Comparative analysis of 343 plastid genomes of Solanum section Petota: Insights into potato diversity,phylogeny, and species discrimination

Common potato (Solanum tuberosum L.) and its wild relatives belong to Solanum section Petota. This section's phylogeny and species delimitation are complicated due to various ploidy levels, high heterozygosity, and frequent interspecific hybridization. Compared to the nuclear genome, the plastid genome is more conserved, has a haploid nature, and has a lower nucleotide substitution rate, providing informative alternative insights into the phylogenetic study of section Petota. Here, we analyzed 343 potato plastid genomes from 53 wild and four cultivated species. The diversity of sequences and genomes was comprehensively analyzed. A total of 24 species were placed in a phylogenetic tree based on genomic data for the first time. Overall, our results not only confirmed most existing clades and species boundaries inferred by nuclear evidence but also provided some distinctive species clade belonging and the maternally inherited evidence supporting the hybrid origin of some species. Furthermore, the divergence times between the major potato clades were estimated. In addition, the species discriminatory power of universal barcodes, nuclear ribosomal DNA, and whole and partial plastid genomes and their combinations were thoroughly evaluated; the plastid genome performed best but had limited discriminatory power for all survey species (40%). Overall, our study provided not only new insights into phylogeny and DNA barcoding of potato but also provided valuable genetic data resources for further systematical research of Petota.     

Two-phase species–time relationships in North American land birds

The species–time relationship (STR) is a macroecological pattern describing the increase in the observed species richness with the length of time censused. Understanding STRs is important for understanding the ecological processes underlying temporal turnover and species richness. However, accurate characterization of the STR has been hampered by the influence of sampling. I analysed STRs for 521 breeding bird survey communities. I used a model of sampling effects to demonstrate that the increase in richness was not due exclusively to sampling. I estimated the time scale at which ecological processes became dominant over sampling effects using a two‐phase model combining a sampling phase and either a power function or logarithmic ecological phase. These two‐phase models performed significantly better than sampling alone and better than simple power and logarithmic functions. Most community dynamics were dominated by ecological processes over scales <5 years. This technique provides an example of a rigorous, quantitative approach to separating sampling from ecological processes.     

朱砂叶螨羧酸脂酶最优测试条件的选择

应用二次回归通用旋转组合设计,对朱砂叶螨离体羧酸酯酶测试过程中所需缓冲液pH值、恒温时间、反应温度及底物浓度,设立4因子5水平试验,在考虑4个因子主效应和互作效应的情况下,筛选测试羧酸酯酶的最优条件组合。     

Fitness effects of sex ratio response to host quality and size in the parasitoid wasp Spalangia cameroni

The parasitoid wasp Spalangia cameroni oviposited a greaterproportion of daughters in stable fly pupae than in house flypupae, even when I controlled for stable flies being smallerthan house flies. Sex ratio manipulation in response to hostquality has been modeled as being adaptive through an effectof host quality on the size and hence offspring production ofdaughters. 5. cameronis response to host species may insteadbe adaptive through an effect on larval survivorship, the developmenttime of daughters, and the size of sons. There was greater survivalof daughters than sons on stable flies. Controlling for hostsize, I found that development time of daughters was about 2%less on stable flies than on house flies. The decrease in developmenttime corresponds to a 2% increase in fitness as estimated byr, the intrinsic rate of increase, and is equivalent to abouta 9% increase in offspring production. Sons were about 2% largerfrom house flies than stable flies, which may increase offspringproduction by up to 3%. Host species had no consistent effecton size of daughters or development time of sons. In additionto the response to host species, mothers oviposited a greaterproportion of daughters in larger stable fly hosts. Whetherthis behavior is adaptive is unclear. Although offspring werelarger when they developed on larger stable flies, the rateof increase was less for daughters dian for sons. Effects ofstable fly size on offspring development time were negligible.     

Magnetic resonance imaging in vivo monitoring of T2 relaxation time: Quantitative assessment of primate brain maturation

This work describes quantitative MRI assessment of primate brain maturation. Nine young baboons were followed from the age of one to 30 months. Assessment of myelination was based on the gray/white matter contrast on MR images and the evolution of T2 relaxation time respectively. The brain maturation began in the posterior fossa and progressed to the olfactory bulbs corresponding to decreasing white matter T2 values. Relaxation parameters provide new opportunities to trace the myelination process in vivo.     

An Estimate of Divergence Time of Parazoa and Eumetazoa and That of Cephalochordata and Vertebrata by Aldolase and Triose Phosphate Isomerase Clocks

Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined based on three different models for estimating evolutionary distances. It was shown that the evolutionary rates remain essentially unchanged in comparisons not only between different classes of vertebrates but also between vertebrates and arthropods and even between animals and plants, irrespective of the models used. Thus these enzymes might be useful molecular clocks for inferring divergence times of animal phyla. To know the divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata, the aldolase cDNAs from Ephydatia fluviatilis, a freshwater sponge, and the TPI cDNAs from Ephydatia fluviatilis and Branchiostoma belcheri, an amphioxus, have been cloned and sequenced. Comparisons of the deduced amino acid sequences of aldolase and TPI from the freshwater sponge with known sequences revealed that the Parazoa–Eumetazoa split occurred about 940 million years ago (Ma) as determined by the average of two proteins and three models. Similarly, the aldolase and TPI clocks suggest that vertebrates and amphioxus last shared a common ancestor around 700 Ma and they possibly diverged shortly after the divergence of deuterostomes and protostomes.     

Ditylenchus dipsaci Infestation of Trifolium repens. I. Temperature Effects,Seedling Invasion,and a Field Survey

Rates of development of stem nematode (Ditylenchus dipsaci) in white clover (Trifolium repens) seedlings were found to be linearly related to temperature. Basal developmental temperature (T_b) was 3 °C, and the thermal constant (S) for development of gravid adult females from freshly laid eggs was 270 accumulated day-degrees above the T_b. Only 12% at 20 °C and 4% at 4 °C of the gravid female nematodes inoculated into seedling axils successfully penetrated seedling epidermis. These nematodes slowly migrated within the seedling and after a lag of 5 days at 20 °C started to lay eggs. The maximal rate of egg production was temperature-dependent, being 0.8 and 3.1 eggs female⁻¹ day⁻¹ at 10 and 20 °C, respectively. Nematodes emigrated rapidly from infested stolons when they were immersed in water, with rates being highest at 25 °C and lowest at 4 °C. The sensitivity to temperature of many of the parameters that govern nematode population dynamics indicates that climatic changes will have a marked effect upon this host-parasite system. A study of infested stolons from the field indicated that nematode numbers increased up to 3,000 or more before tissue senesence, triggered by nematode damage, caused a mass emigration of nematodes from the stolon.     

AN ASSESSMENT OF CHANGES WITH TIME IN THE MARKING PATTERNS USED FOR PHOTOIDENTIFICATION OF INDIVIDUAL SPERM WHALES, PHYSETER MACROCEPHALUS

We observed changes with time in the patterns of characteristic fluke markings used to identify sperm whales. Changes were categorized as minor, moderate, or major based on their severity. These change types were found to occur at rates of 0.9%, 11.8%, and 1.3% per individual per year, respectively. Gain and loss rates for each of seven different mark types were also calculated. The highest estimated rate was the gain of small nicks at 0.08 per individual per year. Most individuals identified by us possess at least a few characteristic marks and, therefore, changes of the type observed in this study are unlikely to severely affect their recognizability. For all but one mark type, gain rates were higher than loss rates, indicating that individuals may be accumulating marks with age. Over long periods this could eventually make individuals unrecognizable, with the result that population sizes calculated from these data may be overestimated. As long as photoidentification studies are conducted sufficiently often, and these changes are as gradual as they appear to be, this problem should be minimal.     

An estimate of spin diffusion in a spin subset: Application to iterative distance calculation from 3D 15N NOESY-HMQC

Summary A method for quantification of distances between amide hydrogens using only the 3D NOESY-HMQC experiment recorded on a ¹⁵N-labelled protein is presented. This method is based on an approximate expression of the NOE intensities between amide hydrogens obtained from continuum modelling of the non-amide spins; this expression is used in a distance calculation algorithm. The algorithm has been named CROWD, standing for Continuum approximation of Relaxati On path Ways between Dilute spins. This approximation as well as the CROWD algorithm are tested on a simulated case; the CROWD algorithm is then applied to experimental data, measured on a fragment of bacteriorhodopsin.     

Refocusing revisited: An optimized,gradient-enhanced refocused HSQC and its applications in 2D and 3D NMR and in deuterium exchange experiments

Summary 2D ¹⁵N-¹H correlation spectra are ideal for measuring backbone amide populations to determine amide exchange protection factors in studies of protein folding or other structural features. Most protein NMR spectroscopists use HSQC, which has been shown to be generally superior to HMQC in both resolution and sensitivity. The refocused HSQC experiment is intrinsically less sensitive than the regular HSQC, due to T₂ relaxation during the refocusing delays. However, we show here that, when high ¹⁵N resolution is needed, an optimized refocused HSQC sequence that utilizes a semi-constant time evolution period and pulsed field gradients has better signal-to-noise ratio and resolution, and integrates more accurately, than a similar HSQC. The differences are demonstrated on a 20 kDa protein. The technique can also be applied to 3D NOESY experiments to eliminate strong NH₂ geminal peaks and their truncation artefacts at a modest cost in sensitivity.