The influence of sampling design on tree‐ring‐based quantification of forest growth

Tree‐rings offer one of the few possibilities to empirically quantify and reconstruct forest growth dynamics over years to millennia. Contemporaneously with the growing scientific community employing tree‐ring parameters, recent research has suggested that commonly applied sampling designs (i.e. how and which trees are selected for dendrochronological sampling) may introduce considerable biases in quantifications of forest responses to environmental change. To date, a systematic assessment of the consequences of sampling design on dendroecological and‐climatological conclusions has not yet been performed. Here, we investigate potential biases by sampling a large population of trees and replicating diverse sampling designs. This is achieved by retroactively subsetting the population and specifically testing for biases emerging for climate reconstruction, growth response to climate variability, long‐term growth trends, and quantification of forest productivity. We find that commonly applied sampling designs can impart systematic biases of varying magnitude to any type of tree‐ring‐based investigations, independent of the total number of samples considered. Quantifications of forest growth and productivity are particularly susceptible to biases, whereas growth responses to short‐term climate variability are less affected by the choice of sampling design. The world's most frequently applied sampling design, focusing on dominant trees only, can bias absolute growth rates by up to 459% and trends in excess of 200%. Our findings challenge paradigms, where a subset of samples is typically considered to be representative for the entire population. The only two sampling strategies meeting the requirements for all types of investigations are the (i) sampling of all individuals within a fixed area; and (ii) fully randomized selection of trees. This result advertises the consistent implementation of a widely applicable sampling design to simultaneously reduce uncertainties in tree‐ring‐based quantifications of forest growth and increase the comparability of datasets beyond individual studies, investigators, laboratories, and geographical boundaries.     

Image quality comparison of a nonlinear image-based noise reduction technique with a hybrid-type iterative reconstruction for pediatric computed tomography

PurposeTo compare computed tomography (CT) image properties between a vendor-independent image-based noise reduction technique, Image-space Noise Reduction (iNoir) and a hybrid-type iterative reconstruction technique, Adaptive Statistical Iterative Reconstruction (ASIR).MethodsA cylindrical water phantom, corresponding to pediatric body size, containing soft-tissue-equivalent rod and 12-mg iodine/ml rod was scanned at size-specific dose estimates of 8.4 and 16.7 mGy. For assessments of image quality and noise texture change, task-based system performance function (SPF) and peak frequency difference (PFD) were compared, respectively, among filtered back projection (FBP), IR image with 50%-blending rate (50%ASIR), 100%ASIR, 50%iNoir, and 100%iNoir. Human observer test for pediatric CT images was performed by radiologists.ResultsFor the soft-tissue contrast, SPF² of 100%iNoir was the highest. The average SPF² between 0.1 and 0.5 cycles/mm for 100%iNoir increased by approximately 70% compared with FBP, while ASIR indicted slight increases in the frequency region of >0.2 cycles/mm. For the iodine contrast, 100%iNoir indicated highest values at the spatial frequencies corresponding pediatric artery diameters. The PFDs of iNoir were negligible and lower than that of ASIR. The results of human observer test supported results of SPF² and PFD.ConclusionsCompared with ASIR, iNoir provided better image quality for pediatric abdominal CT without compromising noise texture change.     

The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt

Saccharomyces cerevisiae strain W303 is a widely used model organism. However, little is known about its genetic origins, as it was created in the 1970s from crossing yeast strains of uncertain genealogy. To obtain insights into its ancestry and physiology, we sequenced the genome of its variant W303-K6001, a yeast model of ageing research. The combination of two next-generation sequencing (NGS) technologies (Illumina and Roche/454 sequencing) yielded an 11.8 Mb genome assembly at an N50 contig length of 262 kb. Although sequencing was substantially more precise and sensitive than whole-genome tiling arrays, both NGS platforms produced a number of false positives. At a 378× average coverage, only 74 per cent of called differences to the S288c reference genome were confirmed by both techniques. The consensus W303-K6001 genome differs in 8133 positions from S288c, predicting altered amino acid sequence in 799 proteins, including factors of ageing and stress resistance. The W303-K6001 (85.4%) genome is virtually identical (less than equal to 0.5 variations per kb) to S288c, and thus originates in the same ancestor. Non-S288c regions distribute unequally over the genome, with chromosome XVI the most (99.6%) and chromosome XI the least (54.5%) S288c-like. Several of these clusters are shared with Σ1278B, another widely used S288c-related model, indicating that these strains share a second ancestor. Thus, the W303-K6001 genome pictures details of complex genetic relationships between the model strains that date back to the early days of experimental yeast genetics. Moreover, this study underlines the necessity of combining multiple NGS and genome-assembling techniques for achieving accurate variant calling in genomic studies.     

An ostracod-based calibration function for electrical conductivity reconstruction in lacustrine environments in Patagonia,Southern South America

In the Patagonian region (∼37–56°S) E of the Andes, the salinity and solute composition of lakes is strongly related to their location along the marked W-E decreasing precipitation gradient that is one of the main climatic features of the area. A calibration function (n = 34) based on 12 ostracod species (Ostracoda, Crustacea) was developed by WA-PLS to quantitatively reconstruct electrical conductivity (EC) values as a salinity proxy. The selected one component model had a r² = 0.74 and RMSEP and maximum bias equal to 16% and 31% of the sampled range, respectively, comparable to other published ostracod-based calibration functions. This model was applied to the ostracod record of the closed lake Laguna Cháltel (49°58′S, 71°07′W), comprising seven species and dominated by two species of the genus Limnocythere. In order to evaluate the calibration function’s robustness, the obtained EC values were compared with qualitative lake level and salinity variations inferred through a multiproxy hydrological reconstruction of the lake. Both reconstructions show good overall agreement, with reconstructed EC values in the oligo-mesohaline range (average: 11 060 ± 680 μS/cm) between 4570 and 3190 cal BP, corresponding to the ephemeral and shallow lake phases, and a marked decrease in EC concurrent with a lake level rise, reaching an average EC of 1140 ± 90 μS/cm during the deep lake phase (1720 cal BP to present). The variability in the reconstructed EC values for the ephemeral lake phase showed some inconsistency with the expected trend, which was attributed to time-averaging effects; for its part, the pace of the decrease in EC during the medium-depth phase (3190–1720 cal BP) differed from the expected, which could be due to autigenic effects (redissolution of salts) at the onset of this phase. This comparison not only lends support to the adequacy of the calibration function, but also suggests that its application in the context of a multiproxy study can greatly contribute to distinguish between autigenic and climatic-related controls of paleosalinity in closed lakes, allowing performing more accurate paleoenvironmental inferences on the basis of paleohydrological reconstructions.     

Ornament evolution in dragon lizards: multiple gains and widespread losses reveal a complex history of evolutionary change

The expression in females of ornaments thought to be the target of sexual selection in males is a long-standing puzzle. Two main hypotheses are proposed to account for the existence of conspicuous ornaments in both sexes (mutual ornamentation): genetic correlation between the sexes and sexual selection on females as well as males. We examined the pattern of ornament gains and losses in 240 species of dragon lizards (Agamidae) in order to elucidate the relative contribution of these two factors in the evolution of mutual ornamentation. In addition, we tested whether the type of shelter used by lizards to avoid predators predicts the evolutionary loss or constraint of ornament expression. We found evidence that the origin of female ornaments is broadly consistent with the predictions of the genetic correlation hypothesis. Ornaments appear congruently in both sexes with some lineages subsequently evolving male biased sexual dimorphism, apparently through the process of natural selection for reduced ornamentation in females. Nevertheless, ornaments have also frequently evolved in both sexes independently. This suggests that genetic correlations are potentially weak for several lineages and sexual selection on females is responsible for at least some evolutionary change in this group. Unexpectedly, we found that the evolutionary loss of some ornaments is concentrated more in males than females and this trend cannot be fully explained by our measures of natural selection.     

“Sensory Switching” in Elbow Reconstruction

In the treatment of the soft tissue defect of the elbow, flap reconstruction is necessitated in many cases because of thinness of soft tissue at this region. In addition, reacquirement of tactile sensation is desirable because of the anatomical and specific functions of the elbow. Of three cases treated for elbow defects, one was reconstructed with a pedicled island forearm flap containing the lateral cutaneous nerve of the forearm, another was reconstructed with a venoneuro-accompanying artery fasciocutaneous flap (VNAF flap) containing the basilic vein, and the third with the VNAF flap containing the cephalic vein. The three cases demonstrated a sudden change of sensory territory 4 to 6 months after surgery, which was confirmed by touching the reconstructed region with patients'' eye-closed: from its original territory to the elbow in a “switching”-like action. Here we describe and discuss the concept of “sensory switching.”     

KINALYZER, a computer program for reconstructing sibling groups

A software suite KINALYZER reconstructs full-sibling groups without parental information using data from codominant marker loci such as microsatellites. KINALYZER utilizes a new algorithm for sibling reconstruction in diploid organisms based on combinatorial optimization. KINALYZER makes use of a Minimum 2-Allele Set Cover approach based on Mendelian inheritance rules and finds the smallest number of sibling groups that contain all the individuals in the sample. Also available is a 'Greedy Consensus' approach that reconstructs sibgroups using subsets of loci and finds the consensus of the partial solutions. Unlike likelihood methods for sibling reconstruction, KINALYZER does not require information about population allele frequencies and it makes no assumptions regarding the mating system of the species. KINALYZER is freely available as a web-based service.