Copyright (c) 2010 All rights reserved. http://works.bepress.com/knight Recent documents in Charles A. Knight en-us Wed, 10 Nov 2010 01:32:54 PST 3600 http://works.bepress.com/knight/22 http://works.bepress.com/knight/22 Mon, 08 Nov 2010 12:03:41 PST Small heat shock protein (sHsp) responses were studied for two evergreen perennial shrubs in the northern California chaparral; one common on warm, south-facing slopes (Ceanothus cuneatus), and the other on cooler, north-facing slopes (Prunus ilicifolia). Small Hsp expression was induced experimentally for field collected leaves. Leaf collections were made where the species co-occur. Small Hsp expression was quantified using two antibodies, one specific to a chloroplast 22 kD sHsp and another that detects a broad range of sHsps. Differences between chloroplast sHsp accumulation, which protects thermally labile proteins in PSII, and the general sHsp response were examined. The species from the cooler microclimate, Prunus, had a lower induction temperature and accumulated greater levels of sHsps at low temperatures. Both Prunus and Ceanothus reached peak sHsp expression at 42∘C. The species from the warmer microclimate, Ceanothus, had greater sHsp expression at higher temperatures. Chloroplast sHsp expression generally tracked sHsp expression in Ceanothus, but in Prunus general Hsps were elevated before chloroplast sHsps. Variation between species for sHsp expression (induction temperatures, accumulation levels, and the duration of expression) coupled with the costs of Hsp synthesis, may contribute to differences in the abundance and distribution of plants across environmental gradients. Charles A. Knight Articles http://works.bepress.com/knight/21 http://works.bepress.com/knight/21 Mon, 08 Nov 2010 12:03:40 PST Variation in genome size (GS) has been linked to several facets of the plant phenotype. Recently it was shown that GS is significantly correlated with cell size and the duration of the cell cycle. Here we test the hypothesis that GS might also be a predictor of apical root meristem growth rate (RMGR). We studied eight species of eudicots with varying GS using time-lapse microscopic image analysis. A significant negative exponential relationship was observed between GS and RMGR. Our results show significantly decreased RMGR for large genome species. This relationship represents a significant consequence of GS expansion in plants and may partly explain why genome sizes tend to be small in eudicots. Interestingly, parasitic plants, which do not rely on root growth as much, often have large genomes. Adam Gruner Articles http://works.bepress.com/knight/20 http://works.bepress.com/knight/20 Mon, 08 Nov 2010 12:03:38 PST Here we test whether genome size is a predictor of pollen size. If it were, inferences of ancient genome size would be possible using the abundant paleo-palynolgical record. We performed regression analyses across 464 species of pollen width and genome size. We found a significant positive trend. However, regression analysis using phylogentically independent contrasts did not support the correlated evolution of these traits. Instead, a large split between angiosperms and gymnosperms for both pollen width and genome size was revealed. Sister taxa were not more likely to show a positive contrast when compared to deeper nodes. However, significantly more congeneric species had a positive trend than expected by chance. These results may reflect the strong selection pressure for pollen to be small. Also, because pollen grains are not metabolically active when measured, their biology is different than other cells which have been shown to be strongly related to genome size, such as guard cells. Our findings contrast with previously published research. It was our hope that pollen size could be used as a proxy for inferring the genome size of ancient species. However, our results suggest pollen is not a good candidate for such endeavors. Charles A. Knight Articles http://works.bepress.com/knight/18 http://works.bepress.com/knight/18 Wed, 14 Jul 2010 15:31:51 PDT The evolution of the seed represents a remarkable life-history transition for photosynthetic organisms. Here, we review the recent literature and historical understanding of how and why seeds evolved. Answering the 'how' question involves a detailed understanding of the developmental morphology and anatomy of seeds, as well as the genetic programs that determine seed size. We complement this with a special emphasis on the evolution of dormancy, the characteristic of seeds that allows for long 'distance' time travel. Answering the 'why' question involves proposed hypotheses of how natural selection has operated to favor the seed life-history phenomenon. The recent flurry of research describing the comparative biology of seeds is discussed. The review will be divided into sections dealing with: (1) the development and anatomy of seeds; (2) the endosperm; (3) dormancy; (4) early seed-like structures and the transition to seeds; and (5) the evolution of seed size (mass). In many cases, a special distinction is made between angiosperm and gymnosperm seeds. Finally, we make some recommendations for future research in seed biology. Ada Linkies Articles http://works.bepress.com/knight/19 http://works.bepress.com/knight/19 Wed, 14 Jul 2010 15:31:51 PDT We performed a comparative analysis of defensive and nutritional plant traits responsible for differential herbivory in a series of experimental feeding trials with generalist herbivores. We measured three defensive traits (leaf strength, leaf mass per unit area and endophytic fungal infection) and two nutritional traits (foliar nitrogen and water) for 26 native and eight non-native plant species from coastal California shrublands. Our feeding trials involved three species of generalist herbivore (beet armyworm, cabbage looper and the garden snail) in two types of laboratory feeding trial (single plant species and preference tests). All traits were significantly related to the amount of leaf area consumed, with foliar nitrogen followed by leaf strength explaining most of the variation in herbivore damage. Defensive and nutritional traits were tightly correlated with one another. These correlations were still apparent after incorporation of the phylogenetic relationships of species using independent contrasts, suggesting that there has been repeated selection for certain trait combinations. Non-native species had lower defensive traits and greater nutrient content and therefore experienced greater herbivory damage than natives. Poorly defended, nutrient-rich species (like most of the non-natives in our study) may be better suited for rapid growth and nutrient acquisition, thus reducing the cost of replenishing leaf material lost to herbivores. Nicole Molinari Articles http://works.bepress.com/knight/17 http://works.bepress.com/knight/17 Wed, 19 Aug 2009 15:16:45 PDT • Background and Aims It has been proposed that having too much DNA may carry physiological consequences for plants. The strong correlation between DNA content, cell size and cell division rate could lead to predictable morphological variation in plants, including a negative relationship with leaf mass per unit area (LMA). In addition, the possible increased demand for resources in species with high DNA content may have downstream effects on maximal metabolic efficiency, including decreased metabolic rates. • Methods Tests were made for genome size-dependent variation in LMA and metabolic rates (mass-based photosynthetic rate and dark respiration rate) using our own measurements and data from a plant functional trait database (Glopnet). These associations were tested using two metrics of genome size: bulk DNA amount (2C DNA) and monoploid genome size (1Cx DNA). The data were analysed using an evolutionary framework that included a regression analysis and independent contrasts using a phylogenetic tree with estimates of molecular diversification times. A contribution index for the LMA data set was also calculated to determine which divergences have the greatest influence on the relationship between genome size and LMA. • Key Results and Conclusions A significant negative association was found between bulk DNA amount and LMA in angiosperms. This was primarily a result of influential divergences that may represent early shifts in growth form. However, divergences in bulk DNA amount were positively associated with divergences in LMA, suggesting that the relationship may be indirect and mediated through other traits directly related to genome size. There was a significant negative association between genome size and metabolic rates that was driven by a basal divergence between angiosperms and gymnosperms; no significant independent contrast results were found. Therefore, it is concluded that genome size-dependent constraints acting on metabolic efficiency may not exist within seed plants. Jeremy M. Beaulieu Articles http://works.bepress.com/knight/15 http://works.bepress.com/knight/15 Wed, 19 Aug 2009 15:16:44 PDT Blooms of toxic algae are increasing in magnitude and frequency around the globe, causing extensive economic and environmental impacts. On the west coast of Florida, blooms of the toxic dinoflagellate Karenia brevis (Davis) have been documented annually for the last 30 years causing respiratory irritation in humans, fish kills, and toxin bioaccumulation in shellfish beds. As a result, methods need to be established to monitor and predict bloom formation and transport to mitigate their harmful effects on the surrounding ecosystems and local communities. In the past, monitoring and mitigation efforts have relied on visual confirmation of water discoloration, fish kills, and laborious cell counts, but recently satellite remote sensing has been used to track harmful algal blooms (HABs) along the Florida coast. Unfortunately satellite ocean color is limited by cloud cover, lack of detection below one optical depth, and revisit frequency, all of which can lead to extended periods without data. To address these shortcomings, an optical phytoplankton discriminator (OPD) was developed to detect K. brevis cells in mixed phytoplankton assemblages. The OPD was integrated into autonomous underwater vehicle (AUV) platforms to gather spatially and temporally relevant data that can be used in collaboration with satellite imagery to provide a 3D picture of bloom dynamics over time. In January 2005, a Remote Environmental Monitoring UnitS (REMUS) AUV with an OPD payload was deployed on the west coast of Florida to retrieve a similarity index (SI), which indicates when K. brevis dominates the phytoplankton community. SI was used to monitor a K. brevis bloom in relation to temperature, salinity, chlorophyll, and ocean currents. Current speed, SI, temperature, salinity, and chlorophyll a from the AUV were used to quantify a 1 km displacement of the K. brevis bloom front that was observed over the deployment period. The ability to monitor short term bloom movement will improve monitoring and predictive efforts that are used to provide warnings for local tourism and fishing industries. In addition, understanding the fine scale environmental conditions associated with bloom formation will increase our ability to predict the location and timing of K. brevis bloom formation. This study demonstrates the use of one autonomous platform and provides evidence that a nested array of AUVs and moorings equipped with new sensors, combined with remote sensing, can provide an early warning and monitoring system to reduce the impact of HABs. Ian C. Robbins Articles http://works.bepress.com/knight/16 http://works.bepress.com/knight/16 Wed, 19 Aug 2009 15:16:44 PDT We examined variation in leaf size and specific leaf area (SLA) in relation to the distribution of 22 chaparral shrub species on small-scale gradients of aspect and elevation. Potential incident solar radiation (insolation) was estimated from a geographic information system to quantify microclimate affinities of these species across north- and south-facing slopes. At the community level, leaf size and SLA both declined with increasing insolation, based on average trait values for the species found in plots along the gradient. However, leaf size and SLA were not significantly correlated across species, suggesting that these two traits are decoupled and associated with different aspects of performance along this environmental gradient. For individual species, SLA was negatively correlated with species distributions along the insolation gradient, and was significantly lower in evergreen versus deciduous species. Leaf size exhibited a negative but non-significant trend in relation to insolation distribution of individual species. At the community level, variance in leaf size increased with increasing insolation. For individual species, there was a greater range of leaf size on south-facing slopes, while there was an absence of small-leaved species on north-facing slopes. These results demonstrate that analyses of plant functional traits along environmental gradients based on community level averages may obscure important aspects of trait variation and distribution among the constituent species. D. D. Ackerly Articles http://works.bepress.com/knight/14 http://works.bepress.com/knight/14 Wed, 19 Aug 2009 15:16:43 PDT We studied the physiological basis of local adaptation to drought in Boechera holboellii, a perennial relative of Arabidopsis thaliana, and used cDNA–AFLPs to identify candidate genes showing differential expression in these populations. We compared two populations of B. holboellii from contrasting water environments in a reciprocal transplant experiment, as well as in a laboratory dry-down experiment. We continuously measured the water content of soils using time domain reflectometery (TDR). We compared populations for their water use efficiency (WUE), root/shoot ratios (R:S) and leaf mass per unit area (LMA) in the field and in the laboratory, and identified candidate genes that (i) responded plastically to water stress and (ii) were differentially expressed between the two populations. Genotypes from the drier site had higher WUE, which was attributable to a large reduction in transpirational water loss. The xeric-adapted population also had increased investment in root biomass and greater leaf mass per unit area. Reciprocal transplants in the field had significantly greater survival in their native habitat. In total, 450 cDNA-AFLP fragments showed significant changes between drought and control treatments. Furthermore, some genes showed genotype (population)-specific patterns of up- or down-regulation in response to drought. Three hundred cDNA-AFLP bands were sequenced leading to the identification of cDNAs coding for proteins involved in signal transduction, transcriptional regulation, redox regulation, oxidative stress and pathways involved in stress adaptation. Some of these proteins could contribute a physiological advantage under drought, making them potential targets for natural selection. Charles A. Knight Articles http://works.bepress.com/knight/13 http://works.bepress.com/knight/13 Wed, 19 Aug 2009 15:16:42 PDT The flora of California, a global biodiversity hotspot, includes 2387 endemic plant taxa. With anticipated climate change, we project that up to 66% will experience >80% reductions in range size within a century. These results are comparable with other studies of fewer species or just samples of a region’s endemics. Projected reductions depend on the magnitude of future emissions and on the ability of species to disperse from their current locations. California’s varied terrain could cause species to move in very different directions, breaking up present-day floras. However, our projections also identify regions where species undergoing severe range reductions may persist. Protecting these potential future refugia and facilitating species dispersal will be essential to maintain biodiversity in the face of climate change. Scott R. Loarie Articles http://works.bepress.com/knight/12 http://works.bepress.com/knight/12 Wed, 19 Aug 2009 15:16:42 PDT Interspecific variation in chloroplast low molecular weight (cLMW) HSP (heat shock protein) expression was examined with respect to phylogeny, species specific leaf area, chlorophyll fluorescence, and mean environmental conditions within species ranges. Eight species of Ceanothus (Rhamnaceae) were heat shocked for 4 h at several different temperatures. Leaf samples were collected immediately after the heat shock, and cLMW HSP expression was quantified using Western blots. At 450C species from the subgenus Cerastes had significantly greater cLMW HSP expression than species from the subgenus Ceanothus. Specific leaf area was negatively correlated with cLMW HSP expression after the 450C heat treatment. In addition, chlorophyll fluorescence (Fv/Fm) 1 h after the heat shocks was positively correlated with cLMW HSP expression. Contrary to our prediction, there was no correlation between July maximum temperature within species ranges and cLMW HSP expression. These results suggest that evolutionary differentiation in cLMW HSP expression is associated with leaf physiological parameters and related aspects of life history, yet associations between climatic conditions within species ranges and cLMW HSP expression require further study. Charles A. Knight Articles http://works.bepress.com/knight/11 http://works.bepress.com/knight/11 Wed, 19 Aug 2009 15:16:41 PDT • Across eukaryotes phenotypic correlations with genome size are thought to scale from genome size effects on cell size. However, for plants the genome/cell size link has only been thoroughly documented within ploidy series and small subsets of herbaceous species.• Here, the first large-scale comparative analysis is made of the relationship between genome size and cell size across 101 species of angiosperms of varying growth forms. Guard cell length and epidermal cell area were used as two metrics of cell size and, in addition, stomatal density was measured.• There was a significant positive relationship between genome size and both guard cell length and epidermal cell area and a negative relationship with stomatal density. Independent contrast analyses revealed that these traits are undergoing correlated evolution with genome size. However, the relationship was growth form dependent (nonsignificant results within trees/shrubs), although trees had the smallest genome/cell sizes and the highest stomatal density.• These results confirm the generality of the genome size/cell size relationship. The results also suggest that changes in genome size, with concomitant influences on stomatal size and density, may influence physiology, and perhaps play an important genetic role in determining the ecological and life-history strategy of a species. Jeremy M. Beaulieu Articles http://works.bepress.com/knight/10 http://works.bepress.com/knight/10 Wed, 19 Aug 2009 15:16:40 PDT • We examined whether increased high temperature photosynthetic thermal tolerance (PT), reduced specific leaf area (SLA) and reduced leaf size represent correlated and convergent adaptations for recently diverged Encelia, Salvia, Atriplex and Eriogonum congeneric species pairs from contrasting thermal and water environments (the Mojave Desert and coastal California). We also studied whether variation in PT is associated with inducible small heat shock protein expression (sHsp). • Traits were measured in a common environment (CE) and in the field to partition effects of phenotypic plasticity and genetic divergence. • We found little evidence for convergent adaptation of PT (CE measurements). Field measurements revealed significant plasticity for PT, which was also associated with increased sHsp expression. Compared to coastal congeners desert species had lower SLA in the CE. These differences were magnified in the field. There was a negative correlation between SLA and PT. Desert species also tended to have smaller leaves both in the CE and in the field. • SLA and leaf size reductions represent repeated evolutionary divergences and are perhaps convergent adaptations for species radiating into the desert, while PT is highly plastic and shows little evidence for convergent adaptation in the congeneric species pairs we studied. Charles A. Knight Articles http://works.bepress.com/knight/9 http://works.bepress.com/knight/9 Wed, 19 Aug 2009 15:16:39 PDT Thomas Mitchell-Olds Articles http://works.bepress.com/knight/8 http://works.bepress.com/knight/8 Wed, 19 Aug 2009 15:16:39 PDT The nuclear DNA content of angiosperms varies by several orders of magnitude. Previous studies suggest that variation in 2C DNA content (i.e. the amount of DNA in G1 phase nuclei, also referred to as the 2C-value) is correlated with environmental factors, but there are conflicting reports in the literature concerning the nature of these relationships. We examined variation in 2C DNA content for 401 species in the ecologically diverse California flora in relation to the mean July maximum temperature, January minimum temperature, and annual precipitation within the geographical ranges of these species. Species with small 2C-values predominate in all environments. Species with large 2C-values occur at intermediate July maximum temperatures, and decline in frequency at both extremes of the July temperature gradient, and with decreasing annual precipitation. Our analysis demonstrates the utility of quantile regression for statistical inference of complex distributions such as these. The method supports our observation that relationships between nuclear DNA content and environmental factors are stronger for species with large 2C-values. Charles A. Knight Articles http://works.bepress.com/knight/7 http://works.bepress.com/knight/7 Wed, 19 Aug 2009 15:16:38 PDT Background and Aims Early observations that genome size was positively correlated with cell size formed the basis of hypothesized consequences of genome size variation at higher phenotypic scales. This scaling was supported by several studies showing a positive relationship between genome size and seed mass, and various metrics of growth and leaf morphology. However, many of these studies were undertaken with limited species sets, and often performed within a single genus. Here we seek to generalize the relationship between genome size and the phenotype by examining eight phenotypic traits using large cross-species comparisons involving diverse assemblages of angiosperm and gymnosperm species. These analyses are presented in order of increasing scale (roughly equating to the number of cells required to produce a particular phenotypic trait), following the order of: cell size (guard cell and epidermal), stomatal density, seed mass, leaf mass per unit area (LMA), wood density, photosynthetic rate and finally maximum plant height.Scope The results show that genome size is a strong predictor of phenotypic traits at the cellular level (guard cell length and epidermal cell area had significant positive relationships with genome size). Stomatal density decreased with increasing genome size, but this did not lead to decreased photosynthetic rate. At higher phenotypic scales, the predictive power of genome size generally diminishes (genome size had weak predictive power for both LMA and seed mass), except in the interesting case of maximum plant height (tree species tend to have small genomes). There was no relationship with wood density. The general observation that species with larger genome size have larger seed mass was supported; however, species with small genome size can also have large seed masses. All of these analyses involved robust comparative methods that incorporate the phylogenetic relationships of species.Conclusions Genome size correlations are quite strong at the cellular level but decrease in predictive power with increasing phenotypic scale. Our hope is that these results may lead to new mechanistic hypotheses about why genome size scaling exists at the cellular level, and why nucleotypic consequences diminish at higher phenotypic scales. Charles A. Knight Articles http://works.bepress.com/knight/6 http://works.bepress.com/knight/6 Wed, 19 Aug 2009 15:16:37 PDT • Previous investigators have identified strong positive relationships between genome size and seed mass within species, and across species from the same genus and family.• Here, we make the first broad-scale quantification of this relationship, using data for 1222 species, from 139 families and 48 orders. We analyzed the relationship between genome size and seed mass using a statistical framework that included four different tests.• A quadratic relationship between genome size and seed mass appeared to be driven by the large genome/seed mass gymnosperms and the many small genome size/large seed mass angiosperms. Very small seeds were never associated with very large genomes, possibly indicating a developmental constraint. Independent contrast results showed that divergences in genome size were positively correlated with divergences in seed mass.• Divergences in seed mass have been more closely correlated with divergences in genome size than with divergences in other morphological and ecological variables. Plant growth form is the only variable examined thus far that explains a greater proportion of variation in seed mass than does genome size. Jeremy M. Beaulieu Articles http://works.bepress.com/knight/5 http://works.bepress.com/knight/5 Wed, 19 Aug 2009 15:16:37 PDT Evolutionary variation for accumulation of small heat shock protein (sHsp) may contribute to thermal niche differentiation between species. Here we examine temperature and time-course-dependent variation for sHsp accumulation in a recently diverged pair of Encelia raised in a common environment: Encelia farinosa, common in the Mojave desert, and Encelia californica, which is found along the cool coastal bluffs of southern North America. Both species exhibit peak sHsp accumulation at 42oC. Encelia californica accumulated greater levels of sHsp at temperatures below 42oC, while E. farinosa had greater levels above 42oC. Encelia farinosa accumulates sHsp at temperatures up to 45oC, while E. californica does not synthesize sHsp above 44oC. Both species accumulated significant levels of sHsp while maintaining photosynthetic electron transport Fv/Fm, but above the temperatures that elicited peak sHsp expression, levels of sHsp and Fv/Fm declined in parallel to zero. Encelia californica accumulated greater levels of sHsp more rapidly than E. farinosa following a 15 min, 42oC heat treatment; however, E. farinosa maintained greater Fv/Fm at all time points. Our results indicate that there are significant differences between Encelia species for sHsp accumulation but that these results depend on the duration, magnitude, and recovery time following temperature stress. Charles A. Knight Articles http://works.bepress.com/knight/4 http://works.bepress.com/knight/4 Wed, 19 Aug 2009 15:16:36 PDT • Background and Aims If large genomes are truly saturated with unnecessary ‘junk’ DNA, it would seem natural that there would be costs associated with accumulation and replication of this excess DNA. Here we examine the available evidence to support this hypothesis, which we term the ‘large genome constraint’. We examine the large genome constraint at three scales: evolution, ecology, and the plant phenotype. • Scope In evolution, we tested the hypothesis that plant lineages with large genomes are diversifying more slowly. We found that genera with large genomes are less likely to be highly specious – suggesting a large genome constraint on speciation. In ecology, we found that species with large genomes are under-represented in extreme environments – again suggesting a large genome constraint for the distribution and abundance of species. Ultimately, if these ecological and evolutionary constraints are real, the genome size effect must be expressed in the phenotype and confer selective disadvantages. Therefore, in phenotype, we review data on the physiological correlates of genome size, and present new analyses involving maximum photosynthetic rate and specific leaf area. Most notably, we found that species with large genomes have reduced maximum photosynthetic rates – again suggesting a large genome constraint on plant performance. Finally, we discuss whether these phenotypic correlations may help explain why species with large genomes are trimmed from the evolutionary tree and have restricted ecological distributions. • Conclusion Our review tentatively supports the large genome constraint hypothesis. Charles A. Knight Articles http://works.bepress.com/knight/3 http://works.bepress.com/knight/3 Wed, 19 Aug 2009 15:16:35 PDT The hypothesis that species inhabiting warmer regions have greater photosynthetic tolerance of high temperatures was tested using the temperature-dependent increase in fluorescence (T-Fo). Congeneric species pairs of Atriplex, Salvia, Encelia, and Eriogonum with desert versus coastal distributions were studied in a common environment and in the field. In addition, 21 species with contrasting microclimate distributions were studied at a field site in a northern California chaparral community. The average July maximum temperature within the current distributions of species was quantified using a geographic information system. Four parameters (Tcrit, TS20, T50, and Tmax) of the T-Fo response were used to quantify photosynthetic thermotolerance. In the common environment, only the desert Atriplex species was significantly greater for all T-Fo parameters when compared to its coastal congener. In the field, desert species had significantly greater Tcrit, TS20, T50, and Tmax when compared to coastal species. The magnitude of variation between species and between genera was similar in the common environment and the field. However, Tcrit, TS20, T50 and Tmax were all significantly greater when measured in the field. There was no relationship between T-Fo parameters and the microclimate distribution of the 21 species at the chaparral field site. In addition, T-Fo parameters for all 35 species were not correlated with the average July maximum temperature within the species ranges. However, there was a significant negative correlation between the average annual amount of precipitation inside species’ ranges and TS20. Our results show that photosynthetic thermotolerance is (1) significantly different between genera and species, (2) highly plastic, (3) not necessarily greater for species with warm climate distributions when measured in a common environment, but (4) significantly greater overall for desert species compared to coastal species when measured in the field. Charles A. Knight Articles