceberg surges (Heinrich events) in the glacial North Atlantic, which are characterized by an excitation of Dansgaard–Oeschger events. Based on model results, it is hypothesized that Heinrich events trigger Dansgaard–Oeschger cycles and that furthermore the occurrence of Heinrich events is dependent on the accumulated climatic effect of a series of Dansgaard–Oeschger events. This scenario leads to a coupled ocean–ice sheet oscillation that shares many similarities with the Bond cycle. Further sensitivity experiments reveal that the timescale of the oscillations can be decomposed into stochastic, linear, and nonlinear deterministic components. A schematic bifurcation diagram is used to compare theoretical results with paleoclimatic data

TARGET2 Unlimited: monetary policy implications of asymmetric liquidity management within the Euro area. CEPS Policy Brief No. 248, 13 July 2011

This paper analyses the implications of a continued divergence of TARGET2 balances for monetary policy in the euro area. The accumulation of TARGET2 claims (liabilities) would make the ECB’s liquidity management asymmetric once the TARGET2 claims in core countries have crowded out central bank credit in those regions. Then while providing scarce liquidity to banks in countries with TARGET2 liabilities, the ECB will need to absorb excess liquidity in countries with TARGET2 claims. We discuss three alternatives and their implications for absorbing excess liquidity in core regions: 1) using market-based measures might accelerate the capital flight from periphery to core countries and would add to the accumulation of risky assets by the ECB; 2) conducting non-market based measures, such as imposing differential (unremunerated) reserve requirements, would distort banking markets and would support the development of shadow banking; and 3) staying passive would lead to decreasing interest rates in core Europe entailing inflationary pressure and overinvestment in those regions and possibly future instability of the banking system

Ga+ beam lithography for suspended lateral beams and nanowires

The authors demonstrate the fabrication of suspended nanowires and doubly clamped beams by using a focused ion beam implanted Ga etch mask followed by an inductively coupled plasma reactive ion etching of silicon. This method will demonstrate how a two-step, completely dry fabrication sequence can be tuned to generate nanomechanical structures on either silicon substrates or silicon on insulator (SOI). This method was used to generate lateral nanowires suspended between 2 µm scaled structures with lengths up to 16 µm and widths down to 40 nm on a silicon substrate. The authors also fabricate 10 µm long doubly clamped beams on SOIs that are 20 nm thick and a minimum of 150 nm wide. In situ electrical measurements of the beams demonstrate a reduction of resistivity from > 37.5 Ω cm down to 0.25 Ω cm. Transmission electron microscopy for quantifying both surface roughness and crystallinity of the suspended nanowires was performed. Finally, a dose array for repeatable fabrication of a desired beam width was also experimentally determined

Low-energy electron beam focusing in self-organized porous alumina vacuum windows

Micromachined, micron-thick porous alumina membranes with closed pore endings show high electron transparency above an energy of 5 keV. This is due to the channeling of electrons along the negatively charged insulating pores after surmounting the thin entrance layer. We also find a sharp hightransparency energy window at energies as low as 2 keV which may be the result of a local maximum of channeling, as predicted by simulations, and positive charge up of the entrance layer causing electron electrostatic focusing. Applications for these membranes range from atmospheric electron spectroscopy to self-assembled, nanoscale, large-area electron collimators