Large igneous provinces and silicic large igneous provinces : progress in our understanding over the last 25 years

Large Igneous Provinces are exceptional intraplate igneous events throughout Earth’s history. Their significance and potential global impact is related to the total volume of magma intruded and released during these geologically brief events (peak eruptions are often within 1-5 Myrs duration) where millions to tens of millions of cubic kilometers of magma are produced. In some cases, at least 1% of the Earth’s surface has been directly covered in volcanic rock, being equivalent to the size of small continents with comparable crustal thicknesses. Large Igneous Provinces are thus important, albeit episodic episodes of new crust addition. However, most magmatism is basaltic so that contributions to crustal growth will not always be picked up in zircon geochronology studies that better trace major episodes of extension-related silicic magmatism and the silicic Large Igneous Provinces. Much headway has been made on our understanding of these anomalous igneous events over the last 25 years, driving many new ideas and models. This includes their: 1) global spatial and temporal distribution, with a long-term average of one event approximately every 20 Myrs, but a clear clustering of events at times of supercontinent break-up – Large Igneous Provinces are thus an integral part of the Wilson cycle and are becoming an increasingly important tool in reconnecting dispersed continental fragments; 2) compositional diversity that in part reflects their crustal setting of ocean basins, and continental interiors and margins where in the latter setting, LIP magmatism can be silicicdominant; 3) mineral and energy resources with major PGE and precious metal resources being hosted in these provinces, as well as magmatism impacting on the hydrocarbon potential of volcanic basins and rifted margins through enhancing source rock maturation, providing fluid migration pathways, and trap formation; 4) biospheric, hydrospheric and atmospheric impacts, with Large Igneous Provinces now widely regarded as a key trigger mechanism for mass extinctions, although the exact kill mechanism(s) are still being resolved; 5) role in mantle geodynamics and thermal evolution of the Earth, by potentially recording the transport of material from the lower mantle or core-mantle boundary to the Earth's surface and being a fundamental component in whole mantle convection models; and 6) recognition on the inner planets where the lack of plate tectonics and erosional processes and planetary antiquity means that the very earliest record of LIP events during planetary evolution may be better preserved than on Earth.

Pyroxene thermometry of rhyolite lavas of the Bruneau–Jarbidge eruptive center, Central Snake River Plain

The Bruneau–Jarbidge eruptive center of the central Snake River Plain in southern Idaho, USA produced multiple rhyolite lava flows with volumes of <10 km³ to 200 km³ each from ~11.2 to 8.1 Ma, most of which follow its climactic phase of large-volume explosive volcanism, represented by the Cougar Point Tuff, from 12.7 to 10.5 Ma. These lavas represent the waning stages of silicic volcanism at a major eruptive center of the Yellowstone hotspot track. Here we provide pyroxene compositions and thermometry results from several lavas that demonstrate that the demise of the silicic volcanic system was characterized by sustained, high pre-eruptive magma temperatures (mostly ≥950 °C) prior to the onset of exclusively basaltic volcanism at the eruptive center. Pyroxenes display a variety of textures in single samples, including solitary euhedral crystals as well as glomerocrysts, crystal clots and annealed microgranular inclusions of pyroxene ±magnetite± plagioclase. Pigeonite and augite crystals are unzoned, and there are no detectable differences in major and minor element compositions according to textural variety — mineral compositions in the microgranular inclusions and crystal clots are identical to those of phenocrysts in the host lavas. In contrast to members of the preceding Cougar Point Tuff that host polymodal glass and mineral populations, pyroxene compositions in each of the lavas are characterized by single rather than multiple discrete compositional modes. Collectively, the lavas reproduce and extend the range of Fe–Mg pyroxene compositional modes observed in the Cougar Point Tuff to more Mg-rich varieties. The compositionally homogeneous populations of pyroxene in each of the lavas, as well as the lack of core-to-rim zonation in individual crystals suggest that individual eruptions each were fed by compositionally homogeneous magma reservoirs, and similarities with the Cougar Point Tuff suggest consanguinity of such reservoirs to those that supplied the polymodal Cougar Point Tuff. Pyroxene thermometry results obtained using QUILF equilibria yield pre-eruptive magma temperatures of 905 to 980 °C, and individual modes consistently record higher Ca content and higher temperatures than pyroxenes with equivalent Fe–Mg ratios in the preceding Cougar Point Tuff. As is the case with the Cougar Point Tuff, evidence for up-temperature zonation within single crystals that would be consistent with recycling of sub- or near-solidus material from antecedent magma reservoirs by rapid reheating is extremely rare. Also, the absence of intra-crystal zonation, particularly at crystal rims, is not easily reconciled with cannibalization of caldera fill that subsided into pre-eruptive reservoirs. The textural, compositional and thermometric results rather are consistent with minor re-equilibration to higher temperatures of the unerupted crystalline residue from the explosive phase of volcanism, or perhaps with newly generated magmas from source materials very similar to those for the Cougar Point Tuff. Collectively, the data suggest that most of the pyroxene compositional diversity that is represented by the tuffs and lavas was produced early in the history of the eruptive center and that compositions across this range were preserved or duplicated through much of its lifetime. Mineral compositions and thermometry of the multiple lavas suggest that unerupted magmas residual to the explosive phase of volcanism may have been stored at sustained, high temperatures subsequent to the explosive phase of volcanism. If so, such persistent high temperatures and large eruptive magma volumes likewise require an abundant and persistent supply of basalt magmas to the lower and/or mid-crust, consistent with the tectonic setting of a continental hotspot.

Essential Oil Composition of Diploid and Tetraploid Clones of Ginger (Zingiber officinale Roscoe) Grown in Australia

Ginger oil, obtained by steam distillation of the rhizome of Zingiber officinale Roscoe, is used in the beverage and fragrance industries. Ginger oil displays considerable compositional diversity, but is typically characterized by a high content of sesquiterpene hydrocarbons, including zingiberene, arcurcumene, â-bisabolene, and â-sesquiphellandrene. Australian ginger oil has a reputation for possessing a particular “lemony” aroma, due to its high content of the isomers neral and geranial, often collectively referred to as citral. Fresh rhizomes of 17 clones of Australian ginger, including commercial cultivars and experimental tetraploid clones, were steam distilled 7 weeks post-harvest, and the resulting oils were analyzed by GC-MS. The essential oils of 16 of the 17 clones, including the tetraploid clones and their parent cultivar, were found to be of substantially similar composition. These oils were characterized by very high citral levels (51-71%) and relatively low levels of the sesquiterpene hydrocarbons typical of ginger oil. The citral levels of most of these oils exceeded those previously reported for ginger oils. The neral-to-geranial ratio was shown to be remarkably constant (0.61 ( 0.01) across all 17 clones. One clone, the cultivar “Jamaican”, yielded oil with a substantially different composition, lower citral content and higher levels of sesquiterpene hydrocarbons. Because this cultivar also contains significantly higher concentrations of pungent gingerols, it possesses unique aroma and flavor characteristics, which should be of commercial interest.

Collaborations complexes : modèle théorique et vérification empirique préliminaire en contexte de projets interdisciplinaires et interorganisationnels

La collaboration constitue une stratégie efficace pour aider les organisations et les individus à évoluer dans des environnements dynamiques et complexes, et génère de nombreux avantages cognitifs, affectifs et pécuniaires. De plus en plus, les équipes de travail sont impliquées dans des collaborations complexes, lesquelles requièrent de transiger à travers les frontières nationales, organisationnelles et disciplinaires. Bien que les collaborations complexes soient de plus en plus courantes en milieux organisationnels et étudiées par les scientifiques, peu d’études empiriques ont été réalisées sur le sujet et la documentation inhérente est disséminée dans divers silos parallèles de connaissances, donnant lieu à des modèles conceptuels divergents et incomplets. L’importance croissante de ces formes de collaboration crée l’impératif scientifique et pratique d’en acquérir une meilleure compréhension ainsi que d’identifier et d’évaluer les conditions et les facteurs qui favorisent leur succès et leur efficacité. Cette thèse vise à combler les lacunes susmentionnées et permettre un avancement des connaissances sur le sujet par l’entremise de deux articles répondant à divers objectifs de recherche. Le premier article avance une définition claire des collaborations complexes, en vue de réduire la confusion entourant ce construit. Il présente également la première revue de documentation sur les facteurs favorisant le succès des collaborations complexes, unifiant les résultats issus de divers contextes et disciplines scientifiques. Cette démarche a permis d’identifier 14 variables clés provenant de 26 études empiriques. À partir de ces données, un modèle conceptuel fondé sur des assises théoriques solides et reconnues en psychologie du travail et des organisations est proposé, offrant ainsi un canevas systémique et dynamique du phénomène ainsi qu’une orientation détaillée des pistes de recherches pertinentes. Le deuxième article part des résultats obtenus dans le premier article afin d’évaluer empiriquement les relations entre certains facteurs clés ayant un impact sur des extrants importants de collaborations complexes. L’étude multiphasique est réalisée auprès de 16 équipes de projets (N=93) interdisciplinaires et interorganisationnelles prenant part à des sessions de travail intensives visant la production de concepts novateurs en design intégré lié au développement durable. Les analyses corrélationnelles montrent des liens positifs entre l’ouverture à la diversité, les processus collaboratifs, la viabilité, la performance d’équipe et la performance de projet, ainsi que des liens négatifs entre les conflits et ces mêmes extrants. De plus, les analyses de médiation multiple révèlent qu’une plus grande ouverture à la diversité influence positivement la viabilité, la performance d’équipe et la performance de projet en favorisant les processus collaboratifs efficaces et en réduisant les conflits. Les implications théoriques et pratiques découlant de ces résultats sont discutées.

Chemical composition of basalts and minerals from basalts of the Bouvet triple junction

This study focuses on mafic volcanic rocks from the Bouvet triple junction, which fall into six geochemically distinct groups: (1) N-MORB, the most widespread type, encountered throughout the study area. (2) Subalkaline volcanics, hawaiites and mugearites strongly enriched in lithophile elements and radiogenic isotopes and composing the Bouvet volcanic rise, and compositionally similar basalts and basaltic andesites from the Spiess Ridge, generated in a deeper, fertile mantle region. (3) Relatively weakly enriched basalts, T-MORB derived by the mixing of Type 1 and 2 melts and exposed near the axes of the Mid-Atlantic, Southwest Indian, and America-Antarctic Ridges. (4) Basalts with a degree of trace lithophile element enrichment similar to the Spiess Ridge and Bouvet Island rocks, but higher in K, P, Ti, and Cr. These occur within extensional structures: the rift valley of the Southwest Indian Ridge, grabens of the East Dislocation Zone, and the linear rise between the Spiess Ridge and Bouvet volcano. Their parental melts presumably separated from plume material that spread from the main channels and underwent fluid-involving differentiation in the mantle. (5) A volcanic suite ranging from basalt to rhyolite, characterized by low concentrations of lithophile elements, particularly TiO2, and occurring on the Shona Seamount and other compressional features within the Antarctic and South American plates near the Bouvet triple junction. Unlike Types 1 to 4, which display tholeiitic differentiation trends, this suite is calc-alkaline. Its parental melts were presumably related to the plume material as well but, subsequently, they underwent a profound differentiation involving fluids and assimilated surrounding rocks in closed magma chambers in the upper mantle. Alternatively, the Shona Seamount might be a fragment of an ancient oceanic island arc. (6) Enriched basalts, distinguished from the other enriched rock types in very high P and radiogenic isotope abundances and composing a tectonic uplift near the junction of the three rifts. It thus follows that the main factors responsible for the compositional diversity of volcanic rocks in this region include (i) mantle source heterogeneity, (ii) plume activity, (iii) an intricate geodynamic setup at the triple junction giving rise to stresses in adjacent plate areas, and (iv) the geological prehistory. The slow spreading rate and ensuing inefficient mixing of the heterogeneous mantle material result in strong spatial variations in basaltic compositions.

Geochemistry of North Atlantic Igneous Province basalts

New Sr-Nd-Pb-Hf data require the existence of at least four mantle components in the genesis of basalts from the the North Atlantic Igneous Province (NAIP): (1) one (or more likely a small range of) enriched component(s) within the Iceland plume, (2) a depleted component within the Iceland plume (distinct from the shallow N-MORB source), (3) a depleted sheath surrounding the plume and (4) shallow N-MORB source mantle. These components have been available since the major phase of igneous activity associated with plume head impact during Paleogene times. In Hf-Nd isotope space, samples from Iceland, DSDP Leg 49 (Sites 407, 408 and 409), ODP Legs 152 and 163 (southeast Greenland margin), the Reykjanes Ridge, Kolbeinsey Ridge and DSDP Leg 38 (Site 348) define fields that are oblique to the main ocean island basalt array and extend toward a component with higher 176Hf/177Hf than the N-MORB source available prior to arrival of the plume, as indicated by the compositions of Cretaceous basalts from Goban Spur (~95 Ma). Aside from Goban Spur, only basalts from Hatton Bank on the oceanward side of the Rockall Plateau (DSDP Leg 81) lie consistently within the field of N-MORB, which indicates that the compositional influence of the plume did not reach this far south and east ~55 Ma ago. Thus, Hf-Nd isotope systematics are consistent with previous studies which indicate that shallow MORB-source mantle does not represent the depleted component within the Iceland plume (Thirlwall, J. Geol. Soc. London 152 (1995) 991-996; Hards et al., J. Geol. Soc. London 152 (1995) 1003-1009; Fitton et al., 1997 doi:10.1016/S0012-821X(97)00170-2). They also indicate that the depleted component is a long-lived and intrinsic feature of the Iceland plume, generated during an ancient melting event in which a mineral (such as garnet) with a high Lu/Hf was a residual phase. Collectively, these data suggest a model for the Iceland plume in which a heterogeneous core, derived from the lower mantle, consists of 'enriched' streaks or blobs dispersed in a more depleted matrix. A distinguishing feature of both the enriched and depleted components is high Nb/Y for a given Zr/Y (i.e. positive DeltaNb), but the enriched component has higher Sr and Pb isotope ratios, combined with lower epsilon-Nd and epsilon-Hf. This heterogeneous core is surrounded by a sheath of depleted material, similar to the depleted component of the Iceland plume in its epsilon-Nd and epsilon-Hf, but with lower 87Sr/86Sr, 208Pb/204Pb and negative DeltaNb; this material was probably entrained from near the 670 km discontinuity when the plume stalled at the boundary between the upper and lower mantle. The plume sheath displaced more normal MORB asthenosphere (distinguished by its lower epsilon-Hf for a given epsilon-Nd or Zr/Nb ratio), which existed in the North Atlantic prior to plume impact. Preliminary data on MORBs from near the Azores plume suggest that much of the North Atlantic may be 'polluted' not only by enriched plume material but also by depleted material similar to the Iceland plume sheath. If this hypothesis is correct, it may provide a general explanation for some of the compositional diversity and variations in inferred depth of melting (Klein and Langmuir, 1987 doi:10.1029/JB092iB08p08089) along the MAR in the North Atlantic.

Chemical element concentrations in sediments from DSDP Holes 60-458 and 60-459

The development of laser ablation-inductively coupled plasma-mass spectrometry has revolutionized the analysis of tephras by providing (1) an efficient and precise method for determining abundances of a wide variety of trace elements at low concentrations in individual glass shards and (2) assessment of geochemical heterogeneities within individual ash horizons. This development is important for petrogenetic studies of intraoceanic arc systems, where tephras provide the most complete temporal record of magmatism. Results from the Izu-Bonin and Mariana arc systems indicate that despite close geographical proximity and similar tectonic evolution, they contrast strongly in terms of geochemical evolution since 35 Ma. Whereas the Mariana tephras have exceptional compositional diversity, ranging from low-K (Oligocene), to high-K (Miocene), and subsequently medium-K compositions (Pliocene-Quaternary), the Izu-Bonin arc has been dominated by low-K compositions throughout. The Mariana increases in K are paralleled by increases in abundances of incompatible trace elements and by increased values of diagnostic ratios (e.g., Nb/yb and Th/yb) regarded as monitors of potential mantle-source fertility. The relative uniformity of Nb/yb and Nb/Zr ratios in Izu-Bonin tephras indicates that cyclic processes of backarc basin development and mantle depletion do not necessarily induce large-scale temporal geochemical variations in the associated arc. Temporal variability within the Mariana arc, and its divergence from the Izu-Bonin arc ca. 13 Ma, can be traced to a major injection of subducted sediment in the Mariana system at this time.

Geochemistry of Indian Ocean tephra and Afro-Arabian lavas

Widespread silicic pyroclastic eruptions of the Oligocene Afro-Arabian flood volcanic province (ignimbrites and airfall tuffs) produced up to 20% of the total flood volcanic stratigraphy (>6*10**4 km**3). Volumes of individual ignimbrites and tuffs exposed on land range from ~150 to >2000 km**3 and eight major units (15-100 m thick) were erupted in <2 Myr, placing these amongst the largest-magnitude silicic pyroclastic eruptions on Earth. They are compositionally distinctive time-stratigraphic markers which were deposited as co-ignimbrite ashfall deposits on a near-global scale around the time of the Oi2 cooling anomaly at ~30 Ma. Two ignimbrites from the lower part of the flood volcanic succession in Yemen have been correlated to: (a) the conjugate rifted margin of Ethiopia (>500 km distant); and (b) to two deep sea ash layers sampled by ODP Leg 115 in the Indian Ocean ~2700 km to the southeast. This correlation is based on whole rock analyses of silicic units for isotope ratios (Pb, Nd) and rare earth element compositions, in conjunction with novel in situ Pb isotope laser ablation multicollector inductively coupled plasma mass spectroscopy analysis of groundmass and glass shards. Compositional diversity preserved on the scale of individual ash shards in these deep sea tephra layers record chemical heterogeneity present in the silicic magma chambers that is not evident in the welded on-land deposits. Ages of the ash layers can be established by correlation to precisely dated on-land ignimbrites, and current evidence suggests that while these eruptions may have exacerbated already changing climatic conditions, they both marginally post-date the Oi2 global cooling anomaly.

Essential oil composition of diploid and tetraploid clones of ginger (Zingiber officinale roscoe) grown in Australia

Ginger oil, obtained by steam distillation of the rhizome of Zingiber officinale Roscoe, is used in the beverage and fragrance industries. Ginger oil displays considerable compositional diversity, but is typically characterized by a high content of sesquiterpene hydrocarbons, including zingiberene, arcurcumene, beta-bisabolene, and beta-sesquiphellandrene. Australian ginger oil has a reputation for possessing a particular lemony aroma, due to its high content of the isomers neral and geranial, often collectively referred to as citral. Fresh rhizomes of 17 clones of Australian ginger, including commercial cultivars and experimental tetraploid clones, were steam distilled 7 weeks post-harvest, and the resulting oils were analyzed by GC-MS. The essential oils of 16 of the 17 clones, including the tetraploid clones and their parent cultivar, were found to be of substantially similar composition. These oils were characterized by very high citral levels (51-71%) and relatively low levels of the sesquiterpene hydrocarbons typical of ginger oil. The citral levels of most of these oils exceeded those previously reported for ginger oils. The neral-to-geranial ratio was shown to be remarkably constant (0.61 +/- 0.01) across all 17 clones. One clone, the cultivar Jamaican, yielded oil with a substantially different composition, lower citral content and higher levels of sesquiterpene hydrocarbons. Because this cultivar also contains significantly higher concentrations of pungent gingerols, it possesses unique aroma and flavor characteristics, which should be of commercial interest.

Chilling damage in a changing climate in coastal landscapes of the subtropical zone: a case study from south Florida

Freeze events significantly influence landscape structure and community composition along subtropical coastlines. This is particularly true in south Florida, where such disturbances have historically contributed to patch diversity within the mangrove forest, and have played a part in limiting its inland transgression. With projected increases in mean global temperatures, such instances are likely to become much less frequent in the region, contributing to a reduction in heterogeneity within the mangrove forest itself. To understand the process more clearly, we explored the dynamics of a Dwarf mangrove forest following two chilling events that produced freeze-like symptoms, i.e., leaf browning, desiccation, and mortality, and interpreted the resulting changes within the context of current winter temperatures and projected future scenarios. Structural effects from a 1996 chilling event were dramatic, with mortality and tissue damage concentrated among individuals comprising the Dwarf forest's low canopy. This disturbance promoted understory plant development and provided an opportunity for Laguncularia racemosa to share dominance with Rhizophora mangle. Mortality due to the less severe 2001 event was greatest in the understory, probably because recovery of the protective canopy following the earlier freeze was still incomplete. Stand dynamics were static over the same period in nearby unimpacted sites. The probability of reaching temperatures as low as those recorded at a nearby meteorological station (≤3 °C) under several warming scenarios was simulated by applying 1° incremental temperature increases to a model developed from a 42-year temperature record. According to the model, the frequency of similar chilling events decreased from once every 1.9 years at present to once every 3.4 and 32.5 years with 1 and 4 °C warming, respectively. The large decrease in the frequency of these events would eliminate an important mechanism that maintains Dwarf forest structure, and promotes compositional diversity.

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Genetic Diversity and Adaptation of Date Palm (Phoenix dactylifera L.)

Acquiring sufficient information on the genetic variation, genetic differentiation, and the ecological and genetic relationships among individuals and populations are essential for establishing guidelines on conservation and utilization of the genetic resources of a species, and more particularly when biotic and abiotic stresses are considered. The aim of this study was to assess the extent and pattern of genetic variation in date palm (Phoenix dacttylifera L) cultivars; the genetic diversity and structure in its populations occurring over geographical ranges; the variation in economically and botanically important traits of it and the variation in its drought adaptive traits, in conservation and utilization context. In this study, the genetic diversity and relationships among selected cultivars from Sudan and Morocco were assessed using microsatellite markers. Microsatellite markers were also used to investigate the genetic diversity within and among populations collected from different geographic locations in Sudan. In a separate investigation, fruits of cultivars selected from Sudan, involved morphological and chemical characterization, and morphological and DNA polymorphism of the mother trees were also investigated. Morphological and photosynthetic adjustments to water stress were studied in the five most important date palm cultivars in Sudan, namely, Gondaila, Barakawi, Bitamoda, Khateeb and Laggai; and the mechanism enhancing photosynthetic gas exchange in date palm under water stress was also investigated. Results showed a significant (p < 0.001, t-test) differentiation between Sudan and Morocco groups of cultivars. However, the major feature of all tested cultivars was the complete lack of clustering and the absence of cultivars representing specific clones. The results indicated high genetic as well as compositional and morphological diversity among cultivars; while, compositional and morphological traits were found to be characteristic features that strongly differentiate cultivars as well as phenotypes. High genetic diversity was observed also in different populations. Slight but significant (p < 0.01, AMOVA) divergence was observed for soft and dry types; however, the genetic divergence among populations was relatively weak. The results showed a complex genetic relationships between some of the tested populations especially when isolation by distance was considered. The results of the study also revealed that date palm cultivars and phenotypes possess specific direct or interaction effects due to water availability on a range of morphological and physiological traits. Soft and dry phenotypes responded differently to different levels of water stress, while the dry phenotype was more sensitive and conservative. The results indicated that date palm has high fixation capacity to photosynthetic CO2 supply with interaction effect to water availability, which can be considered as advantageous when coping with stresses that may arise with climate change. In conclusion, although a large amount of diversity exists among date palm germplasm, the findings in this study show that the role of biological nature of the tree, isolation by distance and environmental effects on structuring date palm genome was highly influenced by human impacts. Identity of date palm cultivars as developed and manipulated by date palm growers, in the absence of scientific breeding programmes, may continue to mainly depend on tree morphology and fruit characters. The pattern of genetic differentiation may cover specific morphological and physiological traits that contribute to adaptive mechanisms in each phenotype. These traits can be considered for further studies related to drought adaptation in date palm.

Bayesian statistical analysis of bacterial diversity

Bacteria play an important role in many ecological systems. The molecular characterization of bacteria using either cultivation-dependent or cultivation-independent methods reveals the large scale of bacterial diversity in natural communities, and the vastness of subpopulations within a species or genus. Understanding how bacterial diversity varies across different environments and also within populations should provide insights into many important questions of bacterial evolution and population dynamics. This thesis presents novel statistical methods for analyzing bacterial diversity using widely employed molecular fingerprinting techniques. The first objective of this thesis was to develop Bayesian clustering models to identify bacterial population structures. Bacterial isolates were identified using multilous sequence typing (MLST), and Bayesian clustering models were used to explore the evolutionary relationships among isolates. Our method involves the inference of genetic population structures via an unsupervised clustering framework where the dependence between loci is represented using graphical models. The population dynamics that generate such a population stratification were investigated using a stochastic model, in which homologous recombination between subpopulations can be quantified within a gene flow network. The second part of the thesis focuses on cluster analysis of community compositional data produced by two different cultivation-independent analyses: terminal restriction fragment length polymorphism (T-RFLP) analysis, and fatty acid methyl ester (FAME) analysis. The cluster analysis aims to group bacterial communities that are similar in composition, which is an important step for understanding the overall influences of environmental and ecological perturbations on bacterial diversity. A common feature of T-RFLP and FAME data is zero-inflation, which indicates that the observation of a zero value is much more frequent than would be expected, for example, from a Poisson distribution in the discrete case, or a Gaussian distribution in the continuous case. We provided two strategies for modeling zero-inflation in the clustering framework, which were validated by both synthetic and empirical complex data sets. We show in the thesis that our model that takes into account dependencies between loci in MLST data can produce better clustering results than those methods which assume independent loci. Furthermore, computer algorithms that are efficient in analyzing large scale data were adopted for meeting the increasing computational need. Our method that detects homologous recombination in subpopulations may provide a theoretical criterion for defining bacterial species. The clustering of bacterial community data include T-RFLP and FAME provides an initial effort for discovering the evolutionary dynamics that structure and maintain bacterial diversity in the natural environment.

Compositional Divergence and Convergence in Local Communities and Spatially Structured Landscapes

Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition) are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence) than, less dissimilar (convergence) than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index) using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect). The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community assembly in a spatially explicit and complex context.