Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method

Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes of controlling the traits in soybean is rarely reported. In this study, we identified a total of 48 domestication-related loci based on RAD-seq genotyping of a natural population comprising 286 accessions. Among these, four on chromosome 12 and additional two on chromosomes 11 and 15 were associated with flowering time, and four on chromosomes 11 and 16 were associated with seed size. Of the five genes associated with flowering time and the three genes associated with seed size, three genes Glyma11g18720, Glyma11g15480 and Glyma15g35080 were homologous to Arabidopsis genes, additional five genes were found for the first time to be associated with these two traits. Glyma11g18720 and Glyma05g28130 were co-expressed with five genes homologous to flowering time genes in Arabidopsis, and Glyma11g15480 was co-expressed with 24 genes homologous to seed development genes in Arabidopsis. This study indicates that integration of population divergence analysis, genome-wide association study and expression analysis is an efficient approach to identify candidate domestication-related genes.

Evidence of resilience to past climate change in Southwest Asia: early farming communities and the 9.2 and 8.2 ka events

Climate change is often cited as a major factor in social change. The so-called 8.2 ka event was one of the most pronounced and abrupt Holocene cold and arid events. The 9.2 ka event was similar, albeit of a smaller magnitude. Both events affected the Northern Hemisphere climate and caused cooling and aridification in Southwest Asia. Yet, the impacts of the 8.2 and 9.2 ka events on early farming communities in this region are not well understood. Current hypotheses for an effect of the 8.2 ka event vary from large-scale site abandonment and migration (including the Neolithisation of Europe) to continuation of occupation and local adaptation, while impacts of the 9.2 ka have not previously been systematically studied. In this paper, we present a thorough assessment of available, quality-checked radiocarbon (14C) dates for sites from Southwest Asia covering the time interval between 9500 and 7500 cal BP, which we interpret in combination with archaeological evidence. In this way, the synchronicity between changes observed in the archaeological record and the rapid climate events is tested. It is shown that there is no evidence for a simultaneous and widespread collapse, large-scale site abandonment, or migration at the time of the events. However, there are indications for local adaptation. We conclude that early farming communities were resilient to the abrupt, severe climate changes at 9250 and 8200 cal BP.

Attribution of climate extreme events

There is a tremendous desire to attribute causes to weather and climate events that is often challenging from a physical standpoint. Headlines attributing an event solely to either human-induced climate change or natural variability can be misleading when both are invariably in play. The conventional attribution framework struggles with dynamically driven extremes because of the small signal-to-noise ratios and often uncertain nature of the forced changes. Here, we suggest that a different framing is desirable, which asks why such extremes unfold the way they do. Specifically, we suggest that it is more useful to regard the extreme circulation regime or weather event as being largely unaffected by climate change, and question whether known changes in the climate system's thermodynamic state affected the impact of the particular event. Some examples briefly illustrated include 'snowmaggedon' in February 2010, superstorm Sandy in October 2012 and supertyphoon Haiyan in November 2013, and, in more detail, the Boulder floods of September 2013, all of which were influenced by high sea surface temperatures that had a discernible human component.

Detecting regular sound changes in linguistics as events of concerted evolution

Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family. Results: Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations. Conclusions: We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.

A critical evaluation of the ability of the Spinning Enhanced Visible and Infrared Imager (SEVIRI) thermal infrared red-green-blue rendering to identify dust events: theoretical analysis

Using a combination of idealized radiative transfer simulations and a case study from the first field campaign of the Saharan Mineral Dust Experiment (SAMUM) in southern Morocco, this paper provides a systematic assessment of the limitations of the widely used Spinning Enhanced Visible and Infrared Imager (SEVIRI) red-green-blue (RGB) thermal infrared dust product. Both analyses indicate that the ability of the product to identify dust, via its characteristic pink coloring, is strongly dependent on the column water vapor, the lower tropospheric lapse rate, and dust altitude. In particular, when column water vapor exceeds ∼20–25 mm, dust presence, even for visible optical depths of the order 0.8, is effectively masked. Variability in dust optical properties also has a marked impact on the imagery, primarily as a result of variability in dust composition. There is a moderate sensitivity to the satellite viewing geometry, particularly in moist conditions. The underlying surface can act to confound the signal seen through variations in spectral emissivity, which are predominantly manifested in the 8.7μm SEVIRI channel. In addition, if a temperature inversion is present, typical of early morning conditions over the Sahara and Sahel, an increased dust loading can actually reduce the pink coloring of the RGB image compared to pristine conditions. Attempts to match specific SEVIRI observations to simulations using SAMUM measurements are challenging because of high uncertainties in surface skin temperature and emissivity. Recommendations concerning the use and interpretation of the SEVIRI RGB imagery are provided on the basis of these findings.

Extraction of unexpected rules from Twitter hashtags and its application to sport events

Twitter has become a dependable microblogging tool for real time information dissemination and newsworthy events broadcast. Its users sometimes break news on the network faster than traditional newsagents due to their presence at ongoing real life events at most times. Different topic detection methods are currently used to match Twitter posts to real life news of mainstream media. In this paper, we analyse tweets relating to the English FA Cup finals 2012 by applying our novel method named TRCM to extract association rules present in hash tag keywords of tweets in different time-slots. Our system identify evolving hash tag keywords with strong association rules in each time-slot. We then map the identified hash tag keywords to event highlights of the game as reported in the ground truth of the main stream media. The performance effectiveness measure of our experiments show that our method perform well as a Topic Detection and Tracking approach.

Molecular and phenotypic characterization of the alternative seasonal growth habit and flowering time in barley (Hordeum vulgare ssp. vulgare L.)

Barley can be classified into three major agronomic types, based on its seasonal growth habit (SGH): spring, winter and alternative. Winter varieties require exposure to vernalization to promote subsequent flowering and are autumn-sown. Spring varieties proceed to flowering in the absence of vernalization and are sown in the spring. The ‘alternative’ (also known as ‘facultative’) SGH is only loosely defined and can be sown in autumn or spring. Here, we investigate the molecular genetic basis of alternative barley. Analysis of the major barley vernalization (VRN-H1, VRN-H2) and photoperiod (PPD-H1, PPD-H2) response genes in a collection of 386 varieties found alternative SGH to be characterized by specific allelic combinations. Spring varieties possessed spring loci at one or both of the vernalization response loci, combined with long-day non-responsive ppd-H1 alleles and wild-type alleles at the short-day photoperiod response locus, PPD-H2. Winter varieties possessed winter alleles at both vernalization loci, in combination with the mutant ppd-H2 allele conferring delayed flowering under short-day photoperiods. In contrast, all alternative varieties investigated possessed a single spring allele (either at VRN-H1 or at VRN-H2) combined with mutant ppd-H2 alleles. This allelic combination is found only in alternative types and is diagnostic for alternative SGH in the collection studied. Analysis of flowering time under controlled environment found alternative varieties flowered later than spring control lines, with the difference most pronounced under short-day photoperiods. This work provides genetic characterization of the alternative SGH phenotype, allowing precise manipulation of SGH and flowering time within breeding programmes, and provides the molecular tools for classification of all three SGH categories within national variety registration processes.

Evidence for interplay between genes and maternal stress in utero: monoamine oxidase A polymorphism moderates effects of life events during pregnancy on infant negative emotionality at 5 weeks

The low activity variant of the monoamine oxidase A (MAOA) functional promoter polymorphism, MAOA-LPR, in interaction with adverse environments (G × E) is associated with child and adult antisocial behaviour disorders. MAOA is expressed during foetal development so in utero G × E may influence early neurodevelopment. We tested the hypothesis that MAOA G × E during pregnancy predicts infant negative emotionality soon after birth. In an epidemiological longitudinal study starting in pregnancy, using a two stage stratified design, we ascertained MAOA-LPR status (low vs. high activity variants) from the saliva of 209 infants (104 boys and 105 girls), and examined predictions to observed infant negative emotionality at 5 weeks post-partum from life events during pregnancy. In analyses weighted to provide estimates for the general population, and including possible confounders for life events, there was an MAOA status by life events interaction (P = 0.017). There was also an interaction between MAOA status and neighbourhood deprivation (P = 0.028). Both interactions arose from a greater effect of increasing life events on negative emotionality in the MAOA-LPR low activity, compared with MAOA-LPR high activity infants. The study provides the first evidence of moderation by MAOA-LPR of the effect of the social environment in pregnancy on negative emotionality in infancy, an early risk for the development of child and adult antisocial behaviour disorders.

Modulation of equatorial Pacific westerly/easterly wind events by the Madden-Julian oscillation and convectively-coupled Rossby waves

Synoptic wind events in the equatorial Pacific strongly influence the El Niño/Southern Oscillation (ENSO) evolution. This paper characterizes the spatio-temporal distribution of Easterly (EWEs) and Westerly Wind Events (WWEs) and quantifies their relationship with intraseasonal and interannual large-scale climate variability. We unambiguously demonstrate that the Madden–Julian Oscillation (MJO) and Convectively-coupled Rossby Waves (CRW) modulate both WWEs and EWEs occurrence probability. 86 % of WWEs occur within convective MJO and/or CRW phases and 83 % of EWEs occur within the suppressed phase of MJO and/or CRW. 41 % of WWEs and 26 % of EWEs are in particular associated with the combined occurrence of a CRW/MJO, far more than what would be expected from a random distribution (3 %). Wind events embedded within MJO phases also have a stronger impact on the ocean, due to a tendency to have a larger amplitude, zonal extent and longer duration. These findings are robust irrespective of the wind events and MJO/CRW detection methods. While WWEs and EWEs behave rather symmetrically with respect to MJO/CRW activity, the impact of ENSO on wind events is asymmetrical. The WWEs occurrence probability indeed increases when the warm pool is displaced eastward during El Niño events, an increase that can partly be related to interannual modulation of the MJO/CRW activity in the western Pacific. On the other hand, the EWEs modulation by ENSO is less robust, and strongly depends on the wind event detection method. The consequences of these results for ENSO predictability are discussed.

Increased frequency of extreme La Niña events under greenhouse warming

The El Niño/Southern Oscillation is Earth’s most prominent source of interannual climate variability, alternating irregularly between El Niño and La Niña, and resulting in global disruption of weather patterns, ecosystems, fisheries and agriculture1, 2, 3, 4, 5. The 1998–1999 extreme La Niña event that followed the 1997–1998 extreme El Niño event6 switched extreme El Niño-induced severe droughts to devastating floods in western Pacific countries, and vice versa in the southwestern United States4, 7. During extreme La Niña events, cold sea surface conditions develop in the central Pacific8, 9, creating an enhanced temperature gradient from the Maritime continent to the central Pacific. Recent studies have revealed robust changes in El Niño characteristics in response to simulated future greenhouse warming10, 11, 12, but how La Niña will change remains unclear. Here we present climate modelling evidence, from simulations conducted for the Coupled Model Intercomparison Project phase 5 (ref. 13), for a near doubling in the frequency of future extreme La Niña events, from one in every 23 years to one in every 13 years. This occurs because projected faster mean warming of the Maritime continent than the central Pacific, enhanced upper ocean vertical temperature gradients, and increased frequency of extreme El Niño events are conducive to development of the extreme La Niña events. Approximately 75% of the increase occurs in years following extreme El Niño events, thus projecting more frequent swings between opposite extremes from one year to the next.

Processes driving intraseasonal displacements of the eastern edge of the warm pool: the contribution of westerly wind events

We investigate the processes responsible for the intraseasonal displacements of the eastern edge of the western Pacific warm pool (WPEE), which appear to play a role in the onset and development of El Niño events. We use 25 years of output from an ocean general circulation model experiment that is able to accurately capture the observed displacements of the WPEE, sea level anomalies, and upper ocean zonal currents at intraseasonal time scales in the western and central Pacific Ocean. Our results confirm that WPEE displacements driven by westerly wind events (WWEs) are largely controlled by zonal advection. This paper has also two novel findings: first, the zonal current anomalies responsible for the WPEE advection are driven primarily by local wind stress anomalies and not by intraseasonal wind-forced Kelvin waves as has been shown in most previous studies. Second, we find that intraseasonal WPEE fluctuations that are not related to WWEs are generally caused by intraseasonal variations in net heat flux, in contrast to interannual WPEE displacements that are largely driven by zonal advection. This study hence raises an interesting question: can surface heat flux-induced zonal WPEE motions contribute to El Niño–Southern Oscillation evolution, as WWEs have been shown to be able to do?

The impact of westerly wind bursts and ocean initial state on the development, and diversity of El Niño events

Westerly wind bursts (WWBs) that occur in the western tropical Pacific are believed to play an important role in the development of El Niño events. Here, following the study of Lengaigne et al. (Clim Dyn 23(6):601–620, 2004), we conduct numerical simulations in which we reexamine the response of the climate system to an observed wind burst added to a coupled general circulation model. Two sets of twin ensemble experiments are conducted (each set has control and perturbed experiments). In the first set, the initial ocean heat content of the system is higher than the model climatology (recharged), while in the second set it is nearly normal (neutral). For the recharged state, in the absence of WWBs, a moderate El Niño with a maximum warming in the central Pacific (CP) develops in about a year. In contrast, for the neutral state, there develops a weak La Niña. However, when the WWB is imposed, the situation dramatically changes: the recharged state slides into an El Niño with a maximum warming in the eastern Pacific, while the neutral set produces a weak CP El Niño instead of previous La Niña conditions. The different response of the system to the exact same perturbations is controlled by the initial state of the ocean and the subsequent ocean–atmosphere interactions involving the interplay between the eastward shift of the warm pool and the warming of the eastern equatorial Pacific. Consequently, the observed diversity of El Niño, including the occurrence of extreme events, may depend on stochastic atmospheric processes, modulating El Niño properties within a broad continuum.