Superconductivity in CuxBi2Se3 and its implications for pairing in the undoped topological insulator

Bi2Se3 is one of a handful of known topological insulators. Here we show that copper intercalation in the van der Waals gaps between the Bi2Se3 layers, yielding an electron concentration of ~ 2 x 10^20cm-3, results in superconductivity at 3.8 K in CuxBi2Se3 for x between 0.12 and 0.15. This demonstrates that Cooper pairing is possible in Bi2Se3 at accessible temperatures, with implications for study of the physics of topological insulators and potential devices.Comment: 6 pages, 4 figure

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

Postglacial expansion of the arctic keystone copepod calanus glacialis

Calanus glacialis, a major contributor to zooplankton biomass in the Arctic shelf seas, is a key link between primary production and higher trophic levels that may be sensitive to climate warming. The aim of this study was to explore genetic variation in contemporary populations of this species to infer possible changes during the Quaternary period, and to assess its population structure in both space and time. Calanus glacialis was sampled in the fjords of Spitsbergen (Hornsund and Kongsfjorden) in 2003, 2004, 2006, 2009 and 2012. The sequence of a mitochondrial marker, belonging to the ND5 gene, selected for the study was 1249 base pairs long and distinguished 75 unique haplotypes among 140 individuals that formed three main clades. There was no detectable pattern in the distribution of haplotypes by geographic distance or over time. Interestingly, a Bayesian skyline plot suggested that a 1000-fold increase in population size occurred approximately 10,000 years before present, suggesting a species expansion after the Last Glacial Maximum.GAME from the National Science Centre, the Polish Ministry of Science and Higher Education Iuventus Plus [IP2014 050573]; FCT-PT [CCMAR/Multi/04326/2013]; [2011/03/B/NZ8/02876

Sources of variation in cuticular hydrocarbons in the ant formica exsecta

Phenotypic variation arises from interactions between genotype and environment, although how variation is produced and then maintained remains unclear. The discovery of the nest-mate recognition system in Formica exsecta ants has allowed phenotypic variation in chemical profiles to be quantified across a natural population of 83 colonies. We investigated if this variation was correlated or not with intrinsic (genetic relatedness), extrinsic (location, light, temperature) or social (queen number) factors. (Z)-9-Alkenes and n-alkanes showed different patterns of variance: island (location) explained only 0.2% of the variation in (Z)-9-alkenes, but 21¬–29% in n-alkanes, whereas colony of origin explained 96% and 45–49% of the variation in (Z)-9-alkenes and n-alkanes, respectively. By contrast, within-colony variance of (Z)-9-alkenes was 4%, and 23–34% in n-alkanes, supporting the function of the former as recognition cues. (Z)-9-Alkene and n-alkane profiles were correlated with the genetic distance between colonies. Only n-alkane profiles diverged with increasing spatial distance. Sampling year explained a small (5%), but significant, amount of the variation in the (Z)-9-alkenes, but there was no consistent directional trend. Polygynous colonies and populous monogynous colonies were dominated by a rich C23:1 profile. We found no associations between worker size, mound exposure, or humidity, although effect sizes for the latter two factors were considerable. The results support the conjecture that genetic factors are the most likely source of between-colony variation in cuticular hydrocarbons

Critical mutation rate has an exponential dependence on population size for eukaryotic-length genomes with crossover

The critical mutation rate (CMR) determines the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness (“flattest”). We identify an inverse relationship between CMR and sequence length in an in silico system with a two-peak fitness landscape; CMR decreases to no more than five orders of magnitude above estimates of eukaryotic per base mutation rate. We confirm the CMR reduces exponentially at low population sizes, irrespective of peak radius and distance, and increases with the number of genetic crossovers. We also identify an inverse relationship between CMR and the number of genes, confirming that, for a similar number of genes to that for the plant Arabidopsis thaliana (25,000), the CMR is close to its known wild-type mutation rate; mutation rates for additional organisms were also found to be within one order of magnitude of the CMR. This is the first time such a simulation model has been assigned input and produced output within range for a given biological organism. The decrease in CMR with population size previously observed is maintained; there is potential for the model to influence understanding of populations undergoing bottleneck, stress, and conservation strategy for populations near extinction

Find the weakest link. A comparison between demographic, genetic and demo-genetic metapopulation extinction times

<p>Abstract</p> <p>Background</p> <p>While the ultimate causes of most species extinctions are environmental, environmental constraints have various secondary consequences on evolutionary and ecological processes. The roles of demographic, genetic mechanisms and their interactions in limiting the viabilities of species or populations have stirred much debate and remain difficult to evaluate in the absence of demography-genetics conceptual and technical framework. Here, I computed projected times to metapopulation extinction using (1) a model focusing on the effects of species properties, habitat quality, quantity and temporal variability on the time to demographic extinction; (2) a genetic model focusing on the dynamics of the drift and inbreeding loads under the same species and habitat constraints; (3) a demo-genetic model accounting for demographic-genetic processes and feedbacks.</p> <p>Results</p> <p>Results indicate that a given population may have a high demographic, but low genetic viability or vice versa; and whether genetic or demographic aspects will be the most limiting to overall viability depends on the constraints faced by the species (e.g., reduction of habitat quantity or quality). As a consequence, depending on metapopulation or species characteristics, incorporating genetic considerations to demographically-based viability assessments may either moderately or severely reduce the persistence time. On the other hand, purely genetically-based estimates of species viability may either underestimate (by neglecting demo-genetic interactions) or overestimate (by neglecting the demographic resilience) true viability.</p> <p>Conclusion</p> <p>Unbiased assessments of the viabilities of species may only be obtained by identifying and considering the most limiting processes (i.e., demography or genetics), or, preferentially, by integrating them.</p

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Wolbachia are maternally-inherited symbiotic bacteria commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. Here we use whole genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe and Africa to predict Wolbachia infection status, estimate cytoplasmic genome copy number, and reconstruct Wolbachia and mtDNA genome sequences. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent incomplete global replacement of ancestral Wolbachia and mtDNA lineages, which is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats.Comment: 41 pages, 5 figure

Limits to the Rate of Adaptive Substitution in Sexual Populations

In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, , that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is , where is the population size, is the rate of beneficial mutations per genome, and is their mean selective advantage. Heritable variance in log fitness due to unlinked loci reduces by under polygamy and under monogamy. With a linear genetic map of length Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on , , , and only through the baseline density: . Under the approximation that the interference due to different sweeps adds up, we show that , implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for ; for higher , the rate of adaptation grows above , but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common—diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time