Evolution of the landscape of Madeira Island: long-term vegetation dynamics

The aim of this thesis was to evaluate historical change of the landscape of Madeira Island and to assess spatial and temporal vegetation dynamics. In current research diverse “retrospective techniques”, such as landscape repeat photography, dendrochronology, and research of historical records were used. These, combined with vegetation relevés, aimed to gather information about landscape change, disturbance history, and vegetation successional patterns. It was found that landscape change, throughout 125 years, was higher in the last five decades manly driven by farming abandonment, building growth and exotic vegetation coverage increase. Pristine vegetation was greatly destroyed since early settlement and by the end of the nineteenth century native vegetation was highly devastated due to recurrent antropogenic disturbances. These actions also helped to block plant succession and to modify floristical assemblages, affecting as well as species richness. In places with less hemeroby, although significant growth of vegetation of lower seral stages was detected, the vegetation of most mature stages headed towards unbalance between recovery and loss, being also very vulnerable to exotic species encroachment. Recovery by native vegetation also occurred in areas formerly occupied by exotic plants and agriculture but it was almost negligible. Vegetation recovery followed the successional model currently proposed, attesting the model itself. Yet, succession was slower than espected, due to lack of favourable conditions and to recurrent disturbances. Probable tempus of each seral stage was obtained by growth rates of woody taxa estimated through dendrochronology. The exotic trees which were the dominant trees in the past (Castanea sativa and Pinus pinaster) almost vanished. Eucalyptus globulus, the current main tree of the exotic forest is being replaced by other cover types as Acacia mearnsii. The latter, along with Arundo donax, Cytisus scoparius and Pittosporum undulatum are currently the exotic species with higher invasive behaviour. However, many other exotic species have also proved to be highly pervasive and came together with the ones referred above to prevent native vegetation regeneration, to diminish biological diversity, and to block early successional phases delaying native forest recovery.

Evolution of thermokarst in East Siberian ice-rich permafrost

Thermokarst lakes and basins are major components of ice-rich permafrost landscapes in East Siberian coastal lowlands and are regarded as indicators of regional climatic changes. We investigate the temporal and spatial dynamics of a 7.5 km**2, partly drained thermokarst basin (alas) using field investigations, remote sensing, Geographic Information Systems (GIS), and sediment analyses. The evolution of the thermokarst basin proceeded in two phases. The first phase started at the Pleistocene/Holocene transition (13 to 12 ka BP) with the initiation of a primary thermokarst lake on the Ice Complex surface. The lake expanded and persisted throughout the early Holocene before it drained abruptly about 5.7 ka BP, thereby creating a > 20 m deep alas with residual lakes. The second phase (5.7 ka BP to present) is characterized by alternating stages of lower and higher thermokarst intensity within the alas that were mainly controlled by local hydrological and relief conditions and accompanied by permafrost aggradation and degradation. It included diverse concurrent processes like lake expansion and stepwise drainage, polygonal ice-wedge growth, and the formation of drainage channels and a pingo, which occurred in different parts of the alas. This more dynamic thermokarst evolution resulted in a complex modern thermokarst landscape. However, on the regional scale, the changes during the second evolutionary phase after drainage of the initial thermokarst lakes were less intense than the early Holocene extensive thermokarst development in East Siberian coastal lowlands as a result of a significant regional change to warmer and wetter climate conditions.

Certain observations concerning the effects of epistasis on complex traits and the evolution of genomes.

Thesis (Ph.D.)--University of Washington, 2016-05

Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

A refined solution to Earth's hidden niobium: implications for evolution of continental crust and mode of core formation

New high-precision niobium (Nb) and tantalum (Ta) concentration data are presented for early Archaean metabasalts, metabasaltic komatiites and their erosion products (mafic metapelites) from SW Greenland and the Acasta gneiss complex, Canada. Individual datasets consistently show sub-chondritic Nb/Ta ratios averaging 15.1+/-11.6. This finding is discussed with regard to two competing models for the solution of the Nb-deficit that characterises the accessible Earth. Firstly, we test whether Nb could have sequestered into the core due to its slightly siderophile (or chalcophile) character under very reducing conditions, as recently proposed from experimental evidence. We demonstrate that troilite inclusions of the Canyon Diablo iron meteorite have Nb and V concentrations in excess of typical chondrites but that the metal phase of the Grant, Toluca and Canyon Diablo iron meteorites do not have significant concentrations of these lithophile elements. We find that if the entire accessible Earth Nb-deficit were explained by Nb in the core, only ca. 17% of the mantle could be depleted and that by 3.7 Ga, continental crust would have already achieved ca. 50% of its present mass. Nb/Ta systematics of late Archaean metabasalts compiled from the literature would further require that by 2.5 Ga, 90% of the present mass of continental crust was already in existence. As an alternative to this explanation, we propose that the average Nb/Ta ratio (15.1+/-11.6) of Earth's oldest mafic rocks is a valid approximation for bulk silicate Earth. This would require that ca. 13% of the terrestrial Nb resided in the Ta-free core. Since the partitioning of Nb between silicate and metal melts depends largely on oxygen fugacity and pressure, this finding could mean that metal/silicate segregation did not occur at the base of a deep magma ocean or that the early mantle was slightly less reducing than generally assumed. A bulk silicate Earth Nb/Ta ratio of 15.1 allows for depletion of up to 40% of the total mantle. This could indicate that in addition to the upper mantle, a portion of the lower mantle is depleted also, or if only the upper mantle were depleted, an additional hidden high Nb/Ta reservoir must exist. Comparison of Nb/Ta systematics between early and late Archaean metabasalts supports the latter idea and indicates deeply subducted high Nb/Ta eclogite slabs could reside in the mantle transition zone or the lower mantle. Accumulation of such slabs appears to have commenced between 2.5 and 2.0 Ga. Regardless of these complexities of terrestrial Nb/Ta systematics, it is shown that the depleted mantle Nb/Th ratio is a very robust proxy for the amount of extracted continental crust, because the temporal evolution of this ratio is dominated by Th-loss to the continents and not Nb-retention in the mantle. We present a new parameterisation of the continental crust volume versus age curve that specifically explores the possibility of lithophile element loss to the core and storage of eclogite slabs in the transition zone. (C) 2003 Elsevier Science B.V. All rights reserved.

40Ar/39Ar constraints on a temporal link between gold mineralization, magmatism, and continental margin transtension in the Jiaodong Gold Province, eastern China

The Jiaodong gold province is the largest gold repository in China. Both mineralization and granitoid hosts are spatially related to the crustal-scale Tan-Lu strike-slip fault system, which developed along the Mesozoic continental margin in eastern China. A series of Ar-40/Ar-39 laser incremental heating analyses of hydrothermal sericite/muscovite from three major gold deposits (Jiaojia, Xincheng, and Wangershan) and igneous biotite from the granodiorite hosts were performed to establish a possible temporal link between gold mineralization, magmatism, and movement along the Tan-Lu fault zone. Magmatic biotite crystals yield well-defined and concordant plateau ages between 124.5+/-0.4 Ma and 124.0+/-0.4 Ma (2sigma), whereas sericite and muscovite samples (a total of 30 single separates) give reproducible plateau ages ranging from 121.0+/-0.4 Ma to 119.2+/-0.2 Ma (2sigma). An integration of our Ar-40/Ar-39 results with age data from other major gold deposits in Jiaodong demonstrates that widespread gold mineralization occurred contemporaneously during a 2-3-m.yr. period. Most gold deposits show intimate spatial associations with abundant mafic to intermediate dikes. The mafic dikes have K-Ar ages of 123.5-119.6 Ma, in excellent agreement with those of the gold deposits. These newly obtained Ar-40/Ar-39 ages, in combination with other independent geological and geochronological data on granodioritic intrusions (130-126 Ma), volcanic rocks (1243.6-114.7 Ma), and deformed rocks within strike-slip faults (132-120 Ma) in Jiaodong or adjacent areas, also support the idea that gold mineralization postdated the granodioritic magmatism but was contemporaneous with mafic magmatism and volcanism, all controlled by the transtensional motion along the Tan-Lu fault in the Early Cretaceous.

Molecular phylogeny and biogeography of the dung beetle genus Temnoplectron Westwood (Scarabaeidae: Scarabaeinae) from Australia’s wet tropics

The landscape of the Australian Wet Tropics can be described as islands of montane rainforest Surrounded by warmer or more xeric habitats. Historical glaciation cycles have caused expansion and contraction of these rainforest islands leading to consistent patterns of genetic divergence within species of vertebrates. To explore whether this dynamic history has promoted speciation in endemic and diverse groups Of insects, we used a combination of mtDNA sequencing and morphological characters to estimate relationships and the tempo of divergence among Australian representatives of the dung beetle genus Temnoplectron. This phylogenetic hypothesis shares a number of well-supported clades with a previously published phylogenetic hypothesis based on morphological data. though statistical support for several nodes is weak. Sister species relationships well-supported in both tree topologies. and a tree obtained by combining the two data sets. suggest that speciation has mostly been allopatric. We identify a number of speciation barriers, which coincide with phylogeographic breaks found in vertebrate species. Large sequence divergences between species emphasize that speciation events are ancient (pre-Pleistocene). The flightless, rainforest species appear to have speciated rapidly. but also in the distant past. (C) 2003 Elsevier Inc. All rights reserved.

Selection pressure-driven evolution of the Epstein-Barr virus-encoded oncogene LMP1 in virus isolates from southeast Asia

The geographically constrained distribution of Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) in southeast Asian populations suggests that both viral and host genetics may influence disease risk. Although susceptibility loci have been mapped within the human genome, the role of viral genetics in the focal distribution of NPC remains an enigma. Here we report a molecular phylogenetic analysis of an NPC-associated viral oncogene, LMP1, in a large panel of EBV isolates from southeast Asia and from Papua New Guinea, Africa, and Australia, regions of the world where NPC is and is not endemic, respectively. This analysis revealed that LMP1 sequences show a distinct geographic structure, indicating that the southeast Asian isolates have evolved as a lineage distinct from those of Papua New Guinea, African, and Australian isolates. Furthermore, a likelihood ratio test revealed that the C termini of the LMP1 sequences of the southeast Asian lineage are under significant positive selection pressure, particularly at some sites within the C-terminal activator regions. We also present evidence that although the N terminus and transmembrane region of LMP1 have undergone recombination, the C-terminal region of the gene has evolved without any history of recombination. Based on these observations, we speculate that selection pressure may be driving the LMP1 sequences in virus isolates from southeast Asia towards a more malignant phenotype, thereby influencing the endemic distribution of NPC in this region.

Evolution of polydnaviruses as insect immune suppressors

Polydnaviruses (PDVs) are endogenous particles that are used by some endoparasitic hymenoptera to disrupt host immunity and development. Recent analyses of encapsidated PDV genes have increased the number of known PDV gene families, which are often closely related to insect genes. Several PDV proteins inactivate host haemocytes by damaging their actin cytoskeleton. These proteins share no significant sequence homology and occur in polyphyletic PDV genera, possibly indicating that convergent evolution has produced functionally similar immune-suppressive molecules causing a haemocyte phenotype characterised by damaged cytoskeleton and inactivation. These phenomena provide further insights into the immune-suppressive activity of PDVs and raise interesting questions about PDV evolution, a topic that has puzzled researchers ever since the discovery of PDVs.

Evolution of the regular zone of histone H1 in Fabaceae plants

An analysis of the historic H1 subtype, H1-1, in eight legumes belonging to four genera of the tribe Vicieae (Pisum, Lathyrus, Lens, and Vicia), revealed an extended region consisting of the tandemly repeated AKPAAK motifs. We named this region the Regular zone (RZ). The AKPAAK motifs are organized into two blocks separated by a short (two or six amino acids) intervening sequence (IS). The distal block contains six AKPAAK motifs, while the number of repeats in the proximal block varies from six in V. faba to seven in the other species. In V. hirsuta, the first two repeated units of the proximal block are octapeptides AKAKPAAK. The apparent rate of synonymous substitutions in the blocks of RZ is much higher than in the rest of the gene. This can be explained by repeat shuffling within each block. In the C-domain of the orthologous H1 subtype froth Medicago truncatula (tribe Trifolieae), a region corresponding to the RZ of Vicieae species was found. It also consists of two blocks of AKPAAK motifs (four and three repeats in the proximal and distal blocks, respectively). These blocks are separated by a 20-amino acid IS. The first 20 amino acids of the Medicago RZ are not part of AKPAAK repeats. We hypothesise that the RZ has most probably evolved as a result of an expansion of AKPAAK repeats from two separate sites in the C-domain. This process started tens of millions of years ago and was most likely directed by positive selection.

Evolution of resistance to sulfadoxine-pyrimethamine in Plasmodium falciparum

The development of resistance to sulfadoxine-pyrimethamine by Plasmodium parasites is a major problem for the effective treatment of malaria, especially P. falciparum malaria. Although the molecular basis for parasite resistance is known, the factors promoting the development and transmission of these resistant parasites are less clear. This paper reports the results of a quantitative comparison of factors previously hypothesized as important for the development of drug resistance, drug dosage, time of treatment, and drug elimination half-life, with an in-host dynamics model of P. falciparum malaria in a malaria-naive host. The results indicate that the development of drug resistance can be categorized into three stages. The first is the selection of existing parasites with genetic mutations in the dihydrofolate reductase or dihydropteroate synthetase gene. This selection is driven by the long half-life of the sulfadoxine-pyrimethamine combination. The second stage involves the selection of parasites with allelic types of higher resistance within the host during an infection. The timing of treatment relative to initiation of a specific anti-P. falciparum EMP1 immune response is an important factor during this stage, as is the treatment dosage. During the third stage, clinical treatment failure becomes prevalent as the parasites develop sufficient resistance mutations to survive therapeutic doses of the drug combination. Therefore, the model output reaffirms the importance of correct treatment of confirmed malaria cases in slowing the development of parasite resistance to sulfadoxine-pyrimethamine.

Frequency and temporal effects in linear optical quantum computing

Typically linear optical quantum computing (LOQC) models assume that all input photons are completely indistinguishable. In practice there will inevitably be nonidealities associated with the photons and the experimental setup which will introduce a degree of distinguishability between photons. We consider a nondeterministic optical controlled-NOT gate, a fundamental LOQC gate, and examine the effect of temporal and spectral distinguishability on its operation. We also consider the effect of utilizing nonideal photon counters, which have finite bandwidth and time response.

Design strategies for controlling the molecular weight and rate using reversible addition-fragmentation chain transfer mediated living radical polymerization

Living radical polymerization has allowed complex polymer architectures to be synthesized in bulk, solution, and water. The most versatile of these techniques is reversible addition-fragmentation chain transfer (RAFT), which allows a wide range of functional and nonfunctional polymers to be made with predictable molecular weight distributions (MWDs), ranging from very narrow to quite broad. The great complexity of the RAFT mechanism and how the kinetic parameters affect the rate of polymerization and MWD are not obvious. Therefore, the aim of this article is to provide useful insights into the important kinetic parameters that control the rate of polymerization and the evolution of the MWD with conversion. We discuss how a change in the chain-transfer constant can affect the evolution of the MWD. It is shown how we can, in principle, use only one RAFT agent to obtain a poly-mer with any MWD. Retardation and inhibition are discussed in terms of (1) the leaving R group reactivity and (2) the intermediate radical termination model versus the slow fragmentation model. (c) 2005 Wiley Periodicals, Inc.

Areal specialization of pyramidal cell structure in the visual cortex of the tree shrew: a new twist revealed in the evolution of cortical circuitry

Cortical pyramidal cells, while having a characteristic morphology, show marked phenotypic variation in primates. Differences have been reported in their size, branching structure and spine density between cortical areas. In particular, there is a systematic increase in the complexity of the structure of pyramidal cells with anterior progression through occipito-temporal cortical visual areas. These differences reflect area-specific specializations in cortical circuitry, which are believed to be important for visual processing. However, it remains unknown as to whether these regional specializations in pyramidal cell structure are restricted to primates. Here we investigated pyramidal cell structure in the visual cortex of the tree shrew, including the primary (V1), second (V2) and temporal dorsal (TD) areas. As in primates, there was a trend for more complex branching structure with anterior progression through visual areas in the tree shrew. However, contrary to the trend reported in primates, cells in the tree shrew tended to become smaller with anterior progression through V1, V2 and TD. In addition, pyramidal cells in V1 of the tree shrew are more than twice as spinous as those in primates. These data suggest that variables that shape the structure of adult cortical pyramidal cells differ among species.

Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations

Human social organization can deeply affect levels of genetic diversity. This fact implies that genetic information can be used to study social structures, which is the basis of ethnogenetics. Recently, methods have been developed to extract this information from genetic data gathered from subdivided populations that have gone through recent spatial expansions, which is typical of most human populations. Here, we perform a Bayesian analysis of mitochondrial and Y chromosome diversity in three matrilocal and three patrilocal groups from northern Thailand to infer the number of males and females arriving in these populations each generation and to estimate the age of their range expansion. We find that the number of male immigrants is 8 times smaller in patrilocal populations than in matrilocal populations, whereas women move 2.5 times more in patrilocal populations than in matrilocal populations. In addition to providing genetic quantification of sex-specific dispersal rates in human populations, we show that although men and women are exchanged at a similar rate between matrilocal populations, there are far fewer men than women moving into patrilocal populations. This finding is compatible with the hypothesis that men are strictly controlling male immigration and promoting female immigration in patrilocal populations and that immigration is much less regulated in matrilocal populations.