Orientational effects in the polarized absorption spectra of molecular aggregates.

We present a detailed theoretical analysis of polarized absorption spectra and linear dichroism of cyanine dye aggregates whose unit cells contain two molecules. The studied threadlike ordered system with a molecular exciton delocalized along its axis can be treated as two chains of conventional molecular aggregates, rotated relative to each other at a certain angle around the aggregate axis. Our approach is based on the general formulas for the effective cross section of light absorption by a molecular aggregate and key points of the molecular exciton theory. We have developed a self-consistent theory for describing the orientational effects in the absorption and dichroic spectra of such supramolecular structures with nonplanar unit cell. It is shown that the spectral behavior of such systems exhibits considerable distinctions from that of conventional cyanine dye aggregates. They consist in the strong dependence of the relative intensities of the J- and H-type spectral bands of the aggregate with a nonplanar unit cell on the angles determining the mutual orientations of the transition dipole moments of constituting molecules and the aggregate axis as well as on the polarization direction of incident light. The derived formulas are reduced to the well-known analytical expressions in the particular case of aggregates with one molecule in the unit cell. The calculations performed within the framework of our excitonic theory combined with available vibronic theory allow us to quite reasonably explain the experimental data for the pseudoisocyanine bromide dye aggregate.

Multilocus Analysis of Phylogenetic Relationships in the Crocidura suaveolens Sensu Lato Species Complex: A Comparison with Mitochondrial Data.

Multilocus analysis was for the first time used to study the phylogeny of the Crocidura suaveolens s. l. species complex. Sequencing data for 16 nuclear genes indicated that several distinct forms exist within the species complex. The structure of the complex did generally not contradict its mitochondrial phylogeny. Siberian shrew showed certain specificity of the nuclear genome, but the degree of its genetic differentiation did not correspond to the species level. Relationships of Crocidura aff. suaveolens from South Gansu and Sichuan with other forms of the species complex were clarified. Shrews from Buryatia and Khentei also belong to this form, but their mtDNA apparently introgressed from C. shantungensis in the past. Hybridization of C. suaveolens s. str. with C. aff. suaveolens and C. güeldenstaedtii occurred recently. Due to multiple introgression events in the history of C. suaveolens s. l., a far larger set of loci is necessary for the analysis of the phylogenetic relationships between its forms.

Phylogeny of the Dipus sagitta Species Complex by Nuclear Gene Sequences.

The northern three-toed jerboa Dipus sagitta had long been considered to be a single polytypic species. High genetic diversity of D. sagitta was earlier revealed on the basis of several mitochondrial and nuclear genes, and several separate species were hypothesized to occur within the taxon. However, the relationships between phylogenetic lineages have not been established because of the small sample size of nuclear genes. In the present work, a far larger set of nuclear DNA loci was used, and thus, a higher resolution of the phylogenetic tree was achieved for ten D. sagitta forms. The structure revealed for the species mainly confirmed the topology and relationships of the mtDNA lineages. Yet the mitochondrial and nuclear phylogenies were not completely consistent. Some of the D. sagitta genetic lineages were therefore assumed to be a product of reticular evolutionary processes. The taxon was concluded to be the diverse species complex D. sagitta sensu lato, in which long-diverged lineages are not always reproductively isolated.

Continuous absorption and emission of light by the heteronuclear rare gas (ArXe)+ and (KrXe)+ ions.

Studies of radiative transitions between ground and charge transfer excited terms of heteronuclear rare-gas (ArXe)+ and (KrXe)+ ions with small and moderate dissociation energies (D0 ArXe+ =179 and D0 KrXe+ =389 meV) are reported. Potential energy curves and dipole transition matrix elements are evaluated using ab initio calculations based on the CASSCF method followed by the NEVPT2 treatment and perturbative description of relativistic effects as implemented in the ORCA suite. We develop an efficient approach for the calculations of Boltzmann-averaged cross sections, rate constants, and absorption and emission coefficients associated with the integral contributions of bound-bound and bound-free transitions from a manifold of rovibrational states of the (RgXe)+ ion. A similar approach is used for the description of the free-free and free-bound transitions between different electronic terms of a quasimolecular (RgXe)+ ion temporarily formed during a collision of Ar or Kr atoms with Xe+ ions. Our method is based on the quantal version of the theory of non-adiabatic transitions in molecular and quasimolecular systems combined with the approximation of a quasicontinuum for rovibrational energy levels. This allowed us to obtain a semianalytic expression for the integral absorption properties particularly relevant at elevated temperatures. We perform a comprehensive analysis of the identified radiative processes in local thermodynamic equilibrium plasmas of rare gas Rg/Xe mixtures containing both atomic, Xe+, and molecular, RgXe+, ions and determine their role in the formation of the absorption and emission spectra in a wide range of wavelengths and gas temperatures. The results obtained are in good agreement with the available experimental data.

Manifestation of the anisotropic properties of the molecular J-aggregate shell in the optical spectra of plexcitonic nanoparticles.

The theoretical studies of light absorption and scattering spectra of the plexcitonic two-layer triangular nanoprisms and three-layer nanospheres are reported. The optical properties of such metal-organic core-shell and core-double-shell nanostructures were previously explained within the framework of pure isotropic models for describing their outer excitonic shell. In this work, we show that the anisotropy of the excitonic shell permittivity can drastically affect the optical spectra of such hybrid nanostructures. This fact is confirmed by directly comparing our theory with some available experimental data, which cannot be treated using conventional isotropic shell models. We have analyzed the influence of the shell anisotropy on the optical spectra and proposed a type of hybrid nanostructure that seems the most convenient for experimental observation of the effects associated with the anisotropy of the excitonic shell. A strong dependence of the anisotropic properties of the J-aggregate shell on the material of the intermediate spacer layer is demonstrated. This allows proposing a new way to effectively control the optical properties of metal-organic nanostructures by selecting the spacer material. Our results extend the understanding of physical effects in optics of plexcitonic nanostructures to more complex systems with the anisotropic and multi-excitonic properties of their molecular aggregate shell.

Spectral-band replication phenomenon in a single pair of hybrid metal-organic nanospheres and nanodisks caused by plexcitonic coupling.

We study an unusual effect of spectral-band replication in the optical spectra of dimers, consisting of spherical nanoparticles or nanodisks with a silver core and a J-aggregate shell of TDBC-dye. It consists in the emergence of a doubled number of plexcitonic spectral bands compared to the case of a plasmonic dimer and in narrow peaks associated with the resonances of the J-aggregate shell. The plexcitonic bands can be divided into two groups: the "original" bands, accurately reproducing plasmonic peaks, and their "replicas," with a specific mutual arrangement and intensity distributions. The effect is interpreted using the multi-state effective Hamiltonian model describing a strong coupling between the quasi-degenerate Frenkel excitonic modes in the organic shells and multiple plasmonic modes in the pair of Ag-cores. We quantitatively explain some available experimental data on the optical properties of nanodisks and suggest a way for the observation of the replication effect. Our results extend the understanding of the nature of plexcitonic coupling to more complex systems compared to individual metal/J-aggregate nanoparticles.

Optical properties of molecular nanocrystals consisting of J-aggregates of anionic and cationic cyanine dyes.

We report results of experimental studies of the photoabsorption, photoluminescent and photoelectric properties of a new type of multilayer molecular nanocrystals, consisting of highly ordered J-aggregates of one anionic and two cationic J-aggregates of cyanine dyes. In contrast to conventional J-aggregated dyes the multichromic nanocrystals synthesized in this work, are capable of efficient light absorption in three excitonic bands of the visible and near-IR spectral ranges. The spectral peak positions in the absorption bands can be controlled by appropriately selecting a set of dyes a molecular crystal is made of. Our investigations of the photoelectric properties of multichromic crystals have shown that each of them can potentially be used as a photosensitive layer of a photocell with photoconductivity in three peaks of excitonic absorption. The synthesized nanocrystals are attractive for the creation of thin-film organic photodetectors with a large photosensitive area and varied photoabsorption spectra, excitonic waveguides and for some other applications in organic and hybrid photonics and optoelectronics.

Is the Center of Origin of Long-tailed Hamster Cricetulus longicaudatus Milne-Edwards 1867 (Rodentia, Cricetidae) Located in Tibet?

First data on morphological and mitochondrial variation in the long-tailed hamster Cricetulus longicaudatus is presented. In contrast to genetically monomorphic populations of Mongolia and Tuva, the northeastern part of the Qinghai-Tibetian Plateau was found to harbor several divergent mtDNA lineages. This pattern suggests a recent expansion of the long-tailed hamster to the northern part of its recent range, which started from Tibet, presumably, in the late Middle Pleistocene. Several populations from the northern edge of the species range were found to be morphologically but not genetically distinct. The apparent disagreement between genetic and morphological data can be explained by rapid morphological evolution in peripheral isolates.

Molecular phylogenetics and taxonomy of dwarf hamsters Cricetulus Milne-Edwards, 1867 (Cricetidae, Rodentia): description of a new genus and reinstatement of another.

The taxonomy of the genus Cricetulus has been controversial. The phylogenetic relationships both within the genus and among Cricetulus lineages and other genera were examined using a set of five nuclear and two mitochondrial genes. The results demonstrate that Cricetulus in its current treatment is a polyphyletic assemblage because the subgenus Urocricetus is phylogenetically unrelated to all other Cricetulus and is a distant sister group to Phodopus. The grey hamster (C. migratorius) proved to be closer to Cricetus and Allocricetulus than to Cricetulus proper, which includes C. barabensis C. sokolovi and C. longicaudatus. Based on these results Urocricetus is elevated to the rank of a full genus and a new genus Nothocricetulus gen.nov. is described for the grey hamster.

Unexpectedly high genetic diversity of the asiatic short-tailed shrews Blarinella (Mammalia, Lipotyphla, Soricidae).

Genetic diversity of the genus Blarinella was studied using one mitochondrial and four nuclear genes as examples. The first genotyping of shrews from the southeast of Gansu province (China), which is a typical habitat of B. griselda, has been performed. Molecular genetic analysis showed that Blarinella sp. from southern Gansu stand apart among the other representatives of the genus and can be assigned to neither of the known species.

[Microsatellite loci variation and investigation of gene flow between two karyoforms of Cricetulus barabensis sensu lato (Rodentia, Cricetidae)].

We examine the diversity of six microsatellite loci and partial RAG1 exon of "barabensis" and "pseudogriseus" karyoforms in Cricetulus barabensis sensu lato species complex. A total of 435 specimens from 68 localities ranging from Altai to the Far East are investigated. The results of the population structure analysis (factor analysis and NJ tree based on Nei genetic distances) support subdivision into two well-differentiated clusters corresponding to the two karyoforms. These karyoforms are also well differentiated by the level of microsatellite variability. In several "barabensis" specimens, we found microsatellite alleles that are common in "pseudogriseus" populations but are otherwise absent in "barabensis." Most of these specimens originate from a single population in one of the zones of potential contact between karyoforms, Kharkhorin in Central Mongolia. These molecular results are consistent with previously published karyological data in suggesting that rare hybridization events between the two chromosomal races occur in nature.

Phylogenetic position of the Gansu mole Scapanulus oweni Thomas, 1912 and the relationships between strictly fossorial tribes of the family talpidae.

The results of the first molecular study focused on the phylogenetic position of the Gansu mole, Scapanulus oweni are presented. The analysis based on sequences of the mitochondrial cytb gene and five nuclear genes supports the monophyly of the Scalopini tribe including S. oweni and shows that two highly fossorial talpid tribes, Talpini and Scalopini, are not immediate sister taxa. These results highlight the role of morphological parallelism as a potential source of conflict between molecular and morphology-based phylogenies in Talpidae.

[Variability of Cytochrome b Gene and Adjacent Section of Gene tRNA-Thr of Mitochondrial DNA in the Northern Mole Vole Ellobius talpinus (Mammalia, Rodentia)].

The Northern mole vole E. talpinus, despite its wide distribution, is characterized by a stable karyotype (2n = NF = 54) and slight morphological polymorphism. We made a preliminary analysis of a mitochondrial DNA fragment to clarify the level of genetic variation and differentiation of E. talpinus. the complete cytochrome b gene (cyt b, 1143 bp) and a short part of its flanking gene tRNA-Thr (27 bp) were sequenced. We studied 16 specimens from eight localities, including Crimea, the Volga region, the Trans-Volga region, the Southern Urals, Western Siberia, and Eastern Turkmenistan. Mitotypes of E. talpinus were distributed on a ML dendrogram as four distinct clusters: the first (I) contains specimens from the Crimea, the second (II) combines individuals from the Volgograd region and the left bank of the Don River, the third (III) includes those from the Trans-Volga region, Southern Urals, the left bank of the Irtysh River, and Eastern Turkmenistan; the fourth (IV) are those from the right bank of the Irtysh River. These clusters were relatively distant from each other: the mean genetic distances (D) between them are 0.021-0.051. The Eastern mole vole E. tancrei differed from E. talpinus population groups 1.5-2 times more (D = 0.077-0.084) than the latter did among themselves. Such variations indirectly proved the unity of E. talpinus, despite its high intraspecific differentiation for the studied fragment of mitochondrial DNA. This differentiation apparently occurred because of the long isolation of E. talpinus population groups, which was due to geographic barriers, in particular, the large rivers that completely separate the species range meridionally (the Volga River, the Irtysh River). Sociality and underground lifestyle could accelerate the fixation of mutations in disjunct populations. The composition and distribution of intraspecific groups of E. talpinus, which were identified in analysis of the mitochondrial DNA fragment, do not coincide with the subspecies taxonomy. The subspecies E. t. talpinus is actually a complex taxon, including two or three genetically discrete forms (III, IV, and probably II). Moreover, one of the forms (III) occupies the territory where three subspecies, E. t. talpinus, E. t. rufescens, and E. t. transcaspiae, were described.

Comparative cytogenetics of hamsters of the genus Allocricetulus argyropulo 1932 (Cricetidae, Rodentia).

Chromosome painting and G-banding analyses were used to delimit homologous chromosomal segments among 4 taxa of the hamsters genus Allocricetulus Argyropulo 1932 (Cricetidae, Murоidea, Rodentia)--A. curtatus (2n = 20), A. eversmanni eversmanni, A. eversmanni pseudocurtatus, and the hybrid A. eversmanni beljaevi × A. eversmanni pseudocurtatus (all 2n = 26). Comparative maps between the 4 karyotypes were established based on chromosome painting of chromosome-specific probes from the Syrian hamster (Mesocricetus auratus, 2n = 44). A putative ancestral karyotype for the genus Allocricetulus (AAK) was proposed and contains 12-13 ancestral autosomal elements. Integrated maps demonstrate extended conservation of syntenies within this rodent genus and show the predominant role of Robertsonian rearrangements in the karyotype evolution of the genus Allocricetulus. At the cytogenetic level, we clearly demonstrate karyological differences between karyotypes of species (A. curtatus vs. A. eversmanni) and subspecies A. e. eversmanni and A. e. beljaevi versus A. e. pseudocurtatus, but the karyotypes of A. e. eversmanni and A. e. beljaevi are identical at this level of resolution.

[Karyotypes divergence in superspecies complex Cricetulus barabensis sensu lato and their interrelationships in natural contact zones].

Interrelationships between three chromosomal forms of striped hamsters belonging to the superspecies complex Cricetulus barabensis sensu lato (Cricetidae, Rodentia), namely 'barabensis', 'pseudogriseus', and 'griseus', are examined from the standpoint of different biological/genetic species concepts. Craniometric data suggest that differences between the karyotypes are rather of subspecies level. Cytogenetic differences between the karyotypes are also not great and correspond to the level of chromosomal races within a single species. The analysis of mitochondrial gene for cytochrome b (cytb) indicates the level of differences between forms of about 2.3-4.1%. Such a level may correspond to intraspecific differences as well as to differences between allied species. Experiments on hybridization resulted in hybrid litters obtained in different mating combinations of karyotypes. Both hybrid males and females fertility was confirmed, too. In nature, there exist several zones where contact between karyotypes 'barabensis' and 'pseudogriseus' is possible. Within one of such zones, in Central Mongolia, two males with atypical karyotype were detected by use of chromosome analysis. With chromosomes number and form, this karyotype may correspond to the hybrid between second and subsequent generations. However, typing of gene cytb and the intron localized in Y-chromosome (DBY1) did not reveal any traces of recent or ancient hybridization. In the other zone where contact between the karyotypes is possible, in South Buryatia, 'barabensis' and 'pseudogriseus' populations are separated by the River Chika and the distance between them does not exceed 5 km. Nevertheless, no hamsters with non-standard karyotypes and no traces of gene flow are detected by karyological and molecular analyses of these populations. The results of Tajima's test, analysis of pairwise differences distribution and indices of nucleotide diversity obtained in the course of examining gene cytb full nucleotide sequence all suggest that both contact zones studied have formed long ago and the absence of gene flow cannot be explained by their forming in the recent past. Thus, the karyotypes studied appear to be evolutionary lines developing independently from each other.

Molecular systematics and evolutionary biogeography of the genus Talpa (Soricomorpha: Talpidae).

The range of the genus Talpa covers almost all Europe up to Western Asia. This genus has never been the object of comprehensive systematic studies using molecular and genetic techniques, such that the evolutionary relationships among species remain unclear. Talpa shows high levels of endemism, and the influence of past glaciation cycles on the distribution pattern of several species has been hypothesized. In this work, we assessed the molecular systematics of the genus using the mitochondrial gene cytochrome b from eight of the nine extant species of Talpa moles. Furthermore, molecular clock estimations were used to hypothesize a biogeographic scenario in concordance with fossil data. Results suggest a monophyletic origin of the genus and a common ancestor for the western European moles T. europaea, T. caeca, T. romana and T. occidentalis. The eastern species T. altaica and T. caucasica are basally divergent. The estimated ages of divergence among lineages are in accordance with a Miocene origin of the extant moles. The genus likely originated in Asia, spreading into Europe during the Pliocene. The evolution of moles appears to have been driven by changes in moisture levels that influenced extinction and speciation events during the Miocene and the Pliocene. Pleistocene climatic oscillations likely caused the range shrinkages and expansions that led to the current distribution pattern of most Talpa species.