Development of record-breaking statistics for climatological time-series analysis

The number of record-breaking events expected to occur in a strictly stationary time-series depends only on the number of values in the time-series, regardless of distribution. This holds whether the events are record-breaking highs or lows and whether we count from past to present or present to past. However, these symmetries are broken in distinct ways by trends in the mean and variance. We define indices that capture this information and use them to detect weak trends from multiple time-series. Here, we use these methods to answer the following questions: (1) Is there a variability trend among globally distributed surface temperature time-series? We find a significant decreasing variability over the past century for the Global Historical Climatology Network (GHCN). This corresponds to about a 10% change in the standard deviation of inter-annual monthly mean temperature distributions. (2) How are record-breaking high and low surface temperatures in the United States affected by time period? We investigate the United States Historical Climatology Network (USHCN) and find that the ratio of record-breaking highs to lows in 2006 increases as the time-series extend further into the past. When we consider the ratio as it evolves with respect to a fixed start year, we find it is strongly correlated with the ensemble mean. We also compare the ratios for USHCN and GHCN (minus USHCN stations). We find the ratios grow monotonically in the GHCN data set, but not in the USHCN data set. (3) Do we detect either mean or variance trends in annual precipitation within the United States? We find that the total annual and monthly precipitation in the United States (USHCN) has increased over the past century. Evidence for a trend in variance is inconclusive.

Investigating within-canopy variation of functional traits and cellular structure of sugar maple (Acer saccharum) leaves

Patterns of increasing leaf mass per area (LMA), area-based leaf nitrogen (Narea), and carbon isotope composition (δ13C) with increasing height in the canopy have been attributed to light gradients or hydraulic limitation in tall trees. Theoretical optimal distributions of LMA and Narea that scale with light maximize canopy photosynthesis; however, sub-optimal distributions are often observed due to hydraulic constraints on leaf development. Using observational, experimental, and modeling approaches, we investigated the response of leaf functional traits (LMA, density, thickness, and leaf nitrogen), leaf carbon isotope composition (δ13C), and cellular structure to light availability, height, and leaf water potential (Ψl) in an Acer saccharum forest to tease apart the influence of light and hydraulic limitations. LMA, leaf and palisade layer thickness, and leaf density were greater at greater light availability but similar heights, highlighting the strong control of light on leaf morphology and cellular structure. Experimental shading decreased both LMA and area-based leaf nitrogen (Narea) and revealed that LMA and Narea were more strongly correlated with height earlier in the growing season and with light later in the growing season. The supply of CO2 to leaves at higher heights appeared to be constrained by stomatal sensitivity to vapor pressure deficit (VPD) or midday leaf water potential, as indicated by increasing δ13C and VPD and decreasing midday Ψl with height. Model simulations showed that daily canopy photosynthesis was biased during the early growing season when seasonality was not accounted for, and was biased throughout the growing season when vertical gradients in LMA and Narea were not accounted for. Overall, our results suggest that leaves acclimate to light soon after leaf expansion, through an accumulation of leaf carbon, thickening of palisade layers and increased LMA, and reduction in stomatal sensitivity to Ψl or VPD. This period of light acclimation in leaves appears to optimize leaf function over time, despite height-related constraints early in the growing season. Our results imply that vertical gradients in leaf functional traits and leaf acclimation to light should be incorporated in canopy function models in order to refine estimates of canopy photosynthesis.

Arrangement of gene pairs, retrotransposon insertions, and regulation of gene expression in plants

Plant genomes are extremely complex. Myriad factors contribute to their evolution and organization, as well as to the expression and regulation of individual genes. Here we present investigations into several such factors and their influence on genome structure and gene expression: the arrangement of pairs of physically adjacent genes, retrotransposons closely associated with genes, and the effect of retrotransposons on gene pair evolution. All sequenced plant genomes contain a significant fraction of retrotransposons, including that of rice. We investigated the effects of retrotransposons within rice genes and within a 1 kb putative promoter region upstream of each gene. We found that approximately one-sixth of all rice genes are closely associated with retrotransposons. Insertions within a gene’s promoter region tend to block gene expression, while retrotransposons within genes promote the existence of alternative splicing forms. We also identified several other trends in retrotransposon insertion and its effects on gene expression. Several studies have previously noted a connection among genes between physical proximity and correlated expression profiles. To determine the degree to which this correlation depends on an exact physical arrangement, we studied the expression and interspecies conservation of convergent and divergent gene pairs in rice, Arabidopsis, and Populus trichocarpa. Correlated expression among gene pairs was quite common in all three species, yet conserved arrangement was rare. However, conservation of gene pair arrangement was significantly more common among pairs with strongly correlated expression levels. In order to uncover additional properties of gene pair conservation and rearrangement, we performed a comparative analysis of convergent, divergent, and tandem gene pairs in rice, sorghum, maize, and Brachypodium. We noted considerable differences between gene pair types and species. We also constructed a putative evolutionary history for each pair, which led to several interesting discoveries. To further elucidate the causes of gene pair conservation and rearrangement, we identified retrotransposon insertions in and near rice gene pairs. Retrotransposon-associated pairs are less likely to be conserved, although there are significant differences in the possible effect of different types and locations of retrotransposon insertions. The three types of gene pair also varied in their susceptibility to retrotransposon-associated evolutionary changes.