A comparison of androgenetic doubled-haploid,and single seed descent lines in Triticale

Summary Sixty single seed descent (SSD) lines and about 25 anther-derived doubled-haploid (DH) lines were obtained from two triticale crosses. The frequency distributions of 10 quantitative agronomic traits were compared using parametric and non-parametric tests. A multivariate discriminant analysis was subsequently carried out. Gliadin patterns obtained from each line by polyacrylamide gel electrophoresis were used to calculate intra- and inter-population diversities from relative dissimilarity indices. It was found that DH and SSD lines show significant differences in frequency distributions of 1000 grain weight in both crosses, of heading date for one cross, and of lodging susceptibility for the other cross. The results of intra- and inter-population gliadin diversity indicate that although the SSD method theoretically provides more opportunity for recombination to occur than the DH method, it did not produce a greater range of recombinants. Since there is no significant difference between SSD- and DH-line distributions for grain yield, anther culture appears to be an efficient method for producing high yielding homozygous lines from F₁ hybrids of triticale in a relatively short time.     

Genetic variation of recent Alu insertions in human populations

The Alu family of intersperesed repeats is comprised of ovr 500,000 members which may be divided into discrete subfamilies based upon mutations held in common between members. Distinct subfamilies of Alu sequences have amplified within the human genome in recent evolutionary history. Several individual Alu family members have amplified so recently in human evolution that they are variable as to presence and absence at specific loci within different human populations. Here, we report on the distribution of six polymorphic Alu insetions in a survey of 563 individuals from 14 human population groups across several continents. Our results indicate that these polymorphic Alu insertions probably have an African origin and that there is a much smaller amount of genetic variation between European populations than that found between other populations groups. Present address: Department of Pathology, Stanley S. Scott Cancer Center, Louisiana State University Medical Center, 1901 Perdido St., New Orleans, LA 70112 Correspondence to: M.A. Batzer     

Asymptotic line-of-descent distributions

Asymptotic distributions are derived for the number of non-mutant ancestors, at time t in the past, of a sample of n from a neutral infinite alleles model. Either the number of non-mutant ancestors L _n (t) has a normal distribution or n-L_n(t) has a Poisson distribution as n , t 0.     

Hydraulic redistribution affects modeled carbon cycling via soil microbial activity and suppressed fire

Hydraulic redistribution (HR) of water from moist to drier soils, through plant roots, occurs world‐wide in seasonally dry ecosystems. Although the influence of HR on landscape hydrology and plant water use has been amply demonstrated, HR's effects on microbe‐controlled processes sensitive to soil moisture, including carbon and nutrient cycling at ecosystem scales, remain difficult to observe in the field and have not been integrated into a predictive framework. We incorporated a representation of HR into the Community Land Model (CLM4.5) and found the new model improved predictions of water, energy, and system‐scale carbon fluxes observed by eddy covariance at four seasonally dry yet ecologically diverse temperate and tropical AmeriFlux sites. Modeled plant productivity and microbial activities were differentially stimulated by upward HR, resulting at times in increased plant demand outstripping increased nutrient supply. Modeled plant productivity and microbial activities were diminished by downward HR. Overall, inclusion of HR tended to increase modeled annual ecosystem uptake of CO₂ (or reduce annual CO₂ release to the atmosphere). Moreover, engagement of CLM4.5′s ground‐truthed fire module indicated that though HR increased modeled fuel load at all four sites, upward HR also moistened surface soil and hydrated vegetation sufficiently to limit the modeled spread of dry season fire and concomitant very large CO₂ emissions to the atmosphere. Historically, fire has been a dominant ecological force in many seasonally dry ecosystems, and intensification of soil drought and altered precipitation regimes are expected for seasonally dry ecosystems in the future. HR may play an increasingly important role mitigating development of extreme soil water potential gradients and associated limitations on plant and soil microbial activities, and may inhibit the spread of fire in seasonally dry ecosystems.     

A combined steepest descent and genetic algorithm (SD/GA) approach for the optimization of solvation parameters

An accurate solvation model is essential for computer modeling of protein folding and other biomolecular self-assembly processes. Compared to explicit solvent models, implicit solvent models, such as the Poisson-Boltzmann (PB) with solvent accessible surface area model (PB/SA), offer a much faster speed—the most compelling reason for the popularity of these implicit solvent models. Since these implicit solvent models typically use empirical parameters, such as atomic radii and the surface tensions, an optimal fit of these parameters is crucial for the final accuracy of properties such as solvation free energy and folding free energy. In this paper, we proposed a combined approach, namely SD/GA, which takes the advantage of both local optimization with the steepest descent (SD), and global optimization with the genetic algorithm (GA), for parameters optimization in multi-dimensional space. The SD/GA method is then applied to the optimization of solvation parameters in the non-polar cavity term of the PB/SA model. The results show that the newly optimized parameters from SD/GA not only increase the accuracy in the solvation free energies for ～200 organic molecules, but also significantly improve the free energy landscape of a β-hairpin folding. The current SD/GA method can be readily applied to other multi-dimensional parameter space optimization as well.     

Does the circadian clock drift when pilots fly multiple transpacific flights with 1- to 2-day layovers?

On trips with multiple transmeridian flights, pilots experience successive non-24 h day/night cycles with circadian and sleep disruption. One study across a 9-day sequence of transpacific flights (no in-flight sleep, 1-day layovers between flights) reported an average period in the core body temperature rhythm of 24.6 h (circadian drift). Consequently, pilots were sometimes flying through the circadian performance nadir and had to readapt to home base time at the end of the trip. The present study examined circadian drift in trip patterns with longer flights and in-flight sleep. Thirty-nine B747-400 pilots (19 captains, 20 first officers, mean age = 55.5 years) were monitored on 9- to 13-day trips with multiple return flights between East Coast USA and Japan (in 4-pilot crews) and between Japan and Hawaii (in 3-pilot crews), with 1-day layovers between each flight. Measures included total in-flight sleep (actigraphy, log books) and top of descent (TOD) measures of sleepiness (Karolinska Sleepiness Scale), fatigue (Samn–Perelli Crew Status Check) and psychomotor vigilance task (PVT) performance. Circadian rhythms of individual pilots were not monitored. To detect circadian drift, mixed-model analysis of variance examined whether for a given flight, total in-flight sleep and TOD measures varied according to when the flight occurred in the trip sequence. In addition, sleep propensity curves for pre-trip and post-trip days were examined (Chi-square periodogram analyses). Limited data suggest that total in-flight sleep of relief crew at landing may have decreased across successive East Coast USA–Japan (flights 1, 3, 5 or 7; median arrival 03:45 Eastern Daylight Time (EDT)). However, PVT response speed at TOD was faster on East Coast USA–Japan flights later in the trip. On these flights, circadian drift would result in flights later in the trip landing closer to the evening wake maintenance zone, when sleep is difficult and PVT response speeds are fastest. On Japan–East Coast USA flights (flights 2, 4, 6 or 8; median arrival time 14:52 EDT), PVT response speeds were slower on flight 8 than on flight 2. Circadian drift would move these arrivals progressively earlier in the SCN pacemaker cycle, where PVT response speeds are slower. Across the five post-trip days, 12 pilots (Group A) immediately resumed their pre-trip sleep pattern of a single nocturnal sleep episode; 9 pilots (Group B) had a daytime nap on most days that moved progressively earlier until it merged with nocturnal sleep and 17 pilots (Group C) had nocturnal sleep and intermittent naps. Chi-square periodogram analyses of the sleep propensity curves for each group across baseline and post-trip days suggest full adaptation to EDT from post-trip day 1 (dominant period = 24 h). However, in Groups B and C, the patterns of split sleep post-trip compared to pre-trip suggest that this may be misleading. We conclude that the trends in total in-flight sleep and significant changes in PVT performance speed at TOD provide preliminary evidence for circadian drift, as do persistent patterns of split sleep post-trip. However, new measures to track circadian rhythms in individual pilots are needed to confirm these findings.     

Darwin and palaeontology: a re-evaluation of his interpretation of the fossil record

Charles Darwin's empirical research in palaeontology, especially on fossil invertebrates, has been relatively neglected as a source of insight into his thinking, other than to note that he viewed the fossil record as very incomplete. During the Beagle voyage, Darwin gained extensive experience with a wide diversity of fossil taxa, and he thought deeply about the nature of the fossil record. That record was, for him, a major source of evidence for large-scale transmutation, but much less so for natural selection or single lineages. Darwin's interpretation of the fossil record has been criticised for its focus on incompleteness, but the record as he knew it was extremely incomplete. He was compelled to address this in arguing for descent with modification, which was likely his primary goal. Darwin's gradualism has been both misrepresented and exaggerated, and has distracted us from the importance of the fossil record in his thinking, which should be viewed in the context of the multiple, sometimes competing demands of the multifaceted argument he presented in the Origin of Species.     

Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement

Upland cotton (Gossypium hirsutum) is the world's largest source of natural fibre and dominates the global textile industry. Hybrid cotton varieties exhibit strong heterosis that confers high fibre yields, yet the genome‐wide effects of artificial selection that have influenced Upland cotton during its breeding history are poorly understood. Here, we resequenced Upland cotton genomes and constructed a variation map of an intact breeding pedigree comprising seven elite and 19 backbone parents. Compared to wild accessions, the 26 pedigree accessions underwent strong artificial selection during domestication that has resulted in reduced genetic diversity but stronger linkage disequilibrium and higher extents of selective sweeps. In contrast to the backbone parents, the elite parents have acquired significantly improved agronomic traits, with an especially pronounced increase in the lint percentage. Notably, identify by descent (IBD) tracking revealed that the elite parents inherited abundant beneficial trait segments and loci from the backbone parents and our combined analyses led to the identification of a core genomic segment which was inherited in the elite lines from the parents Zhong 7263 and Ejing 1 and that was strongly associated with lint percentage. Additionally, SNP correlation analysis of this core segment showed that a non‐synonymous SNP (A‐to‐G) site in a gene encoding the cell wall‐associated receptor‐like kinase 3 (GhWAKL3) protein was highly correlated with increased lint percentage. Our results substantially increase the valuable genomics resources available for future genetic and functional genomics studies of cotton and reveal insights that will facilitate yield increases in the molecular breeding of cotton.     

Increased runs of homozygosity in the autosomal genome of Brazilian individuals with neurodevelopmental delay/intellectual disability and/or multiple congenital anomalies investigated by chromosomal microarray analysis

Runs of homozygosity (ROH) in the human genome may be clinically relevant. The aim of this study was to report the frequency of increased ROH of the autosomal genome in individuals with neurodevelopmental delay/intellectual disability and/or multiple congenital anomalies, and to compare these data with a control group. Data consisted of calls of homozygosity from 265 patients and 289 controls. In total, 7.2% (19/265) of the patients showed multiple ROH exceeding 1% of autosomal genome, compared to 1.4% (4/289) in the control group (p=0.0006). Homozygosity ranged from 1.38% to 22.12% among patients, and from 1.53 to 2.40% in the control group. In turn, 1.9% (5/265) of patients presented ROH ≥10Mb in a single chromosome, compared to 0.3% (1/289) of individuals from the control group (p=0.0801). By excluding cases with reported consanguineous parents (15/24), the frequency of increased ROH was 3.4% (9/250) among patients and 1.7% (5/289) in the control group, considering multiple ROH exceeding 1% of the autosome genome and ROH ≥10Mb in a single chromosome together, although not statistically significant (p=0.1873). These results reinforce the importance of investigating ROH, which with complementary diagnostic tests can improve the diagnostic yield for patients with such conditions.