The discourse of biology lectures : aspects of its mode and text structure

The present thesis investigates mode related aspects in biology lecture discourse and attempts to identify the position of this variety along the spontaneous spoken versus planned written language continuum. Nine lectures (of 43,000 words) consisting of three sets of three lectures each, given by the three lecturers at Aston University, make up the corpus. The indeterminacy of the results obtained from the investigation of grammatical complexity as measured in subordination motivates the need to take the analysis beyond sentence level to the study of mode related aspects in the use of sentence-initial connectives, sub-topic shifting and paraphrase. It is found that biology lecture discourse combines features typical of speech and writing at sentence as well as discourse level: thus, subordination is more used than co-ordination, but one degree complexity sentence is favoured; some sentence initial connectives are only found in uses typical of spoken language but sub-topic shift signalling (generally introduced by a connective) typical of planned written language is a major feature of the lectures; syntactic and lexical revision and repetition, interrupted structures are found in the sub-topic shift signalling utterance and paraphrase, but the text is also amenable to analysis into sentence like units. On the other hand, it is also found that: (1) while there are some differences in the use of a given feature, inter-speaker variation is on the whole not significant; (2) mode related aspects are often motivated by the didactic function of the variety; and (3) the structuring of the text follows a sequencing whose boundaries are marked by sub-topic shifting and the summary paraphrase. This study enables us to draw four theoretical conclusions: (1) mode related aspects cannot be approached as a simple dichotomy since a combination of aspects of both speech and writing are found in a given feature. It is necessary to go to the level of textual features to identify mode related aspects; (2) homogeneity is dominant in this sample of lectures which suggests that there is a high level of standardization in this variety; (3) the didactic function of the variety is manifested in some mode related aspects; (4) the features studied play a role in the structuring of the text.

Formant-frequency variation and its effects on across-formant grouping in speech perception

How speech is separated perceptually from other speech remains poorly understood. In a series of experiments, perceptual organisation was probed by presenting three-formant (F1+F2+F3) analogues of target sentences dichotically, together with a competitor for F2 (F2C), or for F2+F3, which listeners must reject to optimise recognition. To control for energetic masking, the competitor was always presented in the opposite ear to the corresponding target formant(s). Sine-wave speech was used initially, and different versions of F2C were derived from F2 using separate manipulations of its amplitude and frequency contours. F2Cs with time-varying frequency contours were highly effective competitors, whatever their amplitude characteristics, whereas constant-frequency F2Cs were ineffective. Subsequent studies used synthetic-formant speech to explore the effects of manipulating the rate and depth of formant-frequency change in the competitor. Competitor efficacy was not tuned to the rate of formant-frequency variation in the target sentences; rather, the reduction in intelligibility increased with competitor rate relative to the rate for the target sentences. Therefore, differences in speech rate may not be a useful cue for separating the speech of concurrent talkers. Effects of competitors whose depth of formant-frequency variation was scaled by a range of factors were explored using competitors derived either by inverting the frequency contour of F2 about its geometric mean (plausibly speech-like pattern) or by using a regular and arbitrary frequency contour (triangle wave, not plausibly speech-like) matched to the average rate and depth of variation for the inverted F2C. Competitor efficacy depended on the overall depth of frequency variation, not depth relative to that for the other formants. Furthermore, the triangle-wave competitors were as effective as their more speech-like counterparts. Overall, the results suggest that formant-frequency variation is critical for the across-frequency grouping of formants but that this grouping does not depend on speech-specific constraints.

Formant-frequency variation and its effects on across-formant grouping in speech perception

How speech is separated perceptually from other speech remains poorly understood. In a series of experiments, perceptual organisation was probed by presenting three-formant (F1+F2+F3) analogues of target sentences dichotically, together with a competitor for F2 (F2C), or for F2+F3, which listeners must reject to optimise recognition. To control for energetic masking, the competitor was always presented in the opposite ear to the corresponding target formant(s). Sine-wave speech was used initially, and different versions of F2C were derived from F2 using separate manipulations of its amplitude and frequency contours. F2Cs with time-varying frequency contours were highly effective competitors, whatever their amplitude characteristics, whereas constant-frequency F2Cs were ineffective. Subsequent studies used synthetic-formant speech to explore the effects of manipulating the rate and depth of formant-frequency change in the competitor. Competitor efficacy was not tuned to the rate of formant-frequency variation in the target sentences; rather, the reduction in intelligibility increased with competitor rate relative to the rate for the target sentences. Therefore, differences in speech rate may not be a useful cue for separating the speech of concurrent talkers. Effects of competitors whose depth of formant-frequency variation was scaled by a range of factors were explored using competitors derived either by inverting the frequency contour of F2 about its geometric mean (plausibly speech-like pattern) or by using a regular and arbitrary frequency contour (triangle wave, not plausibly speech-like) matched to the average rate and depth of variation for the inverted F2C. Competitor efficacy depended on the overall depth of frequency variation, not depth relative to that for the other formants. Furthermore, the triangle-wave competitors were as effective as their more speech-like counterparts. Overall, the results suggest that formant-frequency variation is critical for the across-frequency grouping of formants but that this grouping does not depend on speech-specific constraints. © Springer Science+Business Media New York 2013.

Genomic variation of HIV-1 and its effects on drug resistance and molecular epidemiology analyses

In the first part of this study human immunodeficiency virus type 1 (HIV-1) proviral DNA sequences derived from 201 clones of the C2-V3 env region and the first exon of the tat gene were obtained from six MV-1 infected heterosexual couples. These molecular data were used to confirm the epidemiological relationships. The ability of the molecular data to draw such conclusions was also tested with multiple phylogenetic analyses. The tat region was much more useful in establishing epidemiological relationships than the commonly used C2-V3.^ Subsequently, using nucleotide sequences from the first exon of the Tat gene, we tested the hypothesis that a Florida dentist (a common source) infected five of his patients in the course of dental procedures, against the null hypothesis that the dentist and each individual of the dental group independently acquired the virus within the local community. Multiple phylogenetic analyses demonstrated that the sequences of the five patients were significantly more related to each other than to sequences of the controls. Our results using Tat sequences, combined with envelope sequence data, strongly support a common phylogenetic epidemiological relationship among these five patients.^ A third study is presented, which deals with the effects of genomic variations in drug resistance. HIV-1 reverse transcriptase (RT) mutations were detected in DNA from peripheral blood mononuclear cells from 11 of 12 HIV-infected children after 11-20 months of zidovudine monotherapy. The codon 41/215 mutant combination was associated with general decline in health status. Patients developing the codon 70 mutation tended to have a better health status. ^

Ecological genetics of Melaleuca quinquenervia (Myrtaceae): Population variation in Florida and its influence on performance of the biological control agent Oxyops vitiosa (Coleoptera: Curculionidae)

Melaleuca quinquenervia (Cav.) Blake (Myrtaceae) was imported into Florida from Australia over a century ago as a landscape plant. A favorable climate and periodic wildfires helped M. quinquenervia thrive; it now occupies about 200,000 hectares in southern Florida. A biological control (i.e., biocontrol) program against M. quinquenervia has been initiated, but not all biocontrol releases are successful. Some scientists have argued that poor biocontrol agent success may relate to genetic differences among populations of invasive weeds. I tested this premise by determining (1) the number and origins of M. quinquenervia introductions into Florida, (2) whether multiple introduction events resulted in the partitioning of Florida's M. quinquenervia populations into discrete biotypes, and (3) whether Oxyops vitiosa, an Australia snout beetle imported to control this weed, might discriminate among putative M. quinquenervia biotypes. Careful scrutiny of early horticultural catalogs and USDA plant introduction records suggested at least six distinct introduction events. Allozyme analyses indicated that the pattern of these introductions, and the subsequent redistribution of progeny, has resulted in geographic structuring of the populations in southern Florida. For example, trees on Florida's Gulf Coast had a greater effective number of alleles and exhibited greater heterozygosity than trees on the Atlantic Coast. Essential oil yields from M. quinquenervia leaves followed a similar trend; Gulf Coast trees yielded nearly twice as much oil as Atlantic Coast trees when both were grown in a common garden. These differences were partially explained by the predominance of a chemical phenotype (chemotype) very rich in the sesquiterpene (E)-nerolidol in M. quinquenervia trees from the Gulf Coast, but rich in a mixture of the monoterpene 1,8-cineole and the sesquiterpene viridiflorol in trees from the Atlantic Coast. Performance of O. vitiosa differed dramatically in laboratory studies depending on the chemotype of the foliage they were fed. Larval survivorship was four-fold greater on the (E)-nerolidol chemotype. Growth was also greater, with adult O. vitiosa gaining nearly 50% more biomass on the (E)-nerolidol plants than on the second chemotype. The results of this study thus confirmed the premise that plant genotype can affect the population dynamics of insects released as weed biocontrols. ^

Plant biogeography and conservation on a tropical island: Isla del Coco, Costa Rica

Isla del Coco (Cocos Island) is a small volcanic island located in the Pacific 500 km west of Costa Rica. Three collecting trips to Isla del Coco, in addition to herbarium research, were completed in order to assess the floristic diversity of the island. The current flora of Isla del Coco contains 262 plant species of which 37 (19.4%) are endemic. This study reports 58 species as new to the island. Seventy-one species (27.1%) were identified as introduced by humans. In addition, five potentially invasive plant species are identified. Seven vegetation types are identified on the island: bayshore, coastal cliff, riparian, low elevation humid forest, high elevation cloud forest, landslide and islet. ^ The biogeographic affinities of the native and endemic species are with Central America/northern South America and to a lesser extent, the Caribbean. Endemic species in the genus Epidendrum were investigated to determine whether an insular radiation event had produced two species found on Isla del Coco. Phylogenetic analysis of the internal transcribed spacer (ITS) of nuclear ribosomal DNA was not able to disprove that the endemic species in this genus are not sister species. Molecular biogeographic analyses of ITS sequence data determined that the Isla del Coco endemic species in the genera Epidendrum, Pilea and Psychotria are most closely related to Central American/northern South American taxa. No biogeographical links were found between the floras of Isla del Coco and the Galápagos Islands. ^ The native and endemic plant diversity of Isla del Coco is threatened with habitat degradation by introduced pigs and deer, and to a lesser extent, by exotic plant species. The IUCN Red List and RAREplants criteria were used to assess the extinction threat for the 37 endemic plant taxa found on the island. All of the endemic species are considered threatened with extinction at the Critically Endangered (CR) by the IUCN criteria or either CR or Endangered (EN) using RAREplants methodology. ^

Acoustic telemetry studies of bonefish (Albula vulpes ) movement around Andros Island, Bahamas: Implications for species management

Bonefish (Albula spp.) support an economically important catch-and-release recreational fishery, as well as artisanal harvesting, in The Bahamas. Little is known about the large-scale movement patterns of bonefish, yet such information is essential for proper species conservation and management. ^ I used acoustic telemetry to determine large-scale movement patterns of bonefish around Andros, Bahamas, in conjunction with presumed spawning migrations. I conclude that bonefish travel long distances from shallow flats to pre-spawning aggregation sites in proximity to off-shore reef locations. Off-shore movement to deeper reef locations occurs around both new and full moons. This study has also confirmed anecdotal reports that the North Bight is an important spawning migration corridor for bonefish. ^ This information is critical for the protection of bonefish and identifies important habitats (e.g. migration corridors and pre-spawning aggregations) on Andros that warrant protection from coastal degradation or fishing pressures. ^

Relationships Between Hydrology and Soils Describe Vegetation Patterns in Seasonally Flooded Tree Islands of the Southern Everglades, Florida

Tree island ecosystems are important and distinct features of Florida Everglades wetlands. We described the inter-relationships among abiotic factors describing seasonally flooded tree islands and characterized plant–soil relationships in tree islands occurring in a relatively unimpacted area of the Everglades. We used Principal Components Analysis (PCA) to reduce our multi-factor dataset, quantified forest structure and vegetation nutrient dynamics, and related these vegetation parameters to PCA summary variables using linear regression analyses. We found that, of the 21 abiotic parameters used to characterize the ecosystem structure of seasonally flooded tree islands, 13 parameters were significantly correlated with four principal components, and they described 78% of the variance among the study islands. Most variation was described by factors related to soil oxidation and hydrology, exemplifying the sensitivity of tree island structure to hydrologic conditions. PCA summary variables describing tree island structure were related to variability in Chrysobalanus icaco (L.) canopy cover, Ilex cassine (L.) and Salix caroliniana (Michx.) canopy cover, Myrica cerifera (L.) plot frequency, litter turnover, % phosphorus resorption of co-dominant species, and nitrogen nutrient-use efficiency. This study supported findings that vegetation characteristics can be sensitive indicators of variability in tree island ecosystem structure. This study produced valuable, information which was used to recommend ecological targets (i.e. restoration performance measures) for seasonally flooded tree islands in more impacted regions of the Everglades landscape.

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

Background: Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results: We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion: Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

Monitoring of Tree Island Conditions in the Southern Everglades: The Effects of Hurricanes and Hydrology on the Status and Population Dynamics of Sixteen Tropical Hardwood Hammock Tree Islands

In 2005 we began a multi-year intensive monitoring and assessment study of tropical hardwood hammocks within two distinct hydrologic regions in Everglades National Park, under funding from the CERP Monitoring and Assessment Program. In serving as an Annual Report for 2010, this document, reports in detail on the population dynamics and status of tropical hardwood hammocks in Shark Slough and adjacent marl prairies during a 4-year period between 2005 and 2009. 2005-09 was a period that saw a marked drawdown in marsh water levels (July 2006 - July 2008), and an active hurricane season in 2005 with two hurricanes, Hurricane Katrina and Wilma, making landfall over south Florida. Thus much of our focus here is on the responses of these forests to annual variation in marsh water level, and on recovery from disturbance. Most of the data are from 16 rectangular permanent plots of 225-625 m2 , with all trees mapped and tagged, and bi-annual sampling of the tree, sapling, shrub, and herb layer in a nested design. At each visit, canopy photos were taken and later analyzed for determination of interannual variation in leaf area index and canopy openness. Three of the plots were sampled at 2-month intervals, in order to gain a better idea of seasonal dynamics in litterfall and litter turnover. Changes in canopy structure were monitored through a vertical line intercept method.

Spatial and temporal variation of microbial properties in the water column of Florida Bay

Physical and biological properties of the water column of Florida Bay were examined at seven study sites over an eighteen month period. The results indicated seasonality in some parameters, but was not evident in others. The data displayed statistically significant (P < 0.05) differences between study sites indicating spatial variation. The presence of seagrass affected the overlying water column, especially with respect to the biological parameters: those areas overlying seagrass beds displayed statistically significantly higher values than those over sparsely covered or barren areas. During the period of the study, Florida Bay experienced a seagrass die-off event: microbial activity and numbers were statistically significantly higher over areas of dying seagrass than over healthy or dead areas. The results of this study pointed to phosphorus being the controlling, or limiting factor, for microbial activity in the water column of Florida Bay.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Archaeological otoliths as environmental recorders: high resolution sampling of pacific cod (Gadus macrocephalus) otoliths from Kiska Island, Alaska

Archaeological fish otoliths have the potential to serve as proxies for both season of site occupation and palaeoclimate conditions. By sampling along the distinctive sub-annual seasonal bands of the otolith and completing a stable isotope (δ¹⁸O, δ¹³C) analysis, variations within the fish’s environment can be identified. Through the analysis of cod otoliths from two archaeological sites on Kiska Island, Gertrude Cove (KIS-010) and Witchcraft Point (KIS-005), this research evaluates a micromilling methodological approach to extracting climatic data from archaeological cod otoliths. In addition, δ¹⁸Ootolith data and radiocarbon dates frame a discussion of Pacific cod harvesting, site occupation, and changing climatic conditions on Kiska Island. To aid in the interpretation of the archaeological Pacific cod results, archaeological and modern Atlantic cod otoliths were also analyzed as a component of this study to develop. The Atlantic cod otoliths provided the methodological and interpretative framework for the study, and also served to assess the efficacy of this sampling strategy for archaeological materials and to add time-depth to existing datasets. The δ¹⁸Ootolith values successfully illustrate relative variation in ambient water temperature. The Pacific cod δ¹⁸O values demonstrate a weak seasonal signal identifiable up to year 3, followed by relatively stable values until year 6/7 when values continuously increase. Based on the δ¹⁸O values, the Pacific cod were exposed to the coldest water temperatures immediately prior to capture. The lack of a clear cycle of seasonal variation and the continued increase in values towards the otolith edge obscures the season of capture, and indicates that other behavioural, environmental, or methodological factors influenced the otolith δ¹⁸O values. It is suggested that Pacific cod would have been harvested throughout the year, and the presence of cod remains in Aleutian archaeological sites cannot be used as a reliable indicator of summer occupation. In addition, when the δ¹⁸O otolith values are integrated with radiocarbon dates and known climatic regimes, it is demonstrated that climatic conditions play an integral role in the pattern of occupation at Gertrude Cove. Initial site occupation coincides with the end of a neoglacial cooling period, and the most recent and continuous occupation coincides with the end of a localized warming period and the onset of the Little Ice Age (LIA).

The Ross's Gull (Rhodostethia rosea) in North America

The population, distribution and range of the Ross's gull in North America remain poorly understood, as does almost every aspect of its ecology and biology. It breeds at a few disparate locations in the Canadian Arctic and is an annual fall migrant in northern Alaska where tens of thousands occur in the nearshore waters of the Beaufort and Chukchi Seas, but little else is known about the distribution, habitat requirements, migratory routes and wintering areas used by this species. In order to clarify the status of the Ross's gull in North America I sought to discover new breeding sites in the Canadian High Arctic in order to characterize nesting habitat requirements, develop a predictive model with which to identify suitable nesting habitat for Ross's gulls, and refresh outdated estimates of the number of individuals migrating past Point Barrow, Alaska. Taken together, my findings provide a comprehensive account of the current status of the Ross's gull in North America.