Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high‐coverage reference genome for the Siberian roe deer (Capreolus pygargus). We find progressive reductions in effective population size (Ne), despite very large census sizes in modern C. capreolus populations and show that low Ne has impacted the C. capreolus genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among C. capreolus populations, including a historically documented founder population that has been through a severe bottleneck. During each phylogenetic transition there is evidence for selection (e.g. using evidence from non‐synonymous change or population data), including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even‐toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change

Hierarchical non-negative matrix factorization applied to three-dimensional 3T MRSI data for automatic tissue characterization of the prostate

In this study non-negative matrix factorization (NMF) was hierarchically applied to simulated and in vivo three-dimensional 3 T MRSI data of the prostate to extract patterns for tumour and benign tissue and to visualize their spatial distribution. Our studies show that the hierarchical scheme provides more reliable tissue patterns than those obtained by performing only one NMF level. We compared the performance of three different NMF implementations in terms of pattern detection accuracy and efficiency when embedded into the same kind of hierarchical scheme. The simulation and in vivo results show that the three implementations perform similarly, although one of them is more robust and better pinpoints the most aggressive tumour voxel(s) in the dataset. Furthermore, they are able to detect tumour and benign tissue patterns even in spectra with lipid artefacts. Copyright © 2016 John Wiley & Sons, Ltd.status: publishe

Mechanism of Nonlinear Optical Enhancement and Supramolecular Isomerism in 1D Polymeric Zn(II) and Cd(II) Sulfates with Pyridine-4-aldoxime Ligands

Interaction of zinc(II) and cadmium(II) sulfates with pyridine-4-aldoxime (4-pyao) and pyridine-4-amidoxime (4-pyamo) ligands resulted in four 1D metal-organic materials (MOMs) with identical composition, [M(SO 4)A2(H2O)2]n, where M = Zn(II), A = 4-pyao for 1, M = Cd(II), A = 4-pyao for 2, M = Zn(II), A = 4-pyamo for 3, M = Cd(II), A = 4-pyamo for 4, and mononuclear [Zn(SO4)(4- pyamo)2(H2O)3] 5. New coordination polymers represent the mixed-ligand supramolecular isomers different by the twisting of two pyridine-4-oxime ligands in the metal coordination environments, and crystallizing in the different space groups. Conformational preferences and nonlinear optical properties of the 4-pyao and 4-pyamo complexes were investigated using density functional theory. Spectral properties of 1-3 have been also evaluated. The solid-state emission of 1D polymers 1-3 appears to be ligand-based, as the positions of the emission maxima remain practically unchanged from free ligand to complexes. The enhancement of luminescence and two-photon absorption in polymers in comparison with the pure ligands is attributed to the chelation of the ligand to the metal center. The detailed mechanism of this enhancement upon complex formation is analyzed and can be used in future design of metal-organic nonlinear optical materials. © 2014 American Chemical Society