Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like ...coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods.
We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (N
e) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages.
N
e curves of all study species converged 1.0 million yr ago, probably reflecting the time when the walnut genus last shared a common ancestor. This estimate was confirmed by the G-PhoCS estimates of divergence times. But all species did not react similarly to the dramatic climatic oscillations following early Pleistocene cooling, so the timing and amplitude of changes in N
e differed among species and even among conspecific lineages.
The population histories of temperate walnut species were not driven by extrinsic environmental changes alone, and a key role was probably played by species-specific factors such as coevolutionary interactions with specialized pathogens.
East Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists ...today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach. We genotyped 70 populations throughout the distributional range of Asian butternuts (Juglans section Cardiocaryon) using eight chloroplast DNA regions, one single‐copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades. The genetic data consistently identified two clades, one northern, comprising Juglans mandshurica and Juglans ailantifolia, and one southern, comprising Juglans cathayensis. The two clades diverged through climate‐induced vicariance of an ancestral northern range during the mid‐Miocene and remained mostly separate thereafter, with geographical isolation of the Japanese Islands and refugial isolation or secondary contacts in the late Pleistocene producing further subdivision within the northern clade. But beyond all that, we also discovered a role of environmental adaptation in maintaining and/or reinforcing the north–south divergence. Asian butternuts offer a strong case for the existence of a biogeographic divide between the northern and southern parts of East Asia during the Neogene and into the Pleistocene.
Establishing an accurate, simple, and rapid serodiagnosis method aiming for specific cancer antigens is critically important for the clinical diagnosis, therapy, and prognostication of cancer. ...Currently, surface-enhanced Raman scattering (SERS) readout techniques challenge fluorescent-based detection methods in terms of both optical stability and more importantly multiple detection capability, which become more desirable for clinical diagnostics. We thus started using an interference-free mixing SERS emission (m-SERS) readout to simultaneously indicate, for the first time, three specific liver cancer antigens, including α-fetoprotein (AFP), carcinoembryonic antigen (CEA), and ferritin (FER), even in one clinical serum sample. Here, three triple bonds (CN and CC) coded SERS tags contribute separate SERS emissions located at 2105, 2159, and 2227 cm–1, respectively; must have one-to-one correspondence from AFP, to FER, to CEA, In the process of detection, the mature double antibody sandwich allows the formation of microscale core–satellite assembly structure between a magnetic bead (MB) and single SERS tags, and therefore a pure and single SERS emission can be observed under the routine excitation laser spot. Because of the action of magnetic force, the uniform 3D packing of SERS tags absorbed MBs will in contrast generate a so-called m-SERS signals. With the help of enrichment and separation by MBs, the proposed m-SERS immunoassay provides an extremely rapid, sensitive, and accurate solution for multiplex detection of antigens or other biomarkers. Herein, the limit of detection (LOD) for simultaneous m-SERS detection of AFP, CEA, and FER was 0.15, 20, and 4 pg/mL, respectively. As expected for 39 clinical serum samples, simultaneous detection of ternary specific antigens can significantly improve the accuracy of liver cancer diagnosis.
Fosfomycin is a broad-spectrum antibiotic with the activity against both Gram-positive and Gram-negative pathogens by inhibiting the bacterial cell wall synthesis. Given the potential therapeutic ...efficacy of fosfomycin against Campylobacter spp., the aim of the present study was to determine the in vitro fosfomycin susceptibility of Campylobacter isolates from avian sources including poultry and wild birds. A total of eight (1.8%) strains of Campylobacter including five C. jejuni strains isolated from ducks and three C. coli strains isolated from chickens and duck showed resistance to fosfomycin, with MICs ranging from 64 to ≥ 256 μg/mL. The extent of fosfomycin resistance was 0%, 0.9% and 3.9% in wild birds, chicken and ducks respectively. The MIC50, MIC90, and MIC100 values were 8, 32, and 32 μg/mL respectively in wild bird, 32, 32, and 64 μg/mL respectively in chicken, and 32, 32, and ≥ 256 μg/mL respectively in ducks. All eight fosfomycin-resistant Campylobacter strains were multidrug resistant; six were also resistant to fluoroquinolones, ampicillin, and tetracycline, and two were also resistant to fluoroquinolones, ampicillin, tetracycline, and macrolides. However, the fosfomycin resistance gene fosXCC was not detected in the eight fosfomycin-resistant strains. Because food animals can harbor fosfomycin-resistant Campylobacter and transmit them to humans, greater efforts are needed to monitor the prevalence of fosfomycin resistance in Campylobacter strains isolated from such animals.
This article considers identification of sparse Volterra systems. A method based on the almost orthogonal matching pursuit (AOMP) is proposed. The AOMP algorithm allows one to estimate one nonzero ...coefficient at a time until all nonzero coefficients are found without losing the optimality and the sparsity, thus avoiding the curse of dimensionality often encountered in Volterra system identification.
In this paper, source localization by a network of primitive binary sensors under various imperfections are studied. Detailed analysis and mathematical modeling of imperfect binary sensors are ...presented. Imperfections include sensor failures of two types, drifting, uncertainty, and heterogeneity in binary sensor trigger thresholds, presence of noise, and nonradial symmetry of sensing ranges. Theoretical results, including asymptotical convergence, are established, in particular in the presence of substantial outliers due to sensor failure and large noise. Efficient numerical algorithms are proposed and simulated supporting the theoretical analysis.
Block-oriented Nonlinear System Identification deals with an area of research that has been very active since the turn of the millennium. The book makes a pedagogical and cohesive presentation of the ...methods developed in that time.
• Recently, there has been a debate about whether the temperate forests of East Asia merged or fragmented during glacial periods in the Pleistocene. Here, we tested these two opposing views through ...phylogeographical studies of the temperate‐deciduous walnut tree, Juglans mandshurica (Juglandaceae) in northern and northeastern China, as well as Japan and Korea. • We assessed the genetic structure of 33 natural populations using 10 nuclear microsatellite loci and seven chloroplast DNA (cpDNA) fragments. • The cpDNA data showed the complete fixation of two different haplotype lineages in northeastern vs northern populations. This pronounced phylogeographic break was also indicated by nuclear microsatellite data, but there were disparities regarding individual populations. Among those populations fixed for haplotype A (the northeastern group), three were clustered in the northern group and four showed evidence of mixed ancestry based on microsatellite data. • Our results support the hypothesis that two independent refugia were maintained across the range of J. mandshurica in the north of China during the last glacial maximum, contrary to the inference that all temperate forests migrated to the south (25-30°N). The discordance between the patterns revealed by cpDNA and microsatellite data indicate that asymmetrical gene flow has occurred between the two refugia.
Abstract
Background
Persian walnut,
Juglans regia
, occurs naturally from Greece to western China, while its closest relative, the iron walnut,
Juglans sigillata
, is endemic in southwest China; both ...species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them.
Results
We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern
J. regia
and its ancestor into
J. sigillata
, including the shell-thickness gene. Within
J. regia
, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while
J. sigillata
had a constant population size from about 100 to 20 generations ago, followed by a rapid decline.
Conclusions
Both
J. regia
and
J. sigillata
appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced
J. regia
appears to have played a role in the domestication of
J. sigillata.
The detection of viruses is of interest for a number of fields including biomedicine, environmental science, and biosecurity. Of particular interest are methods that do not require expensive ...equipment or trained personnel, especially if the results can be read by the naked eye. A new “double imprinting” method was developed whereby a virus‐bioimprinted hydrogel is further micromolded into a diffraction grating sensor by using imprint‐lithography techniques to give a “Molecularly Imprinted Polymer Gel Laser Diffraction Sensor” (MIP‐GLaDiS). A simple laser transmission apparatus was used to measure diffraction, and the system can read by the naked eye to detect the Apple Stem Pitting Virus (ASPV) at concentrations as low as 10 ng mL−1, thus setting the limit of detection of these hydrogels as low as other antigen‐binding methods such as ELISA or fluorescence‐tag systems.
Eye see it: A strategy for the naked‐eye detection of target compounds by using shrink‐responsive hydrogels is presented. A “double imprinting” method was used, in which a virus‐bioimprinted hydrogel is further micromolded into a diffraction‐grating sensor by using imprint‐lithography techniques. The bioimprinting was performed with an impure extract, which eliminates the need for a pure template.
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