http://www.dspace.cam.ac.uk:80/handle/1810/223858 Wed, 22 May 2013 22:13:44 GMT 2013-05-22T22:13:44Z http://www.dspace.cam.ac.uk:80/handle/1810/243636 Title: Forest dynamics at regional scales: predictive models constrained with inventory data Authors: Lines, Emily Abstract: Forest ecosystems store more carbon than the atmosphere and harbour the majority of the world's biodiversity, yet their response to changing climate is uncertain. Forest simulation models make landscape-level predictions of forest dynamics by scaling from key tree-level processes, but models typically have no climate dependency. In this thesis I demonstrate how large-scale national inventories combined with improvements in computational methods mean that models that incorporate the climate dependency of demographic processes may be parameterised at regional scales. In Chapter One I outline historical approaches to modelling forest dynamics and present a discussion of competing methods of parameterisation and model selection. In Chapter Two I present a model of individual tree mortality in the eastern United States which incorporates species, climatic and competitive effects parameterised using Markov Chain Monte Carlo methods. The remainder of the thesis concentrates on modelling Spanish forest dynamics, so in Chapter Three I present a brief introduction to Spanish forest ecology. In Chapter Four I examine how aboveground allometry - the scaling of tree height and crown shape - varies with climate and competition in Spain for 26 species. Hierarchical modelling suggests that scaling theories based on wood properties do not explain differences between species, but climatic factors, and in particular hydraulic limitations, do. In Chapter Five I parameterise a model of recruitment in Spanish forests using Approximate Bayesian Computation, a novel computational method which allows parameterisation of individual-based models without individual-based data, and demonstrate that it produces ecologically reasonable results. Chapter Six presents a forest dynamics model parameterised for the major native species in Spain and tests whether it is able to reproduce observed species-climate distributions. Finally, in Chapter Seven I discuss the main findings of the thesis and avenues for extending this research. Mon, 11 Jun 2012 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243636 2012-06-11T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239128 Title: Nannoplankton as indicators of climatic variability in the Upper Pliocene Authors: Chepstow-Lusty, Alexander John Abstract: Discoasters are the remains of an enigmatic group of nannoplankton, whose last representatives disappeared globally at 1.89 Ma. The one million years prior to their extinction has been analysed in high time resolution and a global database has been developed from ten sites in the Atlantic, Indian and Pacific Oceans. It has been shown that the variability in Discoaster abundance at low latitudes cannot be attributed solely to changes in sea-surface temperature; discoasters were demonstrated to be suppressed at upwelling sites. In combination with global satellite images of phytoplankton blooms (Lewis, 1989) and maps of modern sea-surface temperatures (CLIMAP, 1981), Discoaster abundance variations were interpreted in terms of the interplay between productivity pressure and sea-surface temperature. Discoasters thrived in the Indian Ocean at Site 709 (4°S) in warm waters with little productivity pressure, whereas Discoaster abundance was suppressed at Sites 677 (l°N) and 662 (l°S) in the Pacific and Atlantic, which although located in warm waters, were affected by upwelling. In addition to the reduced Discoaster abundances associated with upwelling, sea-surface temperature gradients are a significant factor when comparing high and low latitude sites. A marked drop in Discoaster abundance is apparent between 41°N and 56°N (i.e., between Sites 607 and 552). Relative abundances of species in the Discoaster assemblage revealed clearly their contrasting environmental preferences; D. brouweri was produced under a wide range of conditions, favouring warm, low productivity waters; D. asymmetricus and D. tamalis were produced in higher abundances relative to D. brouweri during cooler, low productivity episodes; D. pentaradiatus showed highest absolute abundance in warm, low productivity waters, although increasing in relative abundance at higher latitudes; D. surculus increased in relative abundance in high productivity regions and in cooler waters. At all sites, though most markedly at higher latitudes, Discoaster abundances declined after 2.4 Ma, when glaciation began in the North Atlantic. Tue, 01 Jan 1991 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239128 1991-01-01T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/226324 Title: Role of KNOX genes in the evolution and development of floral nectar spurs Authors: Box, Mathew S Abstract: A key question in biology is how changes in gene function or regulation produce new morphologies during evolution. The nectar spur is an evolutionarily labile structure known to influence speciation in a broad range of angiosperm taxa. Here, the genetic basis of nectar spur development, and the evolution of differences in nectar spur morphology, is investigated in Linaria vulgaris and two closely related species of orchid, the primitively longer-spurred Dactylorhiza fuchsii, and more derived short-spurred D. viridis (Orchidinae, Orchidaceae). Despite considerable morphological and phylogenetic differences, nectar spur ontogeny is fundamentally similar in each of the study species, proceeding from an abaxial bulge formed on the ventral petal relatively late in petal morphogenesis. However, spur development is progenetically curtailed in the short-spurred orchid D. viridis. In each case spur development involves class 1 KNOTTED1-like homeobox (KNOX) proteins. KNOX gene expression is not restricted to the spur-bearing petal, indicating that additional components are required to define nectar spur position, e.g. canonical ABC genes, determinants of floral zygomorphy, and additional (currently unknown) factors. However, constitutive expression of class 1 KNOX proteins in transgenic tobacco produces flowers with ectopic outgrowths on the petals, indicating that KNOX proteins alone are, to some degree, capable of inducing structures similar to nectar spurs in a heterologous host. Interestingly, KNOX gene expression is high in the ovary of all study taxa, suggesting that KNOX proteins may also have been involved in the evolution of this key angiosperm feature. Although principally involved in maintaining indeterminacy in the shoot apical meristem (SAM), members of the KNOX gene family have been co-opted in the evolution and development of compound leaves where they suppress differentiation and extend the morphogenetic potential of the leaf. A similar model is presented here to explain the role of KNOX proteins in nectar spur development. Co-option of KNOX gene expression to the maturing perianth delays cellular differentiation, facilitating the development of the nectar spur but requiring additional, unknown factors, to determine nectar spur fate. As facilitators of nectar spur development, changes in the spatio-temporal patterns of KNOX gene expression may alter the potential for nectar spur development and explain the critical length differences observed between the orchids D. fuchsii and D. viridis (and among other angiosperm taxa). Taken together, the available data indicate that KNOX genes confer a meristematic state upon plant tissues in a variety of morphogenetic contexts, making the gene family a potentially versatile tool to mediate a wide variety of evolutionary transformations. Mon, 07 Jun 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/226324 2010-06-07T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/226160 Title: Physiological and molecular determinants of the Chlamydomonas reinhardtii pyrenoid Authors: Meyer, Moritz Abstract: Aquatic photosynthesis accounts for 50% of the global annual net primary production (NPP), despite frequent low availability and limited diffusion of CO2 in the aquatic milieu, and low affinity for CO2 by the primary carboxylating enzyme, Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Many eukaryotic algae, and a single group of land plants, the hornworts, have an inducible carbon concentrating mechanism (CCM), to overcome these limitations. The efficiency of the CCM is improved when RuBisCO is localised to a subcellular compartment, the pyrenoid, which is hypothesised to act as a diffusion barrier for CO2 . Although the pyrenoid is a major player in global carbon balance (we estimate 10-15% of NPP), it is one of the few remaining prominent cellular features without a precise molecular or physiological definition. Under ambient CO2 , at least 90% of the cellular RuBisCO is packed into a dense matrix, together with the chaperone RuBisCO activase. Thylakoid membranes usually traverse the pyrenoid matrix, and the carboxylating substrate is thought to be delivered to the active sites of the enzyme via a carbonic anhydrase located in the lumen of these thylakoids. The mechanism of aggregation of constituents within the pyrenoid, however, still remains largely unknown. Comprehensive mutant screens have yet to reveal mutants incapable of forming pyrenoids other than those mutants with a defective RuBisCO holoenzyme, whereas DNA microarray studies uncovered little with reference to pyrenoid ultrastructure or aggregation. Taken together, this evidence raises the possibility that the basis of pyrenoid ultrastructure and aggregation lies entirely in sequence variations of RuBisCO itself. This work explored, firstly, the advantages conferred by an active CCM in hornworts and in unicellular algae, compared with the passive CO2 acquisition in most terrestrial plants. A physiological framework to CCM and pyrenoid-based photosynthesis, and isotopic discrimination, was provided by comparing the photosynthetic characteristics of selected bryophytes and algae, differing in chloroplast morphology and degrees of internalisation of gas exchanges. The results showed that on-line, carbon isotope discrimination values were a good indicator of CCM occurrence, as well as liquid-phase diffusion limitation, and biochemical limitations resulting from declining RuBisCO activity and electron transport. The methodology was used to diagnose the presence of an active CCM, and the extent of CO2 leakage. Secondly, the effect of RuBisCO sequence variations on the pyrenoid, and associated CCM, was studied using the model alga Chlamydomonas reinhardtii. The starting premise was the report by Nozaki et al. (2002) that, in some species of the family Chlamydomonaceae, a few amino acid residues within the RuBisCO large subunit (LSU) correlated strongly with pyrenoid formation. The specific roles of seven LSU residues were studied by site-directed mutagenesis. Whilst the mutations reduced the affinity of RuBisCO for CO2 and increased CO2 leakage, compared to wild-type Chlamydomonas, there was no effect on the pyrenoid phenotype. Informed by observations that Chlamydomonas mutants with a hybrid RuBisCO, composed of a native LSU, and higher plant small subunit (SSU), lacked a pyrenoid (Genkov et al., 2010), and that defined SSU alterations were neutral with respect to the pyrenoid (Genkov and Spreitzer, 2006), hitherto unexplored SSU domains were modified. A pyrenoid was successfully restored by replacing jointly the two solvent-exposed α-helices, whereas single α-helix replacements had no effect. However, leakage values indicated that the associated CCM was not fully operative, suggesting important correlates between the RuBisCO SSU and the CCM, besides the conditioning of pyrenoid formation. If the pyrenoid is partly defined by simple sequence variations in the RuBisCO SSU, as suggested by the evidence outlined in this thesis, there is the tantalising possibility that transformation of a biophysical CCM into crop plants could be a tractable approach for the future. Description: Thesis is under embargo due to publisher requirements. Mon, 07 Jun 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/226160 2010-06-07T23:00:00Z