Mitogenomes revealed the history of bison colonization of Northern Plains after the Last Glacial Maximum.

American bison demonstrated differential patterns of extinction, survival, and expansion since the terminal Pleistocene. We determined population dynamics of the Northern Great Plains bison using 40 mitochondrial genomes from radiocarbon dated remains with the age ranging from 12,226 to 167 calibrated years before present. Population dynamics correlated with environmental and anthropogenic factors and was characterized by three primary periods: terminal Pleistocene population growth starting 14,000 years ago, mid Holocene demographic stability between 6700 and 2700 years ago, and late Holocene population decline in the last 2700 years. Most diversification of mtDNA haplotypes occurred in the early Holocene when bison colonized new territories opened by retreating ice sheets. Holocene mtDNA lineages were not found in modern bison and lacked association with archaeological sites and morphological forms.

Genetic variation of the mitochondrial DNA control region across plains bison herds in USA and Canada.

Once numbering in the tens of millions, bison (Bison bison) have faced a broad range of challenges over the past century, including genetic impacts from the population bottleneck in the 1800s, and significant loss and fragmentation of habitat resulting in little opportunity for population growth on remaining small, geographically isolated reserves. To identify best practices for bison stewardship against this backdrop, managers must understand the genetic composition of existing conservation herds. This study characterized 14 plains bison (Bison bison bison) herds managed by the U.S. Department of Interior and Parks Canada Agency based on complete mtDNA control region sequences. Among 209 bison, we detected 11 major mtDNA control region haplotypes based on nucleotide substitutions and 23 sub-haplotypes where indels are considered. We determined matrilineal relationships between the herds and compared our genetic findings to historic records. The recent common ancestry of modern bison deriving from small, scattered groups combined with gene flow through foundation and translocation events between herds during the last 100 years, is reflected in Fst value (0.21), haplotype (0.48 ± 0.04) and nucleotide (0.004 ± 0.002) diversities, and mean number of pairwise differences (3.38 ± 1.74). Genetic diversity was distributed unevenly among herds, with 21.41% of genetic variation observed between herds. Median joining network, together with trends in the Tajima's D and Fs tests, revealed two patterns in the recent evolution of mtDNA sequences in bison: mutational process has generated diversity with a Hap 1 haplotype epicenter, and missed mtDNA haplotypes exist in the network due to bottleneck, loss through management practices, or incomplete sampling of specimens across conservation herds. This work significantly expands characterization of the genetic diversity among bison conservation herds, providing additional decision support for managers considering restoring gene flow to achieve long-term species viability.

Effect of the chemical structure of a tetradentate equatorial ligand on the spin-crossover properties of the Fe (III) complexes chain structures: Electron paramagnetic resonance study.

The effect of the chemical structure of the equatorial ligand on the spin state of the Fe (III) ion in a series of 1-D chain complexes of the general formula [Fe(L)(tvp)]BPh4 ·nCH3 OH, where L = dianions of Schiff base containing a different number of aromatic groups: N,N'-ethylenebis (salicylaldimine) (salen) 1, N,N'-ethylenebis (acetylacetone)2,2'-imine (acen) 2, N,N'-ethylenebis (benzoylacetylacetone)2,2'-imine (bzacen) 3, and tvp = 1,2-di(4-pyridyl)ethylene, was studied by ultraviolet-visible (UV-vis) and electron paramagnetic resonance (EPR) methods. The values of exchange interactions, thermodynamic parameters of spin-crossover, and electronic structure features of the Fe (III) complexes were estimated from the EPR data. The substitution of a fragment of the equatorial ligand L in the series salen-acen-bzacen changes the local symmetry of the complex in the 1-D chain, thereby affecting the spin variable properties.

Spin crossover properties of Fe(III) complexes in [Fe (bzacen)(tvp)]BPh4 ·nSolv chain structures: EPR study.

Two types of Fe(III) polynuclear iron(III) 1D-chain coordination compounds of the general formula [Fe (L)(tvp)]BPh4 nSolv, where L = dianion of N,N'-ethylenebis (benzoylacetylacetone)2,2'-imine (bzacen), tvp = 1,2-di(4-pyridyl)ethylene were synthesized and studied by the electron paramagnetic resonance (EPR) and magnetic susceptibility methods in the temperature range (100-300) К. Two types of spin-variable complexes are formed depending on the time of precipitation of the complexes from the same solution leading to differently solvated species. They have different characteristics of the local ligand field and the spin transition behavior. The thermodynamic parameters of spin transitions were determined from the temperature dependence of the EPR signals integral intensity. The energy levels splitting values obtained by analyzing g-factors of low-spin Fe(III) centers evidenced not only on the crucial role of low-symmetry distortions on the principal possibility of spin-crossover processes, but also on the temperature peculiarities of spin transitions.

Isotopic paleoecology of Northern Great Plains bison during the Holocene.

Bison (Bison bison) are one of the few terrestrial megafauna to survive the transition into the Holocene and provide a unique opportunity to study a species on a broad spatiotemporal scale. Today, bison are primarily managed in small and isolated herds with little known about their ancestral ecology. We studied the carbon and nitrogen isotopes of Northern Great Plains bison from the terminal Pleistocene and throughout the Holocene to gain insight into their paleoecology. This time span is contemporary with the first population bottleneck experienced by bison at the end of the Pleistocene and includes the second bottleneck which occurred in the late 19th century. Results were compared with modern bison herd isotopic values from Theodore Roosevelt National Park (TRNP). Patterns of isotopic variation found in bison over time indicate significant (δ13C p = 0.0008, δ15N p = 0.002) differences in diet composition and correlate with climate throughout the Holocene. Isotopic relationships described here reveal the plasticity of ancient bison in unrestricted rangelands during periods of climatic fluctuations. Managers at TRNP and elsewhere should pursue opportunities to expand bison range to maximize forage opportunities for the species in the face of future environmental change.

Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park.

Feral horses in Theodore Roosevelt National Park (TRNP) represent an iconic era of the North Dakota Badlands. Their uncertain history raises management questions regarding origins, genetic diversity, and long-term genetic viability. Hair samples with follicles were collected from 196 horses in the Park and used to sequence the control region of mitochondrial DNA (mtDNA) and to profile 12 autosomal short tandem repeat (STR) markers. Three mtDNA haplotypes found in the TRNP horses belonged to haplogroups L and B. The control region variation was low with haplotype diversity of 0.5271, nucleotide diversity of 0.0077 and mean pairwise difference of 2.93. We sequenced one mitochondrial genome from each haplotype determined by the control region. Two complete mtDNA sequences of haplogroup L were closely related to the mtDNA of American Paint horse. The TRNP haplotype B did not have close matches in GenBank. The phylogenetic test placed this sequence in a group consisting of two horses from China, one from Yakutia, and one from Italy raising a possibility of historical transportation of horses from Siberia and East Asia to North America. Autosomal STR loci were polymorphic and indicated that the TRNP horses were distinctly different from 48 major horse breeds. Heterozygosity, mean number of alleles, and other measures of diversity indicated that TRNP herd diversity was below that observed for most other feral herds and domestic breeds. Both mtDNA and STRs demonstrated that the existing genetic data sets of horses are insufficient to determine the exact origins of the TRNP horses. However, measures of nuclear and mitochondrial diversity have elucidated management needs. It is recommended that new genetic stock be introduced and that adaptive management principles are employed to ensure that unique mitochondrial lineages are preserved and genetic diversity is increased and maintained over time.

A Basic Phase Diagram of Neuronal Dynamics.

The extreme complexity of the brain has attracted the attention of neuroscientists and other researchers for a long time. More recently, the neuromorphic hardware has matured to provide a new powerful tool to study neuronal dynamics. Here, we study neuronal dynamics using different settings on a neuromorphic chip built with flexible parameters of neuron models. Our unique setting in the network of leaky integrate-and-fire (LIF) neurons is to introduce a weak noise environment. We observed three different types of collective neuronal activities, or phases, separated by sharp boundaries, or phase transitions. From this, we construct a rudimentary phase diagram of neuronal dynamics and demonstrate that a noise-induced chaotic phase (N-phase), which is dominated by neuronal avalanche activity (intermittent aperiodic neuron firing), emerges in the presence of noise and its width grows with the noise intensity. The dynamics can be manipulated in this N-phase. Our results and comparison with clinical data is consistent with the literature and our previous work showing that healthy brain must reside in the N-phase. We argue that the brain phase diagram with further refinement may be used for the diagnosis and treatment of mental disease and also suggest that the dynamics may be manipulated to serve as a means of new information processing (e.g., for optimization). Neuromorphic chips, similar to the one we used but with a variety of neuron models, may be used to further enhance the understanding of human brain function and accelerate the development of neuroscience research.

Assembly of Nitrofurazan and Nitrofuroxan Frameworks for High-Performance Energetic Materials.

The design of novel energetic materials with improved performance, optimized parameters, and environmental compatibility remains a challenging task. In this study, new high-energy materials based on isomeric dinitrobi-1,2,5-oxadiazole structures comprising nitrofurazan and nitrofuroxan subunits were synthesized. Due to planarity and strong noncovalent interactions, these materials display high density values as determined by single-crystal X-ray diffraction. The thermal, impact, and friction sensitivities of both isomers are similar to that of nitroesters. Their high detonation performance along with the combined benefits of high density, high heat of formation, and good oxygen balance make the synthesized compounds promising as explosives and highly-energetic oxidizers.

Whole Human Mitochondrial DNA Sequencing.

Mitochondrial DNA (mtDNA) can help in the identification of biological evidence recovered from crime scenes and human remains. Typically the hypervariable regions are targeted for sequencing; however, more discriminating profiles are obtained if the whole genome is sequenced. Different approaches exist as to how best amplify and sequence whole mtDNA from forensic specimens. Here, we describe a method based on two-round PCR, combining multiplex and simplex PCRs. This method has been used in the analysis of mitochondrial genomes from archival saliva samples applied to FTA® cards after 10 years of transportation and preservation, without special protection. It is expected that this technique can be also used for the analysis of other old biological specimens directly or with modifications related to the level of DNA degradation.

Mitochondrial DNA variation in Tajiks living in Tajikistan.

This study aimed to characterize mtDNA control region (positions 16,024-576) of unrelated Tajiks living in Tajikistan. DNA was isolated from saliva specimens stored on FTA cards. The mtDNA fragments were amplified and directly sequenced in forward and reverse directions. Haplogroups were determined using HaploGrep and the diagnostic polymorphisms in the coding region of mtDNA. The Tajik mtDNA pool was characterized by substantial admixture of western and eastern Eurasian haplogroups, 62.6% and 26.4% sequences, respectively. It also contained 9.9% of South Asian and 1.1% of African haplotypes. The Tajik mtDNA sequences belonged to 90 different haplotypes defined by 148 transitions and 13 transversions in 156 of 1122 nucleotide sites. The Tajik mtDNA pool demonstrated the high genetic variation with genetic diversity of 0.999±0.002, nucleotide diversity of 0.014±0.007, and the mean number of pairwise nucleotide differences of 15.38±6.93. The random match probability and the power of discrimination were 0.0112 and 0.9888, respectively. Ethno-territorial groups of Tajiks demonstrated significant genetic differentiation with 2.67% of the genetic variance explained by differences between subpopulations. This study provides the insight into the mtDNA pool of Tajiks living in Tajikistan. The data should be taken into account in forensic identifications based on mtDNA.

Hominin evolution and gene flow in the Pleistocene Africa.

Africa demonstrates a complex process of the hominin evolution with a series of adaptive radiations during several millions of years that led to diverse morphological forms. Recently, Hammer et al. (2011) and Harvati et al. (2011) provided integrated morphological and genetic evidence of interbreeding between modern humans and unknown archaic hominins in Africa as recently as 35,000 years ago. However, a genetic evidence of hybridization between hominin lineages during the Lower and Middle Pleistocene epochs is unknown and the direct retrieval of DNA from extinct lineages of African hominins remains elusive. The availability of both nuclear and mitochondrial genome sequences from modern humans, Neanderthals, and Denisovans allows collecting nuclear DNA sequences of mitochondrial origin (numts) inserted into the nuclear genome of the ancestral hominin lineages and drawing conclusions about the hominin evolution in the remote past. The mtDNA and numt analysis uncovered a deep division of mtDNA lineages that existed in African hominins in the Middle Pleistocene. The first cluster included the human and Neanderthal-like mtDNA sequences while the second consisted of DNA sequences that are known today as mtAncestor-1, a nuclear fossil of the mtDNA, and the Denisova mtDNA isolated from a bone and a tooth found in southern Siberia. The two groups initially diverged 610,000-1,110,000 years ago. Approximately 220,000 years after the primary split, the Denisova - mtAncestor-1 mtDNA lineages mixed with the mtDNA pool of an ancestral population of Neanderthals and modern humans. This admixture after the profound division is demonstrated by the transposition of the Denisova-like mtDNA sequence into the nuclear genome of an ancestor of Neanderthals and modern humans. This finding suggests the matrilineal genetic structure among the Middle Pleistocene hominins as well as the existence of gene flow between African hominin lineages. Through paleogenomic analyses, it is impossible to exclude the theory that population structure and gene flow in African hominins influenced the admixture pattern observed in the nuclear genomes of non-Africans.

Topological field theory of dynamical systems. II.

This paper is a continuation of the study [Chaos.22.033134] of the relation between the stochastic dynamical systems (DS) and the Witten-type topological field theories (TFT). Here, it is discussed that the stochastic expectation values of a DS must be complemented on the TFT side by (-1)(F^), where F^ is the ghost number operator. The role of this inclusion is to unfold the natural path-integral representation of the TFT, i.e., the Witten index that equals up to a topological constant to the partition function of the stochastic noise, into the physical partition function of TFT/DS. It is also shown that on the DS side, the TFT's wavefunctions are the conditional probability densities.

Topological field theory of dynamical systems.

Here, it is shown that the path-integral representation of any stochastic or deterministic continuous-time dynamical model is a cohomological or Witten-type topological field theory, i.e., a model with global topological supersymmetry (Q-symmetry). As many other supersymmetries, Q-symmetry must be perturbatively stable due to what is generically known as non-renormalization theorems. As a result, all (equilibrium) dynamical models are divided into three major categories: Markovian models with unbroken Q-symmetry, chaotic models with Q-symmetry spontaneously broken on the mean-field level by, e.g., fractal invariant sets (e.g., strange attractors), and intermittent or self-organized critical (SOC) models with Q-symmetry dynamically broken by the condensation of instanton-antiinstanton configurations (earthquakes, avalanches, etc.) SOC is a full-dimensional phase separating chaos and Markovian dynamics. In the deterministic limit, however, antiinstantons disappear and SOC collapses into the "edge of chaos." Goldstone theorem stands behind spatio-temporal self-similarity of Q-broken phases known under such names as algebraic statistics of avalanches, 1/f noise, sensitivity to initial conditions, etc. Other fundamental differences of Q-broken phases is that they can be effectively viewed as quantum dynamics and that they must also have time-reversal symmetry spontaneously broken. Q-symmetry breaking in non-equilibrium situations (quenches, Barkhausen effect, etc.) is also briefly discussed.

Self-organized criticality as Witten-type topological field theory with spontaneously broken Becchi-Rouet-Stora-Tyutin symmetry.

Here, a scenario is proposed, according to which a generic self-organized critical (SOC) system can be looked upon as a Witten-type topological field theory (W-TFT) with spontaneously broken Becchi-Rouet-Stora-Tyutin (BRST) symmetry. One of the conditions for the SOC is the slow driving noise, which unambiguously suggests Stratonovich interpretation of the corresponding stochastic differential equation (SDE). This, in turn, necessitates the use of Parisi-Sourlas-Wu stochastic quantization procedure, which straightforwardly leads to a model with BRST-exact action, i.e., to a W-TFT. In the parameter space of the SDE, there must exist full-dimensional regions where the BRST symmetry is spontaneously broken by instantons, which in the context of SOC are essentially avalanches. In these regions, the avalanche-type SOC dynamics is liberated from overwise a rightful dynamics-less W-TFT, and a Goldstone mode of Fadeev-Popov ghosts exists. Goldstinos represent moduli of instantons (avalanches) and being gapless are responsible for the critical avalanche distribution in the low-energy, long-wavelength limit. The above arguments are robust against moderate variations of the SDE's parameters and the criticality is "self-tuned." The proposition of this paper suggests that the machinery of W-TFTs may find its applications in many different areas of modern science studying various physical realizations of SOC. It also suggests that there may in principle exist a connection between some SOC's and the concept of topological quantum computing.

Genome digging: insight into the mitochondrial genome of Homo.

BACKGROUND: A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt) on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1) into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split. PRINCIPAL FINDINGS: Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2) with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively. CONCLUSIONS: This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N)/d(S) dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective population size and possessed genetic diversity comparable with those of chimpanzee and gorilla.

Voltage-controlled ferromagnetic order in MnGe quantum dots.

Here, we speculate that room temperature voltage-controlled ferromagnetic ordering may become a founding phenomenon for the next generation of low-power spintronics nanodevices and discuss the special role of dilute magnetic semiconductors as the most reliable material basis to date. Then, we report on our latest experimental achievements in the voltage manipulation of the ferromagnetism in MnGe quantum dots, experimentally demonstrating the capacity of pushing the Curie temperature further above room temperature for technological applications.

Hydrodynamic tensor density functional theory with correct susceptibility.

In a previous work the authors developed a family of orbital-free tensor equations for the density functional theory [J. Chem. Phys. 124, 024105 (2006)]. The theory is a combination of the coupled hydrodynamic moment equation hierarchy with a cumulant truncation of the one-body electron density matrix. A basic ingredient in the theory is how to truncate the series of equation of motion for the moments. In the original work the authors assumed that the cumulants vanish above a certain order (N). Here the authors show how to modify this assumption to obtain the correct susceptibilities. This is done for N=3, a level above the previous study. At the desired truncation level a few relevant terms are added, which, with the right combination of coefficients, lead to excellent agreement with the Kohn-Sham Lindhard susceptibilities for an uninteracting system. The approach is also powerful away from linear response, as demonstrated in a nonperturbative study of a jellium with a repulsive core, where excellent matching with Kohn-Sham simulations is obtained, while the Thomas-Fermi and von Weiszacker methods show significant deviations. In addition, time-dependent linear response studies at the new N=3 level demonstrate the author's previous assertion that as the order of the theory is increased new additional transverse sound modes appear mimicking the random phase approximation transverse dispersion region.

Nonlinear signal mixing in a three-terminal molecular wire.

The authors study the electronic response of two simple molecular devices to a bichromatic field, where the device acts as a mixer. Two closely related model systems are considered: one is a benzene molecule and the other is a single grapheme sheet, and in both cases the systems are connected to three polyacetylene chains. The electronic response to the dichromatic alternating electric fields is studied by following the electron density fluctuation along the chain lengths. In both cases the electron transfer follows the field frequency at low electric fields. At higher amplitude, a significant amount of nonlinear mixing resulting in new combinations of the input frequencies is found in the spectrum. The influence of gating on the output frequencies is also shown.

Orbital-free tensor density functional theory.

We propose a family of time-dependent orbital-free density-based theories that go beyond the usual current-density description of electrons or other particles. The theories deal with physical quantities that characterize the one-particle density matrix and consequently the kinetics of the particles. We analyze the first two theories in the family. The "lowest-order" theory is quantum hydrodynamics. The second one yields not only the longitudinal plasmon collective excitations, but also the transverse phonon modes that are associated with elementary excitations in Fermi liquids. The theories should make it feasible to do large orbital-free simulations of time-dependent and stationary systems.

Spintronics birefringence with an extended molecular loop-wire or spiral coupling.

A ring with spin-orbit effects coupled to a conducting wire is shown to exhibit a phase delay which is spin dependent. The key is that the coupling of the ring to the wire is over an extended spatial range and not just along a single point; this breaks the symmetry and makes the ring states couple differently to forward and backward moving wire states. This results, for properly injected spin states, in a spin-flipping probability which is dependent on the energy of the injected electron and can therefore be easily controlled. Several systems are presented and shown to exhibit this effect including the basic ring which couples to a wire as well as a ring which mediates between two wires, and a spiral between two wires.