Changing landscapes: Compositional and phenological shifts in New Zealand's natural grassland

Vegetation in a wide range of ecosystems across the globe is responding to recent anthropogenic climate change. There are two key ecological responses in plants associated with recent anthropogenic climate change: shifts in species’ geographic distributions (range shifts) and shifts in the timing of key life cycle events (phenological shifts). These shifts can lead to temporal and spatial changes in vegetation composition and growth activity and hence ecosystem function. Understanding the patterns and processes of these shifts is crucial for the successful management of natural ecosystems under ongoing anthropogenic environmental change. This thesis investigates recent spatiotemporal compositional and phenological shifts in New Zealand’s natural grassland ecosystems and identifies potential topographical and climatic drivers of these shifts. Three grassland types in New Zealand are investigated (Alpine, Tall Tussock and Low Producing grasslands). They are characterised by high levels of indigenous endemic plant biodiversity and cover a wide elevation range. This thesis primarily utilises remote sensing information for quantifying growth dynamics and vegetation patterns in these grasslands over the last 16 years and across large spatial scales, i.e., the catchment of the river Clutha/Mata-Au River in South Island, New Zealand. Shrub encroachment in grassland ecosystems is a globally observed example of compositional shifts in ecosystems associated with recent anthropogenic climate change. In New Zealand, where extensive area of current grassland habitats exist because of anthropogenic deforestation, shrub encroachment into grasslands has two distinct facets: firstly the invasion of non-native shrub species into native grasslands (i.e., exotic shrub invasion) and secondly the dispersal of native woody and shrub species into native grasslands (i.e., native shrub recovery). Propagule pressure is a measurement of species’ seed source size in neighbourhood of a focal area, and it is a key determinant of the degree to which a location gets colonised by individuals from species present in the neighbourhood. The spatial patterns of potential native and exotic shrub propagule pressure on three grassland types in New Zealand were quantified with the assumption that proximity of higher shrub coverage indicates higher shrub propagule availability. Results show that Alpine grasslands are mostly surrounded by native shrublands, while Low producing grassland are most at risk from exotic shrub invasion from neighbouring areas. High native and exotic shrub propagule pressure does not generally coincide spatially, however, it occurs in very similar climates for Low Producing grassland but not for Alpine and Tall Tussock grassland. The analysis of recent shrub encroachment over the last five years in a tussock grassland area in the central South Island showed a 0.35% year-1 increase in shrub cover in grassland area located in immediate neighbourhood of shrub. Shrub encroachment speed was strongly correlated with shrub cover in the neighbourhood. Recent shrub encroachment into grasslands was most pronounced in areas with neighbouring shrub cover of greater than 40%. A wide range of species and ecosystems worldwide have shown changes in the timing of life cycle events and growing seasons in a direction congruent with recent anthropogenic climate changes. In this study, temporal trends over the last 16 years in the start, peak and end dates of the growing season were analysed using remotely sensed data on the Normalised Difference Vegetation Index (NDVI) in New Zealand’s three main grassland types. Overall, 90% of Alpine, 86% of Tall Tussock and 89% of Low Producing grassland areas showed an advancing start of the growing season over the last 16 years. In these areas start of the growing advanced by 7.2, 6.0 and 8.8 days per decade in Alpine, Tall Tussock and Low Producing grassland, respectively. Only small changes in timing of the end of the growing season were observed in the three grassland types. The length of growing season extended by 3.2, 5.2 and 7.1 days per decade in three grassland types. Landscape topography (elevation and aspect) played an important role in particular in alpine grasslands: the start of the growing season was strongly correlated with elevation (later start with increasing elevation), while the end of the growing season was strongly correlated with aspect (later end of season on more south-facing slopes). The start of season was delayed by 7.5, 5.1 and 3.7 days/100 m elevation increase in Alpine, Tall Tussock and Low producing grassland, separately. The end of season was advanced by 1.7 (Alpine), 1.3 (Tall Tussock) and delayed by 0.3 (Low Producing) days/10-degree-south on the slopes in these three grassland types. The results from this thesis show that recent shrub invasion into New Zealand grasslands is highest near shrub areas once a threshold of shrub cover in the neighbourhood is reached. Shrub encroachment was highest at lower elevations and on north-facing slopes. It also highlighted a measurable shift to an earlier start and extended length of the growing season in New Zealand’s main grassland types over the last 16 years, but the magnitude of these shifts showed considerable geographic variation. Importantly, this study has shown a high degree of topographical control on the timing of the growing in New Zealand’s grasslands with elevation and aspect acting differentially on start and end of the growing season. This highlights the importance of landscape heterogeneity and microclimates for ecosystem responses to climate change. This study shows that remotely sensed data can be successfully used to elucidate ecosystem-level shifts in temporal dynamics and spatial patterns of vegetation growth in grassland ecosystems

Selecting Genes by Test Statistics

Gene selection is an important issue in analyzing multiclass microarray data. Among many proposed selection methods, the traditional ANOVA F test statistic has been employed to identify informative genes for both class prediction (classification) and discovery problems. However, the F test statistic assumes an equal variance. This assumption may not be realistic for gene expression data. This paper explores other alternative test statistics which can handle heterogeneity of the variances. We study five such test statistics, which include Brown-Forsythe test statistic and Welch test statistic. Their performance is evaluated and compared with that of F statistic over different classification methods applied to publicly available microarray datasets

Party Secretaries in Chinese Higher Education Institutions, Who Are They?

With approximately 30 million students the Chinese higher education system is the largest in the world. In every publicly funded institution there is a communist party secretary, however, little is known about these party secretaries. The purpose of the study was to understand who these people were. We collected data from 1,751 party secretaries in Chinese higher education institutions and grouped party secretaries into eight types according to the institutions where they worked. We conducted multidimensional scaling analysis and cluster analysis to explore the differences among the eight party secretary types and to put them into categories. In addition, we compared the findings from this study to those from another study investigating the characteristics of higher education institution presidents to examine the differences between party secretaries and presidents. We conclude that party secretaries from whom data were collected are on average 55 years old, 92 percent are males, 76 percent are at the rank of professor, 29 percent have a doctorate degree, and 9 percent have an overseas degree. The eight types of party secretaries can be put into two categories; those in the first category are older, have been in position longer, and more of them have a doctorate degree. In comparison, party secretaries are more likely to be administrative leaders whereas presidents are more likely to be academic leaders

Recent trends in the timing of the growing season in New Zealand’s natural and semi-natural grasslands

We investigate the temporal dynamics of shifts in phenological responses of a range of key stages of the growing season in New Zealand’s three indigenous grassland types over the last 16 years (2001–2016). A near-daily Normalized Difference Vegetation Index (NDVI) time series from MODerate Resolution Imaging Spectroradiometer (MODIS) was used to extract five annual growth phenology indices, namely the Start, End, Length, Peak and Peak NDVI of a growing season. The start of the growing season advanced (i.e. happened earlier) by a median of 7.2, 6.0 and 8.8 days per decade in Alpine, Tall Tussock and Low Producing grassland, whereas the end of the season advanced by a median of 4.5, 0.4 and 0.4 days in the three types respectively. The length of growing season was extended by 3.2, 5.2 and 7.1 days per decade in these three grassland types. Over 86% of the investigated grassland areas showed an advancing (earlier) start of the growing season, and 74% of Alpine grassland showed a trend toward an earlier end of season. Over 63% of all grassland types showed an increase in growing season length. A trend toward earlier growing season peak and overall increasing NDVI in the three grassland types indicate a tendency for increasing vegetation vitality in grassland ecosystems in recent years. The start of growing season was correlated with atmospheric pressure (negatively) and precipitation (positively) changes in winter–spring months, while the timing of the season end is positively correlated with air temperature and solar radiation in summer–autumn months. Our study shows that different grassland types differ in magnitude–but not in direction–of their recent shifts in timing of key growing season stages with high-alpine grasslands showing the strongest response. This study highlights the usefulness of remote sensing for monitoring ecosystem-level phenological shifts over large areas and long time periods

The value of enhanced CT scanning for predicting lymph node metastasis along the right recurrent laryngeal nerve in esophageal squamous cell carcinoma

Background: The right recurrent laryngeal nerve (RRLN) is the region most prone to lymph node metastasis in esophageal squamous cell carcinoma (ESCC). Nodal involvement may be underestimated by traditional imaging prediction criteria, such as a short axis diameter of 10 mm. The purpose of this study was to determine a more accurate imaging criterion to guide clinical treatment strategy selection. Methods: The clinical data of 307 patients with thoracic ESCC who underwent surgery at Shanghai Chest Hospital between January 2018 and December 2018 were retrospectively analyzed. Utilizing 1-mm layer thickness enhanced computed tomography (CT), the RRLN lymph node short diameter (LNSD) size was measured. Univariate and multivariate analyses were performed to determine the risk factors for lymph node metastasis along the RRLN. Results: In our study, RRLN lymph node metastasis occurred in 60 (19.5%) patients and general lymph node metastasis occurred in 150 (48.9%) patients. Of the resected lymph nodes along the RRLN, 14.5% (121/832) were positive. Multivariate analysis identified LNSD [odds ratio (OR), 1.236] as an independent risk factor for RRLN lymph node metastasis. In CT evaluation, a short diameter of 6.5 mm in the RRLN lymph nodes is a critical predictor of metastasis at this site (sensitivity =50%, specificity =83.4%) and a larger short diameter was associated with a higher risk of metastasis (P<0.001). Conclusions: A 6.5 mm cutoff in LNSD can be applied to clinically predict lymph node metastasis in the RRLN region for patients with ESCC

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

Current HIV-1 vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in ~20% of HIV-1-infected individuals, and details of their generation could provide a roadmap for effective vaccination. Here we report the isolation, evolution and structure of a broadly neutralizing antibody from an African donor followed from time of infection. The mature antibody, CH103, neutralized ~55% of HIV-1 isolates, and its co-crystal structure with gp120 revealed a novel loop-based mechanism of CD4-binding site recognition. Virus and antibody gene sequencing revealed concomitant virus evolution and antibody maturation. Notably, the CH103-lineage unmutated common ancestor avidly bound the transmitted/founder HIV-1 envelope glycoprotein, and evolution of antibody neutralization breadth was preceded by extensive viral diversification in and near the CH103 epitope. These data elucidate the viral and antibody evolution leading to induction of a lineage of HIV-1 broadly neutralizing antibodies and provide insights into strategies to elicit similar antibodies via vaccination

Changing landscapes: Compositional and phenological shifts in New Zealand's natural grassland

Vegetation in a wide range of ecosystems across the globe is responding to recent anthropogenic climate change. There are two key ecological responses in plants associated with recent anthropogenic climate change: shifts in species’ geographic distributions (range shifts) and shifts in the timing of key life cycle events (phenological shifts). These shifts can lead to temporal and spatial changes in vegetation composition and growth activity and hence ecosystem function. Understanding the patterns and processes of these shifts is crucial for the successful management of natural ecosystems under ongoing anthropogenic environmental change. This thesis investigates recent spatiotemporal compositional and phenological shifts in New Zealand’s natural grassland ecosystems and identifies potential topographical and climatic drivers of these shifts. Three grassland types in New Zealand are investigated (Alpine, Tall Tussock and Low Producing grasslands). They are characterised by high levels of indigenous endemic plant biodiversity and cover a wide elevation range. This thesis primarily utilises remote sensing information for quantifying growth dynamics and vegetation patterns in these grasslands over the last 16 years and across large spatial scales, i.e., the catchment of the river Clutha/Mata-Au River in South Island, New Zealand. Shrub encroachment in grassland ecosystems is a globally observed example of compositional shifts in ecosystems associated with recent anthropogenic climate change. In New Zealand, where extensive area of current grassland habitats exist because of anthropogenic deforestation, shrub encroachment into grasslands has two distinct facets: firstly the invasion of non-native shrub species into native grasslands (i.e., exotic shrub invasion) and secondly the dispersal of native woody and shrub species into native grasslands (i.e., native shrub recovery). Propagule pressure is a measurement of species’ seed source size in neighbourhood of a focal area, and it is a key determinant of the degree to which a location gets colonised by individuals from species present in the neighbourhood. The spatial patterns of potential native and exotic shrub propagule pressure on three grassland types in New Zealand were quantified with the assumption that proximity of higher shrub coverage indicates higher shrub propagule availability. Results show that Alpine grasslands are mostly surrounded by native shrublands, while Low producing grassland are most at risk from exotic shrub invasion from neighbouring areas. High native and exotic shrub propagule pressure does not generally coincide spatially, however, it occurs in very similar climates for Low Producing grassland but not for Alpine and Tall Tussock grassland. The analysis of recent shrub encroachment over the last five years in a tussock grassland area in the central South Island showed a 0.35% year-1 increase in shrub cover in grassland area located in immediate neighbourhood of shrub. Shrub encroachment speed was strongly correlated with shrub cover in the neighbourhood. Recent shrub encroachment into grasslands was most pronounced in areas with neighbouring shrub cover of greater than 40%. A wide range of species and ecosystems worldwide have shown changes in the timing of life cycle events and growing seasons in a direction congruent with recent anthropogenic climate changes. In this study, temporal trends over the last 16 years in the start, peak and end dates of the growing season were analysed using remotely sensed data on the Normalised Difference Vegetation Index (NDVI) in New Zealand’s three main grassland types. Overall, 90% of Alpine, 86% of Tall Tussock and 89% of Low Producing grassland areas showed an advancing start of the growing season over the last 16 years. In these areas start of the growing advanced by 7.2, 6.0 and 8.8 days per decade in Alpine, Tall Tussock and Low Producing grassland, respectively. Only small changes in timing of the end of the growing season were observed in the three grassland types. The length of growing season extended by 3.2, 5.2 and 7.1 days per decade in three grassland types. Landscape topography (elevation and aspect) played an important role in particular in alpine grasslands: the start of the growing season was strongly correlated with elevation (later start with increasing elevation), while the end of the growing season was strongly correlated with aspect (later end of season on more south-facing slopes). The start of season was delayed by 7.5, 5.1 and 3.7 days/100 m elevation increase in Alpine, Tall Tussock and Low producing grassland, separately. The end of season was advanced by 1.7 (Alpine), 1.3 (Tall Tussock) and delayed by 0.3 (Low Producing) days/10-degree-south on the slopes in these three grassland types. The results from this thesis show that recent shrub invasion into New Zealand grasslands is highest near shrub areas once a threshold of shrub cover in the neighbourhood is reached. Shrub encroachment was highest at lower elevations and on north-facing slopes. It also highlighted a measurable shift to an earlier start and extended length of the growing season in New Zealand’s main grassland types over the last 16 years, but the magnitude of these shifts showed considerable geographic variation. Importantly, this study has shown a high degree of topographical control on the timing of the growing in New Zealand’s grasslands with elevation and aspect acting differentially on start and end of the growing season. This highlights the importance of landscape heterogeneity and microclimates for ecosystem responses to climate change. This study shows that remotely sensed data can be successfully used to elucidate ecosystem-level shifts in temporal dynamics and spatial patterns of vegetation growth in grassland ecosystems

Geographic versus environmental space: Patterns of potential native and exotic woody propagule pressure on New Zealand's indigenous grasslands

Indigenous grassland ecosystems worldwide are increasingly subject to shrub encroachment. A key factor determining encroachment patterns is the availability of shrub propagules in the areas surrounding the grasslands. We here provide a multi-scale spatial analysis of the geographic distribution (geographic space) and the climatic conditions (environmental space) of potential native and exotic shrub propagule pressure for New Zealand’s main grassland types. We show that alpine grasslands are most at risk from native, and low-producing grasslands are most at risk from exotic shrub propagule pressure. Inferred spatial patterns of potential propagule pressure differ between the local, landscape and regional scale